Starting phenix.real_space_refine on Fri Mar 6 15:35:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mph_9189/03_2026/6mph_9189.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mph_9189/03_2026/6mph_9189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6mph_9189/03_2026/6mph_9189.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mph_9189/03_2026/6mph_9189.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6mph_9189/03_2026/6mph_9189.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mph_9189/03_2026/6mph_9189.map" } resolution = 3.8 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= 0.014 sd= 0.126 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 165 5.16 5 C 20157 2.51 5 N 5316 2.21 5 O 6454 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32092 Number of models: 1 Model: "" Number of chains: 72 Chain: "1" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 915 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "2" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 858 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "3" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 915 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "4" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 858 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "6" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "A" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "B" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "C" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "D" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "E" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "H" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 915 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "L" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 858 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "M" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "N" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 787 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "Q" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1029 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 7, 'TRANS': 121} Chain: "R" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "X" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "Y" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "Z" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 787 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "a" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 787 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "f" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1029 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 7, 'TRANS': 121} Chain: "g" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1029 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 7, 'TRANS': 121} Chain: "h" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "i" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "F" 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: "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: 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: "J" 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: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 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: "U" 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" 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: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" 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: "d" 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: "e" 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: "j" 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: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" 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: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "r" 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: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 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: 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: "w" 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: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "y" 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: "z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "0" 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: "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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "9" 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: "AA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "BA" 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: "CA" 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: "DA" 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: "6" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.31, per 1000 atoms: 0.23 Number of scatterers: 32092 At special positions: 0 Unit cell: (157.94, 156.88, 152.64, 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 165 16.00 O 6454 8.00 N 5316 7.00 C 20157 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS 1 22 " - pdb=" SG CYS 1 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 23 " - pdb=" SG CYS 2 88 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 22 " - pdb=" SG CYS 3 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 23 " - pdb=" SG CYS 4 88 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 598 " - pdb=" SG CYS 6 604 " distance=2.02 Simple disulfide: pdb=" SG CYS 6 605 " - pdb=" SG CYS A 501 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 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 B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 433 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 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 M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 103 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 109 " - pdb=" SG CYS Q 112 " distance=2.03 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 23 " - pdb=" SG CYS Z 88 " distance=2.03 Simple disulfide: pdb=" SG CYS a 23 " - pdb=" SG CYS a 88 " distance=2.03 Simple disulfide: pdb=" SG CYS f 22 " - pdb=" SG CYS f 103 " distance=2.03 Simple disulfide: pdb=" SG CYS f 109 " - pdb=" SG CYS f 112 " distance=2.03 Simple disulfide: pdb=" SG CYS g 22 " - pdb=" SG CYS g 103 " distance=2.03 Simple disulfide: pdb=" SG CYS g 109 " - pdb=" SG CYS g 112 " 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 0 4 " - " MAN 0 5 " " MAN S 4 " - " MAN S 5 " " MAN n 4 " - " MAN n 5 " ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " BMA 9 3 " - " MAN 9 4 " " BMA F 3 " - " MAN F 4 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " " BMA S 3 " - " MAN S 4 " " BMA W 3 " - " MAN W 4 " " BMA c 3 " - " MAN c 4 " " BMA e 3 " - " MAN e 4 " " BMA j 3 " - " MAN j 4 " " BMA n 3 " - " MAN n 4 " " BMA r 3 " - " MAN r 4 " " BMA t 3 " - " MAN t 4 " " BMA v 3 " - " MAN v 4 " " BMA w 3 " - " MAN w 4 " " BMABA 3 " - " MANBA 4 " " BMACA 3 " - " MANCA 4 " " BMADA 3 " - " MANDA 4 " ALPHA1-6 " BMA 0 3 " - " MAN 0 6 " " BMA 9 3 " - " MAN 9 5 " " BMA F 3 " - " MAN F 5 " " BMA J 3 " - " MAN J 5 " " BMA S 3 " - " MAN S 6 " " BMA W 3 " - " MAN W 5 " " BMA j 3 " - " MAN j 5 " " BMA n 3 " - " MAN n 6 " " BMA r 3 " - " MAN r 5 " " BMA t 3 " - " MAN t 5 " " BMA w 3 " - " MAN w 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 5 1 " - " NAG 5 2 " " NAG 7 1 " - " NAG 7 2 " " NAG 8 1 " - " NAG 8 2 " " NAG 8 2 " - " BMA 8 3 " " NAG 9 1 " - " NAG 9 2 " " NAG 9 2 " - " BMA 9 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " 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 b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " 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 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 z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " " NAGAA 2 " - " BMAAA 3 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGCA 2 " - " BMACA 3 " " NAGDA 1 " - " NAGDA 2 " " NAGDA 2 " - " BMADA 3 " NAG-ASN " NAG 5 1 " - " ASN C 295 " " NAG 6 701 " - " ASN 6 637 " " NAG 8 1 " - " ASN C 363 " " NAG 9 1 " - " ASN C 386 " " NAG A 635 " - " ASN A 339 " " NAG A 647 " - " ASN A 88 " " NAG B 634 " - " ASN B 339 " " NAG B 646 " - " ASN B 88 " " NAG C 635 " - " ASN C 339 " " NAG C 647 " - " ASN C 88 " " NAG D 701 " - " ASN D 637 " " NAG E 701 " - " ASN E 637 " " NAG F 1 " - " ASN A 332 " " NAG K 1 " - " ASN A 160 " " NAG T 1 " - " ASN A 295 " " NAG V 1 " - " ASN A 363 " " NAG W 1 " - " ASN A 386 " " NAG b 1 " - " ASN A 392 " " NAG c 1 " - " ASN B 332 " " NAG k 1 " - " ASN B 160 " " NAG o 1 " - " ASN B 295 " " NAG q 1 " - " ASN B 363 " " NAG r 1 " - " ASN B 386 " " NAG s 1 " - " ASN B 392 " " NAG t 1 " - " ASN C 332 " " NAG x 1 " - " ASN C 160 " " NAGAA 1 " - " ASN C 392 " Time building additional restraints: 3.05 Conformation dependent library (CDL) restraints added in 1.5 seconds 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7038 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 78 sheets defined 14.5% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain '1' and resid 60 through 64 Processing helix chain '1' and resid 83 through 87 removed outlier: 3.527A pdb=" N THR 1 87 " --> pdb=" O ALA 1 84 " (cutoff:3.500A) Processing helix chain '2' and resid 79 through 83 removed outlier: 3.513A pdb=" N ASP 2 82 " --> pdb=" O GLU 2 79 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL 2 83 " --> pdb=" O ALA 2 80 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 79 through 83' Processing helix chain '3' and resid 60 through 64 Processing helix chain '3' and resid 83 through 87 removed outlier: 3.535A pdb=" N THR 3 87 " --> pdb=" O ALA 3 84 " (cutoff:3.500A) Processing helix chain '4' and resid 79 through 83 removed outlier: 3.532A pdb=" N ASP 4 82 " --> pdb=" O GLU 4 79 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL 4 83 " --> pdb=" O ALA 4 80 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 79 through 83' Processing helix chain '6' and resid 529 through 534 Processing helix chain '6' and resid 537 through 543 Processing helix chain '6' and resid 570 through 595 removed outlier: 3.673A pdb=" N LYS 6 574 " --> pdb=" O VAL 6 570 " (cutoff:3.500A) Processing helix chain '6' and resid 611 through 616 removed outlier: 4.107A pdb=" N SER 6 615 " --> pdb=" O ASN 6 611 " (cutoff:3.500A) Processing helix chain '6' and resid 618 through 626 removed outlier: 3.537A pdb=" N ILE 6 622 " --> pdb=" O ASN 6 618 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TRP 6 623 " --> pdb=" O LEU 6 619 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP 6 624 " --> pdb=" O SER 6 620 " (cutoff:3.500A) Processing helix chain '6' and resid 627 through 635 Processing helix chain '6' and resid 641 through 664 Processing helix chain 'A' and resid 57 through 62 removed outlier: 3.690A pdb=" N TYR A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 115 Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.554A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.537A pdb=" N THR A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.807A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 62 removed outlier: 3.680A pdb=" N TYR B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 67 removed outlier: 4.184A pdb=" N HIS B 66 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASN B 67 " --> pdb=" O GLU B 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 63 through 67' Processing helix chain 'B' and resid 100 through 115 Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.520A pdb=" N CYS B 126 " --> pdb=" O THR B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 198 Processing helix chain 'B' and resid 335 through 350 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 475 through 480 removed outlier: 3.832A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 removed outlier: 3.667A pdb=" N TYR C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 67 removed outlier: 4.166A pdb=" N HIS C 66 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN C 67 " --> pdb=" O GLU C 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 63 through 67' Processing helix chain 'C' and resid 100 through 115 Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.605A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 480 removed outlier: 3.832A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 537 through 543 Processing helix chain 'D' and resid 570 through 595 removed outlier: 3.662A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 616 removed outlier: 4.110A pdb=" N SER D 615 " --> pdb=" O ASN D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 626 removed outlier: 3.555A pdb=" N ILE D 622 " --> pdb=" O ASN D 618 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TRP D 623 " --> pdb=" O LEU D 619 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP D 624 " --> pdb=" O SER D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 641 through 664 Processing helix chain 'E' and resid 523 through 527 removed outlier: 3.578A pdb=" N ALA E 526 " --> pdb=" O LEU E 523 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 523 through 527' Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 537 through 543 Processing helix chain 'E' and resid 570 through 595 removed outlier: 3.654A pdb=" N LYS E 574 " --> pdb=" O VAL E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 616 removed outlier: 4.113A pdb=" N SER E 615 " --> pdb=" O ASN E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 626 removed outlier: 3.551A pdb=" N ILE E 622 " --> pdb=" O ASN E 618 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TRP E 623 " --> pdb=" O LEU E 619 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP E 624 " --> pdb=" O SER E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 641 through 664 Processing helix chain 'H' and resid 60 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.553A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.536A pdb=" N ASP L 82 " --> pdb=" O GLU L 79 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.903A pdb=" N SER M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'Q' and resid 62 through 65 removed outlier: 3.618A pdb=" N GLN Q 65 " --> pdb=" O ARG Q 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 62 through 65' Processing helix chain 'Q' and resid 94 through 98 removed outlier: 3.687A pdb=" N THR Q 98 " --> pdb=" O PRO Q 95 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 87 removed outlier: 3.910A pdb=" N SER X 87 " --> pdb=" O ALA X 84 " (cutoff:3.500A) Processing helix chain 'Y' and resid 83 through 87 removed outlier: 3.936A pdb=" N SER Y 87 " --> pdb=" O ALA Y 84 " (cutoff:3.500A) Processing helix chain 'Z' and resid 79 through 83 Processing helix chain 'a' and resid 79 through 83 Processing helix chain 'f' and resid 62 through 65 removed outlier: 3.624A pdb=" N GLN f 65 " --> pdb=" O ARG f 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 62 through 65' Processing helix chain 'f' and resid 94 through 98 removed outlier: 3.683A pdb=" N THR f 98 " --> pdb=" O PRO f 95 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 65 removed outlier: 3.662A pdb=" N GLN g 65 " --> pdb=" O ARG g 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 62 through 65' Processing helix chain 'g' and resid 94 through 98 removed outlier: 3.623A pdb=" N THR g 98 " --> pdb=" O PRO g 95 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain '1' and resid 11 through 12 removed outlier: 3.812A pdb=" N VAL 1 12 " --> pdb=" O THR 1 110 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP 1 34 " --> pdb=" O TYR 1 50 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TYR 1 50 " --> pdb=" O TRP 1 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP 1 36 " --> pdb=" O ILE 1 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 18 through 19 Processing sheet with id=AA4, first strand: chain '2' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain '2' and resid 45 through 49 removed outlier: 6.569A pdb=" N TRP 2 35 " --> pdb=" O LEU 2 47 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR 2 49 " --> pdb=" O LEU 2 33 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU 2 33 " --> pdb=" O TYR 2 49 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY 2 84 " --> pdb=" O VAL 2 104 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL 2 104 " --> pdb=" O GLY 2 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '3' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain '3' and resid 11 through 12 removed outlier: 3.820A pdb=" N VAL 3 12 " --> pdb=" O THR 3 110 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TRP 3 34 " --> pdb=" O TYR 3 50 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N TYR 3 50 " --> pdb=" O TRP 3 34 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TRP 3 36 " --> pdb=" O ILE 3 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '3' and resid 18 through 19 Processing sheet with id=AA9, first strand: chain '4' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain '4' and resid 45 through 49 removed outlier: 6.558A pdb=" N TRP 4 35 " --> pdb=" O LEU 4 47 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TYR 4 49 " --> pdb=" O LEU 4 33 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU 4 33 " --> pdb=" O TYR 4 49 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY 4 84 " --> pdb=" O VAL 4 104 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL 4 104 " --> pdb=" O GLY 4 84 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '6' and resid 603 through 609 removed outlier: 3.542A pdb=" N VAL A 38 " --> pdb=" O CYS 6 604 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR 6 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N VAL A 36 " --> pdb=" O THR 6 606 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AB4, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.817A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.759A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AB7, first strand: chain 'A' and resid 201 through 203 Processing sheet with id=AB8, first strand: chain 'A' and resid 260 through 261 removed outlier: 6.927A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 11.152A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 12.024A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.529A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.018A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN A 295 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 271 through 274 removed outlier: 11.018A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.529A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.024A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.152A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 302 through 312 removed outlier: 6.021A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 495 through 499 removed outlier: 5.149A pdb=" N VAL B 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR E 606 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 38 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS E 604 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 45 through 47 Processing sheet with id=AC4, first strand: chain 'B' and resid 75 through 76 removed outlier: 3.799A pdb=" N VAL B 75 " --> pdb=" O CYS B 54 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.761A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 169 through 177 Processing sheet with id=AC7, first strand: chain 'B' and resid 201 through 203 Processing sheet with id=AC8, first strand: chain 'B' and resid 260 through 261 removed outlier: 6.950A pdb=" N LEU B 260 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLY B 451 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 11.204A pdb=" N THR B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 11.622A pdb=" N ILE B 453 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 12.054A pdb=" N PHE B 288 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 10.546A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 11.010A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER B 334 " --> pdb=" O GLN B 293 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 271 through 274 removed outlier: 11.010A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 10.546A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 12.054A pdb=" N PHE B 288 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 11.622A pdb=" N ILE B 453 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 11.204A pdb=" N THR B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLY B 451 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER B 393 " --> pdb=" O PHE B 361 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 302 through 312 removed outlier: 6.042A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 495 through 499 removed outlier: 5.133A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR D 606 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 38 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS D 604 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AD4, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.803A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.779A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AD7, first strand: chain 'C' and resid 201 through 203 Processing sheet with id=AD8, first strand: chain 'C' and resid 260 through 261 removed outlier: 6.945A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 11.161A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 12.011A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.516A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.970A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 271 through 273 removed outlier: 10.970A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.516A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.011A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 11.161A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 302 through 312 removed outlier: 6.014A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'H' and resid 18 through 19 Processing sheet with id=AE4, first strand: chain 'H' and resid 46 through 52 removed outlier: 6.755A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE6, first strand: chain 'L' and resid 45 through 49 removed outlier: 6.559A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL L 104 " --> pdb=" O GLY L 84 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 5 through 7 Processing sheet with id=AE8, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.749A pdb=" N THR M 95 " --> pdb=" O TYR M 33 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR M 33 " --> pdb=" O THR M 95 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 11 through 12 Processing sheet with id=AF1, first strand: chain 'N' and resid 12 through 13 removed outlier: 3.589A pdb=" N VAL N 13 " --> pdb=" O ILE N 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'N' and resid 19 through 26 removed outlier: 4.135A pdb=" N ALA N 71 " --> pdb=" O CYS N 23 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 44 through 48 removed outlier: 6.589A pdb=" N TRP N 35 " --> pdb=" O ILE N 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Q' and resid 3 through 5 Processing sheet with id=AF5, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.610A pdb=" N ILE Q 34 " --> pdb=" O TRP Q 50 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TRP Q 50 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP Q 36 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY Q 44 " --> pdb=" O ILE Q 40 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 10 through 12 Processing sheet with id=AF7, first strand: chain 'R' and resid 5 through 6 Processing sheet with id=AF8, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.057A pdb=" N LEU R 11 " --> pdb=" O GLU R 105 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TRP R 34 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.057A pdb=" N LEU R 11 " --> pdb=" O GLU R 105 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'X' and resid 5 through 7 Processing sheet with id=AG2, first strand: chain 'X' and resid 11 through 12 removed outlier: 3.738A pdb=" N THR X 95 " --> pdb=" O TYR X 33 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR X 33 " --> pdb=" O THR X 95 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP X 34 " --> pdb=" O TYR X 50 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR X 50 " --> pdb=" O TRP X 34 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N TRP X 36 " --> pdb=" O ILE X 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'X' and resid 11 through 12 Processing sheet with id=AG4, first strand: chain 'Y' and resid 5 through 7 Processing sheet with id=AG5, first strand: chain 'Y' and resid 11 through 12 removed outlier: 3.766A pdb=" N THR Y 95 " --> pdb=" O TYR Y 33 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TYR Y 33 " --> pdb=" O THR Y 95 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP Y 34 " --> pdb=" O TYR Y 50 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR Y 50 " --> pdb=" O TRP Y 34 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TRP Y 36 " --> pdb=" O ILE Y 48 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 11 through 12 Processing sheet with id=AG7, first strand: chain 'Z' and resid 12 through 13 removed outlier: 3.579A pdb=" N VAL Z 13 " --> pdb=" O ILE Z 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'Z' and resid 19 through 26 removed outlier: 4.067A pdb=" N ALA Z 71 " --> pdb=" O CYS Z 23 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Z' and resid 44 through 48 removed outlier: 6.610A pdb=" N TRP Z 35 " --> pdb=" O ILE Z 47 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'a' and resid 12 through 13 removed outlier: 3.584A pdb=" N VAL a 13 " --> pdb=" O ILE a 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'a' and resid 19 through 26 removed outlier: 4.087A pdb=" N ALA a 71 " --> pdb=" O CYS a 23 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'a' and resid 44 through 48 removed outlier: 6.601A pdb=" N TRP a 35 " --> pdb=" O ILE a 47 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'f' and resid 3 through 5 Processing sheet with id=AH5, first strand: chain 'f' and resid 10 through 12 removed outlier: 6.564A pdb=" N ILE f 34 " --> pdb=" O TRP f 50 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TRP f 50 " --> pdb=" O ILE f 34 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TRP f 36 " --> pdb=" O ILE f 48 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY f 44 " --> pdb=" O ILE f 40 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'f' and resid 10 through 12 Processing sheet with id=AH7, first strand: chain 'g' and resid 3 through 5 Processing sheet with id=AH8, first strand: chain 'g' and resid 10 through 12 removed outlier: 6.563A pdb=" N ILE g 34 " --> pdb=" O TRP g 50 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TRP g 50 " --> pdb=" O ILE g 34 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP g 36 " --> pdb=" O ILE g 48 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'g' and resid 10 through 12 Processing sheet with id=AI1, first strand: chain 'h' and resid 5 through 6 Processing sheet with id=AI2, first strand: chain 'h' and resid 10 through 13 removed outlier: 6.054A pdb=" N LEU h 11 " --> pdb=" O GLU h 105 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP h 34 " --> pdb=" O LEU h 47 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'h' and resid 10 through 13 removed outlier: 6.054A pdb=" N LEU h 11 " --> pdb=" O GLU h 105 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'i' and resid 5 through 6 Processing sheet with id=AI5, first strand: chain 'i' and resid 10 through 13 removed outlier: 6.043A pdb=" N LEU i 11 " --> pdb=" O GLU i 105 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TRP i 34 " --> pdb=" O LEU i 47 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'i' and resid 10 through 13 removed outlier: 6.043A pdb=" N LEU i 11 " --> pdb=" O GLU i 105 " (cutoff:3.500A) 1130 hydrogen bonds defined for protein. 2817 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: 7.30 Time building geometry restraints manager: 3.92 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: 9634 1.34 - 1.46: 7150 1.46 - 1.57: 15811 1.57 - 1.69: 1 1.69 - 1.81: 216 Bond restraints: 32812 Sorted by residual: bond pdb=" C1 NAG B 646 " pdb=" O5 NAG B 646 " ideal model delta sigma weight residual 1.406 1.473 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C1 NAG C 647 " pdb=" O5 NAG C 647 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.03e+00 bond pdb=" C1 MAN t 4 " pdb=" C2 MAN t 4 " ideal model delta sigma weight residual 1.526 1.581 -0.055 2.00e-02 2.50e+03 7.60e+00 bond pdb=" C1 MAN v 4 " pdb=" O5 MAN v 4 " ideal model delta sigma weight residual 1.399 1.454 -0.055 2.00e-02 2.50e+03 7.56e+00 bond pdb=" C1 MAN e 4 " pdb=" O5 MAN e 4 " ideal model delta sigma weight residual 1.399 1.454 -0.055 2.00e-02 2.50e+03 7.50e+00 ... (remaining 32807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 43908 3.04 - 6.08: 584 6.08 - 9.11: 121 9.11 - 12.15: 3 12.15 - 15.19: 3 Bond angle restraints: 44619 Sorted by residual: angle pdb=" C ASN A 332 " pdb=" N VAL A 333 " pdb=" CA VAL A 333 " ideal model delta sigma weight residual 122.11 128.03 -5.92 1.12e+00 7.97e-01 2.79e+01 angle pdb=" CA LEU C 494 " pdb=" CB LEU C 494 " pdb=" CG LEU C 494 " ideal model delta sigma weight residual 116.30 131.49 -15.19 3.50e+00 8.16e-02 1.88e+01 angle pdb=" N PHE f 115 " pdb=" CA PHE f 115 " pdb=" C PHE f 115 " ideal model delta sigma weight residual 109.81 119.38 -9.57 2.21e+00 2.05e-01 1.87e+01 angle pdb=" N PHE Q 115 " pdb=" CA PHE Q 115 " pdb=" C PHE Q 115 " ideal model delta sigma weight residual 109.81 119.27 -9.46 2.21e+00 2.05e-01 1.83e+01 angle pdb=" CA LEU B 494 " pdb=" CB LEU B 494 " pdb=" CG LEU B 494 " ideal model delta sigma weight residual 116.30 131.27 -14.97 3.50e+00 8.16e-02 1.83e+01 ... (remaining 44614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.16: 19957 23.16 - 46.33: 942 46.33 - 69.49: 197 69.49 - 92.65: 209 92.65 - 115.81: 117 Dihedral angle restraints: 21422 sinusoidal: 10430 harmonic: 10992 Sorted by residual: dihedral pdb=" CA GLN L 50 " pdb=" C GLN L 50 " pdb=" N VAL L 51 " pdb=" CA VAL L 51 " ideal model delta harmonic sigma weight residual 180.00 -137.35 -42.65 0 5.00e+00 4.00e-02 7.28e+01 dihedral pdb=" CA GLN 4 50 " pdb=" C GLN 4 50 " pdb=" N VAL 4 51 " pdb=" CA VAL 4 51 " ideal model delta harmonic sigma weight residual -180.00 -137.41 -42.59 0 5.00e+00 4.00e-02 7.26e+01 dihedral pdb=" CA GLN 2 50 " pdb=" C GLN 2 50 " pdb=" N VAL 2 51 " pdb=" CA VAL 2 51 " ideal model delta harmonic sigma weight residual -180.00 -137.76 -42.24 0 5.00e+00 4.00e-02 7.14e+01 ... (remaining 21419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 5033 0.110 - 0.220: 295 0.220 - 0.330: 40 0.330 - 0.441: 0 0.441 - 0.551: 3 Chirality restraints: 5371 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.08e+01 chirality pdb=" C1 NAG s 1 " pdb=" ND2 ASN B 392 " pdb=" C2 NAG s 1 " pdb=" O5 NAG s 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.58e+00 chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN A 392 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.36e+00 ... (remaining 5368 not shown) Planarity restraints: 5490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE Q 115 " 0.050 5.00e-02 4.00e+02 7.56e-02 9.13e+00 pdb=" N PRO Q 116 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO Q 116 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO Q 116 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE g 115 " 0.050 5.00e-02 4.00e+02 7.48e-02 8.95e+00 pdb=" N PRO g 116 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO g 116 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO g 116 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE f 115 " -0.048 5.00e-02 4.00e+02 7.28e-02 8.48e+00 pdb=" N PRO f 116 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO f 116 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO f 116 " -0.041 5.00e-02 4.00e+02 ... (remaining 5487 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 9327 2.81 - 3.33: 26640 3.33 - 3.85: 54080 3.85 - 4.38: 59156 4.38 - 4.90: 102943 Nonbonded interactions: 252146 Sorted by model distance: nonbonded pdb=" OG1 THR B 373 " pdb=" N HIS B 374 " model vdw 2.286 3.120 nonbonded pdb=" OG1 THR C 373 " pdb=" N HIS C 374 " model vdw 2.290 3.120 nonbonded pdb=" OG1 THR A 373 " pdb=" N HIS A 374 " model vdw 2.294 3.120 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP g 79 " model vdw 2.298 3.040 nonbonded pdb=" OH TYR B 318 " pdb=" OD2 ASP Q 79 " model vdw 2.314 3.040 ... (remaining 252141 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: 0.07 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'S' selection = chain 'n' } ncs_group { reference = chain '1' selection = chain '3' selection = chain 'H' } ncs_group { reference = chain '2' selection = chain '4' selection = chain 'L' } ncs_group { reference = chain '5' selection = chain '7' selection = chain 'G' selection = chain 'O' selection = chain 'T' selection = chain 'U' selection = chain 'd' selection = chain 'l' selection = chain 'o' selection = chain 'p' selection = chain 'u' selection = chain 'y' } ncs_group { reference = chain '6' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain '8' selection = chain 'AA' selection = chain 'K' selection = chain 'P' selection = chain 'V' selection = chain 'b' selection = chain 'k' selection = chain 'm' selection = chain 'q' selection = chain 's' selection = chain 'x' selection = chain 'z' } ncs_group { reference = chain '9' selection = chain 'F' selection = chain 'J' selection = chain 'W' selection = chain 'j' selection = chain 'r' selection = chain 't' selection = chain 'w' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'BA' selection = chain 'CA' selection = chain 'DA' selection = chain 'I' selection = chain 'c' selection = chain 'e' selection = chain 'v' } ncs_group { reference = chain 'M' selection = chain 'X' selection = chain 'Y' } ncs_group { reference = chain 'N' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = chain 'Q' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'R' selection = chain 'h' selection = chain 'i' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.870 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: 0.050 Extract box with map and model: 0.630 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 30.690 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 32997 Z= 0.320 Angle : 0.979 15.191 45120 Z= 0.466 Chirality : 0.059 0.551 5371 Planarity : 0.006 0.076 5463 Dihedral : 18.405 115.815 14222 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.27 % Favored : 94.57 % Rotamer: Outliers : 6.01 % Allowed : 7.18 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.46 (0.11), residues: 3777 helix: -2.59 (0.18), residues: 429 sheet: -1.79 (0.13), residues: 1239 loop : -2.59 (0.11), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 503 TYR 0.016 0.002 TYR f 87 PHE 0.025 0.002 PHE C 288 TRP 0.020 0.002 TRP A 96 HIS 0.008 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00664 (32812) covalent geometry : angle 0.92611 (44619) SS BOND : bond 0.00398 ( 54) SS BOND : angle 1.23976 ( 108) hydrogen bonds : bond 0.12858 ( 1064) hydrogen bonds : angle 7.70509 ( 2817) link_ALPHA1-2 : bond 0.00316 ( 3) link_ALPHA1-2 : angle 1.64334 ( 9) link_ALPHA1-3 : bond 0.00508 ( 18) link_ALPHA1-3 : angle 1.64684 ( 54) link_ALPHA1-6 : bond 0.00293 ( 11) link_ALPHA1-6 : angle 1.76889 ( 33) link_BETA1-4 : bond 0.00822 ( 72) link_BETA1-4 : angle 3.78145 ( 216) link_NAG-ASN : bond 0.00950 ( 27) link_NAG-ASN : angle 4.21957 ( 81) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 615 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 70 LEU cc_start: 0.9177 (mt) cc_final: 0.8878 (mp) REVERT: 1 94 ARG cc_start: 0.8316 (tmm160) cc_final: 0.7868 (ttp80) REVERT: 2 3 VAL cc_start: 0.9238 (t) cc_final: 0.9021 (p) REVERT: 3 94 ARG cc_start: 0.8119 (tmm160) cc_final: 0.7496 (ttp80) REVERT: 4 3 VAL cc_start: 0.9281 (t) cc_final: 0.9040 (p) REVERT: 4 5 THR cc_start: 0.8265 (m) cc_final: 0.8022 (p) REVERT: 6 535 MET cc_start: 0.8557 (mmt) cc_final: 0.8334 (tpp) REVERT: 6 584 GLU cc_start: 0.8558 (tt0) cc_final: 0.8355 (tt0) REVERT: 6 601 LYS cc_start: 0.8698 (mttt) cc_final: 0.8393 (ttpp) REVERT: 6 657 GLU cc_start: 0.9312 (tt0) cc_final: 0.9027 (tm-30) REVERT: 6 659 ASP cc_start: 0.9201 (t0) cc_final: 0.8893 (m-30) REVERT: A 37 THR cc_start: 0.9248 (OUTLIER) cc_final: 0.8854 (p) REVERT: A 138 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8106 (tp) REVERT: A 475 MET cc_start: 0.8890 (mmm) cc_final: 0.8668 (mmm) REVERT: A 494 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8837 (pt) REVERT: B 138 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8081 (tp) REVERT: B 475 MET cc_start: 0.8937 (mmm) cc_final: 0.8706 (mmm) REVERT: C 138 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8236 (tp) REVERT: C 494 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8892 (pt) REVERT: D 543 ASN cc_start: 0.8952 (m-40) cc_final: 0.8721 (t0) REVERT: D 595 ILE cc_start: 0.9298 (pt) cc_final: 0.8796 (pt) REVERT: D 629 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.9197 (mp) REVERT: D 633 LYS cc_start: 0.9579 (mttt) cc_final: 0.9372 (mtmm) REVERT: D 651 ASN cc_start: 0.9245 (t0) cc_final: 0.8917 (p0) REVERT: D 657 GLU cc_start: 0.9225 (tt0) cc_final: 0.9024 (tm-30) REVERT: D 659 ASP cc_start: 0.9182 (t0) cc_final: 0.8954 (m-30) REVERT: E 601 LYS cc_start: 0.8743 (mttt) cc_final: 0.8413 (ttpp) REVERT: E 629 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.8942 (mt) REVERT: E 633 LYS cc_start: 0.9554 (mttt) cc_final: 0.9354 (mtmm) REVERT: E 638 TYR cc_start: 0.8507 (m-80) cc_final: 0.7995 (m-10) REVERT: E 659 ASP cc_start: 0.9245 (t0) cc_final: 0.8935 (m-30) REVERT: H 94 ARG cc_start: 0.8402 (tmm160) cc_final: 0.7727 (ttp80) REVERT: L 3 VAL cc_start: 0.9215 (t) cc_final: 0.8976 (p) REVERT: N 54 ARG cc_start: 0.8622 (ptt-90) cc_final: 0.8349 (ptt90) REVERT: N 62 PHE cc_start: 0.8457 (m-80) cc_final: 0.8241 (m-10) REVERT: N 67 THR cc_start: 0.9475 (OUTLIER) cc_final: 0.9042 (p) REVERT: R 10 ILE cc_start: 0.9511 (mt) cc_final: 0.9291 (mm) REVERT: X 82 VAL cc_start: 0.8783 (t) cc_final: 0.8366 (t) REVERT: Y 100 LYS cc_start: 0.9500 (mptt) cc_final: 0.9274 (mmmm) REVERT: Z 54 ARG cc_start: 0.8554 (ptt-90) cc_final: 0.8353 (ptm160) REVERT: Z 67 THR cc_start: 0.9438 (OUTLIER) cc_final: 0.9030 (p) REVERT: a 28 LEU cc_start: 0.9182 (mp) cc_final: 0.8903 (mp) REVERT: a 54 ARG cc_start: 0.8574 (ptt-90) cc_final: 0.8253 (ptt90) REVERT: a 67 THR cc_start: 0.9416 (OUTLIER) cc_final: 0.8897 (p) REVERT: f 32 TYR cc_start: 0.9004 (m-80) cc_final: 0.8779 (m-10) REVERT: h 10 ILE cc_start: 0.9523 (mt) cc_final: 0.9299 (mm) REVERT: h 32 MET cc_start: 0.8551 (tpp) cc_final: 0.8053 (tpp) REVERT: h 50 ASP cc_start: 0.8858 (t0) cc_final: 0.8331 (t0) REVERT: h 51 THR cc_start: 0.9563 (OUTLIER) cc_final: 0.9344 (p) REVERT: h 70 ASP cc_start: 0.8929 (m-30) cc_final: 0.8418 (m-30) REVERT: h 104 LEU cc_start: 0.8666 (tp) cc_final: 0.8449 (mt) REVERT: i 32 MET cc_start: 0.8364 (tpp) cc_final: 0.7110 (tpp) REVERT: i 104 LEU cc_start: 0.8482 (tp) cc_final: 0.8149 (mt) outliers start: 200 outliers final: 45 residues processed: 797 average time/residue: 0.2314 time to fit residues: 278.8734 Evaluate side-chains 377 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 320 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 4 residue 33 LEU Chi-restraints excluded: chain 6 residue 536 THR Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain f residue 37 VAL Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain g residue 51 ILE Chi-restraints excluded: chain h residue 51 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.0570 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.0980 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 5.9990 overall best weight: 1.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 58 ASN 1 65 ASN 2 38 GLN 3 58 ASN 3 65 ASN 4 38 GLN 6 577 GLN 6 611 ASN ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 GLN A 203 GLN A 287 GLN ** B 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN B 203 GLN B 287 GLN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN C 156 ASN C 203 GLN C 287 GLN D 577 GLN D 611 ASN E 577 GLN E 611 ASN H 58 ASN H 65 ASN L 38 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 GLN ** X 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 6 GLN f 118 GLN g 6 GLN g 118 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.063797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.044898 restraints weight = 146956.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.046512 restraints weight = 71680.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.047529 restraints weight = 47234.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.048156 restraints weight = 36912.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.048515 restraints weight = 31978.492| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32997 Z= 0.147 Angle : 0.774 14.752 45120 Z= 0.366 Chirality : 0.048 0.416 5371 Planarity : 0.005 0.060 5463 Dihedral : 15.967 81.968 7364 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.13 % Allowed : 13.20 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.57 (0.12), residues: 3777 helix: -0.78 (0.24), residues: 399 sheet: -1.46 (0.13), residues: 1251 loop : -2.08 (0.12), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG h 39 TYR 0.020 0.001 TYR Z 49 PHE 0.019 0.002 PHE 1 107 TRP 0.016 0.001 TRP 1 54 HIS 0.009 0.001 HIS M 3 Details of bonding type rmsd covalent geometry : bond 0.00318 (32812) covalent geometry : angle 0.73157 (44619) SS BOND : bond 0.00433 ( 54) SS BOND : angle 0.87184 ( 108) hydrogen bonds : bond 0.03643 ( 1064) hydrogen bonds : angle 6.62028 ( 2817) link_ALPHA1-2 : bond 0.00498 ( 3) link_ALPHA1-2 : angle 1.56152 ( 9) link_ALPHA1-3 : bond 0.01028 ( 18) link_ALPHA1-3 : angle 2.39327 ( 54) link_ALPHA1-6 : bond 0.00373 ( 11) link_ALPHA1-6 : angle 1.77814 ( 33) link_BETA1-4 : bond 0.00519 ( 72) link_BETA1-4 : angle 2.84109 ( 216) link_NAG-ASN : bond 0.00505 ( 27) link_NAG-ASN : angle 3.32441 ( 81) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 406 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 76 ASN cc_start: 0.8957 (t0) cc_final: 0.8677 (t0) REVERT: 1 94 ARG cc_start: 0.8041 (tmm160) cc_final: 0.7649 (ttp80) REVERT: 2 24 ARG cc_start: 0.9033 (mtt90) cc_final: 0.8725 (mmt90) REVERT: 2 45 ARG cc_start: 0.8914 (tpm170) cc_final: 0.8563 (tpm170) REVERT: 4 24 ARG cc_start: 0.9051 (mtt90) cc_final: 0.8814 (mmt90) REVERT: 6 571 TRP cc_start: 0.7115 (m-90) cc_final: 0.6660 (m-10) REVERT: 6 574 LYS cc_start: 0.8698 (ptmt) cc_final: 0.8404 (ptpp) REVERT: 6 659 ASP cc_start: 0.9191 (t0) cc_final: 0.8837 (m-30) REVERT: B 475 MET cc_start: 0.8823 (mmm) cc_final: 0.8609 (mmm) REVERT: C 114 GLN cc_start: 0.8913 (mm-40) cc_final: 0.8682 (tm-30) REVERT: D 629 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9229 (mp) REVERT: D 651 ASN cc_start: 0.9324 (t0) cc_final: 0.8957 (p0) REVERT: D 659 ASP cc_start: 0.9153 (t0) cc_final: 0.8881 (m-30) REVERT: E 581 LEU cc_start: 0.9589 (tp) cc_final: 0.9296 (tt) REVERT: E 601 LYS cc_start: 0.8763 (mttt) cc_final: 0.8330 (ttpp) REVERT: E 629 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9070 (mt) REVERT: E 638 TYR cc_start: 0.8495 (m-80) cc_final: 0.7935 (m-10) REVERT: E 659 ASP cc_start: 0.9118 (t0) cc_final: 0.8866 (m-30) REVERT: H 94 ARG cc_start: 0.8069 (tmm160) cc_final: 0.7568 (ttp80) REVERT: M 23 ASN cc_start: 0.8815 (t0) cc_final: 0.8540 (t0) REVERT: M 100 MET cc_start: 0.8948 (mpp) cc_final: 0.8585 (mpp) REVERT: N 47 ILE cc_start: 0.9278 (pt) cc_final: 0.8844 (mt) REVERT: N 54 ARG cc_start: 0.8611 (ptt-90) cc_final: 0.8308 (ptt90) REVERT: N 96 TRP cc_start: 0.8004 (m100) cc_final: 0.7604 (m100) REVERT: Q 118 GLN cc_start: 0.8893 (tm-30) cc_final: 0.8592 (tm-30) REVERT: R 37 GLN cc_start: 0.9125 (tt0) cc_final: 0.8858 (tm-30) REVERT: X 23 ASN cc_start: 0.8697 (t0) cc_final: 0.8394 (t0) REVERT: X 64 LYS cc_start: 0.9033 (tppt) cc_final: 0.8405 (tppt) REVERT: X 100 MET cc_start: 0.8936 (mpp) cc_final: 0.8298 (mmm) REVERT: Y 23 ASN cc_start: 0.9027 (t0) cc_final: 0.8727 (t0) REVERT: Y 53 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.7247 (p0) REVERT: Z 96 TRP cc_start: 0.8080 (m100) cc_final: 0.7497 (m100) REVERT: Z 100 GLU cc_start: 0.8418 (pm20) cc_final: 0.8161 (pm20) REVERT: a 28 LEU cc_start: 0.9094 (mp) cc_final: 0.8877 (mp) REVERT: a 96 TRP cc_start: 0.7914 (m100) cc_final: 0.7576 (m100) REVERT: g 111 TYR cc_start: 0.8723 (m-80) cc_final: 0.8173 (m-80) REVERT: h 1 GLU cc_start: 0.7355 (pt0) cc_final: 0.6833 (mp0) REVERT: h 32 MET cc_start: 0.8337 (tpp) cc_final: 0.7817 (tpp) REVERT: h 70 ASP cc_start: 0.9089 (m-30) cc_final: 0.8874 (p0) REVERT: i 32 MET cc_start: 0.7889 (tpp) cc_final: 0.7418 (tpp) outliers start: 104 outliers final: 58 residues processed: 499 average time/residue: 0.2222 time to fit residues: 170.7388 Evaluate side-chains 378 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 317 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 513 VAL Chi-restraints excluded: chain 6 residue 536 THR Chi-restraints excluded: chain 6 residue 538 THR Chi-restraints excluded: chain 6 residue 604 CYS Chi-restraints excluded: chain 6 residue 639 THR Chi-restraints excluded: chain 6 residue 641 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 604 CYS Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 80 ASP Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 109 VAL Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 79 ASP Chi-restraints excluded: chain g residue 51 ILE Chi-restraints excluded: chain h residue 63 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 120 optimal weight: 0.8980 chunk 370 optimal weight: 7.9990 chunk 319 optimal weight: 0.0010 chunk 365 optimal weight: 7.9990 chunk 186 optimal weight: 2.9990 chunk 329 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 231 optimal weight: 20.0000 chunk 38 optimal weight: 5.9990 chunk 300 optimal weight: 9.9990 chunk 283 optimal weight: 7.9990 overall best weight: 3.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 30AHIS ** 2 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 30AHIS ** 4 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 GLN ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN ** B 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30AHIS ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN M 5 GLN ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 5 GLN ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.061634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.042584 restraints weight = 149852.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.044114 restraints weight = 73375.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.045079 restraints weight = 48615.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.045653 restraints weight = 38237.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.046031 restraints weight = 33331.573| |-----------------------------------------------------------------------------| r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 32997 Z= 0.267 Angle : 0.795 12.164 45120 Z= 0.375 Chirality : 0.048 0.408 5371 Planarity : 0.004 0.053 5463 Dihedral : 14.177 80.198 7326 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.21 % Allowed : 13.62 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.13 (0.13), residues: 3777 helix: -0.35 (0.24), residues: 438 sheet: -1.23 (0.14), residues: 1215 loop : -1.77 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG f 62 TYR 0.017 0.002 TYR D 638 PHE 0.025 0.002 PHE f 115 TRP 0.015 0.002 TRP B 96 HIS 0.005 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00584 (32812) covalent geometry : angle 0.75255 (44619) SS BOND : bond 0.00392 ( 54) SS BOND : angle 1.06285 ( 108) hydrogen bonds : bond 0.03650 ( 1064) hydrogen bonds : angle 6.36403 ( 2817) link_ALPHA1-2 : bond 0.00278 ( 3) link_ALPHA1-2 : angle 1.63350 ( 9) link_ALPHA1-3 : bond 0.00903 ( 18) link_ALPHA1-3 : angle 2.23270 ( 54) link_ALPHA1-6 : bond 0.00358 ( 11) link_ALPHA1-6 : angle 1.75092 ( 33) link_BETA1-4 : bond 0.00444 ( 72) link_BETA1-4 : angle 2.77734 ( 216) link_NAG-ASN : bond 0.00656 ( 27) link_NAG-ASN : angle 3.59860 ( 81) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 325 time to evaluate : 0.990 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: 1 76 ASN cc_start: 0.9192 (t0) cc_final: 0.8981 (t0) REVERT: 1 94 ARG cc_start: 0.7954 (tmm160) cc_final: 0.7604 (ttp80) REVERT: 2 45 ARG cc_start: 0.9041 (tpm170) cc_final: 0.8677 (tpm170) REVERT: 3 3 GLN cc_start: 0.8063 (mp10) cc_final: 0.7779 (mp10) REVERT: 4 24 ARG cc_start: 0.9058 (mtt90) cc_final: 0.8754 (mmt90) REVERT: 6 584 GLU cc_start: 0.8784 (tt0) cc_final: 0.8568 (tm-30) REVERT: 6 654 GLU cc_start: 0.9200 (tp30) cc_final: 0.8993 (tp30) REVERT: A 100 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8909 (ptp) REVERT: A 373 THR cc_start: 0.9630 (t) cc_final: 0.9368 (t) REVERT: B 475 MET cc_start: 0.8899 (mmm) cc_final: 0.8649 (mmm) REVERT: C 107 ASP cc_start: 0.8700 (m-30) cc_final: 0.8468 (m-30) REVERT: C 114 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8719 (tm-30) REVERT: D 601 LYS cc_start: 0.8877 (mttt) cc_final: 0.8624 (ttmm) REVERT: D 659 ASP cc_start: 0.9117 (t0) cc_final: 0.8856 (m-30) REVERT: E 584 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8190 (tm-30) REVERT: E 601 LYS cc_start: 0.8872 (mttt) cc_final: 0.8633 (ttmm) REVERT: E 659 ASP cc_start: 0.9136 (t0) cc_final: 0.8804 (m-30) REVERT: H 64 LYS cc_start: 0.8497 (mtmm) cc_final: 0.8185 (ptpp) REVERT: H 94 ARG cc_start: 0.8027 (tmm160) cc_final: 0.7530 (ttp80) REVERT: M 100 MET cc_start: 0.8956 (mpp) cc_final: 0.8660 (mmm) REVERT: N 20 ARG cc_start: 0.6965 (mtm-85) cc_final: 0.6684 (mtm-85) REVERT: N 54 ARG cc_start: 0.8609 (ptt-90) cc_final: 0.8247 (ptt90) REVERT: N 67 THR cc_start: 0.9485 (OUTLIER) cc_final: 0.9046 (p) REVERT: Q 3 GLN cc_start: 0.8169 (mp10) cc_final: 0.7546 (mp10) REVERT: Q 118 GLN cc_start: 0.8983 (tm-30) cc_final: 0.8660 (tm-30) REVERT: X 30 ARG cc_start: 0.8760 (tpp80) cc_final: 0.8112 (tpp80) REVERT: X 44 GLN cc_start: 0.8307 (pp30) cc_final: 0.7992 (pp30) REVERT: X 53 ASP cc_start: 0.7966 (p0) cc_final: 0.7158 (p0) REVERT: Y 30 ARG cc_start: 0.8755 (tpp80) cc_final: 0.8231 (tpp80) REVERT: Y 53 ASP cc_start: 0.7875 (p0) cc_final: 0.7214 (p0) REVERT: Y 64 LYS cc_start: 0.9071 (tppt) cc_final: 0.8715 (tppt) REVERT: Y 100 MET cc_start: 0.8892 (mpp) cc_final: 0.8256 (mpp) REVERT: Z 67 THR cc_start: 0.9463 (OUTLIER) cc_final: 0.9021 (p) REVERT: a 20 ARG cc_start: 0.6639 (mtm-85) cc_final: 0.6386 (mtm-85) REVERT: a 28 LEU cc_start: 0.9246 (mp) cc_final: 0.8864 (mp) REVERT: a 67 THR cc_start: 0.9423 (OUTLIER) cc_final: 0.9007 (p) REVERT: g 94 THR cc_start: 0.9507 (OUTLIER) cc_final: 0.9303 (t) REVERT: g 111 TYR cc_start: 0.8797 (m-80) cc_final: 0.8280 (m-80) REVERT: h 32 MET cc_start: 0.8473 (tpp) cc_final: 0.7964 (tpp) REVERT: i 32 MET cc_start: 0.8141 (tpp) cc_final: 0.7740 (tpp) REVERT: i 79 ASP cc_start: 0.9080 (OUTLIER) cc_final: 0.8868 (t70) outliers start: 140 outliers final: 79 residues processed: 448 average time/residue: 0.2012 time to fit residues: 142.5276 Evaluate side-chains 359 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 274 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 4 residue 73 LEU Chi-restraints excluded: chain 4 residue 92 VAL Chi-restraints excluded: chain 6 residue 513 VAL Chi-restraints excluded: chain 6 residue 534 SER Chi-restraints excluded: chain 6 residue 536 THR Chi-restraints excluded: chain 6 residue 538 THR Chi-restraints excluded: chain 6 residue 583 VAL Chi-restraints excluded: chain 6 residue 604 CYS Chi-restraints excluded: chain 6 residue 635 ILE Chi-restraints excluded: chain 6 residue 641 ILE Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 53 PHE Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 598 CYS Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain Q residue 80 ASP Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain X residue 24 VAL Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 48 ILE Chi-restraints excluded: chain Y residue 82 VAL Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain f residue 94 THR Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain h residue 63 VAL Chi-restraints excluded: chain h residue 104 LEU Chi-restraints excluded: chain i residue 79 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 7 optimal weight: 0.6980 chunk 191 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 234 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 235 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 351 optimal weight: 6.9990 chunk 321 optimal weight: 6.9990 chunk 305 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.061903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.042996 restraints weight = 148205.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.044534 restraints weight = 72337.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.045506 restraints weight = 47772.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.046110 restraints weight = 37491.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.046457 restraints weight = 32525.761| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 32997 Z= 0.207 Angle : 0.745 11.944 45120 Z= 0.351 Chirality : 0.047 0.421 5371 Planarity : 0.004 0.056 5463 Dihedral : 12.603 78.851 7320 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.58 % Allowed : 15.42 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.77 (0.13), residues: 3777 helix: 0.38 (0.26), residues: 399 sheet: -1.07 (0.14), residues: 1206 loop : -1.54 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG g 62 TYR 0.016 0.001 TYR 2 87 PHE 0.024 0.002 PHE f 115 TRP 0.014 0.001 TRP E 596 HIS 0.006 0.001 HIS M 3 Details of bonding type rmsd covalent geometry : bond 0.00452 (32812) covalent geometry : angle 0.70349 (44619) SS BOND : bond 0.00381 ( 54) SS BOND : angle 1.02141 ( 108) hydrogen bonds : bond 0.03356 ( 1064) hydrogen bonds : angle 6.15075 ( 2817) link_ALPHA1-2 : bond 0.00282 ( 3) link_ALPHA1-2 : angle 1.60792 ( 9) link_ALPHA1-3 : bond 0.00974 ( 18) link_ALPHA1-3 : angle 2.22443 ( 54) link_ALPHA1-6 : bond 0.00518 ( 11) link_ALPHA1-6 : angle 1.69633 ( 33) link_BETA1-4 : bond 0.00408 ( 72) link_BETA1-4 : angle 2.65563 ( 216) link_NAG-ASN : bond 0.00543 ( 27) link_NAG-ASN : angle 3.42905 ( 81) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 307 time to evaluate : 1.237 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: 1 94 ARG cc_start: 0.7831 (tmm160) cc_final: 0.7563 (ttp80) REVERT: 2 45 ARG cc_start: 0.9047 (tpm170) cc_final: 0.8676 (tpm170) REVERT: 3 3 GLN cc_start: 0.7966 (mp10) cc_final: 0.7765 (mp10) REVERT: 4 24 ARG cc_start: 0.9060 (mtt90) cc_final: 0.8745 (mmt90) REVERT: 4 42 GLN cc_start: 0.6664 (OUTLIER) cc_final: 0.6412 (pt0) REVERT: 6 584 GLU cc_start: 0.8748 (tt0) cc_final: 0.8500 (tm-30) REVERT: 6 601 LYS cc_start: 0.8999 (mttt) cc_final: 0.8507 (ttpp) REVERT: 6 654 GLU cc_start: 0.9284 (tp30) cc_final: 0.9020 (tp30) REVERT: A 100 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.8920 (ptp) REVERT: A 373 THR cc_start: 0.9637 (t) cc_final: 0.9382 (t) REVERT: B 271 MET cc_start: 0.8991 (mmm) cc_final: 0.8790 (mmt) REVERT: B 475 MET cc_start: 0.8860 (mmm) cc_final: 0.8625 (mmm) REVERT: C 104 MET cc_start: 0.9534 (OUTLIER) cc_final: 0.8646 (ttm) REVERT: C 114 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8755 (tm-30) REVERT: D 601 LYS cc_start: 0.8879 (mttt) cc_final: 0.8594 (ttmm) REVERT: D 659 ASP cc_start: 0.9074 (t0) cc_final: 0.8844 (m-30) REVERT: E 584 GLU cc_start: 0.8320 (tm-30) cc_final: 0.8052 (tm-30) REVERT: E 601 LYS cc_start: 0.8912 (mttt) cc_final: 0.8633 (ttmm) REVERT: H 94 ARG cc_start: 0.7893 (tmm160) cc_final: 0.7430 (ttp80) REVERT: M 100 MET cc_start: 0.8899 (mpp) cc_final: 0.8642 (mmm) REVERT: N 20 ARG cc_start: 0.6996 (mtm-85) cc_final: 0.6408 (mtm-85) REVERT: N 54 ARG cc_start: 0.8612 (ptt-90) cc_final: 0.8240 (ptt90) REVERT: N 67 THR cc_start: 0.9490 (OUTLIER) cc_final: 0.9032 (p) REVERT: N 96 TRP cc_start: 0.8181 (m100) cc_final: 0.7666 (m100) REVERT: Q 3 GLN cc_start: 0.8270 (mp10) cc_final: 0.7709 (mp10) REVERT: Q 118 GLN cc_start: 0.8983 (tm-30) cc_final: 0.8662 (tm-30) REVERT: X 30 ARG cc_start: 0.8785 (tpp80) cc_final: 0.8114 (tpp80) REVERT: X 44 GLN cc_start: 0.8310 (pp30) cc_final: 0.8079 (pp30) REVERT: X 53 ASP cc_start: 0.8270 (p0) cc_final: 0.7835 (p0) REVERT: X 64 LYS cc_start: 0.9137 (tppt) cc_final: 0.8836 (tppt) REVERT: X 100 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8236 (mt-10) REVERT: X 100 MET cc_start: 0.8994 (mpp) cc_final: 0.8421 (mmm) REVERT: Y 30 ARG cc_start: 0.8818 (tpp80) cc_final: 0.8311 (tpp80) REVERT: Y 53 ASP cc_start: 0.8038 (p0) cc_final: 0.7045 (p0) REVERT: Y 64 LYS cc_start: 0.9064 (tppt) cc_final: 0.8651 (tppt) REVERT: Z 67 THR cc_start: 0.9485 (OUTLIER) cc_final: 0.9011 (p) REVERT: Z 96 TRP cc_start: 0.7996 (m100) cc_final: 0.7530 (m100) REVERT: a 20 ARG cc_start: 0.6735 (mtm-85) cc_final: 0.6507 (mtm-85) REVERT: a 67 THR cc_start: 0.9439 (OUTLIER) cc_final: 0.9056 (p) REVERT: g 111 TYR cc_start: 0.8765 (m-80) cc_final: 0.8273 (m-80) REVERT: h 32 MET cc_start: 0.8451 (tpp) cc_final: 0.7986 (tpp) REVERT: i 32 MET cc_start: 0.8197 (tpp) cc_final: 0.7777 (tpp) REVERT: i 79 ASP cc_start: 0.9095 (t70) cc_final: 0.8893 (t0) outliers start: 119 outliers final: 84 residues processed: 410 average time/residue: 0.2053 time to fit residues: 133.8374 Evaluate side-chains 370 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 280 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 73 LEU Chi-restraints excluded: chain 4 residue 3 VAL Chi-restraints excluded: chain 4 residue 42 GLN Chi-restraints excluded: chain 4 residue 73 LEU Chi-restraints excluded: chain 4 residue 92 VAL Chi-restraints excluded: chain 6 residue 513 VAL Chi-restraints excluded: chain 6 residue 536 THR Chi-restraints excluded: chain 6 residue 583 VAL Chi-restraints excluded: chain 6 residue 604 CYS Chi-restraints excluded: chain 6 residue 635 ILE Chi-restraints excluded: chain 6 residue 641 ILE Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 53 PHE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 534 SER Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain X residue 100 LYS Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 82 VAL Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain f residue 37 VAL Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain f residue 94 THR Chi-restraints excluded: chain g residue 51 ILE Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain i residue 47 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 120 optimal weight: 0.9980 chunk 329 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 296 optimal weight: 7.9990 chunk 205 optimal weight: 3.9990 chunk 288 optimal weight: 10.0000 chunk 200 optimal weight: 9.9990 chunk 189 optimal weight: 0.4980 chunk 76 optimal weight: 6.9990 chunk 139 optimal weight: 0.9990 chunk 203 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 42 GLN ** 2 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 38 GLN ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 HIS C 72 HIS ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.061955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.042863 restraints weight = 150149.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.044404 restraints weight = 73976.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.045391 restraints weight = 49201.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.045976 restraints weight = 38655.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.046317 restraints weight = 33753.031| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 32997 Z= 0.190 Angle : 0.723 12.028 45120 Z= 0.340 Chirality : 0.047 0.417 5371 Planarity : 0.004 0.053 5463 Dihedral : 11.332 77.452 7317 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.94 % Allowed : 15.72 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.58 (0.13), residues: 3777 helix: 0.33 (0.26), residues: 414 sheet: -0.93 (0.15), residues: 1200 loop : -1.39 (0.13), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 1 13 TYR 0.015 0.001 TYR N 49 PHE 0.023 0.002 PHE f 115 TRP 0.015 0.001 TRP B 96 HIS 0.006 0.001 HIS X 3 Details of bonding type rmsd covalent geometry : bond 0.00414 (32812) covalent geometry : angle 0.68166 (44619) SS BOND : bond 0.00333 ( 54) SS BOND : angle 0.98451 ( 108) hydrogen bonds : bond 0.03228 ( 1064) hydrogen bonds : angle 5.96535 ( 2817) link_ALPHA1-2 : bond 0.00282 ( 3) link_ALPHA1-2 : angle 1.58803 ( 9) link_ALPHA1-3 : bond 0.01008 ( 18) link_ALPHA1-3 : angle 2.18368 ( 54) link_ALPHA1-6 : bond 0.00640 ( 11) link_ALPHA1-6 : angle 1.65186 ( 33) link_BETA1-4 : bond 0.00389 ( 72) link_BETA1-4 : angle 2.59373 ( 216) link_NAG-ASN : bond 0.00550 ( 27) link_NAG-ASN : angle 3.42404 ( 81) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 306 time to evaluate : 1.079 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: 1 94 ARG cc_start: 0.7664 (tmm160) cc_final: 0.7437 (ttp80) REVERT: 2 45 ARG cc_start: 0.9103 (tpm170) cc_final: 0.8689 (tpm170) REVERT: 4 24 ARG cc_start: 0.9101 (mtt90) cc_final: 0.8793 (mmt90) REVERT: 4 42 GLN cc_start: 0.6761 (OUTLIER) cc_final: 0.6559 (pt0) REVERT: 6 584 GLU cc_start: 0.8740 (tt0) cc_final: 0.8479 (tm-30) REVERT: 6 601 LYS cc_start: 0.9001 (mttt) cc_final: 0.8589 (ttpp) REVERT: 6 603 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8268 (mm) REVERT: 6 654 GLU cc_start: 0.9314 (tp30) cc_final: 0.9032 (tp30) REVERT: A 100 MET cc_start: 0.9213 (OUTLIER) cc_final: 0.8909 (ptp) REVERT: A 373 THR cc_start: 0.9622 (t) cc_final: 0.9362 (t) REVERT: A 480 ARG cc_start: 0.9430 (OUTLIER) cc_final: 0.8382 (mtm110) REVERT: B 475 MET cc_start: 0.8879 (mmm) cc_final: 0.8645 (mmm) REVERT: C 104 MET cc_start: 0.9543 (OUTLIER) cc_final: 0.8582 (ttm) REVERT: D 601 LYS cc_start: 0.8923 (mttt) cc_final: 0.8613 (ttmm) REVERT: D 659 ASP cc_start: 0.9077 (t0) cc_final: 0.8862 (m-30) REVERT: E 584 GLU cc_start: 0.8330 (tm-30) cc_final: 0.8085 (tm-30) REVERT: E 601 LYS cc_start: 0.8908 (mttt) cc_final: 0.8601 (ttmm) REVERT: E 654 GLU cc_start: 0.9159 (tp30) cc_final: 0.8909 (tp30) REVERT: H 64 LYS cc_start: 0.8507 (mtmm) cc_final: 0.8184 (ptpp) REVERT: H 94 ARG cc_start: 0.7759 (tmm160) cc_final: 0.7360 (ttp80) REVERT: M 100 MET cc_start: 0.8845 (mpp) cc_final: 0.8571 (mmm) REVERT: N 20 ARG cc_start: 0.6987 (mtm-85) cc_final: 0.6761 (mtm-85) REVERT: N 54 ARG cc_start: 0.8626 (ptt-90) cc_final: 0.8252 (ptt90) REVERT: N 67 THR cc_start: 0.9483 (OUTLIER) cc_final: 0.8997 (p) REVERT: N 96 TRP cc_start: 0.8170 (m100) cc_final: 0.7625 (m100) REVERT: Q 3 GLN cc_start: 0.8321 (mp10) cc_final: 0.7733 (mp10) REVERT: Q 118 GLN cc_start: 0.9052 (tm-30) cc_final: 0.8717 (tm-30) REVERT: R 32 MET cc_start: 0.8535 (tpp) cc_final: 0.8017 (tpp) REVERT: R 79 ASP cc_start: 0.8714 (t0) cc_final: 0.8512 (t0) REVERT: X 30 ARG cc_start: 0.8821 (tpp80) cc_final: 0.8128 (tpp80) REVERT: X 44 GLN cc_start: 0.8302 (pp30) cc_final: 0.8068 (pp30) REVERT: X 53 ASP cc_start: 0.8422 (p0) cc_final: 0.7802 (p0) REVERT: X 100 MET cc_start: 0.8938 (mpp) cc_final: 0.8662 (mmm) REVERT: Y 30 ARG cc_start: 0.8838 (tpp80) cc_final: 0.8293 (tpp80) REVERT: Y 53 ASP cc_start: 0.8135 (p0) cc_final: 0.7014 (p0) REVERT: Y 64 LYS cc_start: 0.9070 (tppt) cc_final: 0.8621 (tppt) REVERT: Z 67 THR cc_start: 0.9503 (OUTLIER) cc_final: 0.9025 (p) REVERT: a 20 ARG cc_start: 0.6751 (mtm-85) cc_final: 0.6531 (mtm-85) REVERT: a 67 THR cc_start: 0.9441 (OUTLIER) cc_final: 0.8907 (p) REVERT: a 96 TRP cc_start: 0.8178 (m100) cc_final: 0.7686 (m100) REVERT: g 111 TYR cc_start: 0.8746 (m-80) cc_final: 0.8314 (m-80) REVERT: h 32 MET cc_start: 0.8260 (tpp) cc_final: 0.7688 (tpp) REVERT: h 77 LYS cc_start: 0.9158 (mtmt) cc_final: 0.8946 (mtmt) REVERT: i 32 MET cc_start: 0.8220 (tpp) cc_final: 0.7850 (tpp) REVERT: i 79 ASP cc_start: 0.9137 (t70) cc_final: 0.8927 (t0) outliers start: 131 outliers final: 92 residues processed: 421 average time/residue: 0.1933 time to fit residues: 130.1911 Evaluate side-chains 377 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 277 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 73 LEU Chi-restraints excluded: chain 4 residue 3 VAL Chi-restraints excluded: chain 4 residue 42 GLN Chi-restraints excluded: chain 4 residue 73 LEU Chi-restraints excluded: chain 4 residue 92 VAL Chi-restraints excluded: chain 6 residue 513 VAL Chi-restraints excluded: chain 6 residue 522 PHE Chi-restraints excluded: chain 6 residue 536 THR Chi-restraints excluded: chain 6 residue 538 THR Chi-restraints excluded: chain 6 residue 583 VAL Chi-restraints excluded: chain 6 residue 598 CYS Chi-restraints excluded: chain 6 residue 603 ILE Chi-restraints excluded: chain 6 residue 604 CYS Chi-restraints excluded: chain 6 residue 635 ILE Chi-restraints excluded: chain 6 residue 641 ILE Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 480 ARG Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 53 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 534 SER Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain E residue 598 CYS Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain E residue 647 GLU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain X residue 24 VAL Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain X residue 100 LYS Chi-restraints excluded: chain Y residue 82 VAL Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain f residue 94 THR Chi-restraints excluded: chain g residue 51 ILE Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain i residue 47 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 250 optimal weight: 7.9990 chunk 31 optimal weight: 30.0000 chunk 247 optimal weight: 2.9990 chunk 339 optimal weight: 7.9990 chunk 333 optimal weight: 1.9990 chunk 245 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 244 optimal weight: 10.0000 chunk 70 optimal weight: 0.0020 chunk 101 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 overall best weight: 2.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 HIS ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 HIS ** 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 = 0.3354 r_free = 0.3354 target = 0.061651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.042461 restraints weight = 149056.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.044009 restraints weight = 72504.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.045004 restraints weight = 47948.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.045607 restraints weight = 37534.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.045971 restraints weight = 32559.291| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32997 Z= 0.191 Angle : 0.723 12.073 45120 Z= 0.339 Chirality : 0.046 0.412 5371 Planarity : 0.004 0.052 5463 Dihedral : 10.714 76.366 7317 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.85 % Allowed : 16.65 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.48 (0.14), residues: 3777 helix: 0.47 (0.26), residues: 414 sheet: -0.93 (0.14), residues: 1233 loop : -1.29 (0.14), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 3 13 TYR 0.019 0.001 TYR 4 87 PHE 0.023 0.002 PHE f 115 TRP 0.014 0.001 TRP D 571 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00417 (32812) covalent geometry : angle 0.68208 (44619) SS BOND : bond 0.00325 ( 54) SS BOND : angle 0.97073 ( 108) hydrogen bonds : bond 0.03162 ( 1064) hydrogen bonds : angle 5.86807 ( 2817) link_ALPHA1-2 : bond 0.00260 ( 3) link_ALPHA1-2 : angle 1.59691 ( 9) link_ALPHA1-3 : bond 0.01004 ( 18) link_ALPHA1-3 : angle 2.20593 ( 54) link_ALPHA1-6 : bond 0.00700 ( 11) link_ALPHA1-6 : angle 1.64184 ( 33) link_BETA1-4 : bond 0.00390 ( 72) link_BETA1-4 : angle 2.56861 ( 216) link_NAG-ASN : bond 0.00546 ( 27) link_NAG-ASN : angle 3.39982 ( 81) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 294 time to evaluate : 0.911 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: 4 45 ARG cc_start: 0.8475 (ttm170) cc_final: 0.8041 (ttp-170) REVERT: 6 584 GLU cc_start: 0.8791 (tt0) cc_final: 0.8494 (tm-30) REVERT: 6 601 LYS cc_start: 0.9009 (mttt) cc_final: 0.8668 (ttpp) REVERT: 6 603 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8171 (mm) REVERT: 6 654 GLU cc_start: 0.9342 (tp30) cc_final: 0.9080 (tp30) REVERT: A 100 MET cc_start: 0.9267 (OUTLIER) cc_final: 0.8910 (ptp) REVERT: A 373 THR cc_start: 0.9636 (t) cc_final: 0.9380 (t) REVERT: A 480 ARG cc_start: 0.9416 (OUTLIER) cc_final: 0.8528 (mtm110) REVERT: B 475 MET cc_start: 0.8910 (mmm) cc_final: 0.8668 (mmm) REVERT: C 104 MET cc_start: 0.9570 (OUTLIER) cc_final: 0.8648 (ttm) REVERT: D 601 LYS cc_start: 0.8942 (mttt) cc_final: 0.8585 (ttmm) REVERT: E 584 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8110 (tm-30) REVERT: E 601 LYS cc_start: 0.8960 (mttt) cc_final: 0.8655 (ttmm) REVERT: H 94 ARG cc_start: 0.7675 (tmm160) cc_final: 0.7301 (ttp80) REVERT: M 100 MET cc_start: 0.8853 (mpp) cc_final: 0.8541 (mmm) REVERT: N 54 ARG cc_start: 0.8643 (ptt-90) cc_final: 0.8251 (ptm-80) REVERT: N 67 THR cc_start: 0.9473 (OUTLIER) cc_final: 0.8977 (p) REVERT: N 96 TRP cc_start: 0.8182 (m100) cc_final: 0.7557 (m100) REVERT: Q 3 GLN cc_start: 0.8327 (mp10) cc_final: 0.7738 (mp10) REVERT: Q 118 GLN cc_start: 0.9076 (tm-30) cc_final: 0.8686 (tm-30) REVERT: R 79 ASP cc_start: 0.8651 (t0) cc_final: 0.8397 (t0) REVERT: X 30 ARG cc_start: 0.8876 (tpp80) cc_final: 0.8171 (tpp80) REVERT: X 44 GLN cc_start: 0.8285 (pp30) cc_final: 0.8045 (pp30) REVERT: X 53 ASP cc_start: 0.8517 (p0) cc_final: 0.7852 (p0) REVERT: X 100 MET cc_start: 0.8950 (mpp) cc_final: 0.8350 (mmm) REVERT: Y 30 ARG cc_start: 0.8866 (tpp80) cc_final: 0.8343 (tpp80) REVERT: Y 53 ASP cc_start: 0.8223 (p0) cc_final: 0.7009 (p0) REVERT: Y 64 LYS cc_start: 0.9015 (tppt) cc_final: 0.8570 (tppt) REVERT: Z 67 THR cc_start: 0.9493 (OUTLIER) cc_final: 0.9015 (p) REVERT: a 20 ARG cc_start: 0.6748 (mtm-85) cc_final: 0.6538 (mtm-85) REVERT: a 67 THR cc_start: 0.9444 (OUTLIER) cc_final: 0.8896 (p) REVERT: a 96 TRP cc_start: 0.8217 (m100) cc_final: 0.7672 (m100) REVERT: f 3 GLN cc_start: 0.8217 (mp10) cc_final: 0.8000 (mp10) REVERT: g 111 TYR cc_start: 0.8753 (m-80) cc_final: 0.8385 (m-80) REVERT: h 32 MET cc_start: 0.8320 (tpp) cc_final: 0.7719 (tpp) REVERT: h 77 LYS cc_start: 0.9207 (mtmt) cc_final: 0.9002 (mtmt) REVERT: i 32 MET cc_start: 0.8195 (tpp) cc_final: 0.7829 (tpp) REVERT: i 79 ASP cc_start: 0.9197 (t70) cc_final: 0.8832 (t0) REVERT: i 81 GLU cc_start: 0.8814 (pm20) cc_final: 0.8456 (pm20) outliers start: 128 outliers final: 96 residues processed: 407 average time/residue: 0.1984 time to fit residues: 129.0263 Evaluate side-chains 386 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 283 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 73 LEU Chi-restraints excluded: chain 4 residue 3 VAL Chi-restraints excluded: chain 4 residue 73 LEU Chi-restraints excluded: chain 4 residue 92 VAL Chi-restraints excluded: chain 6 residue 513 VAL Chi-restraints excluded: chain 6 residue 522 PHE Chi-restraints excluded: chain 6 residue 536 THR Chi-restraints excluded: chain 6 residue 583 VAL Chi-restraints excluded: chain 6 residue 603 ILE Chi-restraints excluded: chain 6 residue 604 CYS Chi-restraints excluded: chain 6 residue 635 ILE Chi-restraints excluded: chain 6 residue 639 THR Chi-restraints excluded: chain 6 residue 641 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 480 ARG Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 53 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain E residue 598 CYS Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain E residue 647 GLU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain X residue 24 VAL Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain f residue 37 VAL Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain f residue 94 THR Chi-restraints excluded: chain g residue 51 ILE Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain i residue 47 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 193 optimal weight: 0.0050 chunk 137 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 330 optimal weight: 6.9990 chunk 163 optimal weight: 0.8980 chunk 253 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 208 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 38 GLN ** 2 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 42 GLN C 262 ASN ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.062447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.043280 restraints weight = 149198.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.044849 restraints weight = 72937.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.045814 restraints weight = 48278.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.046436 restraints weight = 38042.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.046812 restraints weight = 32973.528| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32997 Z= 0.135 Angle : 0.702 12.069 45120 Z= 0.327 Chirality : 0.046 0.421 5371 Planarity : 0.004 0.053 5463 Dihedral : 9.870 74.814 7317 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.46 % Allowed : 17.28 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.28 (0.14), residues: 3777 helix: 0.75 (0.27), residues: 396 sheet: -0.81 (0.15), residues: 1233 loop : -1.16 (0.14), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 1 94 TYR 0.019 0.001 TYR 4 87 PHE 0.020 0.001 PHE f 115 TRP 0.020 0.001 TRP D 571 HIS 0.007 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00296 (32812) covalent geometry : angle 0.66293 (44619) SS BOND : bond 0.00252 ( 54) SS BOND : angle 0.94765 ( 108) hydrogen bonds : bond 0.03005 ( 1064) hydrogen bonds : angle 5.68518 ( 2817) link_ALPHA1-2 : bond 0.00312 ( 3) link_ALPHA1-2 : angle 1.63702 ( 9) link_ALPHA1-3 : bond 0.01086 ( 18) link_ALPHA1-3 : angle 2.05716 ( 54) link_ALPHA1-6 : bond 0.00811 ( 11) link_ALPHA1-6 : angle 1.58793 ( 33) link_BETA1-4 : bond 0.00428 ( 72) link_BETA1-4 : angle 2.49305 ( 216) link_NAG-ASN : bond 0.00508 ( 27) link_NAG-ASN : angle 3.26200 ( 81) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 314 time to evaluate : 1.215 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: 4 24 ARG cc_start: 0.9118 (mtt90) cc_final: 0.8910 (mmt90) REVERT: 6 584 GLU cc_start: 0.8779 (tt0) cc_final: 0.8418 (tm-30) REVERT: 6 601 LYS cc_start: 0.9065 (mttt) cc_final: 0.8634 (ttpp) REVERT: 6 603 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8234 (mm) REVERT: 6 654 GLU cc_start: 0.9334 (tp30) cc_final: 0.9052 (tp30) REVERT: A 100 MET cc_start: 0.9253 (OUTLIER) cc_final: 0.8911 (ptp) REVERT: A 373 THR cc_start: 0.9615 (t) cc_final: 0.9342 (t) REVERT: A 480 ARG cc_start: 0.9369 (OUTLIER) cc_final: 0.8433 (mtm110) REVERT: B 125 LEU cc_start: 0.9656 (tp) cc_final: 0.9371 (tp) REVERT: B 426 MET cc_start: 0.8090 (ptm) cc_final: 0.7717 (ptm) REVERT: B 475 MET cc_start: 0.8830 (mmm) cc_final: 0.8568 (mmm) REVERT: C 104 MET cc_start: 0.9535 (OUTLIER) cc_final: 0.8539 (ttm) REVERT: D 601 LYS cc_start: 0.8916 (mttt) cc_final: 0.8550 (ttmm) REVERT: E 584 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8019 (tm-30) REVERT: E 601 LYS cc_start: 0.8864 (mttt) cc_final: 0.8542 (ttmm) REVERT: E 632 ASP cc_start: 0.9232 (t70) cc_final: 0.8975 (t70) REVERT: E 654 GLU cc_start: 0.9075 (tp30) cc_final: 0.8642 (tp30) REVERT: H 64 LYS cc_start: 0.8561 (mtmm) cc_final: 0.8248 (ptpp) REVERT: H 94 ARG cc_start: 0.7501 (tmm160) cc_final: 0.7238 (ttp80) REVERT: M 100 MET cc_start: 0.8784 (mpp) cc_final: 0.8478 (mmm) REVERT: N 54 ARG cc_start: 0.8637 (ptt-90) cc_final: 0.8231 (ptt90) REVERT: N 67 THR cc_start: 0.9472 (OUTLIER) cc_final: 0.8990 (p) REVERT: N 96 TRP cc_start: 0.8128 (m100) cc_final: 0.7534 (m100) REVERT: Q 3 GLN cc_start: 0.8354 (mp10) cc_final: 0.7771 (mp10) REVERT: Q 118 GLN cc_start: 0.9042 (tm-30) cc_final: 0.8613 (tm-30) REVERT: R 32 MET cc_start: 0.8747 (tpp) cc_final: 0.7954 (tpp) REVERT: X 30 ARG cc_start: 0.8911 (tpp80) cc_final: 0.8209 (tpp80) REVERT: X 53 ASP cc_start: 0.8435 (p0) cc_final: 0.7470 (p0) REVERT: X 100 MET cc_start: 0.8903 (mpp) cc_final: 0.8380 (mmm) REVERT: Y 30 ARG cc_start: 0.8875 (tpp80) cc_final: 0.8399 (tpp80) REVERT: Y 53 ASP cc_start: 0.8226 (p0) cc_final: 0.6949 (p0) REVERT: Y 64 LYS cc_start: 0.8963 (tppt) cc_final: 0.8678 (tppt) REVERT: Z 67 THR cc_start: 0.9496 (OUTLIER) cc_final: 0.9023 (p) REVERT: a 20 ARG cc_start: 0.6835 (mtm-85) cc_final: 0.6626 (mtm-85) REVERT: a 67 THR cc_start: 0.9464 (OUTLIER) cc_final: 0.8948 (p) REVERT: a 96 TRP cc_start: 0.8160 (m100) cc_final: 0.7766 (m100) REVERT: f 3 GLN cc_start: 0.8238 (mp10) cc_final: 0.7989 (mp10) REVERT: f 32 TYR cc_start: 0.8921 (m-10) cc_final: 0.8422 (m-10) REVERT: g 111 TYR cc_start: 0.8695 (m-80) cc_final: 0.8368 (m-80) REVERT: h 32 MET cc_start: 0.8186 (tpp) cc_final: 0.7589 (tpp) REVERT: i 32 MET cc_start: 0.7960 (tpp) cc_final: 0.7743 (tpp) REVERT: i 79 ASP cc_start: 0.9193 (t70) cc_final: 0.8849 (t0) REVERT: i 81 GLU cc_start: 0.8808 (pm20) cc_final: 0.8432 (pm20) outliers start: 115 outliers final: 81 residues processed: 413 average time/residue: 0.2074 time to fit residues: 135.8961 Evaluate side-chains 384 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 296 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 2 residue 73 LEU Chi-restraints excluded: chain 4 residue 3 VAL Chi-restraints excluded: chain 4 residue 73 LEU Chi-restraints excluded: chain 4 residue 92 VAL Chi-restraints excluded: chain 6 residue 522 PHE Chi-restraints excluded: chain 6 residue 536 THR Chi-restraints excluded: chain 6 residue 603 ILE Chi-restraints excluded: chain 6 residue 604 CYS Chi-restraints excluded: chain 6 residue 635 ILE Chi-restraints excluded: chain 6 residue 639 THR Chi-restraints excluded: chain 6 residue 641 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 480 ARG Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 53 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 621 GLU Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain X residue 24 VAL Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain Y residue 82 VAL Chi-restraints excluded: chain Y residue 89 ILE Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain f residue 37 VAL Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain f residue 94 THR Chi-restraints excluded: chain g residue 51 ILE Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain h residue 63 VAL Chi-restraints excluded: chain i residue 47 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 215 optimal weight: 5.9990 chunk 321 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 216 optimal weight: 1.9990 chunk 289 optimal weight: 8.9990 chunk 329 optimal weight: 5.9990 chunk 310 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 38 GLN ** 2 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.060265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.041067 restraints weight = 152020.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.042539 restraints weight = 76147.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.043489 restraints weight = 51202.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.044050 restraints weight = 40472.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.044407 restraints weight = 35370.069| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 32997 Z= 0.327 Angle : 0.826 17.155 45120 Z= 0.388 Chirality : 0.048 0.400 5371 Planarity : 0.004 0.061 5463 Dihedral : 10.087 74.681 7314 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.67 % Allowed : 17.46 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.46 (0.14), residues: 3777 helix: 0.74 (0.27), residues: 396 sheet: -0.92 (0.15), residues: 1260 loop : -1.31 (0.14), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 1 13 TYR 0.038 0.002 TYR f 32 PHE 0.027 0.003 PHE g 115 TRP 0.021 0.002 TRP D 571 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00717 (32812) covalent geometry : angle 0.78558 (44619) SS BOND : bond 0.00870 ( 54) SS BOND : angle 1.27825 ( 108) hydrogen bonds : bond 0.03494 ( 1064) hydrogen bonds : angle 5.96226 ( 2817) link_ALPHA1-2 : bond 0.00101 ( 3) link_ALPHA1-2 : angle 1.71663 ( 9) link_ALPHA1-3 : bond 0.00846 ( 18) link_ALPHA1-3 : angle 2.41031 ( 54) link_ALPHA1-6 : bond 0.00673 ( 11) link_ALPHA1-6 : angle 1.68883 ( 33) link_BETA1-4 : bond 0.00468 ( 72) link_BETA1-4 : angle 2.66812 ( 216) link_NAG-ASN : bond 0.00910 ( 27) link_NAG-ASN : angle 3.70751 ( 81) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 277 time to evaluate : 1.000 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: 6 584 GLU cc_start: 0.8745 (tt0) cc_final: 0.8487 (tm-30) REVERT: 6 601 LYS cc_start: 0.9089 (mttt) cc_final: 0.8752 (ttmm) REVERT: 6 654 GLU cc_start: 0.9396 (tp30) cc_final: 0.9141 (tp30) REVERT: A 373 THR cc_start: 0.9685 (t) cc_final: 0.9458 (t) REVERT: A 480 ARG cc_start: 0.9457 (OUTLIER) cc_final: 0.8459 (mtm110) REVERT: B 475 MET cc_start: 0.8892 (mmm) cc_final: 0.8681 (mmm) REVERT: C 104 MET cc_start: 0.9573 (OUTLIER) cc_final: 0.8772 (ttm) REVERT: D 601 LYS cc_start: 0.9001 (mttt) cc_final: 0.8705 (ttmm) REVERT: E 584 GLU cc_start: 0.8271 (tm-30) cc_final: 0.8007 (tm-30) REVERT: E 601 LYS cc_start: 0.8969 (mttt) cc_final: 0.8684 (ttmm) REVERT: E 632 ASP cc_start: 0.9259 (t70) cc_final: 0.8979 (t70) REVERT: E 654 GLU cc_start: 0.9161 (tp30) cc_final: 0.8925 (tp30) REVERT: H 64 LYS cc_start: 0.8573 (mtmm) cc_final: 0.8256 (ptpp) REVERT: H 94 ARG cc_start: 0.7738 (tmm160) cc_final: 0.7277 (ttp80) REVERT: L 42 GLN cc_start: 0.6417 (OUTLIER) cc_final: 0.6215 (pt0) REVERT: M 13 LYS cc_start: 0.9152 (ttpp) cc_final: 0.8932 (ttpp) REVERT: M 100 MET cc_start: 0.9031 (mpp) cc_final: 0.8647 (mmm) REVERT: N 54 ARG cc_start: 0.8641 (ptt-90) cc_final: 0.8233 (ptm-80) REVERT: N 67 THR cc_start: 0.9467 (OUTLIER) cc_final: 0.8957 (p) REVERT: Q 3 GLN cc_start: 0.8389 (mp10) cc_final: 0.7807 (mp10) REVERT: Q 118 GLN cc_start: 0.9178 (tm-30) cc_final: 0.8721 (tm-30) REVERT: R 32 MET cc_start: 0.8936 (tpp) cc_final: 0.8075 (tpp) REVERT: X 30 ARG cc_start: 0.8937 (tpp80) cc_final: 0.8297 (tpp80) REVERT: X 38 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.7637 (tmm-80) REVERT: X 44 GLN cc_start: 0.7779 (pp30) cc_final: 0.7517 (pp30) REVERT: X 53 ASP cc_start: 0.8638 (p0) cc_final: 0.8064 (p0) REVERT: X 100 LYS cc_start: 0.9453 (OUTLIER) cc_final: 0.9183 (mttm) REVERT: X 100 MET cc_start: 0.9011 (mpp) cc_final: 0.8435 (mmm) REVERT: Y 30 ARG cc_start: 0.8975 (tpp80) cc_final: 0.8486 (tpp80) REVERT: Y 38 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8770 (tmm-80) REVERT: Y 53 ASP cc_start: 0.8459 (p0) cc_final: 0.7339 (p0) REVERT: Y 64 LYS cc_start: 0.9061 (tppt) cc_final: 0.8709 (tppt) REVERT: Z 67 THR cc_start: 0.9468 (OUTLIER) cc_final: 0.8968 (p) REVERT: Z 96 TRP cc_start: 0.8007 (m100) cc_final: 0.7156 (m100) REVERT: a 20 ARG cc_start: 0.6856 (mtm-85) cc_final: 0.6655 (mtm-85) REVERT: a 67 THR cc_start: 0.9418 (OUTLIER) cc_final: 0.9001 (p) REVERT: h 32 MET cc_start: 0.8509 (tpp) cc_final: 0.7857 (tpp) REVERT: i 32 MET cc_start: 0.8522 (tpp) cc_final: 0.8073 (tpp) outliers start: 122 outliers final: 85 residues processed: 386 average time/residue: 0.2011 time to fit residues: 123.9101 Evaluate side-chains 364 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 270 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 5 THR Chi-restraints excluded: chain 2 residue 73 LEU Chi-restraints excluded: chain 4 residue 73 LEU Chi-restraints excluded: chain 4 residue 92 VAL Chi-restraints excluded: chain 6 residue 522 PHE Chi-restraints excluded: chain 6 residue 536 THR Chi-restraints excluded: chain 6 residue 598 CYS Chi-restraints excluded: chain 6 residue 604 CYS Chi-restraints excluded: chain 6 residue 635 ILE Chi-restraints excluded: chain 6 residue 641 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 480 ARG Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 53 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 385 CYS Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain D residue 621 GLU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 598 CYS Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 42 GLN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain X residue 24 VAL Chi-restraints excluded: chain X residue 38 ARG Chi-restraints excluded: chain X residue 89 ILE Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain X residue 100 LYS Chi-restraints excluded: chain Y residue 38 ARG Chi-restraints excluded: chain Y residue 82 VAL Chi-restraints excluded: chain Y residue 89 ILE Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 47 ILE Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 94 THR Chi-restraints excluded: chain g residue 51 ILE Chi-restraints excluded: chain g residue 68 VAL Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain h residue 63 VAL Chi-restraints excluded: chain h residue 104 LEU Chi-restraints excluded: chain i residue 47 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 299 optimal weight: 10.0000 chunk 345 optimal weight: 2.9990 chunk 250 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 315 optimal weight: 0.0570 chunk 263 optimal weight: 0.4980 chunk 271 optimal weight: 2.9990 chunk 371 optimal weight: 3.9990 chunk 209 optimal weight: 0.9980 chunk 300 optimal weight: 20.0000 overall best weight: 1.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 44 GLN ** Y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.061810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.042681 restraints weight = 147539.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.044228 restraints weight = 71793.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.045220 restraints weight = 47394.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.045815 restraints weight = 37103.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.046192 restraints weight = 32227.404| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32997 Z= 0.149 Angle : 0.728 17.384 45120 Z= 0.342 Chirality : 0.046 0.419 5371 Planarity : 0.004 0.051 5463 Dihedral : 9.343 73.755 7312 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.92 % Allowed : 18.67 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.25 (0.14), residues: 3777 helix: 0.64 (0.26), residues: 417 sheet: -0.80 (0.15), residues: 1233 loop : -1.12 (0.14), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG 3 13 TYR 0.020 0.001 TYR 2 87 PHE 0.022 0.002 PHE g 115 TRP 0.019 0.001 TRP D 571 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00326 (32812) covalent geometry : angle 0.69114 (44619) SS BOND : bond 0.00291 ( 54) SS BOND : angle 0.95463 ( 108) hydrogen bonds : bond 0.03086 ( 1064) hydrogen bonds : angle 5.74145 ( 2817) link_ALPHA1-2 : bond 0.00274 ( 3) link_ALPHA1-2 : angle 1.66628 ( 9) link_ALPHA1-3 : bond 0.00997 ( 18) link_ALPHA1-3 : angle 2.01258 ( 54) link_ALPHA1-6 : bond 0.00824 ( 11) link_ALPHA1-6 : angle 1.49337 ( 33) link_BETA1-4 : bond 0.00423 ( 72) link_BETA1-4 : angle 2.48856 ( 216) link_NAG-ASN : bond 0.00518 ( 27) link_NAG-ASN : angle 3.24655 ( 81) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 304 time to evaluate : 1.242 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: 4 24 ARG cc_start: 0.9125 (mtt90) cc_final: 0.8915 (mmt90) REVERT: 6 584 GLU cc_start: 0.8760 (tt0) cc_final: 0.8439 (tm-30) REVERT: 6 601 LYS cc_start: 0.9054 (mttt) cc_final: 0.8763 (ttmm) REVERT: 6 654 GLU cc_start: 0.9359 (tp30) cc_final: 0.9057 (tp30) REVERT: A 373 THR cc_start: 0.9620 (t) cc_final: 0.9353 (t) REVERT: B 125 LEU cc_start: 0.9680 (tp) cc_final: 0.9389 (tp) REVERT: B 475 MET cc_start: 0.8811 (mmm) cc_final: 0.8584 (mmm) REVERT: C 104 MET cc_start: 0.9540 (OUTLIER) cc_final: 0.8572 (ttm) REVERT: D 601 LYS cc_start: 0.8936 (mttt) cc_final: 0.8574 (ttmm) REVERT: E 542 ARG cc_start: 0.9555 (ttm170) cc_final: 0.9153 (ttp80) REVERT: E 601 LYS cc_start: 0.8856 (mttt) cc_final: 0.8561 (ttmm) REVERT: E 632 ASP cc_start: 0.9206 (t70) cc_final: 0.8924 (t70) REVERT: H 64 LYS cc_start: 0.8548 (mtmm) cc_final: 0.8222 (ptpp) REVERT: H 94 ARG cc_start: 0.7543 (tmm160) cc_final: 0.7257 (ttp80) REVERT: M 13 LYS cc_start: 0.9218 (ttpp) cc_final: 0.8946 (ttpp) REVERT: N 25 GLU cc_start: 0.7808 (tp30) cc_final: 0.7282 (pp20) REVERT: N 54 ARG cc_start: 0.8660 (ptt-90) cc_final: 0.8256 (ptt90) REVERT: N 67 THR cc_start: 0.9480 (OUTLIER) cc_final: 0.8974 (p) REVERT: N 96 TRP cc_start: 0.8164 (m100) cc_final: 0.7514 (m100) REVERT: Q 3 GLN cc_start: 0.8413 (mp10) cc_final: 0.7836 (mp10) REVERT: Q 118 GLN cc_start: 0.9090 (tm-30) cc_final: 0.8660 (tm-30) REVERT: R 32 MET cc_start: 0.8778 (tpp) cc_final: 0.7877 (tpp) REVERT: X 30 ARG cc_start: 0.8895 (tpp80) cc_final: 0.8179 (tpp80) REVERT: X 38 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.7611 (tmm-80) REVERT: X 53 ASP cc_start: 0.8582 (p0) cc_final: 0.7530 (p0) REVERT: X 100 MET cc_start: 0.8972 (mpp) cc_final: 0.8714 (mmt) REVERT: Y 30 ARG cc_start: 0.8895 (tpp80) cc_final: 0.8403 (tpp80) REVERT: Y 53 ASP cc_start: 0.8414 (p0) cc_final: 0.7130 (p0) REVERT: Z 67 THR cc_start: 0.9491 (OUTLIER) cc_final: 0.9003 (p) REVERT: a 20 ARG cc_start: 0.6864 (mtm-85) cc_final: 0.6653 (mtm-85) REVERT: a 61 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.6665 (ptt90) REVERT: a 67 THR cc_start: 0.9444 (OUTLIER) cc_final: 0.8885 (p) REVERT: a 96 TRP cc_start: 0.8203 (m100) cc_final: 0.7800 (m100) REVERT: f 31 ASP cc_start: 0.8797 (p0) cc_final: 0.8581 (p0) REVERT: g 3 GLN cc_start: 0.8313 (mp10) cc_final: 0.8077 (mp10) REVERT: g 43 LYS cc_start: 0.9563 (mmmm) cc_final: 0.9299 (mmmm) REVERT: h 32 MET cc_start: 0.8347 (tpp) cc_final: 0.7685 (tpp) REVERT: i 32 MET cc_start: 0.8324 (tpp) cc_final: 0.8048 (tmm) REVERT: i 79 ASP cc_start: 0.9215 (OUTLIER) cc_final: 0.8809 (t0) REVERT: i 81 GLU cc_start: 0.8819 (pm20) cc_final: 0.8430 (pm20) outliers start: 97 outliers final: 74 residues processed: 388 average time/residue: 0.2053 time to fit residues: 126.1122 Evaluate side-chains 369 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 288 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 2 residue 73 LEU Chi-restraints excluded: chain 4 residue 73 LEU Chi-restraints excluded: chain 4 residue 92 VAL Chi-restraints excluded: chain 6 residue 513 VAL Chi-restraints excluded: chain 6 residue 522 PHE Chi-restraints excluded: chain 6 residue 536 THR Chi-restraints excluded: chain 6 residue 604 CYS Chi-restraints excluded: chain 6 residue 635 ILE Chi-restraints excluded: chain 6 residue 641 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 53 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 621 GLU Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain X residue 24 VAL Chi-restraints excluded: chain X residue 38 ARG Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain Y residue 82 VAL Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 61 ARG Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 94 THR Chi-restraints excluded: chain g residue 51 ILE Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain h residue 63 VAL Chi-restraints excluded: chain i residue 47 LEU Chi-restraints excluded: chain i residue 79 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 161 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 308 optimal weight: 5.9990 chunk 300 optimal weight: 20.0000 chunk 168 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 227 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 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 = 0.3351 r_free = 0.3351 target = 0.061520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.042298 restraints weight = 149028.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.043845 restraints weight = 72227.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.044846 restraints weight = 47675.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.045443 restraints weight = 37267.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.045806 restraints weight = 32370.777| |-----------------------------------------------------------------------------| r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 32997 Z= 0.185 Angle : 0.745 17.117 45120 Z= 0.350 Chirality : 0.046 0.419 5371 Planarity : 0.004 0.053 5463 Dihedral : 9.114 72.488 7311 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.77 % Allowed : 18.85 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.26 (0.14), residues: 3777 helix: 0.59 (0.26), residues: 414 sheet: -0.78 (0.15), residues: 1254 loop : -1.13 (0.14), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 3 13 TYR 0.019 0.001 TYR N 49 PHE 0.022 0.002 PHE g 115 TRP 0.027 0.001 TRP D 571 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00409 (32812) covalent geometry : angle 0.70759 (44619) SS BOND : bond 0.00332 ( 54) SS BOND : angle 0.95962 ( 108) hydrogen bonds : bond 0.03181 ( 1064) hydrogen bonds : angle 5.68859 ( 2817) link_ALPHA1-2 : bond 0.00218 ( 3) link_ALPHA1-2 : angle 1.61014 ( 9) link_ALPHA1-3 : bond 0.00930 ( 18) link_ALPHA1-3 : angle 2.01430 ( 54) link_ALPHA1-6 : bond 0.00761 ( 11) link_ALPHA1-6 : angle 1.50002 ( 33) link_BETA1-4 : bond 0.00406 ( 72) link_BETA1-4 : angle 2.51635 ( 216) link_NAG-ASN : bond 0.00584 ( 27) link_NAG-ASN : angle 3.35470 ( 81) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 287 time to evaluate : 1.120 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: 6 584 GLU cc_start: 0.8759 (tt0) cc_final: 0.8454 (tm-30) REVERT: 6 601 LYS cc_start: 0.9026 (mttt) cc_final: 0.8616 (ttmm) REVERT: 6 654 GLU cc_start: 0.9378 (tp30) cc_final: 0.9086 (tp30) REVERT: A 373 THR cc_start: 0.9613 (t) cc_final: 0.9340 (t) REVERT: B 426 MET cc_start: 0.8432 (ptm) cc_final: 0.8150 (ptm) REVERT: B 475 MET cc_start: 0.8822 (mmm) cc_final: 0.8600 (mmm) REVERT: C 104 MET cc_start: 0.9556 (OUTLIER) cc_final: 0.8660 (ttm) REVERT: D 601 LYS cc_start: 0.8957 (mttt) cc_final: 0.8583 (ttmm) REVERT: E 584 GLU cc_start: 0.8572 (tm-30) cc_final: 0.7755 (tm-30) REVERT: E 601 LYS cc_start: 0.8938 (mttt) cc_final: 0.8631 (ttmm) REVERT: E 632 ASP cc_start: 0.9232 (t70) cc_final: 0.8943 (t70) REVERT: H 64 LYS cc_start: 0.8566 (mtmm) cc_final: 0.8250 (ptpp) REVERT: H 94 ARG cc_start: 0.7509 (tmm160) cc_final: 0.7219 (ttp80) REVERT: M 13 LYS cc_start: 0.9217 (ttpp) cc_final: 0.8941 (ttpp) REVERT: N 25 GLU cc_start: 0.7890 (tp30) cc_final: 0.7283 (pp20) REVERT: N 54 ARG cc_start: 0.8649 (ptt-90) cc_final: 0.8232 (ptm-80) REVERT: N 67 THR cc_start: 0.9493 (OUTLIER) cc_final: 0.8980 (p) REVERT: N 96 TRP cc_start: 0.8222 (m100) cc_final: 0.7541 (m100) REVERT: Q 3 GLN cc_start: 0.8411 (mp10) cc_final: 0.7795 (mp10) REVERT: Q 118 GLN cc_start: 0.9144 (tm-30) cc_final: 0.8690 (tm-30) REVERT: X 30 ARG cc_start: 0.8924 (tpp80) cc_final: 0.8240 (tpp80) REVERT: X 38 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.7630 (tmm-80) REVERT: X 53 ASP cc_start: 0.8664 (p0) cc_final: 0.7673 (p0) REVERT: X 100 MET cc_start: 0.8994 (mpp) cc_final: 0.8570 (mmt) REVERT: Y 30 ARG cc_start: 0.8929 (tpp80) cc_final: 0.8407 (tpp80) REVERT: Y 38 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.8761 (tmm-80) REVERT: Y 53 ASP cc_start: 0.8502 (p0) cc_final: 0.7279 (p0) REVERT: Z 25 GLU cc_start: 0.7762 (tp30) cc_final: 0.7475 (pp20) REVERT: Z 67 THR cc_start: 0.9484 (OUTLIER) cc_final: 0.8991 (p) REVERT: a 20 ARG cc_start: 0.6880 (mtm-85) cc_final: 0.6671 (mtm-85) REVERT: a 61 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.6672 (ptt90) REVERT: a 67 THR cc_start: 0.9439 (OUTLIER) cc_final: 0.8883 (p) REVERT: a 96 TRP cc_start: 0.8216 (m100) cc_final: 0.7816 (m100) REVERT: f 31 ASP cc_start: 0.8751 (p0) cc_final: 0.8426 (p0) REVERT: g 3 GLN cc_start: 0.8320 (mp10) cc_final: 0.8092 (mp10) REVERT: g 43 LYS cc_start: 0.9574 (mmmm) cc_final: 0.9303 (mmmm) REVERT: h 32 MET cc_start: 0.8317 (tpp) cc_final: 0.7692 (tpp) outliers start: 92 outliers final: 74 residues processed: 366 average time/residue: 0.2106 time to fit residues: 120.6474 Evaluate side-chains 363 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 282 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 2 residue 73 LEU Chi-restraints excluded: chain 4 residue 3 VAL Chi-restraints excluded: chain 4 residue 73 LEU Chi-restraints excluded: chain 4 residue 92 VAL Chi-restraints excluded: chain 6 residue 522 PHE Chi-restraints excluded: chain 6 residue 536 THR Chi-restraints excluded: chain 6 residue 604 CYS Chi-restraints excluded: chain 6 residue 635 ILE Chi-restraints excluded: chain 6 residue 641 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 53 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 621 GLU Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain E residue 513 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain X residue 24 VAL Chi-restraints excluded: chain X residue 38 ARG Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain Y residue 38 ARG Chi-restraints excluded: chain Y residue 82 VAL Chi-restraints excluded: chain Y residue 89 ILE Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Z residue 67 THR Chi-restraints excluded: chain a residue 61 ARG Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 94 THR Chi-restraints excluded: chain g residue 51 ILE Chi-restraints excluded: chain g residue 94 THR Chi-restraints excluded: chain h residue 63 VAL Chi-restraints excluded: chain i residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 178 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 359 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 332 optimal weight: 0.8980 chunk 66 optimal weight: 0.0870 chunk 256 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 205 optimal weight: 9.9990 chunk 157 optimal weight: 7.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN L 37 GLN M 5 GLN M 23 ASN M 68 HIS ** X 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.062555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.043461 restraints weight = 148174.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.045022 restraints weight = 72431.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.046022 restraints weight = 47845.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.046633 restraints weight = 37524.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.046988 restraints weight = 32532.509| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32997 Z= 0.126 Angle : 0.725 17.281 45120 Z= 0.341 Chirality : 0.045 0.428 5371 Planarity : 0.004 0.052 5463 Dihedral : 8.623 71.525 7311 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.65 % Allowed : 19.18 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.13 (0.14), residues: 3777 helix: 0.84 (0.27), residues: 399 sheet: -0.65 (0.15), residues: 1221 loop : -1.10 (0.14), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 4 24 TYR 0.019 0.001 TYR 2 87 PHE 0.019 0.001 PHE g 115 TRP 0.028 0.001 TRP A 427 HIS 0.007 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00278 (32812) covalent geometry : angle 0.68996 (44619) SS BOND : bond 0.00241 ( 54) SS BOND : angle 0.87600 ( 108) hydrogen bonds : bond 0.03025 ( 1064) hydrogen bonds : angle 5.55113 ( 2817) link_ALPHA1-2 : bond 0.00313 ( 3) link_ALPHA1-2 : angle 1.67639 ( 9) link_ALPHA1-3 : bond 0.00983 ( 18) link_ALPHA1-3 : angle 1.85633 ( 54) link_ALPHA1-6 : bond 0.00839 ( 11) link_ALPHA1-6 : angle 1.44944 ( 33) link_BETA1-4 : bond 0.00448 ( 72) link_BETA1-4 : angle 2.46967 ( 216) link_NAG-ASN : bond 0.00508 ( 27) link_NAG-ASN : angle 3.16335 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5455.81 seconds wall clock time: 95 minutes 31.10 seconds (5731.10 seconds total)