Starting phenix.real_space_refine on Sat Aug 8 10:28:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q09_72094/08_2026/9q09_72094.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q09_72094/08_2026/9q09_72094.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q09_72094/08_2026/9q09_72094.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q09_72094/08_2026/9q09_72094.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q09_72094/08_2026/9q09_72094.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q09_72094/08_2026/9q09_72094.map" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 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: 4 Type Number sf(0) Gaussians S 138 5.16 5 C 16802 2.51 5 N 4406 2.21 5 O 5584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26930 Number of models: 1 Model: "" Number of chains: 67 Chain: "A" Number of atoms: 3573 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 452, 3559 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 452, 3559 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 bond proxies already assigned to first conformer: 3617 Chain: "B" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1038 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 1029 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 130, 1023 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 130, 1023 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1034 Chain: "D" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 942 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "E" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 855 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain: "G" Number of atoms: 3565 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 452, 3559 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 452, 3559 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 bond proxies already assigned to first conformer: 3626 Chain: "H" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 942 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "I" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3559 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "J" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1018 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "K" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 942 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "L" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 855 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain: "M" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 855 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain: "h" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1026 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "l" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "d" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1026 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "e" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "k" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1026 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "m" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "R" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "X" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "Y" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Z" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "T" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "W" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "s" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "t" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "u" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "y" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "5" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "6" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "8" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "9" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" C1 MAN P 4 " occ=0.79 ... (9 atoms not shown) pdb=" O6 MAN P 4 " occ=0.79 residue: pdb=" C1 MAN R 4 " occ=0.76 ... (9 atoms not shown) pdb=" O6 MAN R 4 " occ=0.76 residue: pdb=" C1 MAN Y 6 " occ=0.92 ... (9 atoms not shown) pdb=" O6 MAN Y 6 " occ=0.92 residue: pdb=" C1 MAN S 4 " occ=0.74 ... (9 atoms not shown) pdb=" O6 MAN S 4 " occ=0.74 residue: pdb=" C1 MAN T 4 " occ=0.79 ... (9 atoms not shown) pdb=" O6 MAN T 4 " occ=0.79 residue: pdb=" C1 MAN s 6 " occ=0.86 ... (9 atoms not shown) pdb=" O6 MAN s 6 " occ=0.86 residue: pdb=" C1 MAN t 4 " occ=0.88 ... (9 atoms not shown) pdb=" O6 MAN t 4 " occ=0.88 residue: pdb=" C1 MAN y 6 " occ=0.73 ... (9 atoms not shown) pdb=" O6 MAN y 6 " occ=0.73 Time building chain proxies: 7.41, per 1000 atoms: 0.28 Number of scatterers: 26930 At special positions: 0 Unit cell: (157.542, 176.89, 172.283, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 138 16.00 O 5584 8.00 N 4406 7.00 C 16802 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.05 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.02 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 92 " distance=2.03 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 88 " distance=2.03 Simple disulfide: pdb=" SG CYS d 22 " - pdb=" SG CYS d 92 " distance=2.03 Simple disulfide: pdb=" SG CYS e 23 " - pdb=" SG CYS e 88 " distance=2.03 Simple disulfide: pdb=" SG CYS k 22 " - pdb=" SG CYS k 92 " distance=2.03 Simple disulfide: pdb=" SG CYS m 23 " - pdb=" SG CYS m 88 " 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 Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN P 4 " - " MAN P 5 " " MAN R 4 " - " MAN R 5 " " MAN S 4 " - " MAN S 5 " " MAN T 4 " - " MAN T 5 " " MAN V 4 " - " MAN V 5 " " MAN X 4 " - " MAN X 5 " " MAN X 5 " - " MAN X 6 " " MAN u 4 " - " MAN u 5 " " MAN u 5 " - " MAN u 6 " " MAN w 4 " - " MAN w 5 " " MAN w 5 " - " MAN w 6 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " " MAN X 7 " - " MAN X 8 " " BMA Y 3 " - " MAN Y 6 " " MAN Y 4 " - " MAN Y 5 " " BMA Z 3 " - " MAN Z 4 " " BMA s 3 " - " MAN s 6 " " MAN s 4 " - " MAN s 5 " " BMA t 3 " - " MAN t 4 " " BMA u 3 " - " MAN u 4 " " MAN u 7 " - " MAN u 8 " " BMA w 3 " - " MAN w 4 " " MAN w 7 " - " MAN w 8 " " BMA y 3 " - " MAN y 6 " " MAN y 4 " - " MAN y 5 " ALPHA1-6 " BMA P 3 " - " MAN P 6 " " BMA R 3 " - " MAN R 6 " " BMA S 3 " - " MAN S 6 " " BMA T 3 " - " MAN T 6 " " BMA X 3 " - " MAN X 7 " " MAN X 7 " - " MAN X 9 " " BMA Y 3 " - " MAN Y 4 " " BMA s 3 " - " MAN s 4 " " BMA t 3 " - " MAN t 5 " " BMA u 3 " - " MAN u 7 " " MAN u 7 " - " MAN u 9 " " BMA w 3 " - " MAN w 7 " " MAN w 7 " - " MAN w 9 " " BMA y 3 " - " MAN y 4 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 7 1 " - " NAG 7 2 " " NAG 8 1 " - " NAG 8 2 " " NAG 9 1 " - " NAG 9 2 " " NAG F 1 " - " NAG F 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " NAG-ASN " NAG 0 1 " - " ASN A 448 " " NAG 1 1 " - " ASN A 276 " " NAG 2 1 " - " ASN I 160 " " NAG 3 1 " - " ASN I 355 " " NAG 4 1 " - " ASN I 197 " " NAG 5 1 " - " ASN I 295 " " NAG 6 1 " - " ASN I 301 " " NAG 7 1 " - " ASN I 392 " " NAG 8 1 " - " ASN I 448 " " NAG 9 1 " - " ASN I 276 " " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 462 " " NAG A 603 " - " ASN A 234 " " NAG A 604 " - " ASN A 339 " " NAG B 701 " - " ASN B 618 " " NAG B 702 " - " ASN B 637 " " NAG C 701 " - " ASN C 637 " " NAG C 702 " - " ASN C 618 " " NAG F 1 " - " ASN A 133 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 462 " " NAG G 603 " - " ASN G 234 " " NAG G 604 " - " ASN G 339 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 133 " " NAG I 603 " - " ASN I 462 " " NAG I 604 " - " ASN I 234 " " NAG I 605 " - " ASN I 339 " " NAG N 1 " - " ASN A 137 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN G 137 " " NAG R 1 " - " ASN G 363 " " NAG S 1 " - " ASN A 363 " " NAG T 1 " - " ASN I 363 " " NAG U 1 " - " ASN I 137 " " NAG V 1 " - " ASN I 262 " " NAG W 1 " - " ASN I 156 " " NAG X 1 " - " ASN A 332 " " NAG Y 1 " - " ASN G 262 " " NAG Z 1 " - " ASN G 156 " " NAG a 1 " - " ASN G 276 " " NAG b 1 " - " ASN A 160 " " NAG c 1 " - " ASN A 355 " " NAG f 1 " - " ASN A 197 " " NAG g 1 " - " ASN A 295 " " NAG i 1 " - " ASN A 301 " " NAG j 1 " - " ASN A 392 " " NAG n 1 " - " ASN G 355 " " NAG o 1 " - " ASN G 197 " " NAG p 1 " - " ASN G 295 " " NAG q 1 " - " ASN G 301 " " NAG r 1 " - " ASN G 392 " " NAG s 1 " - " ASN A 386 " " NAG t 1 " - " ASN I 386 " " NAG u 1 " - " ASN I 332 " " NAG v 1 " - " ASN G 160 " " NAG w 1 " - " ASN G 332 " " NAG x 1 " - " ASN G 448 " " NAG y 1 " - " ASN G 386 " " NAG z 1 " - " ASN G 133 " Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.4 seconds 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5814 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 60 sheets defined 13.7% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.806A pdb=" N HIS A 105 " --> pdb=" O VAL A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.547A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 152 Processing helix chain 'A' and resid 334 through 354 removed outlier: 4.014A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.619A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 570 through 595 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 664 removed outlier: 3.667A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 536 removed outlier: 3.692A pdb=" N MET C 535 " --> pdb=" O ALA C 532 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR C 536 " --> pdb=" O ALA C 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 532 through 536' Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 569 through 596 removed outlier: 3.704A pdb=" N LYS C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN C 575 " --> pdb=" O TRP C 571 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL C 580 " --> pdb=" O LEU C 576 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TRP C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 641 through 663 removed outlier: 4.027A pdb=" N GLU C 647 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 663 " --> pdb=" O ASP C 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'G' and resid 58 through 63 removed outlier: 4.008A pdb=" N THR G 63 " --> pdb=" O LYS G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 115 Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 335 through 354 removed outlier: 4.218A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE G 353 " --> pdb=" O LEU G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.596A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 474 through 479 removed outlier: 3.792A pdb=" N ASP G 477 " --> pdb=" O ASP G 474 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'I' and resid 57 through 61 Processing helix chain 'I' and resid 100 through 115 removed outlier: 3.925A pdb=" N THR I 106 " --> pdb=" O GLU I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 197 No H-bonds generated for 'chain 'I' and resid 195 through 197' Processing helix chain 'I' and resid 335 through 354 removed outlier: 3.642A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.647A pdb=" N THR I 373 " --> pdb=" O LEU I 369 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 538 through 543 removed outlier: 3.690A pdb=" N ASN J 543 " --> pdb=" O VAL J 539 " (cutoff:3.500A) Processing helix chain 'J' and resid 570 through 596 removed outlier: 3.568A pdb=" N LYS J 574 " --> pdb=" O VAL J 570 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TRP J 596 " --> pdb=" O LEU J 592 " (cutoff:3.500A) Processing helix chain 'J' and resid 618 through 622 Processing helix chain 'J' and resid 627 through 635 Processing helix chain 'J' and resid 638 through 663 removed outlier: 3.714A pdb=" N LEU J 663 " --> pdb=" O ASP J 659 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 30 No H-bonds generated for 'chain 'K' and resid 28 through 30' Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'L' and resid 27C through 31 removed outlier: 4.188A pdb=" N GLY L 30 " --> pdb=" O HIS L 27C" (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR L 31 " --> pdb=" O VAL L 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 27C through 31' Processing helix chain 'h' and resid 63 through 67 removed outlier: 4.063A pdb=" N ARG h 66 " --> pdb=" O LEU h 63 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL h 67 " --> pdb=" O LYS h 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 63 through 67' Processing helix chain 'h' and resid 100D through 100H Processing helix chain 'd' and resid 100D through 100H Processing helix chain 'k' and resid 100D through 100H Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 4.703A pdb=" N VAL A 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 removed outlier: 4.004A pdb=" N LYS A 189 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 302 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 330 through 333 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 466 through 470 Processing sheet with id=AA7, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.883A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AA9, first strand: chain 'B' and resid 603 through 609 removed outlier: 3.857A pdb=" N VAL G 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.357A pdb=" N GLY D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 34 through 35 Processing sheet with id=AB4, first strand: chain 'E' and resid 3 through 5 Processing sheet with id=AB5, first strand: chain 'E' and resid 9 through 13 removed outlier: 3.791A pdb=" N LEU E 11 " --> pdb=" O ARG E 103 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR E 87 " --> pdb=" O TYR E 36 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU E 48 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLN E 37 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N TYR E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG E 49 " --> pdb=" O ALA E 54C" (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 19 through 21 removed outlier: 3.523A pdb=" N LEU E 21 " --> pdb=" O LEU E 73 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 45 through 47 removed outlier: 4.219A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AB9, first strand: chain 'G' and resid 169 through 177 Processing sheet with id=AC1, first strand: chain 'G' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 259 through 261 current: chain 'G' and resid 284 through 287 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 284 through 287 current: chain 'G' and resid 315 through 322 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 315 through 322 current: chain 'G' and resid 393 through 395 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 393 through 395 current: chain 'G' and resid 465 through 470 No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'G' and resid 374 through 378 removed outlier: 3.673A pdb=" N GLU G 381 " --> pdb=" O CYS G 378 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 423 through 424 Processing sheet with id=AC4, first strand: chain 'H' and resid 3 through 7 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 3 through 7 current: chain 'H' and resid 77 through 82 No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.101A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N GLU H 33 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS H 35 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN H 39 " --> pdb=" O VAL H 89 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 494 through 499 removed outlier: 4.016A pdb=" N VAL I 36 " --> pdb=" O THR J 606 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 45 through 47 Processing sheet with id=AC8, first strand: chain 'I' and resid 75 through 76 Processing sheet with id=AC9, first strand: chain 'I' and resid 91 through 94 removed outlier: 4.007A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 169 through 177 Processing sheet with id=AD2, first strand: chain 'I' and resid 200 through 203 removed outlier: 3.695A pdb=" N ALA I 433 " --> pdb=" O ALA I 200 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 271 through 273 removed outlier: 6.942A pdb=" N GLN I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER I 334 " --> pdb=" O GLN I 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 330 through 334 current: chain 'I' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 381 through 385 current: chain 'I' and resid 465 through 470 Processing sheet with id=AD4, first strand: chain 'I' and resid 304 through 312 removed outlier: 6.600A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AD6, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.167A pdb=" N GLY K 10 " --> pdb=" O THR K 110 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 57 through 59 removed outlier: 5.634A pdb=" N GLU K 33 " --> pdb=" O GLY K 95 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 38 through 39 Processing sheet with id=AD9, first strand: chain 'L' and resid 3 through 5 Processing sheet with id=AE1, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.798A pdb=" N LEU L 11 " --> pdb=" O ARG L 103 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 19 through 21 removed outlier: 3.533A pdb=" N LEU L 21 " --> pdb=" O LEU L 73 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 54B through 54D removed outlier: 3.714A pdb=" N ARG L 49 " --> pdb=" O ALA L 54C" (cutoff:3.500A) removed outlier: 6.795A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ARG L 49 " --> pdb=" O ILE L 33 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE L 33 " --> pdb=" O ARG L 49 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 3 through 5 Processing sheet with id=AE5, first strand: chain 'M' and resid 9 through 13 removed outlier: 6.728A pdb=" N LEU M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP M 85 " --> pdb=" O GLN M 38 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR M 87 " --> pdb=" O TYR M 36 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU M 48 " --> pdb=" O TRP M 35 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLN M 37 " --> pdb=" O TYR M 46 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N TYR M 46 " --> pdb=" O GLN M 37 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 18 through 21 removed outlier: 3.526A pdb=" N LEU M 21 " --> pdb=" O LEU M 73 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'h' and resid 33 through 40 removed outlier: 6.730A pdb=" N TRP h 34 " --> pdb=" O TYR h 50 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N TYR h 50 " --> pdb=" O TRP h 34 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N TRP h 36 " --> pdb=" O ILE h 48 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE h 48 " --> pdb=" O TRP h 36 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'h' and resid 44 through 51 current: chain 'h' and resid 100N through 100P Processing sheet with id=AE8, first strand: chain 'h' and resid 100 through 100A Processing sheet with id=AE9, first strand: chain 'l' and resid 10 through 13 Processing sheet with id=AF1, first strand: chain 'l' and resid 19 through 22 Processing sheet with id=AF2, first strand: chain 'l' and resid 45 through 48 removed outlier: 6.371A pdb=" N TRP l 35 " --> pdb=" O ILE l 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'd' and resid 33 through 40 removed outlier: 6.751A pdb=" N TRP d 34 " --> pdb=" O TYR d 50 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N TYR d 50 " --> pdb=" O TRP d 34 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N TRP d 36 " --> pdb=" O ILE d 48 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE d 48 " --> pdb=" O TRP d 36 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER d 40 " --> pdb=" O GLY d 44 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 58 through 59 current: chain 'd' and resid 100N through 100P Processing sheet with id=AF4, first strand: chain 'd' and resid 71 through 72 Processing sheet with id=AF5, first strand: chain 'd' and resid 100 through 100A Processing sheet with id=AF6, first strand: chain 'e' and resid 9 through 13 removed outlier: 5.992A pdb=" N ILE e 9 " --> pdb=" O THR e 103 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR e 105 " --> pdb=" O ILE e 9 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE e 11 " --> pdb=" O THR e 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'e' and resid 19 through 22 Processing sheet with id=AF8, first strand: chain 'e' and resid 45 through 48 removed outlier: 6.477A pdb=" N TRP e 35 " --> pdb=" O ILE e 47 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'k' and resid 5 through 7 Processing sheet with id=AG1, first strand: chain 'k' and resid 33 through 40 removed outlier: 6.740A pdb=" N TRP k 34 " --> pdb=" O TYR k 50 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N TYR k 50 " --> pdb=" O TRP k 34 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N TRP k 36 " --> pdb=" O ILE k 48 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE k 48 " --> pdb=" O TRP k 36 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'k' and resid 57 through 59 current: chain 'k' and resid 100N through 100P Processing sheet with id=AG2, first strand: chain 'k' and resid 71 through 72 Processing sheet with id=AG3, first strand: chain 'k' and resid 100 through 100A Processing sheet with id=AG4, first strand: chain 'm' and resid 9 through 13 Processing sheet with id=AG5, first strand: chain 'm' and resid 19 through 22 Processing sheet with id=AG6, first strand: chain 'm' and resid 45 through 48 removed outlier: 6.658A pdb=" N TRP m 35 " --> pdb=" O ILE m 47 " (cutoff:3.500A) 638 hydrogen bonds defined for protein. 1597 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: 5.35 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8212 1.34 - 1.47: 7471 1.47 - 1.60: 11614 1.60 - 1.72: 0 1.72 - 1.85: 186 Bond restraints: 27483 Sorted by residual: bond pdb=" N ILE A 277 " pdb=" CA ILE A 277 " ideal model delta sigma weight residual 1.459 1.509 -0.050 1.25e-02 6.40e+03 1.62e+01 bond pdb=" N ASP A 141 " pdb=" CA ASP A 141 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.70e-03 1.06e+04 9.24e+00 bond pdb=" N ASP A 140 " pdb=" CA ASP A 140 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.95e+00 bond pdb=" C SER l 67A" pdb=" N PRO l 67B" ideal model delta sigma weight residual 1.333 1.354 -0.020 1.01e-02 9.80e+03 3.97e+00 bond pdb=" N ARG A 151 " pdb=" CA ARG A 151 " ideal model delta sigma weight residual 1.459 1.479 -0.021 1.25e-02 6.40e+03 2.71e+00 ... (remaining 27478 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 36656 2.15 - 4.29: 592 4.29 - 6.44: 57 6.44 - 8.58: 12 8.58 - 10.73: 6 Bond angle restraints: 37323 Sorted by residual: angle pdb=" C ASN l 50 " pdb=" N ASN l 51 " pdb=" CA ASN l 51 " ideal model delta sigma weight residual 121.54 132.27 -10.73 1.91e+00 2.74e-01 3.16e+01 angle pdb=" C ASN m 50 " pdb=" N ASN m 51 " pdb=" CA ASN m 51 " ideal model delta sigma weight residual 121.54 131.82 -10.28 1.91e+00 2.74e-01 2.90e+01 angle pdb=" C GLY A 152 " pdb=" N GLU A 153 " pdb=" CA GLU A 153 " ideal model delta sigma weight residual 120.29 114.57 5.72 1.42e+00 4.96e-01 1.62e+01 angle pdb=" N ARG A 151 " pdb=" CA ARG A 151 " pdb=" C ARG A 151 " ideal model delta sigma weight residual 111.71 107.16 4.55 1.15e+00 7.56e-01 1.56e+01 angle pdb=" C ASN e 50 " pdb=" N ASN e 51 " pdb=" CA ASN e 51 " ideal model delta sigma weight residual 121.54 128.75 -7.21 1.91e+00 2.74e-01 1.43e+01 ... (remaining 37318 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.22: 16651 25.22 - 50.44: 1486 50.44 - 75.66: 250 75.66 - 100.88: 62 100.88 - 126.10: 47 Dihedral angle restraints: 18496 sinusoidal: 9399 harmonic: 9097 Sorted by residual: dihedral pdb=" CD ARG A 151 " pdb=" NE ARG A 151 " pdb=" CZ ARG A 151 " pdb=" NH1 ARG A 151 " ideal model delta sinusoidal sigma weight residual 0.00 85.93 -85.93 1 1.00e+01 1.00e-02 8.92e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual -86.00 -0.25 -85.75 1 1.00e+01 1.00e-02 8.89e+01 dihedral pdb=" CB CYS G 54 " pdb=" SG CYS G 54 " pdb=" SG CYS G 74 " pdb=" CB CYS G 74 " ideal model delta sinusoidal sigma weight residual 93.00 10.64 82.36 1 1.00e+01 1.00e-02 8.32e+01 ... (remaining 18493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 4599 0.140 - 0.280: 47 0.280 - 0.421: 5 0.421 - 0.561: 0 0.561 - 0.701: 1 Chirality restraints: 4652 Sorted by residual: chirality pdb=" C1 NAG z 1 " pdb=" ND2 ASN G 133 " pdb=" C2 NAG z 1 " pdb=" O5 NAG z 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" C1 NAG B 702 " pdb=" ND2 ASN B 637 " pdb=" C2 NAG B 702 " pdb=" O5 NAG B 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" C1 NAG C 702 " pdb=" ND2 ASN C 618 " pdb=" C2 NAG C 702 " pdb=" O5 NAG C 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.08e+00 ... (remaining 4649 not shown) Planarity restraints: 4574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 151 " -1.097 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG A 151 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG A 151 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 151 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 151 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER l 67A" 0.037 5.00e-02 4.00e+02 5.58e-02 4.99e+00 pdb=" N PRO l 67B" -0.097 5.00e-02 4.00e+02 pdb=" CA PRO l 67B" 0.028 5.00e-02 4.00e+02 pdb=" CD PRO l 67B" 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN l 50 " -0.010 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" C ASN l 50 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN l 50 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN l 51 " -0.012 2.00e-02 2.50e+03 ... (remaining 4571 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 6805 2.80 - 3.33: 23608 3.33 - 3.85: 43315 3.85 - 4.38: 50551 4.38 - 4.90: 88372 Nonbonded interactions: 212651 Sorted by model distance: nonbonded pdb=" O ASN l 50 " pdb=" ND2 ASN l 51 " model vdw 2.278 3.120 nonbonded pdb=" O4 NAG Z 2 " pdb=" O2 BMA Z 3 " model vdw 2.366 2.432 nonbonded pdb=" O5 MAN X 7 " pdb=" O6 MAN X 7 " model vdw 2.394 2.432 nonbonded pdb=" O2 BMA Z 3 " pdb=" O3 BMA Z 3 " model vdw 2.404 2.432 nonbonded pdb=" O5 MAN w 9 " pdb=" O6 MAN w 9 " model vdw 2.406 2.432 ... (remaining 212646 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 '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'F' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'f' selection = chain 'g' selection = chain 'i' selection = chain 'j' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 'v' selection = chain 'x' selection = chain 'z' } ncs_group { reference = (chain 'A' and (resid 31 through 102 or resid 104 through 177 or resid 179 throu \ gh 245 or resid 247 through 604)) selection = (chain 'G' and (resid 31 through 102 or resid 104 through 177 or resid 179 throu \ gh 245 or resid 247 through 604)) selection = (chain 'I' and (resid 31 through 102 or resid 104 through 177 or resid 179 throu \ gh 245 or resid 247 through 604)) } ncs_group { reference = (chain 'B' and (resid 515 through 547 or resid 569 through 651 or resid 653 thro \ ugh 664)) selection = (chain 'C' and (resid 515 through 547 or resid 569 through 651 or resid 653 thro \ ugh 664)) selection = (chain 'J' and (resid 515 through 651 or resid 653 through 664)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'U' selection = chain 'W' selection = chain 'Z' } ncs_group { reference = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'Y' selection = chain 's' selection = chain 'y' } ncs_group { reference = chain 'V' selection = chain 't' } ncs_group { reference = chain 'X' selection = chain 'u' selection = chain 'w' } ncs_group { reference = chain 'd' selection = chain 'h' selection = chain 'k' } ncs_group { reference = chain 'e' selection = chain 'l' selection = chain 'm' } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 7.910 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: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.200 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 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 : 0.003 0.050 27700 Z= 0.143 Angle : 0.726 17.857 37929 Z= 0.344 Chirality : 0.048 0.701 4652 Planarity : 0.008 0.492 4513 Dihedral : 19.160 126.100 12547 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.32 % Favored : 92.46 % Rotamer: Outliers : 5.46 % Allowed : 29.71 % Favored : 64.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.15), residues: 3132 helix: 0.57 (0.29), residues: 386 sheet: -1.26 (0.16), residues: 976 loop : -1.64 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 617 TYR 0.026 0.001 TYR B 638 PHE 0.012 0.001 PHE K 67 TRP 0.018 0.001 TRP h 34 HIS 0.003 0.001 HIS L 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (27483) covalent geometry : angle 0.65655 / 0.33 (37323) SS BOND : bond 0.00410 / 0.23 ( 45) SS BOND : angle 1.56696 / 1.07 ( 90) hydrogen bonds : bond 0.15124 / 9.82 ( 638) hydrogen bonds : angle 6.78224 / 4.66 ( 1597) link_ALPHA1-2 : bond 0.00526 / 0.30 ( 11) link_ALPHA1-2 : angle 2.50366 / 1.68 ( 33) link_ALPHA1-3 : bond 0.01035 / 0.63 ( 24) link_ALPHA1-3 : angle 1.87260 / 1.34 ( 72) link_ALPHA1-6 : bond 0.00683 / 0.41 ( 14) link_ALPHA1-6 : angle 1.61299 / 1.12 ( 42) link_BETA1-4 : bond 0.00593 / 0.36 ( 62) link_BETA1-4 : angle 2.03764 / 1.43 ( 186) link_NAG-ASN : bond 0.00525 / 0.34 ( 61) link_NAG-ASN : angle 3.55735 / 2.69 ( 183) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 317 time to evaluate : 0.878 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: A 72 HIS cc_start: 0.6585 (OUTLIER) cc_final: 0.5204 (m-70) REVERT: A 150 MET cc_start: 0.6777 (mmm) cc_final: 0.6392 (mmm) REVERT: A 151 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.5904 (tpt-90) REVERT: A 446 VAL cc_start: 0.8972 (OUTLIER) cc_final: 0.8705 (t) REVERT: A 500 ARG cc_start: 0.7707 (mtt90) cc_final: 0.7316 (mtt-85) REVERT: B 576 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7339 (mp) REVERT: B 588 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7368 (ttm170) REVERT: D 13 LYS cc_start: 0.7835 (mmmm) cc_final: 0.7083 (tppt) REVERT: D 100 ASP cc_start: 0.7752 (m-30) cc_final: 0.7032 (p0) REVERT: E 3 ILE cc_start: 0.8874 (mt) cc_final: 0.8421 (pt) REVERT: E 83 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7237 (pp20) REVERT: G 56 SER cc_start: 0.8211 (m) cc_final: 0.7198 (p) REVERT: G 66 HIS cc_start: 0.7382 (OUTLIER) cc_final: 0.6993 (m-70) REVERT: G 69 TRP cc_start: 0.7049 (OUTLIER) cc_final: 0.5858 (p90) REVERT: G 323 ILE cc_start: 0.9132 (tt) cc_final: 0.8579 (pt) REVERT: G 485 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8106 (ptmm) REVERT: H 83 ARG cc_start: 0.7985 (mtt180) cc_final: 0.7239 (mtm-85) REVERT: I 33 ASN cc_start: 0.6892 (OUTLIER) cc_final: 0.6246 (p0) REVERT: I 46 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7935 (mttp) REVERT: I 69 TRP cc_start: 0.8350 (OUTLIER) cc_final: 0.7505 (m100) REVERT: I 129 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8689 (mt) REVERT: I 153 GLU cc_start: 0.7865 (tp30) cc_final: 0.7313 (tt0) REVERT: I 164 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.6956 (mm-30) REVERT: I 189 LYS cc_start: 0.6975 (OUTLIER) cc_final: 0.6731 (mmmt) REVERT: I 303 THR cc_start: 0.9136 (m) cc_final: 0.8754 (p) REVERT: J 522 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7301 (t80) REVERT: J 588 ARG cc_start: 0.8121 (ttm170) cc_final: 0.7228 (tpt90) REVERT: K 105 GLN cc_start: 0.8328 (mm-40) cc_final: 0.8124 (mm-40) REVERT: M 78 LEU cc_start: 0.6650 (OUTLIER) cc_final: 0.6415 (tt) REVERT: h 39 ARG cc_start: 0.6154 (tpt90) cc_final: 0.5783 (tmt170) REVERT: h 43 LYS cc_start: 0.7128 (OUTLIER) cc_final: 0.6617 (ttpp) REVERT: h 51 VAL cc_start: 0.8685 (p) cc_final: 0.8197 (t) REVERT: h 69 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6781 (tt) REVERT: d 100 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8630 (mt-10) REVERT: e 20 ARG cc_start: 0.7486 (mmt-90) cc_final: 0.7194 (mmt-90) REVERT: e 39 ARG cc_start: 0.7330 (mtm-85) cc_final: 0.6968 (mtt90) REVERT: e 52 GLN cc_start: 0.8362 (mt0) cc_final: 0.8074 (mm110) REVERT: k 43 LYS cc_start: 0.5635 (OUTLIER) cc_final: 0.5077 (tptp) REVERT: k 50 TYR cc_start: 0.7661 (p90) cc_final: 0.7446 (p90) REVERT: k 56 ASP cc_start: 0.5982 (OUTLIER) cc_final: 0.4609 (t0) REVERT: k 100 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7450 (mmt) outliers start: 144 outliers final: 109 residues processed: 444 average time/residue: 0.1642 time to fit residues: 116.7331 Evaluate side-chains 444 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 312 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 425 ASN Chi-restraints excluded: chain G residue 462 ASN Chi-restraints excluded: chain G residue 485 LYS Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 189 LYS Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 249 HIS Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 462 ASN Chi-restraints excluded: chain J residue 515 ILE Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 528 SER Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 622 ILE Chi-restraints excluded: chain J residue 623 TRP Chi-restraints excluded: chain J residue 625 ASN Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain h residue 17 THR Chi-restraints excluded: chain h residue 37 ILE Chi-restraints excluded: chain h residue 43 LYS Chi-restraints excluded: chain h residue 48 ILE Chi-restraints excluded: chain h residue 53 LYS Chi-restraints excluded: chain h residue 59 TYR Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 78 VAL Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain l residue 12 SER Chi-restraints excluded: chain l residue 20 ARG Chi-restraints excluded: chain l residue 23 CYS Chi-restraints excluded: chain l residue 51 ASN Chi-restraints excluded: chain l residue 85 ASP Chi-restraints excluded: chain l residue 88 CYS Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 102 THR Chi-restraints excluded: chain d residue 37 ILE Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 69 LEU Chi-restraints excluded: chain d residue 92 CYS Chi-restraints excluded: chain d residue 100 GLU Chi-restraints excluded: chain d residue 105 THR Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 65 SER Chi-restraints excluded: chain e residue 88 CYS Chi-restraints excluded: chain e residue 95 THR Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain k residue 43 LYS Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 57 THR Chi-restraints excluded: chain k residue 59 TYR Chi-restraints excluded: chain k residue 100 THR Chi-restraints excluded: chain k residue 100 MET Chi-restraints excluded: chain m residue 88 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.0010 chunk 132 optimal weight: 0.0670 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 4.9990 overall best weight: 0.8128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.153920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.106898 restraints weight = 58339.276| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 3.76 r_work: 0.3061 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.0444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27700 Z= 0.138 Angle : 0.710 17.661 37929 Z= 0.314 Chirality : 0.048 0.677 4652 Planarity : 0.003 0.046 4513 Dihedral : 13.665 108.659 7138 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.26 % Favored : 92.52 % Rotamer: Outliers : 6.08 % Allowed : 28.82 % Favored : 65.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.15), residues: 3132 helix: 0.82 (0.29), residues: 385 sheet: -1.17 (0.16), residues: 979 loop : -1.62 (0.14), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG l 61 TYR 0.018 0.001 TYR B 638 PHE 0.013 0.001 PHE M 62 TRP 0.012 0.001 TRP A 69 HIS 0.003 0.001 HIS G 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (27483) covalent geometry : angle 0.64079 / 0.30 (37323) SS BOND : bond 0.00326 / 0.20 ( 45) SS BOND : angle 1.32551 / 0.92 ( 90) hydrogen bonds : bond 0.03849 / 2.55 ( 638) hydrogen bonds : angle 5.29167 / 3.64 ( 1597) link_ALPHA1-2 : bond 0.00736 / 0.41 ( 11) link_ALPHA1-2 : angle 2.51705 / 1.70 ( 33) link_ALPHA1-3 : bond 0.01216 / 0.74 ( 24) link_ALPHA1-3 : angle 1.98220 / 1.33 ( 72) link_ALPHA1-6 : bond 0.00894 / 0.52 ( 14) link_ALPHA1-6 : angle 2.00634 / 1.36 ( 42) link_BETA1-4 : bond 0.00573 / 0.35 ( 62) link_BETA1-4 : angle 2.03935 / 1.43 ( 186) link_NAG-ASN : bond 0.00545 / 0.34 ( 61) link_NAG-ASN : angle 3.46709 / 2.66 ( 183) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 333 time to evaluate : 0.728 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: A 72 HIS cc_start: 0.6813 (OUTLIER) cc_final: 0.5493 (m-70) REVERT: A 99 ASN cc_start: 0.8752 (t0) cc_final: 0.8537 (t0) REVERT: A 138 ILE cc_start: 0.6680 (OUTLIER) cc_final: 0.6374 (tt) REVERT: A 150 MET cc_start: 0.7143 (mmm) cc_final: 0.6921 (mmm) REVERT: A 151 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.6151 (tpt90) REVERT: A 446 VAL cc_start: 0.8995 (OUTLIER) cc_final: 0.8760 (t) REVERT: A 482 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7627 (mt-10) REVERT: A 500 ARG cc_start: 0.7830 (mtt90) cc_final: 0.7535 (mtt-85) REVERT: B 588 ARG cc_start: 0.8258 (ttt-90) cc_final: 0.7862 (ttp-170) REVERT: B 638 TYR cc_start: 0.8530 (m-10) cc_final: 0.8248 (m-10) REVERT: D 13 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7285 (tppt) REVERT: G 66 HIS cc_start: 0.7369 (OUTLIER) cc_final: 0.6993 (m-70) REVERT: G 69 TRP cc_start: 0.7543 (OUTLIER) cc_final: 0.6505 (p90) REVERT: H 83 ARG cc_start: 0.7852 (mtt180) cc_final: 0.7428 (mtm-85) REVERT: I 69 TRP cc_start: 0.8507 (OUTLIER) cc_final: 0.7687 (m100) REVERT: I 153 GLU cc_start: 0.7668 (tp30) cc_final: 0.7348 (tt0) REVERT: I 164 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7320 (mm-30) REVERT: I 189 LYS cc_start: 0.6954 (OUTLIER) cc_final: 0.6734 (mmmt) REVERT: I 334 SER cc_start: 0.8323 (t) cc_final: 0.8117 (m) REVERT: J 522 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.7186 (t80) REVERT: J 588 ARG cc_start: 0.8272 (ttm170) cc_final: 0.7728 (tpt90) REVERT: K 82 ASN cc_start: 0.7849 (t0) cc_final: 0.7309 (t0) REVERT: L 45 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.8049 (ttt180) REVERT: M 78 LEU cc_start: 0.6772 (OUTLIER) cc_final: 0.6515 (tt) REVERT: h 39 ARG cc_start: 0.6511 (tpt90) cc_final: 0.6010 (tpt90) REVERT: h 43 LYS cc_start: 0.7156 (OUTLIER) cc_final: 0.6685 (ttpp) REVERT: h 51 VAL cc_start: 0.8795 (p) cc_final: 0.8320 (t) REVERT: h 69 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7257 (tt) REVERT: e 20 ARG cc_start: 0.7536 (mmt-90) cc_final: 0.7278 (mmt-90) REVERT: k 43 LYS cc_start: 0.5668 (OUTLIER) cc_final: 0.5178 (tptp) REVERT: k 56 ASP cc_start: 0.5918 (OUTLIER) cc_final: 0.4666 (t0) REVERT: k 100 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7688 (mmt) REVERT: m 51 ASN cc_start: 0.8467 (OUTLIER) cc_final: 0.8162 (p0) outliers start: 161 outliers final: 93 residues processed: 469 average time/residue: 0.1590 time to fit residues: 120.2262 Evaluate side-chains 434 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 321 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 385 CYS Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 462 ASN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 189 LYS Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 249 HIS Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 432 GLN Chi-restraints excluded: chain I residue 462 ASN Chi-restraints excluded: chain I residue 464 THR Chi-restraints excluded: chain J residue 515 ILE Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 622 ILE Chi-restraints excluded: chain J residue 623 TRP Chi-restraints excluded: chain J residue 625 ASN Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain h residue 17 THR Chi-restraints excluded: chain h residue 37 ILE Chi-restraints excluded: chain h residue 43 LYS Chi-restraints excluded: chain h residue 48 ILE Chi-restraints excluded: chain h residue 53 LYS Chi-restraints excluded: chain h residue 59 TYR Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 71 LEU Chi-restraints excluded: chain h residue 78 VAL Chi-restraints excluded: chain l residue 58 ILE Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 75 ILE Chi-restraints excluded: chain l residue 88 CYS Chi-restraints excluded: chain l residue 102 THR Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 37 ILE Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 69 LEU Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 70 THR Chi-restraints excluded: chain e residue 75 ILE Chi-restraints excluded: chain e residue 88 CYS Chi-restraints excluded: chain e residue 95 THR Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain k residue 43 LYS Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 59 TYR Chi-restraints excluded: chain k residue 60 SER Chi-restraints excluded: chain k residue 79 SER Chi-restraints excluded: chain k residue 100 MET Chi-restraints excluded: chain m residue 13 VAL Chi-restraints excluded: chain m residue 51 ASN Chi-restraints excluded: chain m residue 95 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 133 optimal weight: 0.8980 chunk 224 optimal weight: 0.0470 chunk 262 optimal weight: 10.0000 chunk 146 optimal weight: 0.5980 chunk 170 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 288 optimal weight: 30.0000 chunk 272 optimal weight: 0.6980 chunk 191 optimal weight: 0.8980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 GLN D 82BASN ** l 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.154712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.107510 restraints weight = 66583.140| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 4.05 r_work: 0.3059 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.0622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27700 Z= 0.126 Angle : 0.694 17.644 37929 Z= 0.308 Chirality : 0.047 0.663 4652 Planarity : 0.003 0.049 4513 Dihedral : 12.391 108.393 7029 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.03 % Favored : 92.71 % Rotamer: Outliers : 6.12 % Allowed : 28.57 % Favored : 65.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.15), residues: 3132 helix: 0.97 (0.29), residues: 385 sheet: -1.03 (0.17), residues: 952 loop : -1.63 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 83 TYR 0.014 0.001 TYR k 50 PHE 0.010 0.001 PHE d 100K TRP 0.013 0.001 TRP A 69 HIS 0.003 0.001 HIS G 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (27483) covalent geometry : angle 0.62862 / 0.29 (37323) SS BOND : bond 0.00291 / 0.18 ( 45) SS BOND : angle 1.14991 / 0.79 ( 90) hydrogen bonds : bond 0.03512 / 2.34 ( 638) hydrogen bonds : angle 4.97634 / 3.42 ( 1597) link_ALPHA1-2 : bond 0.00779 / 0.45 ( 11) link_ALPHA1-2 : angle 2.55540 / 1.71 ( 33) link_ALPHA1-3 : bond 0.01221 / 0.75 ( 24) link_ALPHA1-3 : angle 1.94187 / 1.28 ( 72) link_ALPHA1-6 : bond 0.00976 / 0.58 ( 14) link_ALPHA1-6 : angle 2.08335 / 1.42 ( 42) link_BETA1-4 : bond 0.00587 / 0.36 ( 62) link_BETA1-4 : angle 1.98278 / 1.39 ( 186) link_NAG-ASN : bond 0.00549 / 0.34 ( 61) link_NAG-ASN : angle 3.30756 / 2.55 ( 183) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 323 time to evaluate : 0.991 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: A 57 ASP cc_start: 0.8520 (t0) cc_final: 0.8281 (t70) REVERT: A 72 HIS cc_start: 0.6807 (OUTLIER) cc_final: 0.5515 (m-70) REVERT: A 138 ILE cc_start: 0.6675 (OUTLIER) cc_final: 0.6409 (tt) REVERT: A 150 MET cc_start: 0.7174 (mmm) cc_final: 0.6938 (mmm) REVERT: A 151 ARG cc_start: 0.7091 (OUTLIER) cc_final: 0.5889 (mmm-85) REVERT: A 482 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7628 (mt-10) REVERT: B 588 ARG cc_start: 0.8302 (ttt-90) cc_final: 0.7936 (ttm170) REVERT: B 638 TYR cc_start: 0.8549 (m-10) cc_final: 0.8315 (m-10) REVERT: D 13 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7258 (tppt) REVERT: G 66 HIS cc_start: 0.7396 (OUTLIER) cc_final: 0.7054 (m-70) REVERT: G 69 TRP cc_start: 0.7630 (OUTLIER) cc_final: 0.6488 (p90) REVERT: H 3 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.8086 (pt0) REVERT: H 83 ARG cc_start: 0.7893 (mtt180) cc_final: 0.7495 (mtm-85) REVERT: I 33 ASN cc_start: 0.7122 (OUTLIER) cc_final: 0.6557 (p0) REVERT: I 69 TRP cc_start: 0.8498 (OUTLIER) cc_final: 0.7673 (m100) REVERT: I 153 GLU cc_start: 0.7688 (tp30) cc_final: 0.7344 (tt0) REVERT: I 164 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7394 (mm-30) REVERT: I 213 ILE cc_start: 0.8656 (mm) cc_final: 0.8425 (mt) REVERT: J 522 PHE cc_start: 0.7728 (OUTLIER) cc_final: 0.7135 (t80) REVERT: J 588 ARG cc_start: 0.8302 (ttm170) cc_final: 0.7763 (tpt90) REVERT: K 19 ARG cc_start: 0.8308 (ttt-90) cc_final: 0.8085 (ttt90) REVERT: L 45 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8099 (ttt180) REVERT: h 39 ARG cc_start: 0.6611 (tpt90) cc_final: 0.6191 (tpt90) REVERT: h 43 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6720 (ttpp) REVERT: h 51 VAL cc_start: 0.8787 (p) cc_final: 0.8342 (t) REVERT: h 69 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7409 (tt) REVERT: d 100 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8481 (mt-10) REVERT: e 20 ARG cc_start: 0.7552 (mmt-90) cc_final: 0.7307 (mmt-90) REVERT: k 100 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7752 (mmt) outliers start: 162 outliers final: 107 residues processed: 457 average time/residue: 0.1621 time to fit residues: 119.1780 Evaluate side-chains 440 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 316 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 234 ASN Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 385 CYS Chi-restraints excluded: chain G residue 462 ASN Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 249 HIS Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 432 GLN Chi-restraints excluded: chain I residue 444 ARG Chi-restraints excluded: chain I residue 462 ASN Chi-restraints excluded: chain I residue 464 THR Chi-restraints excluded: chain J residue 515 ILE Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 622 ILE Chi-restraints excluded: chain J residue 623 TRP Chi-restraints excluded: chain J residue 625 ASN Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain h residue 17 THR Chi-restraints excluded: chain h residue 37 ILE Chi-restraints excluded: chain h residue 43 LYS Chi-restraints excluded: chain h residue 48 ILE Chi-restraints excluded: chain h residue 53 LYS Chi-restraints excluded: chain h residue 63 LEU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain l residue 58 ILE Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 75 ILE Chi-restraints excluded: chain l residue 85 ASP Chi-restraints excluded: chain l residue 88 CYS Chi-restraints excluded: chain l residue 102 THR Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 37 ILE Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 69 LEU Chi-restraints excluded: chain d residue 79 SER Chi-restraints excluded: chain d residue 100 GLU Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 75 ILE Chi-restraints excluded: chain e residue 88 CYS Chi-restraints excluded: chain e residue 95 THR Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain k residue 59 TYR Chi-restraints excluded: chain k residue 60 SER Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 100 THR Chi-restraints excluded: chain k residue 100 MET Chi-restraints excluded: chain m residue 13 VAL Chi-restraints excluded: chain m residue 51 ASN Chi-restraints excluded: chain m residue 88 CYS Chi-restraints excluded: chain m residue 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 34 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 270 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 241 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 222 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 GLN D 82BASN I 183 GLN ** l 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 51 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.150653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.103682 restraints weight = 50532.866| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 3.23 r_work: 0.3003 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 27700 Z= 0.248 Angle : 0.797 18.228 37929 Z= 0.358 Chirality : 0.050 0.716 4652 Planarity : 0.004 0.047 4513 Dihedral : 12.144 109.211 7010 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.15 % Favored : 91.62 % Rotamer: Outliers : 7.52 % Allowed : 27.05 % Favored : 65.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.15), residues: 3132 helix: 0.76 (0.29), residues: 376 sheet: -1.21 (0.17), residues: 958 loop : -1.70 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 83 TYR 0.016 0.002 TYR D 50 PHE 0.018 0.002 PHE G 383 TRP 0.017 0.001 TRP h 34 HIS 0.005 0.001 HIS G 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.25 (27483) covalent geometry : angle 0.72079 / 0.34 (37323) SS BOND : bond 0.00452 / 0.28 ( 45) SS BOND : angle 1.51868 / 1.06 ( 90) hydrogen bonds : bond 0.04368 / 2.90 ( 638) hydrogen bonds : angle 5.12347 / 3.53 ( 1597) link_ALPHA1-2 : bond 0.00644 / 0.37 ( 11) link_ALPHA1-2 : angle 2.66001 / 1.78 ( 33) link_ALPHA1-3 : bond 0.01172 / 0.72 ( 24) link_ALPHA1-3 : angle 2.01581 / 1.32 ( 72) link_ALPHA1-6 : bond 0.00939 / 0.55 ( 14) link_ALPHA1-6 : angle 2.03306 / 1.38 ( 42) link_BETA1-4 : bond 0.00541 / 0.33 ( 62) link_BETA1-4 : angle 2.23445 / 1.56 ( 186) link_NAG-ASN : bond 0.00587 / 0.37 ( 61) link_NAG-ASN : angle 3.94127 / 3.01 ( 183) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 312 time to evaluate : 0.922 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: A 72 HIS cc_start: 0.6941 (OUTLIER) cc_final: 0.6564 (p90) REVERT: A 138 ILE cc_start: 0.6773 (OUTLIER) cc_final: 0.6424 (tt) REVERT: A 150 MET cc_start: 0.7508 (mmm) cc_final: 0.7169 (mmm) REVERT: A 151 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.5968 (mmt180) REVERT: A 482 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7739 (mt-10) REVERT: A 500 ARG cc_start: 0.7838 (mtt90) cc_final: 0.7609 (mtt-85) REVERT: B 588 ARG cc_start: 0.8299 (ttt-90) cc_final: 0.7943 (ttm170) REVERT: B 638 TYR cc_start: 0.8587 (m-10) cc_final: 0.8372 (m-10) REVERT: D 13 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7310 (tppt) REVERT: E 51 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8445 (tttp) REVERT: E 83 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7329 (pp20) REVERT: G 66 HIS cc_start: 0.7490 (OUTLIER) cc_final: 0.7129 (m-70) REVERT: G 69 TRP cc_start: 0.7654 (OUTLIER) cc_final: 0.6823 (p90) REVERT: G 323 ILE cc_start: 0.9240 (tt) cc_final: 0.8843 (pt) REVERT: H 3 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8137 (pt0) REVERT: H 83 ARG cc_start: 0.7907 (mtt180) cc_final: 0.7548 (mtm-85) REVERT: I 33 ASN cc_start: 0.7257 (OUTLIER) cc_final: 0.6744 (p0) REVERT: I 69 TRP cc_start: 0.8587 (OUTLIER) cc_final: 0.7813 (m100) REVERT: I 86 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7923 (mt) REVERT: I 153 GLU cc_start: 0.7663 (tp30) cc_final: 0.7386 (tt0) REVERT: J 522 PHE cc_start: 0.7824 (OUTLIER) cc_final: 0.7245 (t80) REVERT: J 588 ARG cc_start: 0.8312 (ttm170) cc_final: 0.7749 (tpt90) REVERT: L 45 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8204 (ttt180) REVERT: M 54 ASP cc_start: 0.8526 (t0) cc_final: 0.8243 (t0) REVERT: M 78 LEU cc_start: 0.6732 (OUTLIER) cc_final: 0.6482 (tt) REVERT: h 39 ARG cc_start: 0.6629 (tpt90) cc_final: 0.6234 (tpt90) REVERT: h 43 LYS cc_start: 0.7257 (OUTLIER) cc_final: 0.6753 (ttpp) REVERT: h 51 VAL cc_start: 0.8798 (p) cc_final: 0.8397 (t) REVERT: h 69 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7356 (tt) REVERT: h 100 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8264 (mt-10) REVERT: d 100 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8623 (mt-10) REVERT: e 20 ARG cc_start: 0.7500 (mmt-90) cc_final: 0.7247 (mmt-90) REVERT: k 100 MET cc_start: 0.7946 (mmt) cc_final: 0.7329 (mmt) REVERT: m 85 ASP cc_start: 0.6781 (OUTLIER) cc_final: 0.6086 (m-30) outliers start: 200 outliers final: 140 residues processed: 482 average time/residue: 0.1645 time to fit residues: 127.8546 Evaluate side-chains 469 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 308 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 234 ASN Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 280 ASN Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 462 ASN Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 231 LYS Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 249 HIS Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 432 GLN Chi-restraints excluded: chain I residue 444 ARG Chi-restraints excluded: chain I residue 464 THR Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain I residue 504 ARG Chi-restraints excluded: chain J residue 515 ILE Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 529 THR Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 622 ILE Chi-restraints excluded: chain J residue 623 TRP Chi-restraints excluded: chain J residue 625 ASN Chi-restraints excluded: chain J residue 630 GLN Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain h residue 17 THR Chi-restraints excluded: chain h residue 37 ILE Chi-restraints excluded: chain h residue 43 LYS Chi-restraints excluded: chain h residue 48 ILE Chi-restraints excluded: chain h residue 53 LYS Chi-restraints excluded: chain h residue 59 TYR Chi-restraints excluded: chain h residue 63 LEU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 71 LEU Chi-restraints excluded: chain h residue 78 VAL Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain h residue 100 GLU Chi-restraints excluded: chain h residue 100 THR Chi-restraints excluded: chain l residue 58 ILE Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 72 THR Chi-restraints excluded: chain l residue 75 ILE Chi-restraints excluded: chain l residue 85 ASP Chi-restraints excluded: chain l residue 88 CYS Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 102 THR Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 37 ILE Chi-restraints excluded: chain d residue 46 GLU Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 79 SER Chi-restraints excluded: chain d residue 100 GLU Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 58 ILE Chi-restraints excluded: chain e residue 70 THR Chi-restraints excluded: chain e residue 75 ILE Chi-restraints excluded: chain e residue 88 CYS Chi-restraints excluded: chain e residue 95 THR Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 59 TYR Chi-restraints excluded: chain k residue 60 SER Chi-restraints excluded: chain k residue 79 SER Chi-restraints excluded: chain k residue 100 THR Chi-restraints excluded: chain m residue 13 VAL Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain m residue 85 ASP Chi-restraints excluded: chain m residue 88 CYS Chi-restraints excluded: chain m residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 281 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 310 optimal weight: 6.9990 chunk 86 optimal weight: 0.0050 chunk 28 optimal weight: 0.7980 chunk 297 optimal weight: 5.9990 chunk 119 optimal weight: 0.6980 chunk 174 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 301 optimal weight: 0.0570 chunk 252 optimal weight: 2.9990 overall best weight: 0.9114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 HIS ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 GLN D 82BASN ** l 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 50 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.153424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.105855 restraints weight = 65076.214| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.94 r_work: 0.3037 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27700 Z= 0.146 Angle : 0.718 17.946 37929 Z= 0.321 Chirality : 0.047 0.684 4652 Planarity : 0.003 0.040 4513 Dihedral : 11.550 109.479 6999 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.00 % Favored : 92.81 % Rotamer: Outliers : 6.16 % Allowed : 28.23 % Favored : 65.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.15), residues: 3132 helix: 1.09 (0.30), residues: 370 sheet: -1.10 (0.17), residues: 943 loop : -1.65 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 83 TYR 0.010 0.001 TYR e 49 PHE 0.011 0.001 PHE G 383 TRP 0.017 0.001 TRP h 34 HIS 0.003 0.001 HIS G 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (27483) covalent geometry : angle 0.64898 / 0.30 (37323) SS BOND : bond 0.00339 / 0.22 ( 45) SS BOND : angle 1.34195 / 0.94 ( 90) hydrogen bonds : bond 0.03634 / 2.43 ( 638) hydrogen bonds : angle 4.89413 / 3.36 ( 1597) link_ALPHA1-2 : bond 0.00764 / 0.44 ( 11) link_ALPHA1-2 : angle 2.58816 / 1.74 ( 33) link_ALPHA1-3 : bond 0.01251 / 0.77 ( 24) link_ALPHA1-3 : angle 1.86948 / 1.18 ( 72) link_ALPHA1-6 : bond 0.01051 / 0.60 ( 14) link_ALPHA1-6 : angle 1.94213 / 1.36 ( 42) link_BETA1-4 : bond 0.00572 / 0.35 ( 62) link_BETA1-4 : angle 2.04636 / 1.44 ( 186) link_NAG-ASN : bond 0.00530 / 0.34 ( 61) link_NAG-ASN : angle 3.53641 / 2.72 ( 183) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 318 time to evaluate : 0.890 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: A 72 HIS cc_start: 0.6732 (OUTLIER) cc_final: 0.5524 (m-70) REVERT: A 99 ASN cc_start: 0.8743 (t0) cc_final: 0.8515 (t0) REVERT: A 150 MET cc_start: 0.7369 (mmm) cc_final: 0.7029 (mmm) REVERT: A 482 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7653 (mt-10) REVERT: B 576 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7613 (mp) REVERT: B 588 ARG cc_start: 0.8299 (ttt-90) cc_final: 0.7958 (ttm170) REVERT: D 13 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7252 (tppt) REVERT: G 66 HIS cc_start: 0.7429 (OUTLIER) cc_final: 0.7032 (m-70) REVERT: G 69 TRP cc_start: 0.7622 (OUTLIER) cc_final: 0.6665 (p90) REVERT: G 323 ILE cc_start: 0.9242 (tt) cc_final: 0.8856 (pt) REVERT: H 3 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.8112 (pt0) REVERT: H 83 ARG cc_start: 0.7864 (mtt180) cc_final: 0.7480 (mtm-85) REVERT: I 33 ASN cc_start: 0.7133 (OUTLIER) cc_final: 0.6585 (p0) REVERT: I 69 TRP cc_start: 0.8535 (OUTLIER) cc_final: 0.7771 (m100) REVERT: I 153 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7352 (tt0) REVERT: J 522 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.7213 (t80) REVERT: J 588 ARG cc_start: 0.8230 (ttm170) cc_final: 0.7714 (tpt90) REVERT: K 19 ARG cc_start: 0.8268 (ttt-90) cc_final: 0.8040 (ttt90) REVERT: L 45 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8135 (ttt180) REVERT: M 54 ASP cc_start: 0.8398 (t0) cc_final: 0.8114 (t0) REVERT: M 78 LEU cc_start: 0.6728 (OUTLIER) cc_final: 0.6465 (tt) REVERT: h 43 LYS cc_start: 0.7276 (OUTLIER) cc_final: 0.6803 (ttpp) REVERT: h 51 VAL cc_start: 0.8789 (p) cc_final: 0.8424 (t) REVERT: h 69 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7316 (tt) REVERT: h 100 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8229 (mt-10) REVERT: d 100 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8610 (mt-10) REVERT: e 20 ARG cc_start: 0.7542 (mmt-90) cc_final: 0.7272 (mmt-90) REVERT: k 100 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7377 (mmt) outliers start: 162 outliers final: 124 residues processed: 454 average time/residue: 0.1637 time to fit residues: 119.7560 Evaluate side-chains 448 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 306 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 462 ASN Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 153 GLU Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 249 HIS Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 385 CYS Chi-restraints excluded: chain I residue 432 GLN Chi-restraints excluded: chain I residue 462 ASN Chi-restraints excluded: chain I residue 464 THR Chi-restraints excluded: chain I residue 504 ARG Chi-restraints excluded: chain J residue 515 ILE Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 529 THR Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 622 ILE Chi-restraints excluded: chain J residue 623 TRP Chi-restraints excluded: chain J residue 625 ASN Chi-restraints excluded: chain J residue 630 GLN Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain h residue 17 THR Chi-restraints excluded: chain h residue 37 ILE Chi-restraints excluded: chain h residue 43 LYS Chi-restraints excluded: chain h residue 53 LYS Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 78 VAL Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain h residue 100 GLU Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 75 ILE Chi-restraints excluded: chain l residue 85 ASP Chi-restraints excluded: chain l residue 88 CYS Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 95 THR Chi-restraints excluded: chain l residue 102 THR Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 37 ILE Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 79 SER Chi-restraints excluded: chain d residue 100 GLU Chi-restraints excluded: chain d residue 103 ASN Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 70 THR Chi-restraints excluded: chain e residue 75 ILE Chi-restraints excluded: chain e residue 88 CYS Chi-restraints excluded: chain e residue 95 THR Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain k residue 57 THR Chi-restraints excluded: chain k residue 59 TYR Chi-restraints excluded: chain k residue 60 SER Chi-restraints excluded: chain k residue 79 SER Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 100 THR Chi-restraints excluded: chain k residue 100 MET Chi-restraints excluded: chain m residue 13 VAL Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain m residue 88 CYS Chi-restraints excluded: chain m residue 95 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 44 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 271 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 144 optimal weight: 0.0270 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 GLN l 8 GLN ** l 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.153193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.106107 restraints weight = 58888.166| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.66 r_work: 0.3053 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27700 Z= 0.147 Angle : 0.709 17.820 37929 Z= 0.317 Chirality : 0.047 0.678 4652 Planarity : 0.003 0.041 4513 Dihedral : 11.150 109.145 6992 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.70 % Favored : 92.10 % Rotamer: Outliers : 7.08 % Allowed : 27.64 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.15), residues: 3132 helix: 1.03 (0.30), residues: 376 sheet: -1.11 (0.17), residues: 961 loop : -1.60 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG h 39 TYR 0.036 0.001 TYR B 638 PHE 0.011 0.001 PHE A 317 TRP 0.018 0.001 TRP h 34 HIS 0.003 0.001 HIS G 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (27483) covalent geometry : angle 0.64010 / 0.30 (37323) SS BOND : bond 0.00338 / 0.22 ( 45) SS BOND : angle 1.31324 / 0.91 ( 90) hydrogen bonds : bond 0.03559 / 2.37 ( 638) hydrogen bonds : angle 4.79621 / 3.29 ( 1597) link_ALPHA1-2 : bond 0.00793 / 0.46 ( 11) link_ALPHA1-2 : angle 2.64789 / 1.76 ( 33) link_ALPHA1-3 : bond 0.01234 / 0.78 ( 24) link_ALPHA1-3 : angle 1.86320 / 1.18 ( 72) link_ALPHA1-6 : bond 0.01017 / 0.56 ( 14) link_ALPHA1-6 : angle 1.86973 / 1.35 ( 42) link_BETA1-4 : bond 0.00564 / 0.34 ( 62) link_BETA1-4 : angle 2.04326 / 1.43 ( 186) link_NAG-ASN : bond 0.00511 / 0.33 ( 61) link_NAG-ASN : angle 3.47953 / 2.69 ( 183) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 315 time to evaluate : 0.772 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: A 72 HIS cc_start: 0.6739 (OUTLIER) cc_final: 0.5519 (m-70) REVERT: A 150 MET cc_start: 0.7420 (mmm) cc_final: 0.6984 (mmm) REVERT: A 151 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.5910 (mmm-85) REVERT: A 482 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7678 (mt-10) REVERT: B 576 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7643 (mp) REVERT: B 588 ARG cc_start: 0.8292 (ttt-90) cc_final: 0.7905 (ttm170) REVERT: B 638 TYR cc_start: 0.8354 (m-10) cc_final: 0.8106 (m-10) REVERT: C 624 ASP cc_start: 0.8444 (m-30) cc_final: 0.8152 (m-30) REVERT: D 13 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7243 (tppt) REVERT: E 51 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8378 (tttp) REVERT: E 83 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7152 (pp20) REVERT: G 66 HIS cc_start: 0.7361 (OUTLIER) cc_final: 0.6998 (m-70) REVERT: G 69 TRP cc_start: 0.7603 (OUTLIER) cc_final: 0.6627 (p90) REVERT: G 323 ILE cc_start: 0.9255 (tt) cc_final: 0.8851 (pt) REVERT: H 3 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8100 (pt0) REVERT: H 83 ARG cc_start: 0.7904 (mtt180) cc_final: 0.7504 (mtm-85) REVERT: I 33 ASN cc_start: 0.7145 (OUTLIER) cc_final: 0.6585 (p0) REVERT: I 69 TRP cc_start: 0.8540 (OUTLIER) cc_final: 0.7772 (m100) REVERT: I 87 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: I 153 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7350 (tt0) REVERT: J 522 PHE cc_start: 0.7664 (OUTLIER) cc_final: 0.7145 (t80) REVERT: J 588 ARG cc_start: 0.8214 (ttm170) cc_final: 0.7672 (tpt90) REVERT: K 19 ARG cc_start: 0.8279 (ttt-90) cc_final: 0.8060 (ttt90) REVERT: K 34 MET cc_start: 0.9060 (mmm) cc_final: 0.8744 (mmt) REVERT: L 45 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8092 (ttt180) REVERT: M 54 ASP cc_start: 0.8401 (t0) cc_final: 0.8110 (t0) REVERT: M 78 LEU cc_start: 0.6702 (OUTLIER) cc_final: 0.6451 (tt) REVERT: h 43 LYS cc_start: 0.7308 (OUTLIER) cc_final: 0.6779 (ttpp) REVERT: h 51 VAL cc_start: 0.8792 (p) cc_final: 0.8438 (t) REVERT: h 69 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7316 (tt) REVERT: h 100 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8202 (mt-10) REVERT: d 100 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8588 (mt-10) REVERT: e 20 ARG cc_start: 0.7513 (mmt-90) cc_final: 0.7251 (mmt-90) REVERT: k 100 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7272 (mmt) outliers start: 186 outliers final: 133 residues processed: 470 average time/residue: 0.1606 time to fit residues: 122.0306 Evaluate side-chains 462 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 307 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 280 ASN Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 462 ASN Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 126 CYS Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 153 GLU Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 249 HIS Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 334 SER Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 385 CYS Chi-restraints excluded: chain I residue 432 GLN Chi-restraints excluded: chain I residue 462 ASN Chi-restraints excluded: chain I residue 464 THR Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain I residue 504 ARG Chi-restraints excluded: chain J residue 515 ILE Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 529 THR Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 623 TRP Chi-restraints excluded: chain J residue 625 ASN Chi-restraints excluded: chain J residue 630 GLN Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain M residue 72 ILE Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain h residue 17 THR Chi-restraints excluded: chain h residue 37 ILE Chi-restraints excluded: chain h residue 43 LYS Chi-restraints excluded: chain h residue 53 LYS Chi-restraints excluded: chain h residue 63 LEU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 71 LEU Chi-restraints excluded: chain h residue 78 VAL Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain h residue 100 GLU Chi-restraints excluded: chain l residue 20 ARG Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 75 ILE Chi-restraints excluded: chain l residue 85 ASP Chi-restraints excluded: chain l residue 88 CYS Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 95 THR Chi-restraints excluded: chain l residue 102 THR Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 37 ILE Chi-restraints excluded: chain d residue 46 GLU Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 79 SER Chi-restraints excluded: chain d residue 100 GLU Chi-restraints excluded: chain d residue 103 ASN Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 70 THR Chi-restraints excluded: chain e residue 75 ILE Chi-restraints excluded: chain e residue 88 CYS Chi-restraints excluded: chain e residue 95 THR Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 57 THR Chi-restraints excluded: chain k residue 59 TYR Chi-restraints excluded: chain k residue 60 SER Chi-restraints excluded: chain k residue 79 SER Chi-restraints excluded: chain k residue 100 THR Chi-restraints excluded: chain k residue 100 MET Chi-restraints excluded: chain m residue 13 VAL Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain m residue 88 CYS Chi-restraints excluded: chain m residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 51 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 228 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 251 optimal weight: 8.9990 chunk 292 optimal weight: 9.9990 chunk 224 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 GLN C 616 ASN ** l 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.149220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.101595 restraints weight = 53277.715| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.53 r_work: 0.3006 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 27700 Z= 0.308 Angle : 0.840 18.519 37929 Z= 0.381 Chirality : 0.052 0.739 4652 Planarity : 0.004 0.057 4513 Dihedral : 11.566 109.191 6990 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.70 % Favored : 91.11 % Rotamer: Outliers : 7.41 % Allowed : 27.42 % Favored : 65.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.15), residues: 3132 helix: 0.36 (0.28), residues: 394 sheet: -1.25 (0.17), residues: 955 loop : -1.73 (0.14), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG h 39 TYR 0.023 0.002 TYR B 638 PHE 0.021 0.002 PHE G 383 TRP 0.015 0.002 TRP h 34 HIS 0.005 0.001 HIS K 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00742 / 0.31 (27483) covalent geometry : angle 0.76218 / 0.36 (37323) SS BOND : bond 0.00545 / 0.35 ( 45) SS BOND : angle 1.76835 / 1.23 ( 90) hydrogen bonds : bond 0.04662 / 3.10 ( 638) hydrogen bonds : angle 5.14267 / 3.54 ( 1597) link_ALPHA1-2 : bond 0.00668 / 0.40 ( 11) link_ALPHA1-2 : angle 2.76924 / 1.83 ( 33) link_ALPHA1-3 : bond 0.01170 / 0.75 ( 24) link_ALPHA1-3 : angle 1.97679 / 1.28 ( 72) link_ALPHA1-6 : bond 0.00897 / 0.50 ( 14) link_ALPHA1-6 : angle 1.93729 / 1.39 ( 42) link_BETA1-4 : bond 0.00547 / 0.33 ( 62) link_BETA1-4 : angle 2.35565 / 1.66 ( 186) link_NAG-ASN : bond 0.00667 / 0.42 ( 61) link_NAG-ASN : angle 4.10510 / 3.08 ( 183) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 300 time to evaluate : 0.899 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: A 72 HIS cc_start: 0.7093 (OUTLIER) cc_final: 0.6557 (p-80) REVERT: A 150 MET cc_start: 0.7565 (mmm) cc_final: 0.7129 (mmm) REVERT: A 151 ARG cc_start: 0.7180 (OUTLIER) cc_final: 0.5813 (mmm160) REVERT: B 576 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7943 (mp) REVERT: B 588 ARG cc_start: 0.8497 (ttt-90) cc_final: 0.8013 (ttm170) REVERT: D 13 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7227 (tppt) REVERT: E 51 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8469 (tttp) REVERT: E 83 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7489 (pp20) REVERT: G 66 HIS cc_start: 0.7469 (OUTLIER) cc_final: 0.7067 (m-70) REVERT: G 69 TRP cc_start: 0.7717 (OUTLIER) cc_final: 0.7037 (p90) REVERT: G 323 ILE cc_start: 0.9318 (tt) cc_final: 0.8854 (pt) REVERT: G 485 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8591 (ptmm) REVERT: H 3 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8201 (pt0) REVERT: I 33 ASN cc_start: 0.7253 (OUTLIER) cc_final: 0.6745 (p0) REVERT: I 69 TRP cc_start: 0.8611 (OUTLIER) cc_final: 0.7871 (m100) REVERT: I 86 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8021 (mt) REVERT: I 87 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7252 (mp0) REVERT: I 153 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7659 (tt0) REVERT: J 522 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.7524 (t80) REVERT: J 588 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7830 (tpt90) REVERT: L 45 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8342 (ttt180) REVERT: M 54 ASP cc_start: 0.8749 (t0) cc_final: 0.8444 (t0) REVERT: M 78 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6404 (tt) REVERT: h 43 LYS cc_start: 0.7356 (OUTLIER) cc_final: 0.6829 (ttpp) REVERT: h 51 VAL cc_start: 0.8831 (p) cc_final: 0.8513 (t) REVERT: h 69 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7159 (tt) REVERT: h 95 THR cc_start: 0.6814 (t) cc_final: 0.6603 (t) REVERT: h 100 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8410 (mt-10) REVERT: d 100 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8738 (mt-10) REVERT: k 21 THR cc_start: 0.6569 (OUTLIER) cc_final: 0.6358 (m) REVERT: k 100 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.6922 (mmt) outliers start: 196 outliers final: 142 residues processed: 466 average time/residue: 0.1626 time to fit residues: 122.1664 Evaluate side-chains 459 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 292 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 51 LYS Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 280 ASN Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 462 ASN Chi-restraints excluded: chain G residue 485 LYS Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 126 CYS Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 153 GLU Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 231 LYS Chi-restraints excluded: chain I residue 249 HIS Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 334 SER Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 462 ASN Chi-restraints excluded: chain I residue 464 THR Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain I residue 504 ARG Chi-restraints excluded: chain J residue 515 ILE Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 529 THR Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 588 ARG Chi-restraints excluded: chain J residue 622 ILE Chi-restraints excluded: chain J residue 623 TRP Chi-restraints excluded: chain J residue 625 ASN Chi-restraints excluded: chain J residue 630 GLN Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain M residue 72 ILE Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain h residue 17 THR Chi-restraints excluded: chain h residue 37 ILE Chi-restraints excluded: chain h residue 43 LYS Chi-restraints excluded: chain h residue 53 LYS Chi-restraints excluded: chain h residue 63 LEU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 71 LEU Chi-restraints excluded: chain h residue 78 VAL Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 100 GLU Chi-restraints excluded: chain l residue 58 ILE Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 72 THR Chi-restraints excluded: chain l residue 75 ILE Chi-restraints excluded: chain l residue 85 ASP Chi-restraints excluded: chain l residue 88 CYS Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 95 THR Chi-restraints excluded: chain l residue 102 THR Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 15 SER Chi-restraints excluded: chain d residue 37 ILE Chi-restraints excluded: chain d residue 46 GLU Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 78 VAL Chi-restraints excluded: chain d residue 79 SER Chi-restraints excluded: chain d residue 92 CYS Chi-restraints excluded: chain d residue 100 GLU Chi-restraints excluded: chain d residue 103 ASN Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 58 ILE Chi-restraints excluded: chain e residue 70 THR Chi-restraints excluded: chain e residue 75 ILE Chi-restraints excluded: chain e residue 88 CYS Chi-restraints excluded: chain e residue 95 THR Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain k residue 21 THR Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 57 THR Chi-restraints excluded: chain k residue 59 TYR Chi-restraints excluded: chain k residue 60 SER Chi-restraints excluded: chain k residue 79 SER Chi-restraints excluded: chain k residue 100 THR Chi-restraints excluded: chain k residue 100 MET Chi-restraints excluded: chain m residue 13 VAL Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain m residue 88 CYS Chi-restraints excluded: chain m residue 95 VAL Chi-restraints excluded: chain m residue 97 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 0 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 239 optimal weight: 5.9990 chunk 262 optimal weight: 9.9990 chunk 148 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 253 optimal weight: 0.6980 chunk 64 optimal weight: 0.0570 chunk 126 optimal weight: 1.9990 chunk 225 optimal weight: 0.6980 chunk 200 optimal weight: 0.6980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 575 GLN B 640 GLN M 69 ASN ** l 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 51 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.153744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.115344 restraints weight = 48533.681| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 4.29 r_work: 0.3011 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27700 Z= 0.127 Angle : 0.710 17.742 37929 Z= 0.320 Chirality : 0.047 0.674 4652 Planarity : 0.003 0.044 4513 Dihedral : 10.968 109.583 6989 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.81 % Favored : 93.00 % Rotamer: Outliers : 5.75 % Allowed : 29.64 % Favored : 64.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.15), residues: 3132 helix: 1.11 (0.30), residues: 370 sheet: -1.08 (0.17), residues: 925 loop : -1.65 (0.14), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG h 39 TYR 0.042 0.001 TYR B 638 PHE 0.011 0.001 PHE H 67 TRP 0.022 0.001 TRP h 34 HIS 0.003 0.001 HIS L 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (27483) covalent geometry : angle 0.64232 / 0.30 (37323) SS BOND : bond 0.00385 / 0.25 ( 45) SS BOND : angle 1.43406 / 0.93 ( 90) hydrogen bonds : bond 0.03480 / 2.32 ( 638) hydrogen bonds : angle 4.80086 / 3.29 ( 1597) link_ALPHA1-2 : bond 0.00939 / 0.55 ( 11) link_ALPHA1-2 : angle 2.58926 / 1.72 ( 33) link_ALPHA1-3 : bond 0.01292 / 0.82 ( 24) link_ALPHA1-3 : angle 1.81638 / 1.16 ( 72) link_ALPHA1-6 : bond 0.01039 / 0.56 ( 14) link_ALPHA1-6 : angle 1.95974 / 1.45 ( 42) link_BETA1-4 : bond 0.00607 / 0.37 ( 62) link_BETA1-4 : angle 2.00045 / 1.41 ( 186) link_NAG-ASN : bond 0.00540 / 0.34 ( 61) link_NAG-ASN : angle 3.45183 / 2.66 ( 183) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 315 time to evaluate : 0.910 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: A 72 HIS cc_start: 0.6951 (OUTLIER) cc_final: 0.5484 (m-70) REVERT: A 150 MET cc_start: 0.7351 (mmm) cc_final: 0.6998 (mmm) REVERT: A 151 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.5872 (mmm160) REVERT: A 482 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7696 (mt-10) REVERT: B 576 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7694 (mp) REVERT: B 588 ARG cc_start: 0.8350 (ttt-90) cc_final: 0.7933 (ttm170) REVERT: C 624 ASP cc_start: 0.8426 (m-30) cc_final: 0.8117 (m-30) REVERT: D 13 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7204 (tppt) REVERT: D 82 ASN cc_start: 0.7948 (t0) cc_final: 0.7696 (t0) REVERT: E 83 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7240 (pp20) REVERT: G 66 HIS cc_start: 0.7379 (OUTLIER) cc_final: 0.6953 (m-70) REVERT: G 69 TRP cc_start: 0.7529 (OUTLIER) cc_final: 0.6653 (p90) REVERT: G 323 ILE cc_start: 0.9254 (tt) cc_final: 0.8818 (pt) REVERT: H 3 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8127 (pt0) REVERT: H 83 ARG cc_start: 0.7945 (mtt180) cc_final: 0.7719 (mtm-85) REVERT: I 33 ASN cc_start: 0.7082 (OUTLIER) cc_final: 0.6510 (p0) REVERT: I 69 TRP cc_start: 0.8556 (OUTLIER) cc_final: 0.7763 (m100) REVERT: I 87 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: I 153 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7430 (tt0) REVERT: J 522 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.7279 (t80) REVERT: J 588 ARG cc_start: 0.8264 (ttm170) cc_final: 0.7688 (tpt90) REVERT: K 34 MET cc_start: 0.9031 (mmm) cc_final: 0.8293 (mmt) REVERT: L 45 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8142 (ttt180) REVERT: M 54 ASP cc_start: 0.8450 (t0) cc_final: 0.8160 (t0) REVERT: M 78 LEU cc_start: 0.6650 (OUTLIER) cc_final: 0.6390 (tt) REVERT: h 39 ARG cc_start: 0.6439 (tpt90) cc_final: 0.6031 (tpt90) REVERT: h 43 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.6813 (ttpp) REVERT: h 51 VAL cc_start: 0.8787 (p) cc_final: 0.8448 (t) REVERT: h 69 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7274 (tt) REVERT: h 100 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8258 (mt-10) REVERT: d 100 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8649 (mt-10) REVERT: k 100 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7266 (mmt) outliers start: 150 outliers final: 115 residues processed: 444 average time/residue: 0.1656 time to fit residues: 118.1770 Evaluate side-chains 444 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 308 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 462 ASN Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 126 CYS Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 153 GLU Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 249 HIS Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 334 SER Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 462 ASN Chi-restraints excluded: chain J residue 515 ILE Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 529 THR Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 623 TRP Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain M residue 72 ILE Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain h residue 17 THR Chi-restraints excluded: chain h residue 37 ILE Chi-restraints excluded: chain h residue 43 LYS Chi-restraints excluded: chain h residue 53 LYS Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 78 VAL Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 97 HIS Chi-restraints excluded: chain h residue 100 GLU Chi-restraints excluded: chain l residue 20 ARG Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 75 ILE Chi-restraints excluded: chain l residue 85 ASP Chi-restraints excluded: chain l residue 88 CYS Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 102 THR Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 37 ILE Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 79 SER Chi-restraints excluded: chain d residue 92 CYS Chi-restraints excluded: chain d residue 100 GLU Chi-restraints excluded: chain d residue 103 ASN Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 70 THR Chi-restraints excluded: chain e residue 75 ILE Chi-restraints excluded: chain e residue 88 CYS Chi-restraints excluded: chain e residue 95 THR Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 57 THR Chi-restraints excluded: chain k residue 59 TYR Chi-restraints excluded: chain k residue 60 SER Chi-restraints excluded: chain k residue 79 SER Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 100 THR Chi-restraints excluded: chain k residue 100 MET Chi-restraints excluded: chain m residue 13 VAL Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain m residue 88 CYS Chi-restraints excluded: chain m residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 188 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 90 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 240 optimal weight: 3.9990 chunk 257 optimal weight: 0.9980 chunk 210 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 299 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 136 ASN ** l 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.152608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.105206 restraints weight = 63660.554| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.98 r_work: 0.3029 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27700 Z= 0.168 Angle : 0.732 17.744 37929 Z= 0.330 Chirality : 0.048 0.688 4652 Planarity : 0.004 0.041 4513 Dihedral : 10.821 109.264 6987 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.61 % Favored : 92.20 % Rotamer: Outliers : 5.71 % Allowed : 29.56 % Favored : 64.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.15), residues: 3132 helix: 1.00 (0.30), residues: 376 sheet: -1.03 (0.17), residues: 955 loop : -1.64 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 83 TYR 0.048 0.001 TYR B 638 PHE 0.015 0.001 PHE G 53 TRP 0.017 0.001 TRP h 34 HIS 0.004 0.001 HIS G 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (27483) covalent geometry : angle 0.66051 / 0.31 (37323) SS BOND : bond 0.00453 / 0.28 ( 45) SS BOND : angle 1.90036 / 1.20 ( 90) hydrogen bonds : bond 0.03696 / 2.47 ( 638) hydrogen bonds : angle 4.80135 / 3.29 ( 1597) link_ALPHA1-2 : bond 0.00905 / 0.55 ( 11) link_ALPHA1-2 : angle 2.58748 / 1.70 ( 33) link_ALPHA1-3 : bond 0.01228 / 0.78 ( 24) link_ALPHA1-3 : angle 1.84834 / 1.19 ( 72) link_ALPHA1-6 : bond 0.00822 / 0.50 ( 14) link_ALPHA1-6 : angle 1.86016 / 1.35 ( 42) link_BETA1-4 : bond 0.00564 / 0.34 ( 62) link_BETA1-4 : angle 2.07033 / 1.46 ( 186) link_NAG-ASN : bond 0.00522 / 0.32 ( 61) link_NAG-ASN : angle 3.54429 / 2.73 ( 183) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 311 time to evaluate : 0.754 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: A 72 HIS cc_start: 0.6920 (OUTLIER) cc_final: 0.6478 (p90) REVERT: A 99 ASN cc_start: 0.8749 (t0) cc_final: 0.8518 (t0) REVERT: A 150 MET cc_start: 0.7320 (mmm) cc_final: 0.6945 (mmm) REVERT: A 151 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.5945 (mmm160) REVERT: A 482 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7669 (mt-10) REVERT: B 576 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7649 (mp) REVERT: B 588 ARG cc_start: 0.8301 (ttt-90) cc_final: 0.7917 (ttm170) REVERT: C 624 ASP cc_start: 0.8432 (m-30) cc_final: 0.8138 (m-30) REVERT: D 13 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7242 (tppt) REVERT: D 82 ASN cc_start: 0.7944 (t0) cc_final: 0.7694 (t0) REVERT: E 83 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7227 (pp20) REVERT: G 66 HIS cc_start: 0.7370 (OUTLIER) cc_final: 0.6944 (m-70) REVERT: G 69 TRP cc_start: 0.7562 (OUTLIER) cc_final: 0.6683 (p90) REVERT: G 323 ILE cc_start: 0.9234 (tt) cc_final: 0.8779 (pt) REVERT: H 3 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8127 (pt0) REVERT: H 83 ARG cc_start: 0.7903 (mtt180) cc_final: 0.7420 (mtm-85) REVERT: I 33 ASN cc_start: 0.7116 (OUTLIER) cc_final: 0.6596 (p0) REVERT: I 69 TRP cc_start: 0.8566 (OUTLIER) cc_final: 0.7774 (m100) REVERT: I 87 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: I 153 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7366 (tt0) REVERT: J 522 PHE cc_start: 0.7795 (OUTLIER) cc_final: 0.7268 (t80) REVERT: J 588 ARG cc_start: 0.8211 (ttm170) cc_final: 0.7674 (tpt90) REVERT: K 34 MET cc_start: 0.9032 (mmm) cc_final: 0.8342 (mmt) REVERT: L 45 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8148 (ttt180) REVERT: M 54 ASP cc_start: 0.8514 (t0) cc_final: 0.8188 (t0) REVERT: M 78 LEU cc_start: 0.6640 (OUTLIER) cc_final: 0.6386 (tt) REVERT: h 39 ARG cc_start: 0.6344 (tpt90) cc_final: 0.5929 (tpt90) REVERT: h 43 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.6845 (ttpp) REVERT: h 51 VAL cc_start: 0.8804 (p) cc_final: 0.8482 (t) REVERT: h 69 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7263 (tt) REVERT: h 100 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8237 (mt-10) REVERT: d 2 MET cc_start: 0.6573 (mtp) cc_final: 0.6006 (mtp) REVERT: d 100 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8634 (mt-10) REVERT: k 100 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7137 (mmt) outliers start: 149 outliers final: 123 residues processed: 440 average time/residue: 0.1681 time to fit residues: 118.7254 Evaluate side-chains 447 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 303 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 280 ASN Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain G residue 462 ASN Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 126 CYS Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 153 GLU Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 249 HIS Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 334 SER Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 462 ASN Chi-restraints excluded: chain I residue 504 ARG Chi-restraints excluded: chain J residue 515 ILE Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 529 THR Chi-restraints excluded: chain J residue 537 LEU Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 623 TRP Chi-restraints excluded: chain J residue 630 GLN Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain M residue 72 ILE Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain h residue 17 THR Chi-restraints excluded: chain h residue 37 ILE Chi-restraints excluded: chain h residue 43 LYS Chi-restraints excluded: chain h residue 53 LYS Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 78 VAL Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 100 GLU Chi-restraints excluded: chain l residue 20 ARG Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 75 ILE Chi-restraints excluded: chain l residue 85 ASP Chi-restraints excluded: chain l residue 88 CYS Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 102 THR Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 15 SER Chi-restraints excluded: chain d residue 37 ILE Chi-restraints excluded: chain d residue 46 GLU Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 79 SER Chi-restraints excluded: chain d residue 92 CYS Chi-restraints excluded: chain d residue 100 GLU Chi-restraints excluded: chain d residue 103 ASN Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 70 THR Chi-restraints excluded: chain e residue 75 ILE Chi-restraints excluded: chain e residue 95 THR Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 57 THR Chi-restraints excluded: chain k residue 59 TYR Chi-restraints excluded: chain k residue 60 SER Chi-restraints excluded: chain k residue 79 SER Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 100 THR Chi-restraints excluded: chain k residue 100 MET Chi-restraints excluded: chain m residue 13 VAL Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain m residue 88 CYS Chi-restraints excluded: chain m residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 69 optimal weight: 0.9990 chunk 297 optimal weight: 10.0000 chunk 128 optimal weight: 1.9990 chunk 250 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 143 optimal weight: 0.0770 chunk 253 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** h 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.153330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.106300 restraints weight = 51164.177| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.50 r_work: 0.3077 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27700 Z= 0.149 Angle : 0.711 17.579 37929 Z= 0.321 Chirality : 0.047 0.681 4652 Planarity : 0.003 0.042 4513 Dihedral : 10.538 109.117 6986 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.97 % Favored : 92.84 % Rotamer: Outliers : 5.46 % Allowed : 29.75 % Favored : 64.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.15), residues: 3132 helix: 0.80 (0.29), residues: 394 sheet: -1.02 (0.17), residues: 958 loop : -1.55 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 83 TYR 0.066 0.001 TYR B 638 PHE 0.015 0.001 PHE G 53 TRP 0.018 0.001 TRP h 34 HIS 0.003 0.001 HIS G 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (27483) covalent geometry : angle 0.64311 / 0.31 (37323) SS BOND : bond 0.00406 / 0.27 ( 45) SS BOND : angle 1.62810 / 1.06 ( 90) hydrogen bonds : bond 0.03548 / 2.37 ( 638) hydrogen bonds : angle 4.72562 / 3.23 ( 1597) link_ALPHA1-2 : bond 0.00975 / 0.58 ( 11) link_ALPHA1-2 : angle 2.48762 / 1.64 ( 33) link_ALPHA1-3 : bond 0.01281 / 0.80 ( 24) link_ALPHA1-3 : angle 1.88491 / 1.18 ( 72) link_ALPHA1-6 : bond 0.00815 / 0.50 ( 14) link_ALPHA1-6 : angle 1.57502 / 1.10 ( 42) link_BETA1-4 : bond 0.00568 / 0.34 ( 62) link_BETA1-4 : angle 2.01224 / 1.42 ( 186) link_NAG-ASN : bond 0.00513 / 0.32 ( 61) link_NAG-ASN : angle 3.44737 / 2.67 ( 183) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6264 Ramachandran restraints generated. 3132 Oldfield, 0 Emsley, 3132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 308 time to evaluate : 0.928 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: A 72 HIS cc_start: 0.7055 (OUTLIER) cc_final: 0.6620 (p90) REVERT: A 150 MET cc_start: 0.7503 (mmm) cc_final: 0.7120 (mmm) REVERT: A 151 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.5872 (mmm160) REVERT: A 482 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7857 (mt-10) REVERT: B 576 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7766 (mp) REVERT: B 588 ARG cc_start: 0.8479 (ttt-90) cc_final: 0.7998 (ttm170) REVERT: C 624 ASP cc_start: 0.8468 (m-30) cc_final: 0.8176 (m-30) REVERT: D 13 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7178 (tppt) REVERT: D 82 ASN cc_start: 0.8063 (t0) cc_final: 0.7797 (t0) REVERT: E 83 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7409 (pp20) REVERT: G 66 HIS cc_start: 0.7389 (OUTLIER) cc_final: 0.6972 (m-70) REVERT: G 69 TRP cc_start: 0.7580 (OUTLIER) cc_final: 0.6674 (p90) REVERT: G 323 ILE cc_start: 0.9232 (tt) cc_final: 0.8756 (pt) REVERT: H 3 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8119 (pt0) REVERT: H 83 ARG cc_start: 0.8025 (mtt180) cc_final: 0.7489 (mtm-85) REVERT: I 33 ASN cc_start: 0.7137 (OUTLIER) cc_final: 0.6565 (p0) REVERT: I 69 TRP cc_start: 0.8561 (OUTLIER) cc_final: 0.7714 (m100) REVERT: I 87 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: I 153 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7619 (tt0) REVERT: J 522 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7436 (t80) REVERT: J 588 ARG cc_start: 0.8437 (ttm170) cc_final: 0.7813 (tpt90) REVERT: K 34 MET cc_start: 0.9115 (mmm) cc_final: 0.8425 (mmt) REVERT: L 45 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8254 (ttt180) REVERT: M 78 LEU cc_start: 0.6734 (OUTLIER) cc_final: 0.6482 (tt) REVERT: h 39 ARG cc_start: 0.6413 (tpt90) cc_final: 0.6003 (tpt90) REVERT: h 43 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.6893 (ttpp) REVERT: h 46 GLU cc_start: 0.7418 (tt0) cc_final: 0.7070 (tt0) REVERT: h 100 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8351 (mt-10) REVERT: d 2 MET cc_start: 0.6539 (mtp) cc_final: 0.5868 (mtp) REVERT: d 100 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8680 (mt-10) REVERT: e 39 ARG cc_start: 0.7341 (tpp80) cc_final: 0.6687 (mtt-85) REVERT: k 100 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7047 (mmt) outliers start: 142 outliers final: 117 residues processed: 429 average time/residue: 0.1553 time to fit residues: 107.4495 Evaluate side-chains 441 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 304 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 87 GLU Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 126 CYS Chi-restraints excluded: chain I residue 127 VAL Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 153 GLU Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 249 HIS Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 333 VAL Chi-restraints excluded: chain I residue 334 SER Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 462 ASN Chi-restraints excluded: chain J residue 515 ILE Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 529 THR Chi-restraints excluded: chain J residue 538 THR Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 623 TRP Chi-restraints excluded: chain J residue 630 GLN Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 72 ILE Chi-restraints excluded: chain M residue 72 ILE Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain h residue 17 THR Chi-restraints excluded: chain h residue 37 ILE Chi-restraints excluded: chain h residue 43 LYS Chi-restraints excluded: chain h residue 53 LYS Chi-restraints excluded: chain h residue 78 VAL Chi-restraints excluded: chain h residue 80 LEU Chi-restraints excluded: chain h residue 100 GLU Chi-restraints excluded: chain l residue 20 ARG Chi-restraints excluded: chain l residue 70 THR Chi-restraints excluded: chain l residue 75 ILE Chi-restraints excluded: chain l residue 85 ASP Chi-restraints excluded: chain l residue 88 CYS Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 102 THR Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain d residue 37 ILE Chi-restraints excluded: chain d residue 46 GLU Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 79 SER Chi-restraints excluded: chain d residue 92 CYS Chi-restraints excluded: chain d residue 100 GLU Chi-restraints excluded: chain d residue 103 ASN Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 70 THR Chi-restraints excluded: chain e residue 75 ILE Chi-restraints excluded: chain e residue 95 THR Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 57 THR Chi-restraints excluded: chain k residue 59 TYR Chi-restraints excluded: chain k residue 60 SER Chi-restraints excluded: chain k residue 79 SER Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain k residue 100 MET Chi-restraints excluded: chain m residue 13 VAL Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain m residue 88 CYS Chi-restraints excluded: chain m residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 60 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 158 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 231 optimal weight: 3.9990 chunk 200 optimal weight: 0.7980 chunk 289 optimal weight: 0.9990 chunk 21 optimal weight: 0.0040 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 183 GLN I 195 ASN ** l 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 50 ASN ** m 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.155251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.107768 restraints weight = 58331.964| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 3.75 r_work: 0.3075 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27700 Z= 0.126 Angle : 0.687 17.277 37929 Z= 0.311 Chirality : 0.047 0.666 4652 Planarity : 0.003 0.043 4513 Dihedral : 10.172 108.734 6982 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.26 % Favored : 92.55 % Rotamer: Outliers : 5.38 % Allowed : 29.89 % Favored : 64.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.15), residues: 3132 helix: 1.05 (0.29), residues: 385 sheet: -0.94 (0.17), residues: 952 loop : -1.54 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 83 TYR 0.073 0.001 TYR B 638 PHE 0.014 0.001 PHE G 53 TRP 0.017 0.001 TRP h 34 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (27483) covalent geometry : angle 0.61994 / 0.29 (37323) SS BOND : bond 0.00365 / 0.24 ( 45) SS BOND : angle 1.45863 / 0.96 ( 90) hydrogen bonds : bond 0.03286 / 2.20 ( 638) hydrogen bonds : angle 4.60680 / 3.15 ( 1597) link_ALPHA1-2 : bond 0.01001 / 0.55 ( 11) link_ALPHA1-2 : angle 2.36629 / 1.58 ( 33) link_ALPHA1-3 : bond 0.01234 / 0.78 ( 24) link_ALPHA1-3 : angle 1.94694 / 1.20 ( 72) link_ALPHA1-6 : bond 0.00824 / 0.51 ( 14) link_ALPHA1-6 : angle 1.60837 / 1.14 ( 42) link_BETA1-4 : bond 0.00575 / 0.35 ( 62) link_BETA1-4 : angle 1.92919 / 1.35 ( 186) link_NAG-ASN : bond 0.00544 / 0.35 ( 61) link_NAG-ASN : angle 3.39976 / 2.65 ( 183) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7579.28 seconds wall clock time: 130 minutes 28.16 seconds (7828.16 seconds total)