Starting phenix.real_space_refine on Sat Aug 8 04:43:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fad_28953/08_2026/8fad_28953_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fad_28953/08_2026/8fad_28953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fad_28953/08_2026/8fad_28953_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fad_28953/08_2026/8fad_28953_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fad_28953/08_2026/8fad_28953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fad_28953/08_2026/8fad_28953.map" } resolution = 4.0 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= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11943 atoms to isotropic. 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 96 5.16 5 C 10074 2.51 5 N 2626 2.21 5 O 3414 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16210 Number of models: 1 Model: "" Number of chains: 60 Chain: "B" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1100 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 1, 'TRANS': 136} Chain: "C" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3675 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 22, 'TRANS': 443} Chain breaks: 1 Chain: "D" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1100 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 1, 'TRANS': 136} Chain: "E" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3675 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 22, 'TRANS': 443} Chain breaks: 1 Chain: "A" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3675 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 22, 'TRANS': 443} Chain breaks: 1 Chain: "F" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 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: "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: 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: "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: 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: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 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: 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: "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: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: "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: 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: "h" 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: "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: 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: "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: 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: 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: "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: "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: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 100 Unusual residues: {'83G': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" 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: "E" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 86 Unusual residues: {'83G': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 86 Unusual residues: {'83G': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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 Time building chain proxies: 3.41, per 1000 atoms: 0.21 Number of scatterers: 16210 At special positions: 0 Unit cell: (141.11, 139.74, 124.67, 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 96 16.00 O 3414 8.00 N 2626 7.00 C 10074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " 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=2.04 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 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 D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 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=1, symmetry=0 Links applied ALPHA1-2 " MAN M 4 " - " MAN M 5 " " MAN h 4 " - " MAN h 5 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA c 3 " - " MAN c 4 " " BMA h 3 " - " MAN h 4 " " BMA r 3 " - " MAN r 6 " ALPHA1-6 " BMA M 3 " - " MAN M 6 " " BMA R 3 " - " MAN R 4 " " BMA c 3 " - " MAN c 5 " " BMA r 3 " - " MAN r 4 " " MAN r 4 " - " MAN r 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " 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 Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " 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 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 w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " NAG-ASN " NAG 0 1 " - " ASN A 448 " " NAG 1 1 " - " ASN F 611 " " NAG A 602 " - " ASN A 160 " " NAG A 603 " - " ASN A 188 " " NAG A 604 " - " ASN A 241 " " NAG A 605 " - " ASN A 401 " " NAG B 701 " - " ASN B 616 " " NAG B 702 " - " ASN B 625 " " NAG B 703 " - " ASN B 637 " " NAG C 602 " - " ASN C 160 " " NAG C 603 " - " ASN C 188 " " NAG C 604 " - " ASN C 241 " " NAG C 605 " - " ASN C 356 " " NAG C 606 " - " ASN C 401 " " NAG D 701 " - " ASN D 616 " " NAG D 702 " - " ASN D 625 " " NAG D 703 " - " ASN D 637 " " NAG E 602 " - " ASN E 160 " " NAG E 603 " - " ASN E 188 " " NAG E 604 " - " ASN E 241 " " NAG E 605 " - " ASN E 401 " " NAG F 701 " - " ASN F 616 " " NAG F 702 " - " ASN F 625 " " NAG F 703 " - " ASN F 637 " " NAG G 1 " - " ASN B 611 " " NAG H 1 " - " ASN C 88 " " NAG I 1 " - " ASN C 130 " " NAG J 1 " - " ASN C 156 " " NAG K 1 " - " ASN C 197 " " NAG L 1 " - " ASN C 234 " " NAG M 1 " - " ASN C 262 " " NAG N 1 " - " ASN C 276 " " NAG O 1 " - " ASN C 295 " " NAG P 1 " - " ASN C 301 " " NAG Q 1 " - " ASN C 332 " " NAG R 1 " - " ASN C 339 " " NAG S 1 " - " ASN C 362 " " NAG T 1 " - " ASN C 386 " " NAG U 1 " - " ASN C 392 " " NAG V 1 " - " ASN C 448 " " NAG W 1 " - " ASN D 611 " " NAG X 1 " - " ASN E 88 " " NAG Y 1 " - " ASN E 130 " " NAG Z 1 " - " ASN E 156 " " NAG a 1 " - " ASN E 197 " " NAG b 1 " - " ASN E 234 " " NAG c 1 " - " ASN E 262 " " NAG d 1 " - " ASN E 276 " " NAG e 1 " - " ASN E 295 " " NAG f 1 " - " ASN E 301 " " NAG g 1 " - " ASN E 332 " " NAG h 1 " - " ASN E 339 " " NAG i 1 " - " ASN E 362 " " NAG j 1 " - " ASN E 386 " " NAG k 1 " - " ASN E 392 " " NAG l 1 " - " ASN E 448 " " NAG m 1 " - " ASN A 88 " " NAG n 1 " - " ASN A 130 " " NAG o 1 " - " ASN A 156 " " NAG p 1 " - " ASN A 197 " " NAG q 1 " - " ASN A 234 " " NAG r 1 " - " ASN A 262 " " NAG s 1 " - " ASN A 276 " " NAG t 1 " - " ASN A 295 " " NAG u 1 " - " ASN A 301 " " NAG v 1 " - " ASN A 332 " " NAG w 1 " - " ASN A 339 " " NAG x 1 " - " ASN A 362 " " NAG y 1 " - " ASN A 386 " " NAG z 1 " - " ASN A 392 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 654.4 milliseconds 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3360 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 28 sheets defined 27.4% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'B' and resid 529 through 536 removed outlier: 3.638A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 564 removed outlier: 4.289A pdb=" N LEU B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL B 549 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN B 550 " --> pdb=" O SER B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 removed outlier: 3.524A pdb=" N ILE B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.587A pdb=" N TRP B 631 " --> pdb=" O THR B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 657 Processing helix chain 'C' and resid 58 through 64 removed outlier: 3.869A pdb=" N THR C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.189A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.537A pdb=" N LEU C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 126' Processing helix chain 'C' and resid 177 through 181 Processing helix chain 'C' and resid 335 through 353 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 474 through 484 removed outlier: 4.516A pdb=" N ASN C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR C 484 " --> pdb=" O ARG C 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 535 Processing helix chain 'D' and resid 538 through 564 removed outlier: 3.537A pdb=" N LEU D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 596 Processing helix chain 'D' and resid 618 through 626 Processing helix chain 'D' and resid 627 through 634 removed outlier: 3.980A pdb=" N GLU D 634 " --> pdb=" O GLU D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 657 removed outlier: 4.231A pdb=" N GLY D 640 " --> pdb=" O ASP D 636 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LEU D 641 " --> pdb=" O ASN D 637 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 64 removed outlier: 4.289A pdb=" N ALA E 60 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR E 61 " --> pdb=" O ASP E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.207A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.579A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.635A pdb=" N MET E 373 " --> pdb=" O PRO E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 483 removed outlier: 4.518A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.287A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 481 removed outlier: 4.517A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 3.957A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 536 removed outlier: 3.604A pdb=" N ILE F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 543 removed outlier: 4.259A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.588A pdb=" N GLU F 584 " --> pdb=" O VAL F 580 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 625 removed outlier: 3.830A pdb=" N ASN F 625 " --> pdb=" O MET F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 removed outlier: 4.032A pdb=" N ARG F 633 " --> pdb=" O MET F 629 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU F 634 " --> pdb=" O GLU F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 637 through 657 Processing sheet with id=AA1, first strand: chain 'B' and resid 609 through 610 removed outlier: 4.574A pdb=" N LEU A 34 " --> pdb=" O TRP B 610 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 494 through 499 removed outlier: 3.549A pdb=" N CYS D 604 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 494 through 499 removed outlier: 4.597A pdb=" N LEU C 34 " --> pdb=" O TRP D 610 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.217A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 92 through 94 Processing sheet with id=AA6, first strand: chain 'C' and resid 169 through 174 Processing sheet with id=AA7, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.912A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.299A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.847A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 11.749A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.875A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.551A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 11.361A pdb=" N ASP C 457 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 12.346A pdb=" N ILE C 284 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N SER C 334 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N CYS C 331 " --> pdb=" O LEU C 416 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 271 through 273 removed outlier: 12.346A pdb=" N ILE C 284 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 11.361A pdb=" N ASP C 457 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 11.551A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.875A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.749A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.847A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.299A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR C 467 " --> pdb=" O ASP C 457 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 301 through 308 removed outlier: 6.740A pdb=" N ASN C 301 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE C 322 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 423 through 424 Processing sheet with id=AB2, first strand: chain 'E' and resid 495 through 499 removed outlier: 5.777A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.803A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 92 through 94 Processing sheet with id=AB5, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AB6, first strand: chain 'E' and resid 181 through 183 removed outlier: 3.724A pdb=" N ARG E 192 " --> pdb=" O VAL E 182 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 201 through 203 Processing sheet with id=AB8, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.670A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 9.982A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.177A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.228A pdb=" N SER E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 9.748A pdb=" N VAL E 292 " --> pdb=" O SER E 446 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 9.590A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.670A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR E 467 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 301 through 308 removed outlier: 6.700A pdb=" N ASN E 301 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 329 through 334 removed outlier: 3.596A pdb=" N CYS E 331 " --> pdb=" O LEU E 416 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.591A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 92 through 94 Processing sheet with id=AC5, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AC6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AC7, first strand: chain 'A' and resid 201 through 203 removed outlier: 3.513A pdb=" N TYR A 435 " --> pdb=" O THR A 202 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 260 through 261 removed outlier: 6.670A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.405A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.919A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.622A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.093A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.647A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.100A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 12.265A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 360 through 361 Processing sheet with id=AC9, first strand: chain 'A' and resid 271 through 273 removed outlier: 12.265A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 11.100A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 11.647A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.093A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.622A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.919A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.405A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 443 through 457 current: chain 'A' and resid 413 through 420 Processing sheet with id=AD1, first strand: chain 'A' and resid 301 through 308 removed outlier: 6.743A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) 526 hydrogen bonds defined for protein. 1488 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: 2.36 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3874 1.33 - 1.46: 4337 1.46 - 1.59: 8165 1.59 - 1.72: 1 1.72 - 1.85: 132 Bond restraints: 16509 Sorted by residual: bond pdb=" N GLY E 431 " pdb=" CA GLY E 431 " ideal model delta sigma weight residual 1.442 1.476 -0.034 7.70e-03 1.69e+04 1.93e+01 bond pdb=" C GLY F 640 " pdb=" O GLY F 640 " ideal model delta sigma weight residual 1.234 1.284 -0.051 1.20e-02 6.94e+03 1.78e+01 bond pdb=" N VAL C 182 " pdb=" CA VAL C 182 " ideal model delta sigma weight residual 1.457 1.494 -0.037 9.00e-03 1.23e+04 1.68e+01 bond pdb=" C1 MAN h 4 " pdb=" O5 MAN h 4 " ideal model delta sigma weight residual 1.399 1.473 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" N VAL E 242 " pdb=" CA VAL E 242 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.14e-02 7.69e+03 1.28e+01 ... (remaining 16504 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 21872 3.60 - 7.19: 525 7.19 - 10.79: 35 10.79 - 14.39: 1 14.39 - 17.98: 3 Bond angle restraints: 22436 Sorted by residual: angle pdb=" N ASN F 637 " pdb=" CA ASN F 637 " pdb=" C ASN F 637 " ideal model delta sigma weight residual 112.90 102.80 10.10 1.31e+00 5.83e-01 5.94e+01 angle pdb=" CA ASN B 611 " pdb=" CB ASN B 611 " pdb=" CG ASN B 611 " ideal model delta sigma weight residual 112.60 119.04 -6.44 1.00e+00 1.00e+00 4.15e+01 angle pdb=" CA GLY F 521 " pdb=" C GLY F 521 " pdb=" O GLY F 521 " ideal model delta sigma weight residual 122.23 118.09 4.14 6.90e-01 2.10e+00 3.60e+01 angle pdb=" C3 MAN c 4 " pdb=" C2 MAN c 4 " pdb=" O2 MAN c 4 " ideal model delta sigma weight residual 111.77 129.75 -17.98 3.00e+00 1.11e-01 3.59e+01 angle pdb=" CA ASN C 401 " pdb=" CB ASN C 401 " pdb=" CG ASN C 401 " ideal model delta sigma weight residual 112.60 106.78 5.82 1.00e+00 1.00e+00 3.39e+01 ... (remaining 22431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.45: 11057 28.45 - 56.90: 518 56.90 - 85.35: 111 85.35 - 113.80: 60 113.80 - 142.24: 22 Dihedral angle restraints: 11768 sinusoidal: 6576 harmonic: 5192 Sorted by residual: dihedral pdb=" CB CYS B 598 " pdb=" SG CYS B 598 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual 93.00 166.92 -73.92 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 149.50 -56.50 1 1.00e+01 1.00e-02 4.30e+01 dihedral pdb=" CA CYS C 119 " pdb=" C CYS C 119 " pdb=" N VAL C 120 " pdb=" CA VAL C 120 " ideal model delta harmonic sigma weight residual 180.00 -150.23 -29.77 0 5.00e+00 4.00e-02 3.55e+01 ... (remaining 11765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.297: 2879 0.297 - 0.594: 40 0.594 - 0.891: 12 0.891 - 1.188: 4 1.188 - 1.485: 5 Chirality restraints: 2940 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.92 -1.48 2.00e-02 2.50e+03 5.51e+03 chirality pdb=" C1 NAG w 2 " pdb=" O4 NAG w 1 " pdb=" C2 NAG w 2 " pdb=" O5 NAG w 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.92 -1.48 2.00e-02 2.50e+03 5.49e+03 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-02 2.50e+03 1.53e+03 ... (remaining 2937 not shown) Planarity restraints: 2738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 703 " -0.356 2.00e-02 2.50e+03 3.07e-01 1.18e+03 pdb=" C7 NAG F 703 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG F 703 " -0.111 2.00e-02 2.50e+03 pdb=" N2 NAG F 703 " 0.547 2.00e-02 2.50e+03 pdb=" O7 NAG F 703 " -0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG 1 2 " -0.327 2.00e-02 2.50e+03 2.85e-01 1.01e+03 pdb=" C7 NAG 1 2 " 0.073 2.00e-02 2.50e+03 pdb=" C8 NAG 1 2 " -0.114 2.00e-02 2.50e+03 pdb=" N2 NAG 1 2 " 0.510 2.00e-02 2.50e+03 pdb=" O7 NAG 1 2 " -0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG l 1 " 0.331 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG l 1 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG l 1 " 0.168 2.00e-02 2.50e+03 pdb=" N2 NAG l 1 " -0.502 2.00e-02 2.50e+03 pdb=" O7 NAG l 1 " 0.085 2.00e-02 2.50e+03 ... (remaining 2735 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 158 2.60 - 3.18: 14247 3.18 - 3.75: 24945 3.75 - 4.33: 34494 4.33 - 4.90: 53196 Nonbonded interactions: 127040 Sorted by model distance: nonbonded pdb=" OE1 GLU A 211 " pdb=" O6 MAN r 6 " model vdw 2.027 3.040 nonbonded pdb=" OD1 ASN C 461 " pdb=" OG1 THR C 465 " model vdw 2.135 3.040 nonbonded pdb=" OD1 ASN A 461 " pdb=" OG1 THR A 465 " model vdw 2.136 3.040 nonbonded pdb=" OD1 ASN E 461 " pdb=" OG1 THR E 465 " model vdw 2.136 3.040 nonbonded pdb=" O ASN C 478 " pdb=" OG SER C 481 " model vdw 2.246 3.040 ... (remaining 127035 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 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'm' 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 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain 'A' selection = (chain 'C' and resid 33 through 605) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 520 through 547 or resid 563 through 703)) selection = (chain 'D' and (resid 520 through 547 or resid 563 through 703)) selection = chain 'F' } ncs_group { reference = chain 'J' selection = chain 'N' selection = chain 'Q' selection = chain 'T' selection = chain 'Z' selection = chain 'g' selection = chain 'j' selection = chain 'w' } ncs_group { reference = chain 'M' selection = chain 'r' } ncs_group { reference = chain 'c' selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.470 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 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 : 0.011 0.243 16682 Z= 0.791 Angle : 1.710 35.046 22922 Z= 1.003 Chirality : 0.130 1.485 2940 Planarity : 0.029 0.307 2668 Dihedral : 18.964 142.245 8318 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.90 % Allowed : 9.62 % Favored : 89.48 % Rotamer: Outliers : 3.64 % Allowed : 7.73 % Favored : 88.63 % Cbeta Deviations : 0.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.19), residues: 1777 helix: 0.05 (0.27), residues: 416 sheet: -1.43 (0.24), residues: 390 loop : -2.39 (0.17), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 503 TYR 0.013 0.002 TYR F 586 PHE 0.017 0.001 PHE A 468 TRP 0.032 0.002 TRP A 400 HIS 0.009 0.002 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.01108 / 0.77 (16509) covalent geometry : angle 1.46861 / 0.97 (22436) SS BOND : bond 0.00331 / 0.19 ( 30) SS BOND : angle 1.76146 / 1.06 ( 60) hydrogen bonds : bond 0.19028 / 12.98 ( 505) hydrogen bonds : angle 7.70718 / 5.48 ( 1488) Misc. bond : bond 0.20234 / 10.65 ( 1) link_ALPHA1-2 : bond 0.00819 / 0.39 ( 2) link_ALPHA1-2 : angle 0.87623 / 0.31 ( 6) link_ALPHA1-3 : bond 0.02534 / 1.24 ( 4) link_ALPHA1-3 : angle 3.15396 / 1.59 ( 12) link_ALPHA1-6 : bond 0.00913 / 0.51 ( 5) link_ALPHA1-6 : angle 10.41286 / 5.10 ( 15) link_BETA1-4 : bond 0.03532 / 1.49 ( 61) link_BETA1-4 : angle 5.29549 / 3.76 ( 183) link_NAG-ASN : bond 0.01971 / 1.33 ( 70) link_NAG-ASN : angle 7.41408 / 5.54 ( 210) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 459 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8912 (ttm) cc_final: 0.8346 (ttp) REVERT: B 543 LEU cc_start: 0.9514 (mt) cc_final: 0.9286 (pp) REVERT: B 629 MET cc_start: 0.8105 (mmm) cc_final: 0.7710 (mmm) REVERT: B 638 TYR cc_start: 0.7859 (m-80) cc_final: 0.7580 (m-80) REVERT: B 649 SER cc_start: 0.9434 (p) cc_final: 0.9118 (p) REVERT: B 654 GLU cc_start: 0.8105 (tt0) cc_final: 0.7739 (tt0) REVERT: B 655 LYS cc_start: 0.7006 (mttt) cc_final: 0.6589 (mmtm) REVERT: C 34 LEU cc_start: 0.8712 (mt) cc_final: 0.8324 (mt) REVERT: C 68 VAL cc_start: 0.5921 (OUTLIER) cc_final: 0.4739 (p) REVERT: C 71 THR cc_start: 0.7841 (m) cc_final: 0.7353 (t) REVERT: C 80 ASN cc_start: 0.7551 (t0) cc_final: 0.7106 (t0) REVERT: C 95 MET cc_start: 0.8191 (ppp) cc_final: 0.7574 (ppp) REVERT: C 120 VAL cc_start: 0.8999 (t) cc_final: 0.8348 (t) REVERT: C 190 SER cc_start: 0.8535 (m) cc_final: 0.8309 (p) REVERT: C 244 THR cc_start: 0.9588 (m) cc_final: 0.9194 (p) REVERT: C 256 SER cc_start: 0.9024 (p) cc_final: 0.8728 (p) REVERT: C 475 MET cc_start: 0.8878 (tpp) cc_final: 0.8298 (mmp) REVERT: D 591 GLN cc_start: 0.9075 (tm-30) cc_final: 0.7835 (tm-30) REVERT: D 592 LEU cc_start: 0.9309 (tp) cc_final: 0.9077 (tp) REVERT: D 595 ILE cc_start: 0.8039 (pt) cc_final: 0.7467 (pt) REVERT: D 617 LYS cc_start: 0.8466 (mmmm) cc_final: 0.7834 (tptm) REVERT: D 629 MET cc_start: 0.7930 (mmm) cc_final: 0.7694 (mmm) REVERT: D 651 ASN cc_start: 0.8779 (t0) cc_final: 0.8379 (t0) REVERT: E 37 THR cc_start: 0.8729 (m) cc_final: 0.8454 (p) REVERT: E 39 TYR cc_start: 0.7470 (m-80) cc_final: 0.7134 (m-10) REVERT: E 71 THR cc_start: 0.8695 (m) cc_final: 0.8469 (p) REVERT: E 86 LEU cc_start: 0.8932 (mp) cc_final: 0.8665 (tp) REVERT: E 98 ASN cc_start: 0.8341 (t0) cc_final: 0.8098 (t0) REVERT: E 179 LEU cc_start: 0.9120 (mt) cc_final: 0.8887 (tp) REVERT: E 330 HIS cc_start: 0.8733 (OUTLIER) cc_final: 0.8519 (p-80) REVERT: E 435 TYR cc_start: 0.7807 (t80) cc_final: 0.6663 (t80) REVERT: A 66 HIS cc_start: 0.8576 (m90) cc_final: 0.8269 (m90) REVERT: A 80 ASN cc_start: 0.7875 (t0) cc_final: 0.7519 (p0) REVERT: A 95 MET cc_start: 0.9113 (ppp) cc_final: 0.8877 (ppp) REVERT: A 133 ASP cc_start: 0.6984 (m-30) cc_final: 0.6433 (p0) REVERT: A 193 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8624 (mp) REVERT: A 195 ASN cc_start: 0.8946 (m-40) cc_final: 0.8063 (t0) REVERT: A 245 VAL cc_start: 0.8987 (OUTLIER) cc_final: 0.8756 (m) REVERT: A 302 ASN cc_start: 0.8666 (m-40) cc_final: 0.8347 (m110) REVERT: F 530 MET cc_start: 0.7929 (mtm) cc_final: 0.7382 (mtt) REVERT: F 618 THR cc_start: 0.8516 (OUTLIER) cc_final: 0.8247 (p) REVERT: F 621 MET cc_start: 0.9044 (mmt) cc_final: 0.8842 (mmm) REVERT: F 629 MET cc_start: 0.8860 (tpt) cc_final: 0.8639 (mmm) REVERT: F 632 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8279 (tm-30) REVERT: F 633 ARG cc_start: 0.8860 (mmm-85) cc_final: 0.8110 (mmm-85) REVERT: F 648 GLU cc_start: 0.9443 (pp20) cc_final: 0.9152 (pp20) REVERT: F 652 GLN cc_start: 0.9073 (tm-30) cc_final: 0.8780 (tm-30) outliers start: 58 outliers final: 8 residues processed: 494 average time/residue: 0.1282 time to fit residues: 94.0891 Evaluate side-chains 250 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 237 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain E residue 330 HIS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 627 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 8.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 554 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 ASN C 139 ASN ** C 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN D 624 ASN D 656 ASN E 67 ASN E 72 HIS E 195 ASN E 330 HIS E 428 GLN A 139 ASN A 246 GLN A 428 GLN ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN F 590 GLN ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.083052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.066460 restraints weight = 61677.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.068710 restraints weight = 33959.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.070248 restraints weight = 23142.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.071278 restraints weight = 17954.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.071910 restraints weight = 15177.517| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16682 Z= 0.196 Angle : 1.004 11.673 22922 Z= 0.450 Chirality : 0.055 0.539 2940 Planarity : 0.005 0.053 2668 Dihedral : 17.027 136.073 4945 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.37 % Favored : 92.40 % Rotamer: Outliers : 3.96 % Allowed : 14.64 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.19), residues: 1777 helix: 0.22 (0.25), residues: 431 sheet: -1.17 (0.24), residues: 462 loop : -2.27 (0.18), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 633 TYR 0.012 0.001 TYR F 638 PHE 0.018 0.002 PHE A 382 TRP 0.031 0.002 TRP B 571 HIS 0.008 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (16509) covalent geometry : angle 0.91943 / 0.43 (22436) SS BOND : bond 0.00475 / 0.21 ( 30) SS BOND : angle 0.96043 / 0.66 ( 60) hydrogen bonds : bond 0.06107 / 4.29 ( 505) hydrogen bonds : angle 6.08121 / 4.25 ( 1488) Misc. bond : bond 0.00505 / 0.27 ( 1) link_ALPHA1-2 : bond 0.00448 / 0.21 ( 2) link_ALPHA1-2 : angle 2.03010 / 0.84 ( 6) link_ALPHA1-3 : bond 0.02147 / 1.07 ( 4) link_ALPHA1-3 : angle 2.46518 / 1.20 ( 12) link_ALPHA1-6 : bond 0.01100 / 0.58 ( 5) link_ALPHA1-6 : angle 1.95072 / 0.92 ( 15) link_BETA1-4 : bond 0.00728 / 0.51 ( 61) link_BETA1-4 : angle 3.04576 / 2.26 ( 183) link_NAG-ASN : bond 0.00697 / 0.45 ( 70) link_NAG-ASN : angle 3.26662 / 2.49 ( 210) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 250 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.9017 (ttm) cc_final: 0.8197 (ttm) REVERT: B 557 ARG cc_start: 0.9229 (ttp80) cc_final: 0.8332 (ttp80) REVERT: B 588 ARG cc_start: 0.8873 (ttm170) cc_final: 0.8489 (ttm110) REVERT: B 601 LYS cc_start: 0.8832 (mmtm) cc_final: 0.8307 (mmtt) REVERT: B 622 ILE cc_start: 0.9434 (mm) cc_final: 0.8940 (mm) REVERT: B 628 TRP cc_start: 0.8943 (m100) cc_final: 0.8384 (m100) REVERT: B 629 MET cc_start: 0.8335 (mmm) cc_final: 0.8031 (mmm) REVERT: C 80 ASN cc_start: 0.7118 (t0) cc_final: 0.6713 (t0) REVERT: C 106 GLU cc_start: 0.9060 (pp20) cc_final: 0.8847 (tm-30) REVERT: C 244 THR cc_start: 0.9228 (m) cc_final: 0.9027 (p) REVERT: C 269 GLU cc_start: 0.8605 (pm20) cc_final: 0.8395 (pm20) REVERT: D 584 GLU cc_start: 0.8904 (tt0) cc_final: 0.8469 (mt-10) REVERT: D 617 LYS cc_start: 0.8602 (mmmm) cc_final: 0.8088 (mtpp) REVERT: D 629 MET cc_start: 0.7253 (mmm) cc_final: 0.6887 (mmm) REVERT: D 638 TYR cc_start: 0.8372 (m-80) cc_final: 0.8075 (m-10) REVERT: D 651 ASN cc_start: 0.8728 (t0) cc_final: 0.8414 (t0) REVERT: E 37 THR cc_start: 0.9003 (m) cc_final: 0.8598 (p) REVERT: E 71 THR cc_start: 0.8712 (m) cc_final: 0.8389 (t) REVERT: E 180 ASP cc_start: 0.7359 (m-30) cc_final: 0.7140 (m-30) REVERT: E 373 MET cc_start: 0.8273 (ptt) cc_final: 0.7735 (ppp) REVERT: A 80 ASN cc_start: 0.8108 (t0) cc_final: 0.7833 (p0) REVERT: A 104 MET cc_start: 0.9327 (OUTLIER) cc_final: 0.8903 (tmm) REVERT: A 180 ASP cc_start: 0.7951 (m-30) cc_final: 0.7738 (m-30) REVERT: A 195 ASN cc_start: 0.8580 (m-40) cc_final: 0.8079 (t0) REVERT: A 198 THR cc_start: 0.8852 (p) cc_final: 0.7954 (p) REVERT: A 373 MET cc_start: 0.8139 (ppp) cc_final: 0.7630 (ppp) REVERT: F 530 MET cc_start: 0.8187 (mtm) cc_final: 0.7688 (mtm) REVERT: F 543 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7105 (tm) REVERT: F 584 GLU cc_start: 0.8603 (mp0) cc_final: 0.8375 (mp0) REVERT: F 622 ILE cc_start: 0.9475 (pt) cc_final: 0.9153 (mm) REVERT: F 632 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8294 (tm-30) REVERT: F 633 ARG cc_start: 0.8930 (mmm-85) cc_final: 0.8589 (mmm-85) REVERT: F 652 GLN cc_start: 0.9066 (tm-30) cc_final: 0.8568 (tm-30) outliers start: 63 outliers final: 28 residues processed: 286 average time/residue: 0.1106 time to fit residues: 48.6473 Evaluate side-chains 221 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 400 TRP Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 542 ARG Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 636 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 139 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 135 optimal weight: 7.9990 chunk 76 optimal weight: 30.0000 chunk 35 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 126 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 554 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 HIS ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN D 651 ASN ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.077517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.061014 restraints weight = 64154.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.063070 restraints weight = 35397.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.064479 restraints weight = 24425.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.065410 restraints weight = 19190.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.065974 restraints weight = 16401.965| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.150 16682 Z= 0.260 Angle : 0.956 10.519 22922 Z= 0.437 Chirality : 0.053 0.337 2940 Planarity : 0.005 0.044 2668 Dihedral : 14.317 130.605 4934 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.82 % Favored : 92.01 % Rotamer: Outliers : 4.59 % Allowed : 17.02 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.19), residues: 1777 helix: 0.08 (0.24), residues: 435 sheet: -1.15 (0.22), residues: 489 loop : -2.24 (0.19), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 542 TYR 0.022 0.002 TYR D 586 PHE 0.020 0.002 PHE A 382 TRP 0.024 0.002 TRP D 596 HIS 0.016 0.002 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.26 (16509) covalent geometry : angle 0.89304 / 0.42 (22436) SS BOND : bond 0.00386 / 0.20 ( 30) SS BOND : angle 1.70545 / 1.06 ( 60) hydrogen bonds : bond 0.05737 / 4.01 ( 505) hydrogen bonds : angle 5.71968 / 4.03 ( 1488) Misc. bond : bond 0.00242 / 0.13 ( 1) link_ALPHA1-2 : bond 0.00283 / 0.15 ( 2) link_ALPHA1-2 : angle 1.97605 / 0.79 ( 6) link_ALPHA1-3 : bond 0.02333 / 1.17 ( 4) link_ALPHA1-3 : angle 2.26539 / 1.13 ( 12) link_ALPHA1-6 : bond 0.01260 / 0.63 ( 5) link_ALPHA1-6 : angle 1.44921 / 0.74 ( 15) link_BETA1-4 : bond 0.00701 / 0.48 ( 61) link_BETA1-4 : angle 2.66693 / 1.99 ( 183) link_NAG-ASN : bond 0.00620 / 0.40 ( 70) link_NAG-ASN : angle 2.62943 / 1.95 ( 210) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 200 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.9070 (ttm) cc_final: 0.8452 (ttm) REVERT: B 543 LEU cc_start: 0.9460 (mt) cc_final: 0.8981 (pp) REVERT: B 560 GLU cc_start: 0.9004 (pp20) cc_final: 0.8364 (tp30) REVERT: B 588 ARG cc_start: 0.8798 (ttm170) cc_final: 0.8368 (ttm110) REVERT: B 622 ILE cc_start: 0.9567 (mm) cc_final: 0.9192 (mm) REVERT: B 629 MET cc_start: 0.8406 (mmm) cc_final: 0.8083 (mmm) REVERT: C 80 ASN cc_start: 0.7265 (t0) cc_final: 0.6793 (t0) REVERT: C 104 MET cc_start: 0.9467 (tmm) cc_final: 0.9166 (tmm) REVERT: C 106 GLU cc_start: 0.9178 (pp20) cc_final: 0.8972 (tm-30) REVERT: C 244 THR cc_start: 0.9214 (m) cc_final: 0.9003 (p) REVERT: C 373 MET cc_start: 0.8358 (tmm) cc_final: 0.8114 (tmm) REVERT: D 542 ARG cc_start: 0.8287 (mtt-85) cc_final: 0.7993 (ptp-110) REVERT: D 606 THR cc_start: 0.7175 (t) cc_final: 0.6891 (t) REVERT: D 621 MET cc_start: 0.8745 (ppp) cc_final: 0.8487 (ppp) REVERT: D 629 MET cc_start: 0.7911 (mmm) cc_final: 0.7611 (mmm) REVERT: D 638 TYR cc_start: 0.8600 (m-80) cc_final: 0.8351 (m-10) REVERT: D 651 ASN cc_start: 0.8728 (t160) cc_final: 0.8433 (t0) REVERT: E 37 THR cc_start: 0.9122 (m) cc_final: 0.8454 (p) REVERT: E 71 THR cc_start: 0.8852 (m) cc_final: 0.8636 (p) REVERT: E 373 MET cc_start: 0.8704 (ptt) cc_final: 0.8440 (ptt) REVERT: A 40 TYR cc_start: 0.8842 (t80) cc_final: 0.8266 (t80) REVERT: A 104 MET cc_start: 0.9238 (tmm) cc_final: 0.8826 (tmm) REVERT: A 180 ASP cc_start: 0.8235 (m-30) cc_final: 0.8019 (m-30) REVERT: A 195 ASN cc_start: 0.8452 (m-40) cc_final: 0.7780 (t0) REVERT: A 198 THR cc_start: 0.9125 (p) cc_final: 0.8103 (p) REVERT: A 255 VAL cc_start: 0.9094 (OUTLIER) cc_final: 0.8830 (t) REVERT: A 373 MET cc_start: 0.8026 (ppp) cc_final: 0.7580 (ppp) REVERT: A 394 THR cc_start: 0.8846 (p) cc_final: 0.8625 (t) REVERT: A 475 MET cc_start: 0.9135 (tpp) cc_final: 0.8686 (tpp) REVERT: F 520 LEU cc_start: 0.3507 (OUTLIER) cc_final: 0.3211 (tt) REVERT: F 530 MET cc_start: 0.8781 (mtm) cc_final: 0.8152 (mtm) REVERT: F 577 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8687 (mm-40) REVERT: F 632 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8201 (tm-30) REVERT: F 633 ARG cc_start: 0.8997 (mmm-85) cc_final: 0.8624 (mmm-85) REVERT: F 647 GLU cc_start: 0.8963 (tp30) cc_final: 0.8744 (tp30) outliers start: 73 outliers final: 38 residues processed: 253 average time/residue: 0.0953 time to fit residues: 38.0476 Evaluate side-chains 217 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain D residue 633 ARG Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 388 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 636 ASP Chi-restraints excluded: chain F residue 637 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 30 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 72 optimal weight: 0.4980 chunk 82 optimal weight: 0.9990 chunk 159 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 554 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN C 103 GLN C 343 ASN ** C 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.079029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.062605 restraints weight = 62807.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.064727 restraints weight = 34441.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.066191 restraints weight = 23640.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.067159 restraints weight = 18440.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.067789 restraints weight = 15664.576| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16682 Z= 0.142 Angle : 0.844 15.308 22922 Z= 0.381 Chirality : 0.050 0.326 2940 Planarity : 0.005 0.133 2668 Dihedral : 13.378 129.563 4933 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.98 % Favored : 92.85 % Rotamer: Outliers : 3.39 % Allowed : 19.47 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.19), residues: 1777 helix: 0.45 (0.25), residues: 418 sheet: -1.01 (0.23), residues: 468 loop : -2.14 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 166 TYR 0.032 0.001 TYR B 643 PHE 0.013 0.001 PHE C 468 TRP 0.015 0.002 TRP C 400 HIS 0.005 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (16509) covalent geometry : angle 0.78933 / 0.37 (22436) SS BOND : bond 0.00356 / 0.17 ( 30) SS BOND : angle 1.00378 / 0.62 ( 60) hydrogen bonds : bond 0.05089 / 3.58 ( 505) hydrogen bonds : angle 5.39196 / 3.80 ( 1488) Misc. bond : bond 0.00803 / 0.42 ( 1) link_ALPHA1-2 : bond 0.00204 / 0.10 ( 2) link_ALPHA1-2 : angle 2.04364 / 0.84 ( 6) link_ALPHA1-3 : bond 0.02152 / 1.08 ( 4) link_ALPHA1-3 : angle 2.25060 / 1.11 ( 12) link_ALPHA1-6 : bond 0.01184 / 0.61 ( 5) link_ALPHA1-6 : angle 1.36470 / 0.68 ( 15) link_BETA1-4 : bond 0.00641 / 0.44 ( 61) link_BETA1-4 : angle 2.42591 / 1.83 ( 183) link_NAG-ASN : bond 0.00463 / 0.28 ( 70) link_NAG-ASN : angle 2.28594 / 1.69 ( 210) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 207 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.9087 (ttm) cc_final: 0.8570 (ttm) REVERT: B 543 LEU cc_start: 0.9515 (mt) cc_final: 0.8975 (pp) REVERT: B 588 ARG cc_start: 0.8911 (ttm170) cc_final: 0.8411 (ttm110) REVERT: B 629 MET cc_start: 0.8394 (mmm) cc_final: 0.8016 (mmm) REVERT: C 80 ASN cc_start: 0.7266 (t0) cc_final: 0.6797 (t0) REVERT: C 95 MET cc_start: 0.8682 (ppp) cc_final: 0.8221 (ppp) REVERT: C 106 GLU cc_start: 0.9176 (pp20) cc_final: 0.8949 (tm-30) REVERT: C 211 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8024 (tm-30) REVERT: C 373 MET cc_start: 0.8191 (tmm) cc_final: 0.7930 (tmm) REVERT: D 603 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8487 (tt) REVERT: D 621 MET cc_start: 0.8709 (ppp) cc_final: 0.8475 (ppp) REVERT: D 638 TYR cc_start: 0.8504 (m-80) cc_final: 0.8266 (m-10) REVERT: D 651 ASN cc_start: 0.8621 (t160) cc_final: 0.8220 (t0) REVERT: E 37 THR cc_start: 0.9049 (m) cc_final: 0.8407 (p) REVERT: E 95 MET cc_start: 0.9082 (ptt) cc_final: 0.8869 (ppp) REVERT: E 373 MET cc_start: 0.8728 (ptt) cc_final: 0.8492 (ptt) REVERT: E 426 MET cc_start: 0.8612 (tpp) cc_final: 0.7845 (mmt) REVERT: A 40 TYR cc_start: 0.8828 (t80) cc_final: 0.8288 (t80) REVERT: A 195 ASN cc_start: 0.8354 (m-40) cc_final: 0.7907 (t0) REVERT: A 198 THR cc_start: 0.9100 (p) cc_final: 0.8244 (p) REVERT: A 373 MET cc_start: 0.8151 (ppp) cc_final: 0.7538 (ppp) REVERT: A 475 MET cc_start: 0.9062 (tpp) cc_final: 0.8638 (tpp) REVERT: F 530 MET cc_start: 0.8754 (mtm) cc_final: 0.7971 (mtm) REVERT: F 577 GLN cc_start: 0.9158 (mm-40) cc_final: 0.8744 (mm-40) REVERT: F 584 GLU cc_start: 0.8749 (mp0) cc_final: 0.8532 (mp0) REVERT: F 618 THR cc_start: 0.9354 (m) cc_final: 0.9100 (p) REVERT: F 629 MET cc_start: 0.8888 (mmm) cc_final: 0.8618 (mmm) REVERT: F 632 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8178 (tm-30) REVERT: F 633 ARG cc_start: 0.8940 (mmm-85) cc_final: 0.8527 (mmm-85) REVERT: F 647 GLU cc_start: 0.8985 (tp30) cc_final: 0.8693 (tp30) REVERT: F 652 GLN cc_start: 0.9060 (tm-30) cc_final: 0.8646 (tm-30) outliers start: 54 outliers final: 29 residues processed: 240 average time/residue: 0.1191 time to fit residues: 44.3043 Evaluate side-chains 213 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 636 ASP Chi-restraints excluded: chain F residue 637 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 45 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 156 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 136 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 55.8332 > 50:) overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 554 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN ** C 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.075887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.059622 restraints weight = 64446.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.061598 restraints weight = 35747.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.062938 restraints weight = 24689.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.063824 restraints weight = 19483.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.064417 restraints weight = 16723.490| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 16682 Z= 0.230 Angle : 0.884 12.322 22922 Z= 0.406 Chirality : 0.051 0.341 2940 Planarity : 0.005 0.131 2668 Dihedral : 12.829 129.293 4926 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.27 % Favored : 91.67 % Rotamer: Outliers : 4.33 % Allowed : 20.23 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.19), residues: 1777 helix: 0.47 (0.25), residues: 414 sheet: -1.09 (0.22), residues: 513 loop : -2.12 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG E 166 TYR 0.023 0.001 TYR B 643 PHE 0.017 0.002 PHE A 382 TRP 0.029 0.002 TRP E 69 HIS 0.012 0.002 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.23 (16509) covalent geometry : angle 0.83008 / 0.39 (22436) SS BOND : bond 0.00344 / 0.18 ( 30) SS BOND : angle 1.35473 / 0.73 ( 60) hydrogen bonds : bond 0.05317 / 3.73 ( 505) hydrogen bonds : angle 5.41736 / 3.83 ( 1488) Misc. bond : bond 0.00169 / 0.09 ( 1) link_ALPHA1-2 : bond 0.00094 / 0.05 ( 2) link_ALPHA1-2 : angle 2.11028 / 0.87 ( 6) link_ALPHA1-3 : bond 0.02364 / 1.18 ( 4) link_ALPHA1-3 : angle 2.70793 / 1.35 ( 12) link_ALPHA1-6 : bond 0.01183 / 0.60 ( 5) link_ALPHA1-6 : angle 1.48176 / 0.87 ( 15) link_BETA1-4 : bond 0.00644 / 0.43 ( 61) link_BETA1-4 : angle 2.41127 / 1.85 ( 183) link_NAG-ASN : bond 0.00504 / 0.34 ( 70) link_NAG-ASN : angle 2.33983 / 1.73 ( 210) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 181 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8931 (ttm) cc_final: 0.8496 (ttm) REVERT: B 553 ASN cc_start: 0.9002 (t0) cc_final: 0.8662 (m-40) REVERT: B 588 ARG cc_start: 0.8918 (ttm170) cc_final: 0.8381 (ttm110) REVERT: B 606 THR cc_start: 0.9326 (t) cc_final: 0.9049 (p) REVERT: B 629 MET cc_start: 0.8526 (mmm) cc_final: 0.8084 (mmm) REVERT: B 643 TYR cc_start: 0.8996 (m-80) cc_final: 0.8645 (m-80) REVERT: C 80 ASN cc_start: 0.7226 (t0) cc_final: 0.6701 (t0) REVERT: C 211 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7996 (tm-30) REVERT: D 629 MET cc_start: 0.7757 (mmm) cc_final: 0.7527 (mmm) REVERT: D 638 TYR cc_start: 0.8740 (m-80) cc_final: 0.8484 (m-10) REVERT: D 651 ASN cc_start: 0.8728 (t160) cc_final: 0.8409 (t0) REVERT: E 426 MET cc_start: 0.8696 (tpp) cc_final: 0.8232 (mpp) REVERT: A 40 TYR cc_start: 0.8976 (t80) cc_final: 0.8089 (t80) REVERT: A 104 MET cc_start: 0.9270 (OUTLIER) cc_final: 0.8905 (tmm) REVERT: A 195 ASN cc_start: 0.8402 (m-40) cc_final: 0.7676 (t0) REVERT: A 198 THR cc_start: 0.9221 (p) cc_final: 0.8275 (p) REVERT: A 373 MET cc_start: 0.8065 (ppp) cc_final: 0.7510 (ppp) REVERT: A 390 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9063 (mt) REVERT: A 426 MET cc_start: 0.8717 (mmm) cc_final: 0.8189 (mmm) REVERT: F 530 MET cc_start: 0.8868 (mtm) cc_final: 0.8132 (mtm) REVERT: F 575 GLN cc_start: 0.8956 (pp30) cc_final: 0.8551 (pp30) REVERT: F 577 GLN cc_start: 0.9198 (mm-40) cc_final: 0.8780 (mm-40) REVERT: F 584 GLU cc_start: 0.8850 (mp0) cc_final: 0.8596 (mp0) REVERT: F 618 THR cc_start: 0.9157 (m) cc_final: 0.8845 (p) REVERT: F 629 MET cc_start: 0.8928 (mmm) cc_final: 0.8664 (mmm) REVERT: F 632 GLU cc_start: 0.8384 (tm-30) cc_final: 0.8169 (tm-30) REVERT: F 633 ARG cc_start: 0.9039 (mmm-85) cc_final: 0.8635 (mmm-85) REVERT: F 652 GLN cc_start: 0.9035 (tm-30) cc_final: 0.8614 (tm-30) outliers start: 69 outliers final: 44 residues processed: 230 average time/residue: 0.1168 time to fit residues: 42.0020 Evaluate side-chains 219 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 173 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 535 ILE Chi-restraints excluded: chain D residue 550 GLN Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 388 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 124 PRO Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 636 ASP Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 646 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 84 optimal weight: 9.9990 chunk 152 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 125 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.076110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.059808 restraints weight = 64423.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.061784 restraints weight = 35650.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.063125 restraints weight = 24763.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.064019 restraints weight = 19567.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.064598 restraints weight = 16795.097| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.5239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16682 Z= 0.183 Angle : 0.850 15.478 22922 Z= 0.389 Chirality : 0.050 0.340 2940 Planarity : 0.006 0.215 2668 Dihedral : 12.352 130.692 4924 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.99 % Favored : 91.95 % Rotamer: Outliers : 3.20 % Allowed : 22.68 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.19), residues: 1777 helix: 0.57 (0.25), residues: 408 sheet: -1.02 (0.22), residues: 513 loop : -2.14 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 166 TYR 0.021 0.001 TYR B 643 PHE 0.024 0.001 PHE F 522 TRP 0.024 0.002 TRP E 69 HIS 0.011 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (16509) covalent geometry : angle 0.79631 / 0.38 (22436) SS BOND : bond 0.00376 / 0.18 ( 30) SS BOND : angle 1.88220 / 0.82 ( 60) hydrogen bonds : bond 0.05124 / 3.60 ( 505) hydrogen bonds : angle 5.27567 / 3.73 ( 1488) Misc. bond : bond 0.01143 / 0.60 ( 1) link_ALPHA1-2 : bond 0.00150 / 0.07 ( 2) link_ALPHA1-2 : angle 2.03973 / 0.84 ( 6) link_ALPHA1-3 : bond 0.01999 / 1.00 ( 4) link_ALPHA1-3 : angle 2.42834 / 1.20 ( 12) link_ALPHA1-6 : bond 0.01115 / 0.56 ( 5) link_ALPHA1-6 : angle 1.68741 / 1.17 ( 15) link_BETA1-4 : bond 0.00649 / 0.43 ( 61) link_BETA1-4 : angle 2.29819 / 1.78 ( 183) link_NAG-ASN : bond 0.00434 / 0.29 ( 70) link_NAG-ASN : angle 2.18654 / 1.62 ( 210) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 189 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8910 (ttm) cc_final: 0.8490 (ttm) REVERT: B 543 LEU cc_start: 0.9528 (mt) cc_final: 0.8951 (pp) REVERT: B 588 ARG cc_start: 0.8863 (ttm170) cc_final: 0.8586 (ttm170) REVERT: B 606 THR cc_start: 0.9363 (t) cc_final: 0.9083 (p) REVERT: B 629 MET cc_start: 0.8479 (mmm) cc_final: 0.8055 (mmm) REVERT: B 656 ASN cc_start: 0.8871 (t0) cc_final: 0.8603 (t0) REVERT: C 80 ASN cc_start: 0.7272 (t0) cc_final: 0.6726 (t0) REVERT: C 211 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7886 (tm-30) REVERT: D 629 MET cc_start: 0.7749 (mmm) cc_final: 0.7511 (mmm) REVERT: D 638 TYR cc_start: 0.8726 (m-80) cc_final: 0.8480 (m-10) REVERT: D 651 ASN cc_start: 0.8747 (t160) cc_final: 0.8329 (t0) REVERT: E 37 THR cc_start: 0.9157 (m) cc_final: 0.8535 (p) REVERT: E 426 MET cc_start: 0.8597 (tpp) cc_final: 0.8116 (mpp) REVERT: A 40 TYR cc_start: 0.8984 (t80) cc_final: 0.8775 (t80) REVERT: A 195 ASN cc_start: 0.8436 (m-40) cc_final: 0.7595 (t0) REVERT: A 198 THR cc_start: 0.9202 (p) cc_final: 0.8414 (p) REVERT: A 373 MET cc_start: 0.8275 (ppp) cc_final: 0.7700 (ppp) REVERT: A 475 MET cc_start: 0.9195 (tpp) cc_final: 0.8527 (tpp) REVERT: F 530 MET cc_start: 0.8868 (mtm) cc_final: 0.8127 (mtm) REVERT: F 575 GLN cc_start: 0.8942 (pp30) cc_final: 0.8507 (pp30) REVERT: F 584 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8514 (mp0) REVERT: F 595 ILE cc_start: 0.9280 (mm) cc_final: 0.9066 (mm) REVERT: F 618 THR cc_start: 0.8943 (m) cc_final: 0.8680 (p) REVERT: F 620 ASP cc_start: 0.8502 (p0) cc_final: 0.8235 (p0) REVERT: F 629 MET cc_start: 0.8952 (mmm) cc_final: 0.8692 (mmm) REVERT: F 632 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8229 (tm-30) REVERT: F 633 ARG cc_start: 0.9071 (mmm-85) cc_final: 0.8651 (mmm-85) REVERT: F 652 GLN cc_start: 0.9028 (tm-30) cc_final: 0.8587 (tm-30) outliers start: 51 outliers final: 45 residues processed: 222 average time/residue: 0.1185 time to fit residues: 41.3452 Evaluate side-chains 221 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 175 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 388 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 636 ASP Chi-restraints excluded: chain F residue 637 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 128 optimal weight: 30.0000 chunk 164 optimal weight: 0.5980 chunk 72 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 554 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.075833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.059602 restraints weight = 64332.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.061541 restraints weight = 35720.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.062885 restraints weight = 24774.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.063768 restraints weight = 19565.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.064340 restraints weight = 16820.408| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16682 Z= 0.175 Angle : 0.841 18.764 22922 Z= 0.384 Chirality : 0.049 0.328 2940 Planarity : 0.006 0.213 2668 Dihedral : 11.621 124.342 4924 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.44 % Favored : 91.50 % Rotamer: Outliers : 3.96 % Allowed : 22.17 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.19), residues: 1777 helix: 0.70 (0.25), residues: 403 sheet: -0.91 (0.22), residues: 501 loop : -2.10 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 166 TYR 0.022 0.001 TYR B 643 PHE 0.011 0.001 PHE E 382 TRP 0.026 0.002 TRP C 400 HIS 0.010 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (16509) covalent geometry : angle 0.79375 / 0.37 (22436) SS BOND : bond 0.00626 / 0.42 ( 30) SS BOND : angle 1.31006 / 0.64 ( 60) hydrogen bonds : bond 0.04955 / 3.47 ( 505) hydrogen bonds : angle 5.15454 / 3.63 ( 1488) Misc. bond : bond 0.00592 / 0.31 ( 1) link_ALPHA1-2 : bond 0.00161 / 0.08 ( 2) link_ALPHA1-2 : angle 2.01507 / 0.83 ( 6) link_ALPHA1-3 : bond 0.02088 / 1.04 ( 4) link_ALPHA1-3 : angle 2.34183 / 1.16 ( 12) link_ALPHA1-6 : bond 0.01014 / 0.51 ( 5) link_ALPHA1-6 : angle 1.84115 / 1.34 ( 15) link_BETA1-4 : bond 0.00645 / 0.43 ( 61) link_BETA1-4 : angle 2.22940 / 1.74 ( 183) link_NAG-ASN : bond 0.00417 / 0.28 ( 70) link_NAG-ASN : angle 2.08157 / 1.53 ( 210) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 189 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8860 (ttm) cc_final: 0.8483 (ttm) REVERT: B 542 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8446 (ttt180) REVERT: B 588 ARG cc_start: 0.8885 (ttm170) cc_final: 0.8586 (ttm170) REVERT: B 606 THR cc_start: 0.9362 (t) cc_final: 0.9089 (p) REVERT: B 629 MET cc_start: 0.8478 (mmm) cc_final: 0.8057 (mmm) REVERT: B 636 ASP cc_start: 0.9137 (t0) cc_final: 0.8550 (p0) REVERT: B 643 TYR cc_start: 0.9105 (m-80) cc_final: 0.8743 (m-80) REVERT: B 656 ASN cc_start: 0.8776 (t0) cc_final: 0.8414 (t0) REVERT: C 80 ASN cc_start: 0.7266 (t0) cc_final: 0.6702 (t0) REVERT: C 103 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8646 (tm-30) REVERT: C 133 ASP cc_start: 0.8649 (m-30) cc_final: 0.8158 (t70) REVERT: C 211 GLU cc_start: 0.8343 (tm-30) cc_final: 0.8010 (tm-30) REVERT: C 373 MET cc_start: 0.8352 (tmm) cc_final: 0.8019 (tmm) REVERT: D 599 SER cc_start: 0.7912 (OUTLIER) cc_final: 0.7646 (m) REVERT: D 638 TYR cc_start: 0.8896 (m-80) cc_final: 0.8646 (m-10) REVERT: D 651 ASN cc_start: 0.8787 (t160) cc_final: 0.8445 (t0) REVERT: E 37 THR cc_start: 0.9175 (m) cc_final: 0.8611 (p) REVERT: A 40 TYR cc_start: 0.8988 (t80) cc_final: 0.8021 (t80) REVERT: A 195 ASN cc_start: 0.8263 (m-40) cc_final: 0.7684 (t0) REVERT: A 198 THR cc_start: 0.9230 (p) cc_final: 0.8453 (p) REVERT: A 302 ASN cc_start: 0.9102 (m-40) cc_final: 0.8713 (m-40) REVERT: A 373 MET cc_start: 0.8290 (ppp) cc_final: 0.7654 (ppp) REVERT: A 406 ASN cc_start: 0.8029 (OUTLIER) cc_final: 0.7648 (m110) REVERT: A 475 MET cc_start: 0.9198 (tpp) cc_final: 0.8627 (tpp) REVERT: F 530 MET cc_start: 0.8762 (mtm) cc_final: 0.8159 (mtm) REVERT: F 543 LEU cc_start: 0.8299 (mt) cc_final: 0.8001 (mt) REVERT: F 575 GLN cc_start: 0.9049 (pp30) cc_final: 0.8472 (pp30) REVERT: F 577 GLN cc_start: 0.9081 (mm-40) cc_final: 0.8869 (mm-40) REVERT: F 584 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8515 (mp0) REVERT: F 618 THR cc_start: 0.8963 (m) cc_final: 0.8694 (p) REVERT: F 620 ASP cc_start: 0.8513 (p0) cc_final: 0.7991 (p0) REVERT: F 629 MET cc_start: 0.8950 (mmm) cc_final: 0.8695 (mmm) REVERT: F 632 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8211 (tm-30) REVERT: F 633 ARG cc_start: 0.9069 (mmm-85) cc_final: 0.8649 (mmm-85) outliers start: 63 outliers final: 46 residues processed: 236 average time/residue: 0.1166 time to fit residues: 42.5824 Evaluate side-chains 225 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 174 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 388 THR Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 636 ASP Chi-restraints excluded: chain F residue 637 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 45 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 chunk 118 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 564 HIS ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.074709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.058601 restraints weight = 65075.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.060523 restraints weight = 36165.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.061839 restraints weight = 25147.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.062703 restraints weight = 19862.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.063255 restraints weight = 17090.172| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.5791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 16682 Z= 0.207 Angle : 0.864 18.250 22922 Z= 0.398 Chirality : 0.050 0.332 2940 Planarity : 0.006 0.227 2668 Dihedral : 10.965 121.585 4924 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.61 % Favored : 91.28 % Rotamer: Outliers : 4.02 % Allowed : 22.61 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.19), residues: 1777 helix: 0.65 (0.25), residues: 403 sheet: -0.82 (0.23), residues: 489 loop : -2.10 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG E 166 TYR 0.020 0.001 TYR B 643 PHE 0.014 0.001 PHE A 382 TRP 0.029 0.002 TRP E 69 HIS 0.012 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.21 (16509) covalent geometry : angle 0.81454 / 0.39 (22436) SS BOND : bond 0.00346 / 0.18 ( 30) SS BOND : angle 2.05727 / 0.98 ( 60) hydrogen bonds : bond 0.05178 / 3.63 ( 505) hydrogen bonds : angle 5.19865 / 3.67 ( 1488) Misc. bond : bond 0.00953 / 0.50 ( 1) link_ALPHA1-2 : bond 0.00175 / 0.08 ( 2) link_ALPHA1-2 : angle 1.97759 / 0.81 ( 6) link_ALPHA1-3 : bond 0.01885 / 0.94 ( 4) link_ALPHA1-3 : angle 2.40416 / 1.20 ( 12) link_ALPHA1-6 : bond 0.00906 / 0.46 ( 5) link_ALPHA1-6 : angle 1.58401 / 1.06 ( 15) link_BETA1-4 : bond 0.00658 / 0.44 ( 61) link_BETA1-4 : angle 2.23932 / 1.75 ( 183) link_NAG-ASN : bond 0.00436 / 0.30 ( 70) link_NAG-ASN : angle 2.11320 / 1.54 ( 210) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 177 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8850 (ttm) cc_final: 0.8504 (ttm) REVERT: B 588 ARG cc_start: 0.8838 (ttm170) cc_final: 0.8506 (ttm170) REVERT: B 606 THR cc_start: 0.9409 (t) cc_final: 0.9138 (p) REVERT: B 629 MET cc_start: 0.8382 (mmm) cc_final: 0.7960 (mmm) REVERT: B 643 TYR cc_start: 0.9094 (m-80) cc_final: 0.8691 (m-80) REVERT: B 656 ASN cc_start: 0.8807 (t0) cc_final: 0.8516 (t0) REVERT: C 80 ASN cc_start: 0.7339 (t0) cc_final: 0.6737 (t0) REVERT: C 103 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8663 (tm-30) REVERT: C 133 ASP cc_start: 0.8612 (m-30) cc_final: 0.8133 (t70) REVERT: C 211 GLU cc_start: 0.8356 (tm-30) cc_final: 0.8013 (tm-30) REVERT: D 599 SER cc_start: 0.7964 (OUTLIER) cc_final: 0.7686 (m) REVERT: D 638 TYR cc_start: 0.8972 (m-80) cc_final: 0.8721 (m-10) REVERT: D 651 ASN cc_start: 0.8808 (t160) cc_final: 0.8455 (t0) REVERT: E 373 MET cc_start: 0.9008 (ptt) cc_final: 0.8445 (ptm) REVERT: E 426 MET cc_start: 0.8245 (tpp) cc_final: 0.8037 (mmm) REVERT: A 195 ASN cc_start: 0.8392 (m-40) cc_final: 0.7730 (t0) REVERT: A 198 THR cc_start: 0.9280 (p) cc_final: 0.8690 (p) REVERT: A 373 MET cc_start: 0.8271 (ppp) cc_final: 0.7677 (ppp) REVERT: A 390 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9125 (mt) REVERT: A 406 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7598 (m110) REVERT: A 429 GLU cc_start: 0.9079 (tp30) cc_final: 0.8511 (mp0) REVERT: A 475 MET cc_start: 0.9188 (tpp) cc_final: 0.8757 (tpp) REVERT: F 520 LEU cc_start: 0.5498 (OUTLIER) cc_final: 0.5224 (tt) REVERT: F 530 MET cc_start: 0.8795 (mtm) cc_final: 0.8224 (mtm) REVERT: F 543 LEU cc_start: 0.8316 (mt) cc_final: 0.8098 (mt) REVERT: F 575 GLN cc_start: 0.9075 (pp30) cc_final: 0.8582 (pp30) REVERT: F 577 GLN cc_start: 0.9102 (mm-40) cc_final: 0.8885 (mm-40) REVERT: F 584 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8553 (pm20) REVERT: F 618 THR cc_start: 0.9015 (m) cc_final: 0.8739 (p) REVERT: F 620 ASP cc_start: 0.8540 (p0) cc_final: 0.8166 (p0) REVERT: F 629 MET cc_start: 0.8916 (mmm) cc_final: 0.8562 (mmm) REVERT: F 633 ARG cc_start: 0.9092 (mmm-85) cc_final: 0.8658 (mmm-85) outliers start: 64 outliers final: 49 residues processed: 225 average time/residue: 0.1077 time to fit residues: 38.3704 Evaluate side-chains 226 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 171 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 388 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 124 PRO Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 636 ASP Chi-restraints excluded: chain F residue 637 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 112 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 554 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 564 HIS ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.075014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.059136 restraints weight = 64214.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.061086 restraints weight = 35533.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.062372 restraints weight = 24535.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.063246 restraints weight = 19430.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.063822 restraints weight = 16642.021| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.5926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16682 Z= 0.167 Angle : 0.839 18.995 22922 Z= 0.386 Chirality : 0.049 0.326 2940 Planarity : 0.006 0.253 2668 Dihedral : 10.331 118.693 4924 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.38 % Favored : 91.56 % Rotamer: Outliers : 3.64 % Allowed : 22.80 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.20), residues: 1777 helix: 0.74 (0.26), residues: 403 sheet: -0.74 (0.23), residues: 489 loop : -2.07 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG E 166 TYR 0.023 0.001 TYR B 643 PHE 0.012 0.001 PHE A 382 TRP 0.025 0.002 TRP C 400 HIS 0.006 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (16509) covalent geometry : angle 0.79333 / 0.38 (22436) SS BOND : bond 0.00357 / 0.18 ( 30) SS BOND : angle 1.68778 / 0.80 ( 60) hydrogen bonds : bond 0.04959 / 3.48 ( 505) hydrogen bonds : angle 5.06982 / 3.58 ( 1488) Misc. bond : bond 0.01360 / 0.72 ( 1) link_ALPHA1-2 : bond 0.00245 / 0.12 ( 2) link_ALPHA1-2 : angle 2.00763 / 0.83 ( 6) link_ALPHA1-3 : bond 0.01737 / 0.87 ( 4) link_ALPHA1-3 : angle 2.16986 / 1.07 ( 12) link_ALPHA1-6 : bond 0.00865 / 0.44 ( 5) link_ALPHA1-6 : angle 1.52036 / 0.98 ( 15) link_BETA1-4 : bond 0.00646 / 0.43 ( 61) link_BETA1-4 : angle 2.17430 / 1.71 ( 183) link_NAG-ASN : bond 0.00395 / 0.27 ( 70) link_NAG-ASN : angle 2.01240 / 1.47 ( 210) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 177 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8822 (ttm) cc_final: 0.8505 (ttm) REVERT: B 542 ARG cc_start: 0.8844 (ttt180) cc_final: 0.8156 (ttt180) REVERT: B 588 ARG cc_start: 0.8852 (ttm170) cc_final: 0.8515 (ttm170) REVERT: B 606 THR cc_start: 0.9412 (t) cc_final: 0.9155 (p) REVERT: B 643 TYR cc_start: 0.9152 (m-80) cc_final: 0.8930 (m-80) REVERT: B 656 ASN cc_start: 0.8794 (t0) cc_final: 0.8439 (t0) REVERT: C 80 ASN cc_start: 0.7370 (t0) cc_final: 0.6751 (t0) REVERT: C 103 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8644 (tm-30) REVERT: C 133 ASP cc_start: 0.8553 (m-30) cc_final: 0.8186 (t70) REVERT: C 211 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8012 (tm-30) REVERT: C 373 MET cc_start: 0.8102 (tmm) cc_final: 0.7783 (tmm) REVERT: C 426 MET cc_start: 0.8276 (tpp) cc_final: 0.7569 (mmt) REVERT: D 540 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8030 (tp-100) REVERT: D 599 SER cc_start: 0.7931 (OUTLIER) cc_final: 0.7671 (m) REVERT: D 651 ASN cc_start: 0.8827 (t160) cc_final: 0.8487 (t0) REVERT: E 37 THR cc_start: 0.9209 (m) cc_final: 0.8694 (p) REVERT: E 373 MET cc_start: 0.8989 (ptt) cc_final: 0.8486 (ptm) REVERT: A 40 TYR cc_start: 0.9053 (t80) cc_final: 0.8098 (t80) REVERT: A 195 ASN cc_start: 0.8365 (m-40) cc_final: 0.7697 (t0) REVERT: A 198 THR cc_start: 0.9282 (p) cc_final: 0.8725 (p) REVERT: A 373 MET cc_start: 0.8269 (ppp) cc_final: 0.7660 (ppp) REVERT: A 390 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9118 (mt) REVERT: A 406 ASN cc_start: 0.7992 (OUTLIER) cc_final: 0.7588 (m110) REVERT: A 429 GLU cc_start: 0.9085 (tp30) cc_final: 0.8527 (mp0) REVERT: A 475 MET cc_start: 0.9143 (tpp) cc_final: 0.8508 (tpp) REVERT: F 520 LEU cc_start: 0.5435 (OUTLIER) cc_final: 0.5192 (tt) REVERT: F 543 LEU cc_start: 0.8281 (mt) cc_final: 0.8059 (mt) REVERT: F 575 GLN cc_start: 0.9073 (pp30) cc_final: 0.8486 (pp30) REVERT: F 577 GLN cc_start: 0.9103 (mm-40) cc_final: 0.8900 (mm-40) REVERT: F 584 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8533 (pm20) REVERT: F 618 THR cc_start: 0.8981 (m) cc_final: 0.8660 (p) REVERT: F 633 ARG cc_start: 0.9030 (mmm-85) cc_final: 0.8691 (mmm-85) outliers start: 58 outliers final: 45 residues processed: 220 average time/residue: 0.1030 time to fit residues: 35.8976 Evaluate side-chains 218 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 166 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 388 THR Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 636 ASP Chi-restraints excluded: chain F residue 637 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 16 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 154 optimal weight: 9.9990 chunk 145 optimal weight: 9.9990 chunk 147 optimal weight: 6.9990 chunk 27 optimal weight: 0.2980 chunk 59 optimal weight: 0.0970 chunk 119 optimal weight: 20.0000 chunk 127 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 554 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 461 ASN F 564 HIS ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.075640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.059537 restraints weight = 64549.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.061506 restraints weight = 35563.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.062843 restraints weight = 24611.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.063725 restraints weight = 19365.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.064283 restraints weight = 16631.916| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.6019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 16682 Z= 0.144 Angle : 0.828 19.286 22922 Z= 0.384 Chirality : 0.049 0.328 2940 Planarity : 0.007 0.285 2668 Dihedral : 10.012 115.704 4924 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.33 % Favored : 91.62 % Rotamer: Outliers : 3.14 % Allowed : 23.49 % Favored : 73.37 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.19), residues: 1777 helix: 0.78 (0.25), residues: 401 sheet: -0.65 (0.23), residues: 483 loop : -2.04 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 166 TYR 0.024 0.001 TYR D 586 PHE 0.009 0.001 PHE F 522 TRP 0.026 0.002 TRP C 400 HIS 0.007 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (16509) covalent geometry : angle 0.78591 / 0.38 (22436) SS BOND : bond 0.00314 / 0.16 ( 30) SS BOND : angle 1.44641 / 0.69 ( 60) hydrogen bonds : bond 0.04755 / 3.35 ( 505) hydrogen bonds : angle 5.02889 / 3.54 ( 1488) Misc. bond : bond 0.01992 / 1.05 ( 1) link_ALPHA1-2 : bond 0.00289 / 0.14 ( 2) link_ALPHA1-2 : angle 1.98666 / 0.83 ( 6) link_ALPHA1-3 : bond 0.01919 / 0.96 ( 4) link_ALPHA1-3 : angle 2.18601 / 1.08 ( 12) link_ALPHA1-6 : bond 0.00831 / 0.44 ( 5) link_ALPHA1-6 : angle 1.42190 / 0.87 ( 15) link_BETA1-4 : bond 0.00658 / 0.44 ( 61) link_BETA1-4 : angle 2.12319 / 1.67 ( 183) link_NAG-ASN : bond 0.00392 / 0.26 ( 70) link_NAG-ASN : angle 1.92777 / 1.41 ( 210) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 175 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8897 (ttm) cc_final: 0.8603 (ttm) REVERT: B 542 ARG cc_start: 0.8859 (ttt180) cc_final: 0.8175 (ttt180) REVERT: B 588 ARG cc_start: 0.8844 (ttm170) cc_final: 0.8504 (ttm170) REVERT: B 606 THR cc_start: 0.9383 (t) cc_final: 0.9130 (p) REVERT: B 621 MET cc_start: 0.9412 (ppp) cc_final: 0.8907 (ppp) REVERT: B 643 TYR cc_start: 0.9148 (m-80) cc_final: 0.8886 (m-80) REVERT: B 656 ASN cc_start: 0.8753 (t0) cc_final: 0.8464 (t0) REVERT: C 80 ASN cc_start: 0.7383 (t0) cc_final: 0.6757 (t0) REVERT: C 95 MET cc_start: 0.8788 (ppp) cc_final: 0.8298 (ppp) REVERT: C 103 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8672 (tm-30) REVERT: C 133 ASP cc_start: 0.8553 (m-30) cc_final: 0.8181 (t70) REVERT: C 211 GLU cc_start: 0.8371 (tm-30) cc_final: 0.7996 (tm-30) REVERT: C 373 MET cc_start: 0.8200 (tmm) cc_final: 0.7886 (tmm) REVERT: C 426 MET cc_start: 0.8179 (tpp) cc_final: 0.7480 (mmt) REVERT: D 599 SER cc_start: 0.7881 (OUTLIER) cc_final: 0.7635 (m) REVERT: D 651 ASN cc_start: 0.8811 (t160) cc_final: 0.8478 (t0) REVERT: E 37 THR cc_start: 0.9207 (m) cc_final: 0.8731 (p) REVERT: E 179 LEU cc_start: 0.8962 (mm) cc_final: 0.8306 (tp) REVERT: E 373 MET cc_start: 0.8975 (ptt) cc_final: 0.8470 (ptm) REVERT: E 426 MET cc_start: 0.7791 (mmm) cc_final: 0.7352 (mmt) REVERT: A 40 TYR cc_start: 0.9036 (t80) cc_final: 0.8105 (t80) REVERT: A 195 ASN cc_start: 0.8346 (m-40) cc_final: 0.7434 (t0) REVERT: A 198 THR cc_start: 0.9268 (p) cc_final: 0.8812 (p) REVERT: A 373 MET cc_start: 0.8286 (ppp) cc_final: 0.7658 (ppp) REVERT: A 390 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9153 (mt) REVERT: A 406 ASN cc_start: 0.7958 (OUTLIER) cc_final: 0.7557 (m110) REVERT: A 426 MET cc_start: 0.8575 (tpp) cc_final: 0.8197 (mmm) REVERT: A 429 GLU cc_start: 0.9034 (tp30) cc_final: 0.8449 (mp0) REVERT: A 475 MET cc_start: 0.9089 (tpp) cc_final: 0.8476 (tpp) REVERT: F 520 LEU cc_start: 0.5451 (OUTLIER) cc_final: 0.5218 (tt) REVERT: F 530 MET cc_start: 0.7170 (mtt) cc_final: 0.6720 (mmm) REVERT: F 575 GLN cc_start: 0.9067 (pp30) cc_final: 0.8635 (pp30) REVERT: F 584 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8489 (pm20) REVERT: F 618 THR cc_start: 0.8974 (m) cc_final: 0.8668 (p) REVERT: F 633 ARG cc_start: 0.9033 (mmm-85) cc_final: 0.8826 (mmm-85) outliers start: 50 outliers final: 36 residues processed: 212 average time/residue: 0.1106 time to fit residues: 36.8403 Evaluate side-chains 213 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 171 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 388 THR Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 636 ASP Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 656 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 128 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 76 optimal weight: 0.0170 chunk 161 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 554 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 ASN F 564 HIS ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.075943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.059936 restraints weight = 63965.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.061929 restraints weight = 35136.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.063256 restraints weight = 24194.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.064135 restraints weight = 19071.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.064671 restraints weight = 16325.442| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.6068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.146 16682 Z= 0.154 Angle : 0.903 41.512 22922 Z= 0.421 Chirality : 0.049 0.328 2940 Planarity : 0.004 0.080 2668 Dihedral : 9.830 114.171 4924 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.99 % Favored : 91.95 % Rotamer: Outliers : 2.70 % Allowed : 23.87 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.19), residues: 1777 helix: 0.67 (0.25), residues: 401 sheet: -0.71 (0.23), residues: 462 loop : -2.07 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG E 166 TYR 0.032 0.001 TYR D 586 PHE 0.010 0.001 PHE F 522 TRP 0.026 0.001 TRP C 400 HIS 0.004 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (16509) covalent geometry : angle 0.86809 / 0.41 (22436) SS BOND : bond 0.00352 / 0.16 ( 30) SS BOND : angle 1.35058 / 0.67 ( 60) hydrogen bonds : bond 0.04738 / 3.35 ( 505) hydrogen bonds : angle 5.00052 / 3.51 ( 1488) Misc. bond : bond 0.01868 / 0.98 ( 1) link_ALPHA1-2 : bond 0.00329 / 0.16 ( 2) link_ALPHA1-2 : angle 1.96581 / 0.82 ( 6) link_ALPHA1-3 : bond 0.01927 / 0.96 ( 4) link_ALPHA1-3 : angle 2.15628 / 1.06 ( 12) link_ALPHA1-6 : bond 0.00801 / 0.43 ( 5) link_ALPHA1-6 : angle 1.40211 / 0.84 ( 15) link_BETA1-4 : bond 0.00673 / 0.45 ( 61) link_BETA1-4 : angle 2.10439 / 1.66 ( 183) link_NAG-ASN : bond 0.00386 / 0.26 ( 70) link_NAG-ASN : angle 1.89279 / 1.38 ( 210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2380.07 seconds wall clock time: 42 minutes 14.28 seconds (2534.28 seconds total)