Starting phenix.real_space_refine on Thu Mar 5 09:00:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g4t_29731/03_2026/8g4t_29731.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g4t_29731/03_2026/8g4t_29731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g4t_29731/03_2026/8g4t_29731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g4t_29731/03_2026/8g4t_29731.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g4t_29731/03_2026/8g4t_29731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g4t_29731/03_2026/8g4t_29731.map" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 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 132 5.16 5 C 12909 2.51 5 N 3437 2.21 5 O 4261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 20739 Number of models: 1 Model: "" Number of chains: 63 Chain: "A" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1042 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain breaks: 1 Chain: "B" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1042 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain breaks: 1 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: "F" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1042 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain breaks: 1 Chain: "G" 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: "I" 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: "H" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "L" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 801 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "D" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "J" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "K" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 801 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "M" 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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: "S" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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: "b" 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: "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: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 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: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 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: "q" 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: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" 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: "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: 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: "w" 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: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "4" Number of atoms: 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: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.21, per 1000 atoms: 0.25 Number of scatterers: 20739 At special positions: 0 Unit cell: (139.86, 148.74, 129.87, 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 132 16.00 O 4261 8.00 N 3437 7.00 C 12909 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS C 501 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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=2.03 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 F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 605 " - pdb=" SG CYS I 501 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN R 4 " - " MAN R 5 " " MAN g 4 " - " MAN g 5 " " MAN v 4 " - " MAN v 5 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA R 3 " - " MAN R 4 " " BMA b 3 " - " MAN b 4 " " BMA g 3 " - " MAN g 4 " " BMA q 3 " - " MAN q 4 " " BMA v 3 " - " MAN v 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA R 3 " - " MAN R 6 " " BMA b 3 " - " MAN b 5 " " BMA g 3 " - " MAN g 6 " " BMA q 3 " - " MAN q 5 " " BMA v 3 " - " MAN v 6 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " 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 x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " NAG-ASN " NAG 0 1 " - " ASN I 363 " " NAG 1 1 " - " ASN I 386 " " NAG 2 1 " - " ASN I 392 " " NAG 3 1 " - " ASN I 448 " " NAG 4 1 " - " ASN I 160 " " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 618 " " NAG A 703 " - " ASN A 637 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 601 " - " ASN C 355 " " NAG C 602 " - " ASN C 339 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 637 " " NAG G 601 " - " ASN G 355 " " NAG G 602 " - " ASN G 339 " " NAG I 601 " - " ASN I 355 " " NAG I 602 " - " ASN I 339 " " NAG M 1 " - " ASN C 88 " " NAG N 1 " - " ASN C 133 " " NAG O 1 " - " ASN C 156 " " NAG P 1 " - " ASN C 197 " " NAG Q 1 " - " ASN C 234 " " NAG R 1 " - " ASN C 262 " " NAG S 1 " - " ASN C 276 " " NAG T 1 " - " ASN C 295 " " NAG U 1 " - " ASN C 301 " " NAG V 1 " - " ASN C 332 " " NAG W 1 " - " ASN C 363 " " NAG X 1 " - " ASN C 386 " " NAG Y 1 " - " ASN C 392 " " NAG Z 1 " - " ASN C 448 " " NAG a 1 " - " ASN C 160 " " NAG b 1 " - " ASN G 88 " " NAG c 1 " - " ASN G 133 " " NAG d 1 " - " ASN G 156 " " NAG e 1 " - " ASN G 197 " " NAG f 1 " - " ASN G 234 " " NAG g 1 " - " ASN G 262 " " NAG h 1 " - " ASN G 276 " " NAG i 1 " - " ASN G 295 " " NAG j 1 " - " ASN G 301 " " NAG k 1 " - " ASN G 332 " " NAG l 1 " - " ASN G 363 " " NAG m 1 " - " ASN G 386 " " NAG n 1 " - " ASN G 392 " " NAG o 1 " - " ASN G 448 " " NAG p 1 " - " ASN G 160 " " NAG q 1 " - " ASN I 88 " " NAG r 1 " - " ASN I 133 " " NAG s 1 " - " ASN I 156 " " NAG t 1 " - " ASN I 197 " " NAG u 1 " - " ASN I 234 " " NAG v 1 " - " ASN I 262 " " NAG w 1 " - " ASN I 276 " " NAG x 1 " - " ASN I 295 " " NAG y 1 " - " ASN I 301 " " NAG z 1 " - " ASN I 332 " Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 1.0 seconds 4790 Ramachandran restraints generated. 2395 Oldfield, 0 Emsley, 2395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4496 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 46 sheets defined 18.3% alpha, 36.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 542 removed outlier: 3.958A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 574 removed outlier: 4.569A pdb=" N ILE A 573 " --> pdb=" O THR A 569 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LYS A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 569 through 574' Processing helix chain 'A' and resid 575 through 597 removed outlier: 3.604A pdb=" N ARG A 579 " --> pdb=" O GLN A 575 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 592 " --> pdb=" O ARG A 588 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 removed outlier: 3.758A pdb=" N TRP A 623 " --> pdb=" O LEU A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.589A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 664 removed outlier: 3.642A pdb=" N GLY A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 645 " --> pdb=" O ILE A 641 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP A 664 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.909A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 597 removed outlier: 4.594A pdb=" N ILE B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.707A pdb=" N TRP B 623 " --> pdb=" O LEU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.586A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 664 removed outlier: 3.538A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 98 through 115 removed outlier: 4.120A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.643A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.908A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 575 through 597 removed outlier: 3.741A pdb=" N ARG F 579 " --> pdb=" O GLN F 575 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU F 592 " --> pdb=" O ARG F 588 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU F 593 " --> pdb=" O ASP F 589 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 removed outlier: 3.771A pdb=" N TRP F 623 " --> pdb=" O LEU F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.600A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 664 removed outlier: 3.517A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP F 664 " --> pdb=" O LEU F 660 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 Processing helix chain 'G' and resid 70 through 74 removed outlier: 3.529A pdb=" N ALA G 73 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 115 removed outlier: 4.437A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN G 103 " --> pdb=" O ASN G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 335 through 350 Processing helix chain 'G' and resid 351 through 353 No H-bonds generated for 'chain 'G' and resid 351 through 353' Processing helix chain 'G' and resid 425 through 429 removed outlier: 4.325A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 481 removed outlier: 3.647A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 62 Processing helix chain 'I' and resid 98 through 115 removed outlier: 4.237A pdb=" N GLU I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 removed outlier: 3.505A pdb=" N LEU I 125 " --> pdb=" O LEU I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 350 Processing helix chain 'I' and resid 351 through 353 No H-bonds generated for 'chain 'I' and resid 351 through 353' Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.514A pdb=" N THR I 373 " --> pdb=" O LEU I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 481 removed outlier: 3.648A pdb=" N TRP I 479 " --> pdb=" O MET I 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.505A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.516A pdb=" N HIS D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'K' and resid 79 through 83 removed outlier: 4.222A pdb=" N PHE K 83 " --> pdb=" O SER K 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 5.590A pdb=" N VAL C 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 603 through 609 removed outlier: 5.586A pdb=" N VAL G 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.664A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.911A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AA6, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AA7, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.372A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.554A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 12.280A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 12.050A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.232A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.357A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE C 376 " --> pdb=" O PHE C 383 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 271 through 273 removed outlier: 11.357A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 11.232A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.050A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.280A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.803A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 603 through 609 removed outlier: 5.573A pdb=" N VAL I 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 45 through 47 removed outlier: 4.666A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 75 through 76 removed outlier: 3.880A pdb=" N VAL G 75 " --> pdb=" O CYS G 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AB6, first strand: chain 'G' and resid 169 through 177 Processing sheet with id=AB7, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.357A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.591A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.578A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 12.278A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 12.127A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 11.269A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 11.420A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS G 330 " --> pdb=" O THR G 297 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS G 421 " --> pdb=" O PHE G 382 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU G 381 " --> pdb=" O CYS G 378 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE G 376 " --> pdb=" O PHE G 383 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 271 through 274 removed outlier: 11.420A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 11.269A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 12.127A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 12.278A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.578A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER G 393 " --> pdb=" O PHE G 361 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.769A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 45 through 47 removed outlier: 4.707A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 75 through 76 removed outlier: 3.936A pdb=" N VAL I 75 " --> pdb=" O CYS I 54 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'I' and resid 169 through 177 Processing sheet with id=AC6, first strand: chain 'I' and resid 202 through 203 removed outlier: 6.389A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 259 through 261 removed outlier: 6.547A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.370A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 12.382A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 12.160A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 11.291A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 11.462A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N GLN I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER I 334 " --> pdb=" O GLN I 293 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU I 381 " --> pdb=" O CYS I 378 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE I 376 " --> pdb=" O PHE I 383 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 271 through 274 removed outlier: 11.462A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 11.291A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 12.160A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 12.382A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 10.370A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE I 358 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N PHE I 468 " --> pdb=" O ILE I 358 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER I 393 " --> pdb=" O PHE I 361 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 304 through 312 removed outlier: 6.840A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.394A pdb=" N GLY H 10 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR H 110 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL H 109 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG H 38 " --> pdb=" O TYR H 47 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N TYR H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.394A pdb=" N GLY H 10 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR H 110 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL H 109 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.767A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.458A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU L 33 " --> pdb=" O HIS L 49 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N HIS L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.458A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.717A pdb=" N VAL D 109 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA D 88 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ARG D 38 " --> pdb=" O TYR D 47 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N TYR D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.717A pdb=" N VAL D 109 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA D 88 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ARG D 94 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.731A pdb=" N GLU E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.377A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL E 85 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU E 33 " --> pdb=" O HIS E 49 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N HIS E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.377A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'J' and resid 11 through 12 Processing sheet with id=AE6, first strand: chain 'J' and resid 57 through 59 removed outlier: 5.610A pdb=" N TYR J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ARG J 38 " --> pdb=" O TYR J 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ARG J 94 " --> pdb=" O ASP J 101 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 57 through 59 removed outlier: 5.610A pdb=" N TYR J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ARG J 38 " --> pdb=" O TYR J 47 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.774A pdb=" N GLU K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.605A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA K 84 " --> pdb=" O VAL K 104 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL K 85 " --> pdb=" O GLN K 38 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU K 33 " --> pdb=" O HIS K 49 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N HIS K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.605A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA K 84 " --> pdb=" O VAL K 104 " (cutoff:3.500A) 719 hydrogen bonds defined for protein. 1932 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: 4.10 Time building geometry restraints manager: 2.81 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: 6470 1.34 - 1.46: 5359 1.46 - 1.58: 9129 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 21138 Sorted by residual: bond pdb=" C TRP G 35 " pdb=" N VAL G 36 " ideal model delta sigma weight residual 1.334 1.254 0.079 1.24e-02 6.50e+03 4.11e+01 bond pdb=" C VAL G 36 " pdb=" N THR G 37 " ideal model delta sigma weight residual 1.331 1.259 0.072 1.51e-02 4.39e+03 2.25e+01 bond pdb=" C VAL I 36 " pdb=" N THR I 37 " ideal model delta sigma weight residual 1.331 1.258 0.073 1.55e-02 4.16e+03 2.20e+01 bond pdb=" C VAL C 36 " pdb=" N THR C 37 " ideal model delta sigma weight residual 1.331 1.260 0.071 1.55e-02 4.16e+03 2.12e+01 bond pdb=" C ASN I 136 " pdb=" N ASN I 137 " ideal model delta sigma weight residual 1.333 1.382 -0.049 1.29e-02 6.01e+03 1.46e+01 ... (remaining 21133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 27403 1.43 - 2.86: 1042 2.86 - 4.29: 166 4.29 - 5.72: 49 5.72 - 7.16: 28 Bond angle restraints: 28688 Sorted by residual: angle pdb=" O ASN C 136 " pdb=" C ASN C 136 " pdb=" N ASN C 137 " ideal model delta sigma weight residual 123.40 128.38 -4.98 1.13e+00 7.83e-01 1.94e+01 angle pdb=" CA ASN C 136 " pdb=" C ASN C 136 " pdb=" N ASN C 137 " ideal model delta sigma weight residual 116.26 111.35 4.91 1.27e+00 6.20e-01 1.49e+01 angle pdb=" C ASN C 136 " pdb=" N ASN C 137 " pdb=" CA ASN C 137 " ideal model delta sigma weight residual 122.63 118.37 4.26 1.44e+00 4.82e-01 8.76e+00 angle pdb=" C GLY K 50 " pdb=" N ALA K 51 " pdb=" CA ALA K 51 " ideal model delta sigma weight residual 121.54 126.31 -4.77 1.91e+00 2.74e-01 6.24e+00 angle pdb=" C GLY L 50 " pdb=" N ALA L 51 " pdb=" CA ALA L 51 " ideal model delta sigma weight residual 121.54 126.31 -4.77 1.91e+00 2.74e-01 6.22e+00 ... (remaining 28683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.66: 12793 21.66 - 43.32: 1121 43.32 - 64.98: 249 64.98 - 86.64: 85 86.64 - 108.30: 48 Dihedral angle restraints: 14296 sinusoidal: 7306 harmonic: 6990 Sorted by residual: dihedral pdb=" CB CYS I 201 " pdb=" SG CYS I 201 " pdb=" SG CYS I 433 " pdb=" CB CYS I 433 " ideal model delta sinusoidal sigma weight residual -86.00 -140.35 54.35 1 1.00e+01 1.00e-02 4.01e+01 dihedral pdb=" CB CYS C 201 " pdb=" SG CYS C 201 " pdb=" SG CYS C 433 " pdb=" CB CYS C 433 " ideal model delta sinusoidal sigma weight residual -86.00 -138.42 52.42 1 1.00e+01 1.00e-02 3.75e+01 dihedral pdb=" CB CYS G 201 " pdb=" SG CYS G 201 " pdb=" SG CYS G 433 " pdb=" CB CYS G 433 " ideal model delta sinusoidal sigma weight residual -86.00 -138.17 52.17 1 1.00e+01 1.00e-02 3.71e+01 ... (remaining 14293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2990 0.059 - 0.117: 486 0.117 - 0.176: 83 0.176 - 0.234: 6 0.234 - 0.293: 15 Chirality restraints: 3580 Sorted by residual: chirality pdb=" C1 NAG n 1 " pdb=" ND2 ASN G 392 " pdb=" C2 NAG n 1 " pdb=" O5 NAG n 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN C 392 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C1 NAG u 1 " pdb=" ND2 ASN I 234 " pdb=" C2 NAG u 1 " pdb=" O5 NAG u 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 3577 not shown) Planarity restraints: 3550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 504 " -0.156 9.50e-02 1.11e+02 7.00e-02 3.31e+00 pdb=" NE ARG G 504 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG G 504 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG G 504 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG G 504 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 504 " -0.154 9.50e-02 1.11e+02 6.93e-02 3.28e+00 pdb=" NE ARG C 504 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG C 504 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG C 504 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 504 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU F 657 " -0.006 2.00e-02 2.50e+03 1.24e-02 1.54e+00 pdb=" CD GLU F 657 " 0.021 2.00e-02 2.50e+03 pdb=" OE1 GLU F 657 " -0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU F 657 " -0.008 2.00e-02 2.50e+03 ... (remaining 3547 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 333 2.66 - 3.22: 18522 3.22 - 3.78: 28443 3.78 - 4.34: 40696 4.34 - 4.90: 68471 Nonbonded interactions: 156465 Sorted by model distance: nonbonded pdb=" O3 NAG n 2 " pdb=" O7 NAG n 2 " model vdw 2.105 3.040 nonbonded pdb=" O3 NAG Y 2 " pdb=" O7 NAG Y 2 " model vdw 2.106 3.040 nonbonded pdb=" O3 NAG 2 2 " pdb=" O7 NAG 2 2 " model vdw 2.108 3.040 nonbonded pdb=" O ALA L 25 " pdb=" OG1 THR L 69 " model vdw 2.214 3.040 nonbonded pdb=" OG1 THR B 606 " pdb=" O VAL G 36 " model vdw 2.234 3.040 ... (remaining 156460 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain '4' selection = chain 'a' selection = chain 'p' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' } ncs_group { reference = (chain 'E' and resid 1 through 106) selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'b' selection = chain 'q' } ncs_group { reference = chain 'R' selection = chain 'g' selection = chain 'v' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.670 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:7.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 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 : 0.005 0.079 21309 Z= 0.249 Angle : 0.708 13.532 29159 Z= 0.296 Chirality : 0.049 0.293 3580 Planarity : 0.003 0.070 3490 Dihedral : 17.611 108.297 9674 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.38 % Allowed : 19.61 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.17), residues: 2395 helix: 0.60 (0.27), residues: 420 sheet: 0.22 (0.20), residues: 672 loop : -0.71 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 504 TYR 0.008 0.001 TYR C 217 PHE 0.010 0.001 PHE K 83 TRP 0.008 0.001 TRP I 69 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00510 (21138) covalent geometry : angle 0.65546 (28688) SS BOND : bond 0.00188 ( 42) SS BOND : angle 0.69973 ( 84) hydrogen bonds : bond 0.24756 ( 674) hydrogen bonds : angle 8.26267 ( 1932) link_ALPHA1-2 : bond 0.00241 ( 3) link_ALPHA1-2 : angle 1.97713 ( 9) link_ALPHA1-3 : bond 0.00264 ( 6) link_ALPHA1-3 : angle 1.67610 ( 18) link_ALPHA1-6 : bond 0.00352 ( 6) link_ALPHA1-6 : angle 1.64074 ( 18) link_BETA1-4 : bond 0.00914 ( 54) link_BETA1-4 : angle 3.08656 ( 162) link_NAG-ASN : bond 0.00177 ( 60) link_NAG-ASN : angle 1.81442 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4790 Ramachandran restraints generated. 2395 Oldfield, 0 Emsley, 2395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4790 Ramachandran restraints generated. 2395 Oldfield, 0 Emsley, 2395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 196 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 GLU cc_start: 0.8657 (pt0) cc_final: 0.8397 (pt0) REVERT: F 621 GLU cc_start: 0.8668 (pt0) cc_final: 0.8445 (pt0) REVERT: G 397 SER cc_start: 0.9063 (OUTLIER) cc_final: 0.8721 (m) REVERT: G 504 ARG cc_start: 0.8169 (tpp80) cc_final: 0.7867 (tpp-160) REVERT: H 3 GLN cc_start: 0.8660 (pp30) cc_final: 0.8120 (pm20) REVERT: L 24 ARG cc_start: 0.8455 (ttp80) cc_final: 0.8215 (ttp80) REVERT: L 42 GLN cc_start: 0.7813 (mp10) cc_final: 0.7521 (mp10) REVERT: L 102 THR cc_start: 0.7460 (m) cc_final: 0.7175 (m) REVERT: D 3 GLN cc_start: 0.8552 (pp30) cc_final: 0.8252 (pm20) REVERT: D 18 LEU cc_start: 0.8327 (tm) cc_final: 0.8040 (tt) REVERT: D 87 MET cc_start: 0.8312 (mmp) cc_final: 0.7990 (mmp) REVERT: E 42 GLN cc_start: 0.7616 (mp10) cc_final: 0.7389 (mp10) REVERT: E 102 THR cc_start: 0.7568 (m) cc_final: 0.7327 (m) REVERT: J 3 GLN cc_start: 0.8740 (pp30) cc_final: 0.8454 (pm20) REVERT: K 39 LYS cc_start: 0.8605 (mmtp) cc_final: 0.8326 (mptt) REVERT: K 42 GLN cc_start: 0.8000 (mp10) cc_final: 0.7355 (mp10) outliers start: 29 outliers final: 26 residues processed: 219 average time/residue: 0.8445 time to fit residues: 203.9076 Evaluate side-chains 199 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 397 SER Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 241 SER Chi-restraints excluded: chain I residue 411 ASN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 47 TYR Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain J residue 13 GLN Chi-restraints excluded: chain J residue 47 TYR Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS G 72 HIS I 72 HIS L 100 GLN E 27 GLN E 100 GLN K 27 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.078991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.052290 restraints weight = 48864.179| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 3.87 r_work: 0.2619 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21309 Z= 0.137 Angle : 0.661 9.300 29159 Z= 0.305 Chirality : 0.047 0.275 3580 Planarity : 0.003 0.034 3490 Dihedral : 11.537 80.805 5312 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.52 % Allowed : 19.80 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.17), residues: 2395 helix: 0.92 (0.28), residues: 435 sheet: 0.48 (0.19), residues: 694 loop : -0.68 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 504 TYR 0.010 0.001 TYR L 91 PHE 0.010 0.001 PHE A 519 TRP 0.010 0.001 TRP L 96 HIS 0.005 0.001 HIS I 72 Details of bonding type rmsd covalent geometry : bond 0.00293 (21138) covalent geometry : angle 0.61226 (28688) SS BOND : bond 0.00306 ( 42) SS BOND : angle 0.61921 ( 84) hydrogen bonds : bond 0.05530 ( 674) hydrogen bonds : angle 5.60269 ( 1932) link_ALPHA1-2 : bond 0.00911 ( 3) link_ALPHA1-2 : angle 1.89079 ( 9) link_ALPHA1-3 : bond 0.01179 ( 6) link_ALPHA1-3 : angle 2.35569 ( 18) link_ALPHA1-6 : bond 0.00194 ( 6) link_ALPHA1-6 : angle 1.84397 ( 18) link_BETA1-4 : bond 0.00960 ( 54) link_BETA1-4 : angle 2.58804 ( 162) link_NAG-ASN : bond 0.00287 ( 60) link_NAG-ASN : angle 1.93811 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4790 Ramachandran restraints generated. 2395 Oldfield, 0 Emsley, 2395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4790 Ramachandran restraints generated. 2395 Oldfield, 0 Emsley, 2395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 206 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 GLU cc_start: 0.8759 (pt0) cc_final: 0.8462 (pt0) REVERT: C 72 HIS cc_start: 0.8389 (t-90) cc_final: 0.8181 (t-170) REVERT: C 504 ARG cc_start: 0.8563 (ttp-170) cc_final: 0.8300 (tpp80) REVERT: F 621 GLU cc_start: 0.8849 (pt0) cc_final: 0.8635 (pt0) REVERT: G 426 MET cc_start: 0.9328 (mmm) cc_final: 0.9062 (mmt) REVERT: I 129 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8964 (mt) REVERT: I 155 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8058 (mtpp) REVERT: I 271 MET cc_start: 0.8954 (mmm) cc_final: 0.8750 (mmm) REVERT: I 397 SER cc_start: 0.9075 (OUTLIER) cc_final: 0.8775 (t) REVERT: H 75 LYS cc_start: 0.9149 (mtmm) cc_final: 0.8921 (mttm) REVERT: H 87 MET cc_start: 0.8710 (mmt) cc_final: 0.8489 (mmm) REVERT: H 105 ARG cc_start: 0.8696 (tpt90) cc_final: 0.8472 (tpt90) REVERT: L 39 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8448 (tppt) REVERT: L 42 GLN cc_start: 0.7926 (mp10) cc_final: 0.7604 (mp10) REVERT: L 54 ARG cc_start: 0.8799 (ttm110) cc_final: 0.8456 (ttm110) REVERT: L 82 ASP cc_start: 0.7218 (m-30) cc_final: 0.6991 (m-30) REVERT: D 18 LEU cc_start: 0.8212 (tm) cc_final: 0.7838 (tt) REVERT: D 87 MET cc_start: 0.8380 (mmp) cc_final: 0.8148 (mmt) REVERT: E 42 GLN cc_start: 0.7599 (mp10) cc_final: 0.7399 (mp10) REVERT: E 54 ARG cc_start: 0.8731 (ttm110) cc_final: 0.8466 (ttm110) REVERT: E 79 GLN cc_start: 0.7169 (mp10) cc_final: 0.6880 (mp10) REVERT: E 82 ASP cc_start: 0.6587 (m-30) cc_final: 0.6258 (m-30) REVERT: J 87 MET cc_start: 0.8705 (mmt) cc_final: 0.8496 (mmm) REVERT: J 107 THR cc_start: 0.8792 (t) cc_final: 0.8574 (m) REVERT: K 42 GLN cc_start: 0.8015 (mp10) cc_final: 0.7311 (mp10) REVERT: K 54 ARG cc_start: 0.8782 (ttm110) cc_final: 0.8474 (ttm110) outliers start: 53 outliers final: 19 residues processed: 249 average time/residue: 0.7884 time to fit residues: 217.2788 Evaluate side-chains 211 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 190 GLU Chi-restraints excluded: chain G residue 241 SER Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain I residue 397 SER Chi-restraints excluded: chain H residue 47 TYR Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain J residue 47 TYR Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 77 optimal weight: 2.9990 chunk 29 optimal weight: 0.0970 chunk 150 optimal weight: 4.9990 chunk 218 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 177 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 44 optimal weight: 0.0070 chunk 100 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 230 optimal weight: 2.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 72 HIS I 33 ASN H 3 GLN L 100 GLN D 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.078551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.051341 restraints weight = 49397.988| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 3.98 r_work: 0.2587 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21309 Z= 0.147 Angle : 0.651 9.654 29159 Z= 0.295 Chirality : 0.046 0.265 3580 Planarity : 0.003 0.037 3490 Dihedral : 9.872 67.569 5281 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.86 % Allowed : 19.99 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.17), residues: 2395 helix: 1.04 (0.28), residues: 435 sheet: 0.51 (0.19), residues: 700 loop : -0.70 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 504 TYR 0.010 0.001 TYR E 91 PHE 0.009 0.001 PHE A 519 TRP 0.009 0.001 TRP D 103 HIS 0.003 0.001 HIS G 72 Details of bonding type rmsd covalent geometry : bond 0.00338 (21138) covalent geometry : angle 0.60615 (28688) SS BOND : bond 0.00264 ( 42) SS BOND : angle 0.59764 ( 84) hydrogen bonds : bond 0.05156 ( 674) hydrogen bonds : angle 5.09783 ( 1932) link_ALPHA1-2 : bond 0.00668 ( 3) link_ALPHA1-2 : angle 1.79239 ( 9) link_ALPHA1-3 : bond 0.01185 ( 6) link_ALPHA1-3 : angle 1.70183 ( 18) link_ALPHA1-6 : bond 0.00325 ( 6) link_ALPHA1-6 : angle 1.73005 ( 18) link_BETA1-4 : bond 0.00808 ( 54) link_BETA1-4 : angle 2.44143 ( 162) link_NAG-ASN : bond 0.00207 ( 60) link_NAG-ASN : angle 1.96620 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4790 Ramachandran restraints generated. 2395 Oldfield, 0 Emsley, 2395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4790 Ramachandran restraints generated. 2395 Oldfield, 0 Emsley, 2395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 195 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 GLU cc_start: 0.8783 (pt0) cc_final: 0.8455 (pt0) REVERT: B 621 GLU cc_start: 0.9027 (pt0) cc_final: 0.8295 (pp20) REVERT: C 504 ARG cc_start: 0.8628 (ttp-170) cc_final: 0.8356 (tpp80) REVERT: F 621 GLU cc_start: 0.8898 (pt0) cc_final: 0.8631 (pt0) REVERT: I 129 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8946 (mt) REVERT: I 155 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8092 (mtpp) REVERT: I 397 SER cc_start: 0.9017 (OUTLIER) cc_final: 0.8686 (t) REVERT: H 75 LYS cc_start: 0.9177 (mtmm) cc_final: 0.8949 (mttm) REVERT: H 87 MET cc_start: 0.8663 (mmt) cc_final: 0.8382 (mmm) REVERT: H 105 ARG cc_start: 0.8681 (tpt90) cc_final: 0.8466 (tpt90) REVERT: L 42 GLN cc_start: 0.7899 (mp10) cc_final: 0.7511 (mp10) REVERT: L 54 ARG cc_start: 0.8762 (ttm110) cc_final: 0.8423 (ttm110) REVERT: D 3 GLN cc_start: 0.8655 (pt0) cc_final: 0.7978 (pp30) REVERT: D 18 LEU cc_start: 0.8089 (tm) cc_final: 0.7746 (tt) REVERT: D 83 ARG cc_start: 0.8683 (mtm-85) cc_final: 0.8468 (mtm-85) REVERT: E 18 ARG cc_start: 0.8555 (mmt-90) cc_final: 0.7392 (mmp80) REVERT: E 54 ARG cc_start: 0.8696 (ttm110) cc_final: 0.8409 (ttm110) REVERT: E 79 GLN cc_start: 0.7301 (mp10) cc_final: 0.7069 (mp10) REVERT: J 87 MET cc_start: 0.8772 (mmt) cc_final: 0.8475 (mmm) REVERT: K 42 GLN cc_start: 0.7987 (mp10) cc_final: 0.7230 (mp10) REVERT: K 54 ARG cc_start: 0.8744 (ttm110) cc_final: 0.8456 (ttm110) outliers start: 60 outliers final: 28 residues processed: 242 average time/residue: 0.7492 time to fit residues: 200.8762 Evaluate side-chains 214 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 190 GLU Chi-restraints excluded: chain G residue 241 SER Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain I residue 397 SER Chi-restraints excluded: chain H residue 47 TYR Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain J residue 47 TYR Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 36 optimal weight: 0.9980 chunk 234 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 198 optimal weight: 7.9990 chunk 225 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 69 optimal weight: 0.0980 chunk 204 optimal weight: 3.9990 chunk 192 optimal weight: 10.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 ASN C 377 ASN G 33 ASN H 3 GLN L 100 GLN E 100 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.077405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.050185 restraints weight = 49378.853| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 3.97 r_work: 0.2557 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 21309 Z= 0.228 Angle : 0.694 9.848 29159 Z= 0.317 Chirality : 0.048 0.271 3580 Planarity : 0.004 0.039 3490 Dihedral : 9.186 59.839 5281 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.28 % Allowed : 20.32 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.17), residues: 2395 helix: 0.85 (0.28), residues: 438 sheet: 0.39 (0.19), residues: 680 loop : -0.81 (0.17), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 504 TYR 0.013 0.001 TYR C 217 PHE 0.013 0.001 PHE G 383 TRP 0.011 0.001 TRP K 96 HIS 0.005 0.001 HIS L 49 Details of bonding type rmsd covalent geometry : bond 0.00546 (21138) covalent geometry : angle 0.64853 (28688) SS BOND : bond 0.00327 ( 42) SS BOND : angle 0.82749 ( 84) hydrogen bonds : bond 0.05707 ( 674) hydrogen bonds : angle 5.05969 ( 1932) link_ALPHA1-2 : bond 0.00504 ( 3) link_ALPHA1-2 : angle 1.72318 ( 9) link_ALPHA1-3 : bond 0.01066 ( 6) link_ALPHA1-3 : angle 1.92278 ( 18) link_ALPHA1-6 : bond 0.00241 ( 6) link_ALPHA1-6 : angle 1.77704 ( 18) link_BETA1-4 : bond 0.00773 ( 54) link_BETA1-4 : angle 2.48915 ( 162) link_NAG-ASN : bond 0.00272 ( 60) link_NAG-ASN : angle 2.04580 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4790 Ramachandran restraints generated. 2395 Oldfield, 0 Emsley, 2395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4790 Ramachandran restraints generated. 2395 Oldfield, 0 Emsley, 2395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 189 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 GLU cc_start: 0.8854 (pt0) cc_final: 0.8527 (pt0) REVERT: A 641 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8880 (mp) REVERT: B 621 GLU cc_start: 0.9083 (pt0) cc_final: 0.8665 (pp20) REVERT: B 657 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8254 (tp30) REVERT: C 129 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8871 (mt) REVERT: C 504 ARG cc_start: 0.8620 (ttp-170) cc_final: 0.8342 (tpp80) REVERT: F 621 GLU cc_start: 0.8954 (pt0) cc_final: 0.8670 (pt0) REVERT: F 657 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8225 (tm-30) REVERT: I 129 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.9030 (mt) REVERT: I 155 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8131 (mtpp) REVERT: I 397 SER cc_start: 0.9029 (OUTLIER) cc_final: 0.8669 (t) REVERT: H 12 VAL cc_start: 0.9370 (m) cc_final: 0.9136 (p) REVERT: H 75 LYS cc_start: 0.9189 (mtmm) cc_final: 0.8965 (mttm) REVERT: H 85 GLU cc_start: 0.9045 (pm20) cc_final: 0.8835 (pm20) REVERT: H 87 MET cc_start: 0.8684 (mmt) cc_final: 0.8420 (mmm) REVERT: H 105 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8544 (tpt90) REVERT: L 42 GLN cc_start: 0.7967 (mp10) cc_final: 0.7575 (mp10) REVERT: L 54 ARG cc_start: 0.8758 (ttm110) cc_final: 0.8454 (ttm110) REVERT: L 61 ARG cc_start: 0.6148 (OUTLIER) cc_final: 0.5894 (ptt90) REVERT: D 3 GLN cc_start: 0.8718 (pt0) cc_final: 0.7983 (pp30) REVERT: D 72 ASP cc_start: 0.7734 (t0) cc_final: 0.7269 (t0) REVERT: D 75 LYS cc_start: 0.9366 (mtmm) cc_final: 0.8986 (mttp) REVERT: E 42 GLN cc_start: 0.7396 (mp10) cc_final: 0.7161 (mp10) REVERT: J 87 MET cc_start: 0.8751 (mmt) cc_final: 0.8403 (mmm) REVERT: K 42 GLN cc_start: 0.8007 (mp10) cc_final: 0.7209 (mp10) REVERT: K 54 ARG cc_start: 0.8727 (ttm110) cc_final: 0.8438 (ttm110) outliers start: 69 outliers final: 37 residues processed: 242 average time/residue: 0.7439 time to fit residues: 199.8029 Evaluate side-chains 230 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 185 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 190 GLU Chi-restraints excluded: chain G residue 241 SER Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain I residue 397 SER Chi-restraints excluded: chain H residue 47 TYR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 47 TYR Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 120 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 chunk 170 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 137 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 208 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.078066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.050924 restraints weight = 49056.073| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 3.97 r_work: 0.2575 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21309 Z= 0.162 Angle : 0.658 9.752 29159 Z= 0.297 Chirality : 0.046 0.266 3580 Planarity : 0.003 0.039 3490 Dihedral : 8.636 56.294 5281 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.28 % Allowed : 20.66 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.17), residues: 2395 helix: 0.93 (0.28), residues: 438 sheet: 0.55 (0.19), residues: 694 loop : -0.85 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 504 TYR 0.011 0.001 TYR E 91 PHE 0.014 0.001 PHE L 83 TRP 0.009 0.001 TRP C 479 HIS 0.003 0.001 HIS E 49 Details of bonding type rmsd covalent geometry : bond 0.00381 (21138) covalent geometry : angle 0.61373 (28688) SS BOND : bond 0.00260 ( 42) SS BOND : angle 0.64388 ( 84) hydrogen bonds : bond 0.04992 ( 674) hydrogen bonds : angle 4.85715 ( 1932) link_ALPHA1-2 : bond 0.00499 ( 3) link_ALPHA1-2 : angle 1.93030 ( 9) link_ALPHA1-3 : bond 0.01151 ( 6) link_ALPHA1-3 : angle 1.67568 ( 18) link_ALPHA1-6 : bond 0.00380 ( 6) link_ALPHA1-6 : angle 1.62754 ( 18) link_BETA1-4 : bond 0.00778 ( 54) link_BETA1-4 : angle 2.40671 ( 162) link_NAG-ASN : bond 0.00197 ( 60) link_NAG-ASN : angle 2.00363 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4790 Ramachandran restraints generated. 2395 Oldfield, 0 Emsley, 2395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4790 Ramachandran restraints generated. 2395 Oldfield, 0 Emsley, 2395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 192 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 GLU cc_start: 0.8830 (pt0) cc_final: 0.8473 (pt0) REVERT: A 641 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8847 (mp) REVERT: B 621 GLU cc_start: 0.9074 (pt0) cc_final: 0.8703 (pp20) REVERT: B 657 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8257 (tp30) REVERT: C 129 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8850 (mt) REVERT: C 504 ARG cc_start: 0.8626 (ttp-170) cc_final: 0.8334 (tpp80) REVERT: F 621 GLU cc_start: 0.8961 (pt0) cc_final: 0.8658 (pt0) REVERT: F 657 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8297 (tm-30) REVERT: I 129 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8911 (mt) REVERT: I 139 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8225 (p) REVERT: I 155 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8073 (mtpp) REVERT: I 397 SER cc_start: 0.9025 (OUTLIER) cc_final: 0.8669 (t) REVERT: H 3 GLN cc_start: 0.8464 (pt0) cc_final: 0.7780 (pp30) REVERT: H 75 LYS cc_start: 0.9194 (mtmm) cc_final: 0.8963 (mttm) REVERT: H 80 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8327 (tm) REVERT: H 87 MET cc_start: 0.8653 (mmt) cc_final: 0.8303 (mmm) REVERT: H 105 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8429 (tpt90) REVERT: L 39 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8166 (tppt) REVERT: L 42 GLN cc_start: 0.8014 (mp10) cc_final: 0.7625 (mp10) REVERT: L 54 ARG cc_start: 0.8778 (ttm110) cc_final: 0.8456 (ttm110) REVERT: L 61 ARG cc_start: 0.6095 (OUTLIER) cc_final: 0.5786 (ptt90) REVERT: D 3 GLN cc_start: 0.8694 (pt0) cc_final: 0.8049 (pp30) REVERT: D 18 LEU cc_start: 0.7974 (tp) cc_final: 0.7685 (tt) REVERT: D 72 ASP cc_start: 0.7672 (t0) cc_final: 0.7239 (t0) REVERT: D 75 LYS cc_start: 0.9430 (mtmm) cc_final: 0.9098 (mttp) REVERT: D 86 ASP cc_start: 0.8577 (m-30) cc_final: 0.8117 (m-30) REVERT: D 87 MET cc_start: 0.8687 (mmm) cc_final: 0.8402 (mmt) REVERT: E 18 ARG cc_start: 0.8528 (mmt-90) cc_final: 0.7337 (mmp80) REVERT: E 42 GLN cc_start: 0.7200 (mp10) cc_final: 0.6747 (mp10) REVERT: E 82 ASP cc_start: 0.6853 (m-30) cc_final: 0.6561 (m-30) REVERT: J 3 GLN cc_start: 0.8633 (pt0) cc_final: 0.7711 (pp30) REVERT: K 42 GLN cc_start: 0.8026 (mp10) cc_final: 0.7285 (mp10) REVERT: K 54 ARG cc_start: 0.8757 (ttm110) cc_final: 0.8451 (ttm110) outliers start: 69 outliers final: 36 residues processed: 245 average time/residue: 0.7270 time to fit residues: 197.8802 Evaluate side-chains 231 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 184 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 190 GLU Chi-restraints excluded: chain G residue 241 SER Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain I residue 397 SER Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain H residue 47 TYR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain J residue 47 TYR Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 156 optimal weight: 0.0570 chunk 132 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 218 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.0500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 100 GLN E 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.078630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.051525 restraints weight = 48660.421| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 3.96 r_work: 0.2593 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21309 Z= 0.133 Angle : 0.638 9.749 29159 Z= 0.287 Chirality : 0.045 0.265 3580 Planarity : 0.003 0.049 3490 Dihedral : 8.125 56.458 5281 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.38 % Allowed : 20.85 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.17), residues: 2395 helix: 1.03 (0.28), residues: 438 sheet: 0.59 (0.19), residues: 694 loop : -0.82 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 504 TYR 0.011 0.001 TYR E 91 PHE 0.008 0.001 PHE A 519 TRP 0.009 0.001 TRP C 479 HIS 0.003 0.001 HIS L 49 Details of bonding type rmsd covalent geometry : bond 0.00305 (21138) covalent geometry : angle 0.59464 (28688) SS BOND : bond 0.00233 ( 42) SS BOND : angle 0.56309 ( 84) hydrogen bonds : bond 0.04456 ( 674) hydrogen bonds : angle 4.67254 ( 1932) link_ALPHA1-2 : bond 0.00500 ( 3) link_ALPHA1-2 : angle 1.95655 ( 9) link_ALPHA1-3 : bond 0.01182 ( 6) link_ALPHA1-3 : angle 1.56032 ( 18) link_ALPHA1-6 : bond 0.00463 ( 6) link_ALPHA1-6 : angle 1.50564 ( 18) link_BETA1-4 : bond 0.00793 ( 54) link_BETA1-4 : angle 2.36859 ( 162) link_NAG-ASN : bond 0.00182 ( 60) link_NAG-ASN : angle 1.92987 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4790 Ramachandran restraints generated. 2395 Oldfield, 0 Emsley, 2395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4790 Ramachandran restraints generated. 2395 Oldfield, 0 Emsley, 2395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 189 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 GLU cc_start: 0.8798 (pt0) cc_final: 0.8477 (pt0) REVERT: A 641 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8899 (mp) REVERT: B 621 GLU cc_start: 0.9061 (pt0) cc_final: 0.8687 (pp20) REVERT: C 129 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8831 (mt) REVERT: C 139 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8237 (p) REVERT: C 504 ARG cc_start: 0.8611 (ttp-170) cc_final: 0.8310 (tpp80) REVERT: F 621 GLU cc_start: 0.8956 (pt0) cc_final: 0.8641 (pt0) REVERT: F 657 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8214 (tm-30) REVERT: G 63 THR cc_start: 0.7492 (OUTLIER) cc_final: 0.7252 (p) REVERT: G 139 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8038 (p) REVERT: I 129 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8882 (mt) REVERT: I 155 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8019 (mtpp) REVERT: I 397 SER cc_start: 0.9043 (OUTLIER) cc_final: 0.8692 (t) REVERT: H 3 GLN cc_start: 0.8452 (pt0) cc_final: 0.7820 (pp30) REVERT: H 12 VAL cc_start: 0.9371 (m) cc_final: 0.9162 (p) REVERT: H 75 LYS cc_start: 0.9197 (mtmm) cc_final: 0.8949 (mttm) REVERT: H 80 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8308 (tm) REVERT: H 87 MET cc_start: 0.8765 (mmt) cc_final: 0.8370 (mmm) REVERT: H 105 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8425 (tpt90) REVERT: L 42 GLN cc_start: 0.7988 (mp10) cc_final: 0.7577 (mp10) REVERT: L 54 ARG cc_start: 0.8752 (ttm110) cc_final: 0.8428 (ttm110) REVERT: L 61 ARG cc_start: 0.6003 (OUTLIER) cc_final: 0.5769 (ptt180) REVERT: D 3 GLN cc_start: 0.8667 (pt0) cc_final: 0.7855 (pp30) REVERT: D 18 LEU cc_start: 0.8015 (tp) cc_final: 0.7729 (tt) REVERT: D 87 MET cc_start: 0.8751 (mmm) cc_final: 0.8391 (mmt) REVERT: E 18 ARG cc_start: 0.8517 (mmt-90) cc_final: 0.7399 (mmp80) REVERT: E 42 GLN cc_start: 0.7232 (mp10) cc_final: 0.6869 (mp10) REVERT: E 82 ASP cc_start: 0.6901 (m-30) cc_final: 0.6630 (m-30) REVERT: J 3 GLN cc_start: 0.8622 (pt0) cc_final: 0.7676 (pp30) REVERT: K 42 GLN cc_start: 0.8047 (mp10) cc_final: 0.7330 (mp10) REVERT: K 54 ARG cc_start: 0.8709 (ttm110) cc_final: 0.8416 (ttm110) outliers start: 71 outliers final: 33 residues processed: 246 average time/residue: 0.7404 time to fit residues: 202.1721 Evaluate side-chains 226 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 182 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 190 GLU Chi-restraints excluded: chain G residue 241 SER Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain I residue 397 SER Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain H residue 47 TYR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain J residue 47 TYR Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 133 optimal weight: 0.5980 chunk 86 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 209 optimal weight: 7.9990 chunk 149 optimal weight: 0.9980 chunk 184 optimal weight: 0.1980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.078829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.051744 restraints weight = 48894.803| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 3.97 r_work: 0.2605 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21309 Z= 0.127 Angle : 0.639 9.773 29159 Z= 0.287 Chirality : 0.045 0.265 3580 Planarity : 0.003 0.037 3490 Dihedral : 7.869 56.494 5281 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.81 % Allowed : 21.47 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.17), residues: 2395 helix: 1.32 (0.29), residues: 420 sheet: 0.61 (0.19), residues: 694 loop : -0.70 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 504 TYR 0.011 0.001 TYR E 91 PHE 0.008 0.001 PHE G 53 TRP 0.009 0.001 TRP K 96 HIS 0.003 0.001 HIS E 49 Details of bonding type rmsd covalent geometry : bond 0.00293 (21138) covalent geometry : angle 0.59705 (28688) SS BOND : bond 0.00222 ( 42) SS BOND : angle 0.54448 ( 84) hydrogen bonds : bond 0.04303 ( 674) hydrogen bonds : angle 4.59454 ( 1932) link_ALPHA1-2 : bond 0.00490 ( 3) link_ALPHA1-2 : angle 1.96034 ( 9) link_ALPHA1-3 : bond 0.01192 ( 6) link_ALPHA1-3 : angle 1.46233 ( 18) link_ALPHA1-6 : bond 0.00533 ( 6) link_ALPHA1-6 : angle 1.44770 ( 18) link_BETA1-4 : bond 0.00791 ( 54) link_BETA1-4 : angle 2.34320 ( 162) link_NAG-ASN : bond 0.00175 ( 60) link_NAG-ASN : angle 1.91113 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4790 Ramachandran restraints generated. 2395 Oldfield, 0 Emsley, 2395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4790 Ramachandran restraints generated. 2395 Oldfield, 0 Emsley, 2395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 184 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 GLU cc_start: 0.8799 (pt0) cc_final: 0.8464 (pt0) REVERT: A 641 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8905 (mp) REVERT: C 129 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8823 (mt) REVERT: C 139 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8216 (p) REVERT: C 504 ARG cc_start: 0.8605 (ttp-170) cc_final: 0.8314 (tpp80) REVERT: F 621 GLU cc_start: 0.8982 (pt0) cc_final: 0.8699 (pt0) REVERT: F 657 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8214 (tm-30) REVERT: G 63 THR cc_start: 0.7477 (OUTLIER) cc_final: 0.7240 (p) REVERT: G 139 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.8002 (p) REVERT: I 129 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8868 (mt) REVERT: I 139 THR cc_start: 0.8519 (OUTLIER) cc_final: 0.8157 (p) REVERT: I 155 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8002 (mtpp) REVERT: I 397 SER cc_start: 0.9042 (OUTLIER) cc_final: 0.8694 (t) REVERT: H 3 GLN cc_start: 0.8429 (pt0) cc_final: 0.7805 (pp30) REVERT: H 12 VAL cc_start: 0.9388 (m) cc_final: 0.9172 (p) REVERT: H 75 LYS cc_start: 0.9200 (mtmm) cc_final: 0.8947 (mttm) REVERT: H 80 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8273 (tm) REVERT: H 87 MET cc_start: 0.8748 (mmt) cc_final: 0.8346 (mmm) REVERT: H 105 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8422 (tpt90) REVERT: L 42 GLN cc_start: 0.7977 (mp10) cc_final: 0.7568 (mp10) REVERT: L 54 ARG cc_start: 0.8743 (ttm110) cc_final: 0.8420 (ttm110) REVERT: L 61 ARG cc_start: 0.5969 (OUTLIER) cc_final: 0.5745 (ptt180) REVERT: D 3 GLN cc_start: 0.8641 (pt0) cc_final: 0.7841 (pp30) REVERT: D 18 LEU cc_start: 0.7995 (tp) cc_final: 0.7712 (tt) REVERT: D 72 ASP cc_start: 0.7673 (t0) cc_final: 0.7292 (t0) REVERT: D 87 MET cc_start: 0.8622 (mmm) cc_final: 0.8351 (mmt) REVERT: E 18 ARG cc_start: 0.8491 (mmt-90) cc_final: 0.7363 (mmp80) REVERT: E 42 GLN cc_start: 0.7258 (mp10) cc_final: 0.6686 (mp10) REVERT: J 3 GLN cc_start: 0.8611 (pt0) cc_final: 0.7667 (pp30) REVERT: K 42 GLN cc_start: 0.8081 (mp10) cc_final: 0.7368 (mp10) REVERT: K 54 ARG cc_start: 0.8746 (ttm110) cc_final: 0.8440 (ttm110) outliers start: 59 outliers final: 33 residues processed: 235 average time/residue: 0.7461 time to fit residues: 194.6696 Evaluate side-chains 226 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 241 SER Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 397 SER Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain H residue 47 TYR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain J residue 47 TYR Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 103 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 216 optimal weight: 7.9990 chunk 230 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 77 optimal weight: 0.0060 chunk 23 optimal weight: 2.9990 chunk 222 optimal weight: 4.9990 chunk 196 optimal weight: 9.9990 chunk 229 optimal weight: 0.9980 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 100 GLN E 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.078326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.051176 restraints weight = 48789.408| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 3.96 r_work: 0.2584 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21309 Z= 0.159 Angle : 0.656 9.993 29159 Z= 0.295 Chirality : 0.046 0.268 3580 Planarity : 0.003 0.039 3490 Dihedral : 7.744 56.466 5281 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.71 % Allowed : 21.70 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.17), residues: 2395 helix: 1.27 (0.29), residues: 420 sheet: 0.58 (0.19), residues: 702 loop : -0.72 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 504 TYR 0.010 0.001 TYR J 47 PHE 0.010 0.001 PHE G 383 TRP 0.011 0.001 TRP K 96 HIS 0.004 0.001 HIS L 49 Details of bonding type rmsd covalent geometry : bond 0.00377 (21138) covalent geometry : angle 0.61494 (28688) SS BOND : bond 0.00250 ( 42) SS BOND : angle 0.64424 ( 84) hydrogen bonds : bond 0.04668 ( 674) hydrogen bonds : angle 4.63766 ( 1932) link_ALPHA1-2 : bond 0.00452 ( 3) link_ALPHA1-2 : angle 1.88066 ( 9) link_ALPHA1-3 : bond 0.01084 ( 6) link_ALPHA1-3 : angle 1.43842 ( 18) link_ALPHA1-6 : bond 0.00588 ( 6) link_ALPHA1-6 : angle 1.38413 ( 18) link_BETA1-4 : bond 0.00770 ( 54) link_BETA1-4 : angle 2.35191 ( 162) link_NAG-ASN : bond 0.00194 ( 60) link_NAG-ASN : angle 1.93406 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4790 Ramachandran restraints generated. 2395 Oldfield, 0 Emsley, 2395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4790 Ramachandran restraints generated. 2395 Oldfield, 0 Emsley, 2395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 182 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 641 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8924 (mp) REVERT: B 621 GLU cc_start: 0.9108 (pt0) cc_final: 0.8509 (pp20) REVERT: C 63 THR cc_start: 0.7222 (OUTLIER) cc_final: 0.6951 (p) REVERT: C 129 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8842 (mt) REVERT: C 139 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8201 (p) REVERT: C 504 ARG cc_start: 0.8605 (ttp-170) cc_final: 0.8312 (tpp80) REVERT: F 621 GLU cc_start: 0.9002 (pt0) cc_final: 0.8703 (pt0) REVERT: F 657 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8223 (tm-30) REVERT: G 63 THR cc_start: 0.7466 (OUTLIER) cc_final: 0.7230 (p) REVERT: G 139 THR cc_start: 0.8379 (OUTLIER) cc_final: 0.7993 (p) REVERT: G 504 ARG cc_start: 0.8525 (tpp80) cc_final: 0.8291 (tpp80) REVERT: I 129 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8917 (mt) REVERT: I 139 THR cc_start: 0.8508 (OUTLIER) cc_final: 0.8145 (p) REVERT: I 155 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8080 (mtpp) REVERT: I 397 SER cc_start: 0.9002 (OUTLIER) cc_final: 0.8635 (t) REVERT: I 499 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8277 (p) REVERT: H 3 GLN cc_start: 0.8496 (pt0) cc_final: 0.7904 (pp30) REVERT: H 18 LEU cc_start: 0.7926 (tm) cc_final: 0.7693 (tt) REVERT: H 75 LYS cc_start: 0.9190 (mtmm) cc_final: 0.8937 (mttm) REVERT: H 80 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8271 (tm) REVERT: H 87 MET cc_start: 0.8729 (mmt) cc_final: 0.8315 (mmm) REVERT: H 105 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8432 (tpt90) REVERT: L 42 GLN cc_start: 0.7996 (mp10) cc_final: 0.7597 (mp10) REVERT: L 54 ARG cc_start: 0.8786 (ttm110) cc_final: 0.8508 (ttm110) REVERT: L 61 ARG cc_start: 0.5986 (OUTLIER) cc_final: 0.5756 (ptt180) REVERT: D 3 GLN cc_start: 0.8650 (pt0) cc_final: 0.7866 (pp30) REVERT: D 18 LEU cc_start: 0.8031 (tp) cc_final: 0.7743 (tt) REVERT: D 72 ASP cc_start: 0.7710 (t0) cc_final: 0.7343 (t0) REVERT: D 83 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8445 (mtm110) REVERT: D 85 GLU cc_start: 0.9093 (pm20) cc_final: 0.8831 (pm20) REVERT: D 87 MET cc_start: 0.8630 (mmm) cc_final: 0.8330 (mmp) REVERT: E 18 ARG cc_start: 0.8493 (mmt-90) cc_final: 0.7437 (mmp80) REVERT: E 42 GLN cc_start: 0.7373 (mp10) cc_final: 0.6857 (mp10) REVERT: E 102 THR cc_start: 0.6384 (m) cc_final: 0.6145 (m) REVERT: J 3 GLN cc_start: 0.8631 (pt0) cc_final: 0.7780 (pp30) REVERT: K 42 GLN cc_start: 0.8098 (mp10) cc_final: 0.7375 (mp10) REVERT: K 54 ARG cc_start: 0.8753 (ttm110) cc_final: 0.8441 (ttm110) outliers start: 57 outliers final: 36 residues processed: 233 average time/residue: 0.7248 time to fit residues: 187.6365 Evaluate side-chains 233 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 182 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 241 SER Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain I residue 397 SER Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain H residue 47 TYR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain J residue 47 TYR Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 98 ASP Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 62 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 175 optimal weight: 0.2980 chunk 210 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.079260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.052201 restraints weight = 48960.228| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 3.98 r_work: 0.2618 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21309 Z= 0.111 Angle : 0.624 9.742 29159 Z= 0.280 Chirality : 0.044 0.262 3580 Planarity : 0.003 0.043 3490 Dihedral : 7.522 57.878 5281 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.57 % Allowed : 22.28 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.17), residues: 2395 helix: 1.39 (0.29), residues: 420 sheet: 0.71 (0.19), residues: 687 loop : -0.67 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 504 TYR 0.011 0.001 TYR L 91 PHE 0.007 0.001 PHE G 53 TRP 0.009 0.001 TRP C 479 HIS 0.003 0.001 HIS E 49 Details of bonding type rmsd covalent geometry : bond 0.00251 (21138) covalent geometry : angle 0.58415 (28688) SS BOND : bond 0.00214 ( 42) SS BOND : angle 0.48997 ( 84) hydrogen bonds : bond 0.03926 ( 674) hydrogen bonds : angle 4.45363 ( 1932) link_ALPHA1-2 : bond 0.00500 ( 3) link_ALPHA1-2 : angle 2.04672 ( 9) link_ALPHA1-3 : bond 0.01179 ( 6) link_ALPHA1-3 : angle 1.13592 ( 18) link_ALPHA1-6 : bond 0.00753 ( 6) link_ALPHA1-6 : angle 1.32210 ( 18) link_BETA1-4 : bond 0.00787 ( 54) link_BETA1-4 : angle 2.27307 ( 162) link_NAG-ASN : bond 0.00184 ( 60) link_NAG-ASN : angle 1.86902 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4790 Ramachandran restraints generated. 2395 Oldfield, 0 Emsley, 2395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4790 Ramachandran restraints generated. 2395 Oldfield, 0 Emsley, 2395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 184 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 GLU cc_start: 0.8924 (pt0) cc_final: 0.8326 (pp20) REVERT: A 641 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8898 (mp) REVERT: B 574 LYS cc_start: 0.8773 (mmmt) cc_final: 0.8553 (mtmt) REVERT: B 621 GLU cc_start: 0.9024 (pt0) cc_final: 0.8438 (pp20) REVERT: C 63 THR cc_start: 0.7128 (OUTLIER) cc_final: 0.6854 (p) REVERT: C 129 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8830 (mt) REVERT: C 139 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8202 (p) REVERT: C 504 ARG cc_start: 0.8654 (ttp-170) cc_final: 0.8335 (tpp80) REVERT: F 574 LYS cc_start: 0.8702 (mtmt) cc_final: 0.8495 (mtmt) REVERT: F 621 GLU cc_start: 0.8974 (pt0) cc_final: 0.8676 (pt0) REVERT: F 657 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8158 (tm-30) REVERT: G 63 THR cc_start: 0.7630 (OUTLIER) cc_final: 0.7376 (p) REVERT: G 139 THR cc_start: 0.8350 (OUTLIER) cc_final: 0.7962 (p) REVERT: G 504 ARG cc_start: 0.8561 (tpp80) cc_final: 0.8324 (tpp80) REVERT: I 129 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8858 (mt) REVERT: I 155 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8008 (mtpp) REVERT: I 381 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7767 (mm-30) REVERT: I 499 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8288 (p) REVERT: H 3 GLN cc_start: 0.8462 (pt0) cc_final: 0.8081 (pp30) REVERT: H 18 LEU cc_start: 0.7913 (tm) cc_final: 0.7628 (tt) REVERT: H 75 LYS cc_start: 0.9207 (mtmm) cc_final: 0.8952 (mttm) REVERT: H 80 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8235 (tm) REVERT: H 83 ARG cc_start: 0.8655 (mtp180) cc_final: 0.8362 (mtm110) REVERT: H 87 MET cc_start: 0.8694 (mmt) cc_final: 0.8279 (mmm) REVERT: H 105 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8503 (tpt90) REVERT: L 42 GLN cc_start: 0.7970 (mp10) cc_final: 0.7547 (mp10) REVERT: L 54 ARG cc_start: 0.8784 (ttm110) cc_final: 0.8461 (ttm110) REVERT: L 61 ARG cc_start: 0.5947 (OUTLIER) cc_final: 0.5736 (ptt180) REVERT: D 3 GLN cc_start: 0.8626 (pt0) cc_final: 0.8058 (pp30) REVERT: D 18 LEU cc_start: 0.7989 (tp) cc_final: 0.7748 (tt) REVERT: D 72 ASP cc_start: 0.7708 (t0) cc_final: 0.7380 (t0) REVERT: D 75 LYS cc_start: 0.9449 (mttp) cc_final: 0.9229 (mttp) REVERT: D 87 MET cc_start: 0.8637 (mmm) cc_final: 0.8329 (mmp) REVERT: E 18 ARG cc_start: 0.8481 (mmt-90) cc_final: 0.8271 (mmp80) REVERT: E 42 GLN cc_start: 0.7384 (mp10) cc_final: 0.6859 (mp10) REVERT: J 3 GLN cc_start: 0.8601 (pt0) cc_final: 0.7834 (pp30) REVERT: J 83 ARG cc_start: 0.8812 (mtm-85) cc_final: 0.8431 (ttp-110) REVERT: K 42 GLN cc_start: 0.8069 (mp10) cc_final: 0.7336 (mp10) REVERT: K 54 ARG cc_start: 0.8732 (ttm110) cc_final: 0.8429 (ttm110) REVERT: K 102 THR cc_start: 0.5031 (OUTLIER) cc_final: 0.4787 (t) outliers start: 54 outliers final: 30 residues processed: 232 average time/residue: 0.7846 time to fit residues: 201.4485 Evaluate side-chains 226 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 183 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 241 SER Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain H residue 47 TYR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain J residue 47 TYR Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 186 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 207 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 164 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 37 GLN E 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.079134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.052059 restraints weight = 48909.356| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 3.97 r_work: 0.2608 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21309 Z= 0.123 Angle : 0.636 13.741 29159 Z= 0.284 Chirality : 0.045 0.264 3580 Planarity : 0.003 0.042 3490 Dihedral : 7.471 59.105 5281 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.28 % Allowed : 22.70 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.17), residues: 2395 helix: 1.41 (0.29), residues: 420 sheet: 0.72 (0.19), residues: 687 loop : -0.65 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 504 TYR 0.010 0.001 TYR E 91 PHE 0.008 0.001 PHE C 53 TRP 0.009 0.001 TRP K 96 HIS 0.003 0.001 HIS L 49 Details of bonding type rmsd covalent geometry : bond 0.00285 (21138) covalent geometry : angle 0.59687 (28688) SS BOND : bond 0.00221 ( 42) SS BOND : angle 0.52623 ( 84) hydrogen bonds : bond 0.04079 ( 674) hydrogen bonds : angle 4.44882 ( 1932) link_ALPHA1-2 : bond 0.00475 ( 3) link_ALPHA1-2 : angle 1.90045 ( 9) link_ALPHA1-3 : bond 0.01064 ( 6) link_ALPHA1-3 : angle 1.19761 ( 18) link_ALPHA1-6 : bond 0.00753 ( 6) link_ALPHA1-6 : angle 1.32736 ( 18) link_BETA1-4 : bond 0.00773 ( 54) link_BETA1-4 : angle 2.27126 ( 162) link_NAG-ASN : bond 0.00165 ( 60) link_NAG-ASN : angle 1.85661 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4790 Ramachandran restraints generated. 2395 Oldfield, 0 Emsley, 2395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4790 Ramachandran restraints generated. 2395 Oldfield, 0 Emsley, 2395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 183 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 GLU cc_start: 0.8875 (pt0) cc_final: 0.8224 (pp20) REVERT: A 641 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8912 (mp) REVERT: B 574 LYS cc_start: 0.8773 (mmmt) cc_final: 0.8554 (mtmt) REVERT: B 621 GLU cc_start: 0.9025 (pt0) cc_final: 0.8449 (pp20) REVERT: C 63 THR cc_start: 0.7123 (OUTLIER) cc_final: 0.6850 (p) REVERT: C 129 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8843 (mt) REVERT: C 139 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8176 (p) REVERT: C 504 ARG cc_start: 0.8661 (ttp-170) cc_final: 0.8359 (tpp80) REVERT: F 574 LYS cc_start: 0.8706 (mtmt) cc_final: 0.8505 (mtmt) REVERT: F 621 GLU cc_start: 0.8988 (pt0) cc_final: 0.8678 (pt0) REVERT: F 657 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8188 (tm-30) REVERT: G 63 THR cc_start: 0.7624 (OUTLIER) cc_final: 0.7374 (p) REVERT: G 139 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.7938 (p) REVERT: G 504 ARG cc_start: 0.8652 (tpp80) cc_final: 0.8416 (tpp80) REVERT: I 129 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8889 (mt) REVERT: I 155 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8006 (mtpp) REVERT: I 499 THR cc_start: 0.8751 (OUTLIER) cc_final: 0.8307 (p) REVERT: H 3 GLN cc_start: 0.8448 (pt0) cc_final: 0.8025 (pp30) REVERT: H 75 LYS cc_start: 0.9209 (mtmm) cc_final: 0.8952 (mttm) REVERT: H 80 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8231 (tm) REVERT: H 83 ARG cc_start: 0.8683 (mtp180) cc_final: 0.8452 (mtm110) REVERT: H 87 MET cc_start: 0.8682 (mmt) cc_final: 0.8270 (mmm) REVERT: H 105 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8502 (tpt90) REVERT: L 42 GLN cc_start: 0.7976 (mp10) cc_final: 0.7553 (mp10) REVERT: L 54 ARG cc_start: 0.8779 (ttm110) cc_final: 0.8502 (ttm110) REVERT: L 61 ARG cc_start: 0.5950 (OUTLIER) cc_final: 0.5724 (ptt180) REVERT: D 3 GLN cc_start: 0.8626 (pt0) cc_final: 0.8062 (pp30) REVERT: D 18 LEU cc_start: 0.8006 (tp) cc_final: 0.7775 (tt) REVERT: D 72 ASP cc_start: 0.7726 (t0) cc_final: 0.7410 (t0) REVERT: E 18 ARG cc_start: 0.8480 (mmt-90) cc_final: 0.8272 (mmp80) REVERT: E 42 GLN cc_start: 0.7450 (mp10) cc_final: 0.6794 (mp10) REVERT: J 3 GLN cc_start: 0.8594 (pt0) cc_final: 0.7818 (pp30) REVERT: J 83 ARG cc_start: 0.8828 (mtm-85) cc_final: 0.8427 (ttp-110) REVERT: K 42 GLN cc_start: 0.8079 (mp10) cc_final: 0.7374 (mp10) REVERT: K 102 THR cc_start: 0.4925 (OUTLIER) cc_final: 0.4674 (t) outliers start: 48 outliers final: 32 residues processed: 228 average time/residue: 0.7940 time to fit residues: 200.3102 Evaluate side-chains 227 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 182 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 241 SER Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 139 THR Chi-restraints excluded: chain I residue 155 LYS Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain I residue 450 THR Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain H residue 47 TYR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain J residue 47 TYR Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 180 optimal weight: 3.9990 chunk 200 optimal weight: 0.9990 chunk 191 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 223 optimal weight: 0.8980 chunk 137 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 236 optimal weight: 20.0000 chunk 6 optimal weight: 0.9990 chunk 216 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.079071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.051926 restraints weight = 48761.384| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 3.97 r_work: 0.2608 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21309 Z= 0.132 Angle : 0.634 9.781 29159 Z= 0.285 Chirality : 0.045 0.263 3580 Planarity : 0.003 0.042 3490 Dihedral : 7.458 59.729 5281 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.24 % Allowed : 22.66 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.17), residues: 2395 helix: 1.40 (0.29), residues: 420 sheet: 0.70 (0.19), residues: 693 loop : -0.64 (0.17), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 504 TYR 0.010 0.001 TYR E 91 PHE 0.032 0.001 PHE K 83 TRP 0.010 0.001 TRP K 96 HIS 0.003 0.001 HIS E 49 Details of bonding type rmsd covalent geometry : bond 0.00307 (21138) covalent geometry : angle 0.59467 (28688) SS BOND : bond 0.00231 ( 42) SS BOND : angle 0.54896 ( 84) hydrogen bonds : bond 0.04172 ( 674) hydrogen bonds : angle 4.46982 ( 1932) link_ALPHA1-2 : bond 0.00473 ( 3) link_ALPHA1-2 : angle 1.89434 ( 9) link_ALPHA1-3 : bond 0.01032 ( 6) link_ALPHA1-3 : angle 1.15038 ( 18) link_ALPHA1-6 : bond 0.00773 ( 6) link_ALPHA1-6 : angle 1.32298 ( 18) link_BETA1-4 : bond 0.00766 ( 54) link_BETA1-4 : angle 2.25886 ( 162) link_NAG-ASN : bond 0.00168 ( 60) link_NAG-ASN : angle 1.86729 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6232.88 seconds wall clock time: 107 minutes 0.89 seconds (6420.89 seconds total)