Starting phenix.real_space_refine on Wed Mar 4 18:45:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ohy_20074/03_2026/6ohy_20074.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ohy_20074/03_2026/6ohy_20074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ohy_20074/03_2026/6ohy_20074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ohy_20074/03_2026/6ohy_20074.map" model { file = "/net/cci-nas-00/data/ceres_data/6ohy_20074/03_2026/6ohy_20074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ohy_20074/03_2026/6ohy_20074.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 144 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 102 5.16 5 C 9474 2.51 5 N 2439 2.21 5 O 3177 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15192 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3547 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 24, 'TRANS': 422} Chain breaks: 2 Chain: "B" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 964 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 3547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3547 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 24, 'TRANS': 422} Chain breaks: 2 Chain: "E" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 964 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'TRANS': 119} Chain breaks: 1 Chain: "D" Number of atoms: 3547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3547 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 24, 'TRANS': 422} Chain breaks: 2 Chain: "F" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 964 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'TRANS': 119} Chain breaks: 1 Chain: "G" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "O" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "c" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "q" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.89, per 1000 atoms: 0.26 Number of scatterers: 15192 At special positions: 0 Unit cell: (133.62, 122.4, 121.38, 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 102 16.00 O 3177 8.00 N 2439 7.00 C 9474 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.06 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=1.99 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.04 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " 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=0, symmetry=0 Links applied ALPHA1-3 " BMA N 3 " - " MAN N 4 " " MAN N 4 " - " MAN N 5 " " BMA b 3 " - " MAN b 4 " " MAN b 4 " - " MAN b 5 " " BMA p 3 " - " MAN p 4 " " MAN p 4 " - " MAN p 5 " ALPHA1-6 " BMA N 3 " - " MAN N 7 " " MAN N 4 " - " MAN N 6 " " BMA b 3 " - " MAN b 7 " " MAN b 4 " - " MAN b 6 " " BMA p 3 " - " MAN p 7 " " MAN p 4 " - " MAN p 6 " BETA1-4 " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " BETA1-6 " NAG G 1 " - " FUC G 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG J 1 " - " FUC J 3 " " NAG O 1 " - " FUC O 2 " " NAG S 1 " - " FUC S 2 " " NAG T 1 " - " FUC T 2 " " NAG U 1 " - " FUC U 2 " " NAG X 1 " - " FUC X 3 " " NAG c 1 " - " FUC c 2 " " NAG g 1 " - " FUC g 2 " " NAG h 1 " - " FUC h 2 " " NAG i 1 " - " FUC i 2 " " NAG l 1 " - " FUC l 3 " " NAG q 1 " - " FUC q 2 " " NAG u 1 " - " FUC u 2 " " NAG v 1 " - " FUC v 2 " NAG-ASN " NAG A 607 " - " ASN A 188 " " NAG A 611 " - " ASN A 268 " " NAG A 612 " - " ASN A 301 " " NAG A 626 " - " ASN A 343 " " NAG A 627 " - " ASN A 358 " " NAG A 634 " - " ASN A 442 " " NAG A 637 " - " ASN A 464F" " NAG B 705 " - " ASN B 625 " " NAG C 607 " - " ASN C 188 " " NAG C 611 " - " ASN C 268 " " NAG C 612 " - " ASN C 301 " " NAG C 626 " - " ASN C 343 " " NAG C 627 " - " ASN C 358 " " NAG C 634 " - " ASN C 442 " " NAG C 637 " - " ASN C 464F" " NAG D 607 " - " ASN D 188 " " NAG D 611 " - " ASN D 268 " " NAG D 612 " - " ASN D 301 " " NAG D 626 " - " ASN D 343 " " NAG D 627 " - " ASN D 358 " " NAG D 634 " - " ASN D 442 " " NAG D 637 " - " ASN D 464F" " NAG E 705 " - " ASN E 625 " " NAG F 705 " - " ASN F 625 " " NAG G 1 " - " ASN A 88 " " NAG H 1 " - " ASN A 160 " " NAG I 1 " - " ASN A 156 " " NAG J 1 " - " ASN A 197 " " NAG K 1 " - " ASN A 386 " " NAG L 1 " - " ASN A 236 " " NAG M 1 " - " ASN A 241 " " NAG N 1 " - " ASN A 262 " " NAG O 1 " - " ASN A 412 " " NAG P 1 " - " ASN A 392 " " NAG Q 1 " - " ASN A 334 " " NAG R 1 " - " ASN A 448 " " NAG S 1 " - " ASN B 637 " " NAG T 1 " - " ASN B 616 " " NAG U 1 " - " ASN C 88 " " NAG V 1 " - " ASN C 160 " " NAG W 1 " - " ASN C 156 " " NAG X 1 " - " ASN C 197 " " NAG Y 1 " - " ASN C 386 " " NAG Z 1 " - " ASN C 236 " " NAG a 1 " - " ASN C 241 " " NAG b 1 " - " ASN C 262 " " NAG c 1 " - " ASN C 412 " " NAG d 1 " - " ASN C 392 " " NAG e 1 " - " ASN C 334 " " NAG f 1 " - " ASN C 448 " " NAG g 1 " - " ASN E 637 " " NAG h 1 " - " ASN E 616 " " NAG i 1 " - " ASN D 88 " " NAG j 1 " - " ASN D 160 " " NAG k 1 " - " ASN D 156 " " NAG l 1 " - " ASN D 197 " " NAG m 1 " - " ASN D 386 " " NAG n 1 " - " ASN D 236 " " NAG o 1 " - " ASN D 241 " " NAG p 1 " - " ASN D 262 " " NAG q 1 " - " ASN D 412 " " NAG r 1 " - " ASN D 392 " " NAG s 1 " - " ASN D 334 " " NAG t 1 " - " ASN D 448 " " NAG u 1 " - " ASN F 637 " " NAG v 1 " - " ASN F 616 " Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 656.4 milliseconds 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3192 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 27 sheets defined 25.0% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.185A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.787A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 148 Processing helix chain 'A' and resid 334 through 354 removed outlier: 3.783A pdb=" N GLU A 347 " --> pdb=" O ASN A 343 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE A 352 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 397 removed outlier: 3.699A pdb=" N ILE A 396 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.767A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.505A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 533 removed outlier: 3.589A pdb=" N ALA B 533 " --> pdb=" O MET B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 595 removed outlier: 4.230A pdb=" N VAL B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 618A through 626 removed outlier: 3.668A pdb=" N TYR B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.897A pdb=" N ARG B 633 " --> pdb=" O GLN B 629 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN B 636 " --> pdb=" O ASP B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 652 removed outlier: 3.546A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 660 removed outlier: 3.794A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 116 removed outlier: 4.184A pdb=" N ASP C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.788A pdb=" N LEU C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 148 Processing helix chain 'C' and resid 334 through 354 removed outlier: 3.782A pdb=" N GLU C 347 " --> pdb=" O ASN C 343 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE C 352 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 397 removed outlier: 3.698A pdb=" N ILE C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.766A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 528 removed outlier: 4.506A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 533 removed outlier: 3.590A pdb=" N ALA E 533 " --> pdb=" O MET E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 595 removed outlier: 4.230A pdb=" N VAL E 580 " --> pdb=" O LEU E 576 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP E 589 " --> pdb=" O ARG E 585 " (cutoff:3.500A) Processing helix chain 'E' and resid 618A through 626 removed outlier: 3.668A pdb=" N TYR E 626 " --> pdb=" O ILE E 622 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 636 removed outlier: 3.896A pdb=" N ARG E 633 " --> pdb=" O GLN E 629 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU E 634 " --> pdb=" O GLN E 630 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN E 636 " --> pdb=" O ASP E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 652 removed outlier: 3.545A pdb=" N ILE E 642 " --> pdb=" O TYR E 638 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU E 647 " --> pdb=" O TYR E 643 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR E 651 " --> pdb=" O GLU E 647 " (cutoff:3.500A) Processing helix chain 'E' and resid 652 through 660 removed outlier: 3.793A pdb=" N GLU E 657 " --> pdb=" O GLN E 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 116 removed outlier: 4.185A pdb=" N ASP D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 removed outlier: 3.788A pdb=" N LEU D 125 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 148 Processing helix chain 'D' and resid 334 through 354 removed outlier: 3.782A pdb=" N GLU D 347 " --> pdb=" O ASN D 343 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE D 352 " --> pdb=" O VAL D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 397 removed outlier: 3.699A pdb=" N ILE D 396 " --> pdb=" O ASN D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 481 removed outlier: 3.766A pdb=" N TRP D 479 " --> pdb=" O MET D 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.505A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 533 removed outlier: 3.590A pdb=" N ALA F 533 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 595 removed outlier: 4.230A pdb=" N VAL F 580 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 618A through 626 removed outlier: 3.667A pdb=" N TYR F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.897A pdb=" N ARG F 633 " --> pdb=" O GLN F 629 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN F 636 " --> pdb=" O ASP F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 652 removed outlier: 3.546A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) Processing helix chain 'F' and resid 652 through 660 removed outlier: 3.793A pdb=" N GLU F 657 " --> pdb=" O GLN F 653 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.679A pdb=" N LEU A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.703A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 93 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 removed outlier: 5.113A pdb=" N ASN A 160 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR A 128 " --> pdb=" O ASN A 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 Processing sheet with id=AA7, first strand: chain 'A' and resid 260 through 261 removed outlier: 10.368A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N THR A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.008A pdb=" N VAL A 292 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N ASN A 448 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 10.655A pdb=" N ASP A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 260 through 261 removed outlier: 10.368A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N THR A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.008A pdb=" N VAL A 292 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N ASN A 448 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 10.655A pdb=" N ASP A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 333 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR A 414 " --> pdb=" O ILE A 333 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N PHE A 382 " --> pdb=" O ARG A 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 302 through 310 removed outlier: 6.545A pdb=" N THR A 303 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 36 through 37 Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.678A pdb=" N LEU C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.703A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE C 93 " --> pdb=" O GLU C 237 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLU C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 177 removed outlier: 5.113A pdb=" N ASN C 160 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR C 128 " --> pdb=" O ASN C 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 201 through 203 Processing sheet with id=AB7, first strand: chain 'C' and resid 260 through 261 removed outlier: 10.368A pdb=" N THR C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.773A pdb=" N ILE C 294 " --> pdb=" O THR C 444 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N THR C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.008A pdb=" N VAL C 292 " --> pdb=" O THR C 446 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N ASN C 448 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 10.655A pdb=" N ASP C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 260 through 261 removed outlier: 10.368A pdb=" N THR C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.773A pdb=" N ILE C 294 " --> pdb=" O THR C 444 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N THR C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.008A pdb=" N VAL C 292 " --> pdb=" O THR C 446 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N ASN C 448 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 10.655A pdb=" N ASP C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE C 333 " --> pdb=" O THR C 414 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR C 414 " --> pdb=" O ILE C 333 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N PHE C 382 " --> pdb=" O ARG C 421 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 302 through 310 removed outlier: 6.544A pdb=" N THR C 303 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 36 through 37 Processing sheet with id=AC2, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.678A pdb=" N LEU D 225 " --> pdb=" O VAL D 245 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AC4, first strand: chain 'D' and resid 91 through 94 removed outlier: 3.703A pdb=" N GLU D 91 " --> pdb=" O CYS D 239 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE D 93 " --> pdb=" O GLU D 237 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLU D 237 " --> pdb=" O PHE D 93 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 177 removed outlier: 5.113A pdb=" N ASN D 160 " --> pdb=" O THR D 128 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR D 128 " --> pdb=" O ASN D 160 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 201 through 203 Processing sheet with id=AC7, first strand: chain 'D' and resid 260 through 261 removed outlier: 10.368A pdb=" N THR D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.773A pdb=" N ILE D 294 " --> pdb=" O THR D 444 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N THR D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.008A pdb=" N VAL D 292 " --> pdb=" O THR D 446 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N ASN D 448 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 10.654A pdb=" N ASP D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 260 through 261 removed outlier: 10.368A pdb=" N THR D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.773A pdb=" N ILE D 294 " --> pdb=" O THR D 444 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N THR D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.008A pdb=" N VAL D 292 " --> pdb=" O THR D 446 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N ASN D 448 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 10.654A pdb=" N ASP D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE D 333 " --> pdb=" O THR D 414 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR D 414 " --> pdb=" O ILE D 333 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N PHE D 382 " --> pdb=" O ARG D 421 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 302 through 310 removed outlier: 6.545A pdb=" N THR D 303 " --> pdb=" O GLU D 321 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1215 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: 2.25 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4537 1.34 - 1.46: 3790 1.46 - 1.58: 7006 1.58 - 1.70: 3 1.70 - 1.83: 135 Bond restraints: 15471 Sorted by residual: bond pdb=" C1 MAN p 4 " pdb=" C2 MAN p 4 " ideal model delta sigma weight residual 1.526 1.587 -0.061 2.00e-02 2.50e+03 9.32e+00 bond pdb=" C1 MAN b 4 " pdb=" C2 MAN b 4 " ideal model delta sigma weight residual 1.526 1.586 -0.060 2.00e-02 2.50e+03 9.03e+00 bond pdb=" C1 MAN N 4 " pdb=" C2 MAN N 4 " ideal model delta sigma weight residual 1.526 1.586 -0.060 2.00e-02 2.50e+03 8.96e+00 bond pdb=" C1 NAG D 627 " pdb=" O5 NAG D 627 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.27e+00 bond pdb=" C1 NAG C 627 " pdb=" O5 NAG C 627 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.05e+00 ... (remaining 15466 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 20144 2.39 - 4.79: 727 4.79 - 7.18: 129 7.18 - 9.57: 27 9.57 - 11.97: 15 Bond angle restraints: 21042 Sorted by residual: angle pdb=" N PHE B 519 " pdb=" CA PHE B 519 " pdb=" C PHE B 519 " ideal model delta sigma weight residual 110.50 118.91 -8.41 1.41e+00 5.03e-01 3.56e+01 angle pdb=" N PHE E 519 " pdb=" CA PHE E 519 " pdb=" C PHE E 519 " ideal model delta sigma weight residual 110.50 118.86 -8.36 1.41e+00 5.03e-01 3.51e+01 angle pdb=" N PHE F 519 " pdb=" CA PHE F 519 " pdb=" C PHE F 519 " ideal model delta sigma weight residual 110.50 118.84 -8.34 1.41e+00 5.03e-01 3.50e+01 angle pdb=" C ASN A 412 " pdb=" N MET A 413 " pdb=" CA MET A 413 " ideal model delta sigma weight residual 121.54 131.45 -9.91 1.91e+00 2.74e-01 2.69e+01 angle pdb=" C ASN D 412 " pdb=" N MET D 413 " pdb=" CA MET D 413 " ideal model delta sigma weight residual 121.54 131.40 -9.86 1.91e+00 2.74e-01 2.66e+01 ... (remaining 21037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.14: 10338 24.14 - 48.28: 442 48.28 - 72.42: 80 72.42 - 96.56: 30 96.56 - 120.70: 27 Dihedral angle restraints: 10917 sinusoidal: 5976 harmonic: 4941 Sorted by residual: dihedral pdb=" CA SER F 534 " pdb=" C SER F 534 " pdb=" N VAL F 535 " pdb=" CA VAL F 535 " ideal model delta harmonic sigma weight residual 180.00 131.35 48.65 0 5.00e+00 4.00e-02 9.47e+01 dihedral pdb=" CA SER B 534 " pdb=" C SER B 534 " pdb=" N VAL B 535 " pdb=" CA VAL B 535 " ideal model delta harmonic sigma weight residual 180.00 131.36 48.64 0 5.00e+00 4.00e-02 9.46e+01 dihedral pdb=" CA SER E 534 " pdb=" C SER E 534 " pdb=" N VAL E 535 " pdb=" CA VAL E 535 " ideal model delta harmonic sigma weight residual 180.00 131.37 48.63 0 5.00e+00 4.00e-02 9.46e+01 ... (remaining 10914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2387 0.095 - 0.189: 322 0.189 - 0.283: 18 0.283 - 0.378: 15 0.378 - 0.472: 9 Chirality restraints: 2751 Sorted by residual: chirality pdb=" C1 NAG u 1 " pdb=" ND2 ASN F 637 " pdb=" C2 NAG u 1 " pdb=" O5 NAG u 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.58e+00 chirality pdb=" CB ILE C 391 " pdb=" CA ILE C 391 " pdb=" CG1 ILE C 391 " pdb=" CG2 ILE C 391 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN B 637 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.94e+00 ... (remaining 2748 not shown) Planarity restraints: 2574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 534 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.18e+00 pdb=" C SER B 534 " 0.046 2.00e-02 2.50e+03 pdb=" O SER B 534 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL B 535 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 534 " 0.013 2.00e-02 2.50e+03 2.68e-02 7.16e+00 pdb=" C SER E 534 " -0.046 2.00e-02 2.50e+03 pdb=" O SER E 534 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL E 535 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 534 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.00e+00 pdb=" C SER F 534 " 0.046 2.00e-02 2.50e+03 pdb=" O SER F 534 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL F 535 " -0.016 2.00e-02 2.50e+03 ... (remaining 2571 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3962 2.81 - 3.33: 13306 3.33 - 3.86: 23997 3.86 - 4.38: 26125 4.38 - 4.90: 44042 Nonbonded interactions: 111432 Sorted by model distance: nonbonded pdb=" NH2 ARG D 503 " pdb=" OD1 ASN F 650 " model vdw 2.288 3.120 nonbonded pdb=" NH2 ARG A 503 " pdb=" OD1 ASN B 650 " model vdw 2.316 3.120 nonbonded pdb=" OH TYR E 586 " pdb=" NE2 GLN F 591 " model vdw 2.316 3.120 nonbonded pdb=" O PHE A 93 " pdb=" OH TYR A 233 " model vdw 2.331 3.040 nonbonded pdb=" O PHE D 93 " pdb=" OH TYR D 233 " model vdw 2.331 3.040 ... (remaining 111427 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 1) selection = (chain 'H' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'K' and resid 1) selection = (chain 'L' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'S' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'V' and resid 1) selection = (chain 'W' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'a' and resid 1) selection = (chain 'c' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'e' and resid 1) selection = (chain 'f' and resid 1) selection = (chain 'g' and resid 1) selection = (chain 'h' and resid 1) selection = (chain 'i' and resid 1) selection = (chain 'j' and resid 1) selection = (chain 'k' and resid 1) selection = (chain 'm' and resid 1) selection = (chain 'n' and resid 1) selection = (chain 'o' and resid 1) selection = (chain 'q' and resid 1) selection = (chain 'r' and resid 1) selection = (chain 's' and resid 1) selection = (chain 't' and resid 1) selection = (chain 'u' and resid 1) selection = (chain 'v' and resid 1) } ncs_group { reference = chain 'J' selection = chain 'X' selection = chain 'l' } ncs_group { reference = chain 'N' selection = chain 'b' selection = chain 'p' } 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.860 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.030 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 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 : 0.008 0.061 15630 Z= 0.366 Angle : 1.208 15.872 21486 Z= 0.567 Chirality : 0.068 0.472 2751 Planarity : 0.007 0.060 2508 Dihedral : 14.531 120.701 7626 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.54 % Allowed : 10.53 % Favored : 88.93 % Rotamer: Outliers : 0.40 % Allowed : 2.39 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.74 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.17), residues: 1671 helix: -2.46 (0.20), residues: 333 sheet: -1.20 (0.25), residues: 306 loop : -2.52 (0.17), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 192 TYR 0.017 0.003 TYR C 330 PHE 0.019 0.003 PHE C 53 TRP 0.037 0.004 TRP A 479 HIS 0.007 0.002 HIS C 246 Details of bonding type rmsd covalent geometry : bond 0.00767 (15471) covalent geometry : angle 1.11281 (21042) SS BOND : bond 0.00944 ( 33) SS BOND : angle 1.60203 ( 66) hydrogen bonds : bond 0.18170 ( 426) hydrogen bonds : angle 7.82737 ( 1215) link_ALPHA1-3 : bond 0.00943 ( 6) link_ALPHA1-3 : angle 2.11802 ( 18) link_ALPHA1-6 : bond 0.00068 ( 6) link_ALPHA1-6 : angle 1.81258 ( 18) link_BETA1-4 : bond 0.00759 ( 33) link_BETA1-4 : angle 2.40452 ( 99) link_BETA1-6 : bond 0.00620 ( 15) link_BETA1-6 : angle 1.78914 ( 45) link_NAG-ASN : bond 0.00927 ( 66) link_NAG-ASN : angle 4.65807 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 273 time to evaluate : 0.379 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: A 66 HIS cc_start: 0.7014 (m-70) cc_final: 0.6589 (m-70) REVERT: A 95 MET cc_start: 0.8705 (ttp) cc_final: 0.8431 (tmm) REVERT: A 98 ASN cc_start: 0.8791 (t0) cc_final: 0.8544 (t0) REVERT: A 104 MET cc_start: 0.8911 (tmm) cc_final: 0.8207 (tmm) REVERT: A 371 VAL cc_start: 0.8629 (m) cc_final: 0.8265 (t) REVERT: B 519 PHE cc_start: 0.7824 (OUTLIER) cc_final: 0.7153 (t80) REVERT: B 611 ASN cc_start: 0.7115 (t0) cc_final: 0.6783 (t0) REVERT: B 612 LYS cc_start: 0.7710 (mttt) cc_final: 0.7357 (ttpp) REVERT: B 614 TRP cc_start: 0.7650 (m-10) cc_final: 0.6593 (m-10) REVERT: B 633 ARG cc_start: 0.8516 (mtt-85) cc_final: 0.8204 (ptt90) REVERT: B 652 GLN cc_start: 0.8400 (mt0) cc_final: 0.8186 (mt0) REVERT: B 659 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8370 (mm-30) REVERT: C 66 HIS cc_start: 0.6837 (m-70) cc_final: 0.6578 (m-70) REVERT: C 95 MET cc_start: 0.8853 (ttp) cc_final: 0.8578 (tmm) REVERT: C 98 ASN cc_start: 0.8791 (t0) cc_final: 0.8377 (t0) REVERT: C 104 MET cc_start: 0.8893 (tmm) cc_final: 0.8678 (tmm) REVERT: C 270 THR cc_start: 0.9009 (m) cc_final: 0.8742 (p) REVERT: C 371 VAL cc_start: 0.8590 (m) cc_final: 0.8255 (t) REVERT: C 430 VAL cc_start: 0.5747 (t) cc_final: 0.5384 (t) REVERT: E 611 ASN cc_start: 0.7286 (t0) cc_final: 0.6717 (t0) REVERT: E 612 LYS cc_start: 0.7782 (mttt) cc_final: 0.7532 (ttpp) REVERT: E 633 ARG cc_start: 0.8685 (mtt-85) cc_final: 0.8104 (ptt90) REVERT: E 652 GLN cc_start: 0.8332 (mt0) cc_final: 0.8053 (mt0) REVERT: D 95 MET cc_start: 0.8655 (ttp) cc_final: 0.8449 (tmm) REVERT: D 98 ASN cc_start: 0.8840 (t0) cc_final: 0.8597 (t0) REVERT: D 104 MET cc_start: 0.8852 (tmm) cc_final: 0.8296 (tmm) REVERT: D 371 VAL cc_start: 0.8631 (m) cc_final: 0.8203 (t) REVERT: F 519 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7375 (t80) REVERT: F 611 ASN cc_start: 0.7198 (t0) cc_final: 0.6828 (t0) REVERT: F 612 LYS cc_start: 0.7657 (mttt) cc_final: 0.7272 (ttpp) REVERT: F 633 ARG cc_start: 0.8303 (mtt-85) cc_final: 0.8043 (ptt90) outliers start: 6 outliers final: 3 residues processed: 279 average time/residue: 0.1247 time to fit residues: 50.5188 Evaluate side-chains 150 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 145 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.0670 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 0.5980 overall best weight: 1.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 195 ASN A 249 HIS ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN C 249 HIS ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 GLN E 590 GLN ** E 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 GLN D 249 HIS ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 492 GLN F 590 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.098994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.082948 restraints weight = 42059.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.084743 restraints weight = 29829.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.086027 restraints weight = 23555.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.086935 restraints weight = 19870.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.087458 restraints weight = 17637.762| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15630 Z= 0.181 Angle : 0.884 14.503 21486 Z= 0.414 Chirality : 0.052 0.294 2751 Planarity : 0.005 0.069 2508 Dihedral : 13.818 110.090 4386 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.46 % Favored : 90.25 % Rotamer: Outliers : 0.27 % Allowed : 2.46 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -2.55 (0.19), residues: 1671 helix: -1.11 (0.24), residues: 342 sheet: -1.35 (0.25), residues: 324 loop : -2.08 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 480 TYR 0.027 0.001 TYR F 638 PHE 0.023 0.002 PHE A 376 TRP 0.020 0.002 TRP C 112 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00399 (15471) covalent geometry : angle 0.79681 (21042) SS BOND : bond 0.00323 ( 33) SS BOND : angle 0.83920 ( 66) hydrogen bonds : bond 0.04279 ( 426) hydrogen bonds : angle 5.69110 ( 1215) link_ALPHA1-3 : bond 0.01702 ( 6) link_ALPHA1-3 : angle 3.01870 ( 18) link_ALPHA1-6 : bond 0.00380 ( 6) link_ALPHA1-6 : angle 1.84902 ( 18) link_BETA1-4 : bond 0.00399 ( 33) link_BETA1-4 : angle 1.62742 ( 99) link_BETA1-6 : bond 0.00690 ( 15) link_BETA1-6 : angle 1.63918 ( 45) link_NAG-ASN : bond 0.00575 ( 66) link_NAG-ASN : angle 3.74345 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 196 time to evaluate : 0.546 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: A 370 GLU cc_start: 0.7246 (mp0) cc_final: 0.6569 (tt0) REVERT: B 614 TRP cc_start: 0.7419 (m-10) cc_final: 0.6974 (m-10) REVERT: C 66 HIS cc_start: 0.6608 (m-70) cc_final: 0.6390 (m-70) REVERT: C 370 GLU cc_start: 0.7247 (mp0) cc_final: 0.6689 (tt0) REVERT: E 651 THR cc_start: 0.8560 (p) cc_final: 0.7713 (t) REVERT: D 370 GLU cc_start: 0.6885 (mp0) cc_final: 0.6343 (tt0) REVERT: F 614 TRP cc_start: 0.7182 (m-10) cc_final: 0.6817 (m-10) REVERT: F 648 GLU cc_start: 0.8194 (tt0) cc_final: 0.7882 (tp30) REVERT: F 651 THR cc_start: 0.8653 (p) cc_final: 0.7594 (p) REVERT: F 652 GLN cc_start: 0.7124 (mt0) cc_final: 0.6874 (mp10) outliers start: 4 outliers final: 0 residues processed: 199 average time/residue: 0.1208 time to fit residues: 36.1638 Evaluate side-chains 130 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 160 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 GLN ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 611 ASN ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.098141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.082650 restraints weight = 42605.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.084396 restraints weight = 30613.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.085613 restraints weight = 24242.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.086445 restraints weight = 20582.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.086906 restraints weight = 18331.018| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15630 Z= 0.196 Angle : 0.874 14.177 21486 Z= 0.400 Chirality : 0.052 0.288 2751 Planarity : 0.005 0.062 2508 Dihedral : 12.775 109.893 4386 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.63 % Favored : 90.19 % Rotamer: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -2.36 (0.19), residues: 1671 helix: -0.76 (0.26), residues: 342 sheet: -1.36 (0.23), residues: 360 loop : -2.00 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.021 0.001 TYR F 638 PHE 0.020 0.002 PHE C 376 TRP 0.018 0.001 TRP C 112 HIS 0.007 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00432 (15471) covalent geometry : angle 0.77966 (21042) SS BOND : bond 0.00375 ( 33) SS BOND : angle 1.12750 ( 66) hydrogen bonds : bond 0.03903 ( 426) hydrogen bonds : angle 5.39751 ( 1215) link_ALPHA1-3 : bond 0.01647 ( 6) link_ALPHA1-3 : angle 3.03038 ( 18) link_ALPHA1-6 : bond 0.00395 ( 6) link_ALPHA1-6 : angle 1.80651 ( 18) link_BETA1-4 : bond 0.00389 ( 33) link_BETA1-4 : angle 1.73430 ( 99) link_BETA1-6 : bond 0.01126 ( 15) link_BETA1-6 : angle 2.12032 ( 45) link_NAG-ASN : bond 0.00623 ( 66) link_NAG-ASN : angle 3.77123 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.562 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: B 614 TRP cc_start: 0.7440 (m-10) cc_final: 0.7006 (m-10) REVERT: B 621 VAL cc_start: 0.8305 (t) cc_final: 0.8021 (t) REVERT: E 579 ARG cc_start: 0.7196 (mtt-85) cc_final: 0.6943 (mtm180) REVERT: E 621 VAL cc_start: 0.8513 (t) cc_final: 0.8288 (t) REVERT: D 104 MET cc_start: 0.8544 (tmm) cc_final: 0.8272 (ttp) REVERT: D 423 ILE cc_start: 0.9526 (mt) cc_final: 0.9173 (mt) REVERT: F 611 ASN cc_start: 0.7195 (t0) cc_final: 0.6297 (t0) REVERT: F 612 LYS cc_start: 0.7064 (mttt) cc_final: 0.6557 (ttpp) REVERT: F 614 TRP cc_start: 0.7229 (m-10) cc_final: 0.6665 (m-10) REVERT: F 621 VAL cc_start: 0.8584 (t) cc_final: 0.8301 (t) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1065 time to fit residues: 29.2904 Evaluate side-chains 137 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 101 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 150 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 ASN C 425 ASN ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN D 425 ASN ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.094012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.078658 restraints weight = 43394.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.080260 restraints weight = 31598.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.081375 restraints weight = 25379.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.082124 restraints weight = 21766.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.082573 restraints weight = 19584.021| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 15630 Z= 0.306 Angle : 0.993 13.593 21486 Z= 0.456 Chirality : 0.054 0.327 2751 Planarity : 0.006 0.076 2508 Dihedral : 12.290 107.181 4386 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.95 % Favored : 88.87 % Rotamer: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.62 % 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: -2.49 (0.19), residues: 1671 helix: -0.99 (0.25), residues: 348 sheet: -1.68 (0.23), residues: 372 loop : -1.91 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 503 TYR 0.017 0.002 TYR E 586 PHE 0.023 0.003 PHE C 376 TRP 0.023 0.002 TRP D 112 HIS 0.011 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00696 (15471) covalent geometry : angle 0.90613 (21042) SS BOND : bond 0.00407 ( 33) SS BOND : angle 0.84372 ( 66) hydrogen bonds : bond 0.04387 ( 426) hydrogen bonds : angle 5.64702 ( 1215) link_ALPHA1-3 : bond 0.01619 ( 6) link_ALPHA1-3 : angle 3.43874 ( 18) link_ALPHA1-6 : bond 0.00321 ( 6) link_ALPHA1-6 : angle 1.89656 ( 18) link_BETA1-4 : bond 0.00459 ( 33) link_BETA1-4 : angle 2.21890 ( 99) link_BETA1-6 : bond 0.01351 ( 15) link_BETA1-6 : angle 2.97925 ( 45) link_NAG-ASN : bond 0.00777 ( 66) link_NAG-ASN : angle 3.69678 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.512 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: B 621 VAL cc_start: 0.8401 (t) cc_final: 0.8129 (t) REVERT: C 381 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7715 (mm-30) REVERT: E 621 VAL cc_start: 0.8504 (t) cc_final: 0.8260 (t) REVERT: D 381 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7595 (mm-30) REVERT: F 585 ARG cc_start: 0.8654 (ttt90) cc_final: 0.8221 (ttt90) REVERT: F 611 ASN cc_start: 0.7200 (t0) cc_final: 0.6903 (t0) REVERT: F 612 LYS cc_start: 0.7145 (mttt) cc_final: 0.6657 (ttpp) REVERT: F 621 VAL cc_start: 0.8546 (t) cc_final: 0.8277 (t) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1128 time to fit residues: 30.0745 Evaluate side-chains 130 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 82 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 27 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN D 425 ASN ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.097081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.081915 restraints weight = 43006.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.083689 restraints weight = 29973.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.084957 restraints weight = 23467.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.085757 restraints weight = 19682.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.086461 restraints weight = 17448.479| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15630 Z= 0.171 Angle : 0.863 13.797 21486 Z= 0.390 Chirality : 0.052 0.360 2751 Planarity : 0.005 0.079 2508 Dihedral : 11.371 103.882 4386 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.04 % Favored : 90.84 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.28 (0.19), residues: 1671 helix: -0.56 (0.27), residues: 351 sheet: -1.30 (0.24), residues: 363 loop : -2.01 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 585 TYR 0.015 0.001 TYR A 217 PHE 0.017 0.002 PHE C 376 TRP 0.018 0.001 TRP A 479 HIS 0.008 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00376 (15471) covalent geometry : angle 0.76802 (21042) SS BOND : bond 0.00258 ( 33) SS BOND : angle 0.69810 ( 66) hydrogen bonds : bond 0.03601 ( 426) hydrogen bonds : angle 5.30488 ( 1215) link_ALPHA1-3 : bond 0.01742 ( 6) link_ALPHA1-3 : angle 3.18821 ( 18) link_ALPHA1-6 : bond 0.00454 ( 6) link_ALPHA1-6 : angle 1.79060 ( 18) link_BETA1-4 : bond 0.00364 ( 33) link_BETA1-4 : angle 1.72006 ( 99) link_BETA1-6 : bond 0.01513 ( 15) link_BETA1-6 : angle 2.55436 ( 45) link_NAG-ASN : bond 0.00529 ( 66) link_NAG-ASN : angle 3.71998 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.502 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: B 614 TRP cc_start: 0.7396 (m-10) cc_final: 0.7176 (m-10) REVERT: B 621 VAL cc_start: 0.8272 (t) cc_final: 0.7984 (t) REVERT: C 470 LEU cc_start: 0.7609 (mt) cc_final: 0.7113 (tp) REVERT: E 621 VAL cc_start: 0.8449 (t) cc_final: 0.8195 (t) REVERT: E 652 GLN cc_start: 0.7290 (mp10) cc_final: 0.6609 (mp10) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1048 time to fit residues: 28.5855 Evaluate side-chains 132 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 91 optimal weight: 0.0040 chunk 161 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 40 optimal weight: 0.0870 chunk 75 optimal weight: 8.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.5774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN C 465 ASN D 465 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.099979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.084516 restraints weight = 41982.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.086514 restraints weight = 28327.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.087927 restraints weight = 21596.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.088922 restraints weight = 17808.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.089598 restraints weight = 15491.532| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15630 Z= 0.130 Angle : 0.794 13.817 21486 Z= 0.363 Chirality : 0.050 0.300 2751 Planarity : 0.005 0.085 2508 Dihedral : 10.274 99.150 4386 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 (0.20), residues: 1671 helix: -0.22 (0.27), residues: 357 sheet: -1.50 (0.24), residues: 378 loop : -1.74 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 429 TYR 0.023 0.001 TYR C 217 PHE 0.016 0.001 PHE B 522 TRP 0.022 0.001 TRP C 427 HIS 0.005 0.002 HIS C 375 Details of bonding type rmsd covalent geometry : bond 0.00265 (15471) covalent geometry : angle 0.71446 (21042) SS BOND : bond 0.00263 ( 33) SS BOND : angle 0.63323 ( 66) hydrogen bonds : bond 0.03090 ( 426) hydrogen bonds : angle 5.06003 ( 1215) link_ALPHA1-3 : bond 0.01864 ( 6) link_ALPHA1-3 : angle 3.17126 ( 18) link_ALPHA1-6 : bond 0.00632 ( 6) link_ALPHA1-6 : angle 1.70973 ( 18) link_BETA1-4 : bond 0.00391 ( 33) link_BETA1-4 : angle 1.44802 ( 99) link_BETA1-6 : bond 0.01477 ( 15) link_BETA1-6 : angle 2.48946 ( 45) link_NAG-ASN : bond 0.00452 ( 66) link_NAG-ASN : angle 3.21218 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.528 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: A 475 MET cc_start: 0.7452 (ptm) cc_final: 0.6648 (ttp) REVERT: B 621 VAL cc_start: 0.8270 (t) cc_final: 0.7983 (t) REVERT: B 652 GLN cc_start: 0.7262 (mp10) cc_final: 0.6712 (mp10) REVERT: E 614 TRP cc_start: 0.7619 (m-10) cc_final: 0.7410 (m-10) REVERT: E 621 VAL cc_start: 0.8504 (t) cc_final: 0.8161 (t) REVERT: E 652 GLN cc_start: 0.7044 (mp10) cc_final: 0.6488 (mp10) REVERT: D 470 LEU cc_start: 0.7480 (mt) cc_final: 0.7260 (tt) REVERT: F 621 VAL cc_start: 0.8428 (t) cc_final: 0.8192 (t) REVERT: F 638 TYR cc_start: 0.6577 (m-80) cc_final: 0.6372 (m-10) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.0965 time to fit residues: 26.3597 Evaluate side-chains 131 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 121 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 153 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 203 GLN B 591 GLN C 195 ASN C 310 GLN D 195 ASN D 422 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.098692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.083229 restraints weight = 42450.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.085167 restraints weight = 28938.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.086548 restraints weight = 22247.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.087459 restraints weight = 18443.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.088149 restraints weight = 16211.989| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15630 Z= 0.149 Angle : 0.793 13.412 21486 Z= 0.359 Chirality : 0.049 0.287 2751 Planarity : 0.005 0.091 2508 Dihedral : 9.862 96.132 4386 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.20), residues: 1671 helix: -0.18 (0.27), residues: 357 sheet: -1.38 (0.24), residues: 378 loop : -1.74 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 585 TYR 0.015 0.001 TYR D 217 PHE 0.012 0.002 PHE E 522 TRP 0.019 0.001 TRP A 427 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00329 (15471) covalent geometry : angle 0.71499 (21042) SS BOND : bond 0.00190 ( 33) SS BOND : angle 0.55234 ( 66) hydrogen bonds : bond 0.03107 ( 426) hydrogen bonds : angle 4.99935 ( 1215) link_ALPHA1-3 : bond 0.01861 ( 6) link_ALPHA1-3 : angle 3.34435 ( 18) link_ALPHA1-6 : bond 0.00605 ( 6) link_ALPHA1-6 : angle 1.80340 ( 18) link_BETA1-4 : bond 0.00378 ( 33) link_BETA1-4 : angle 1.55699 ( 99) link_BETA1-6 : bond 0.01378 ( 15) link_BETA1-6 : angle 2.51633 ( 45) link_NAG-ASN : bond 0.00450 ( 66) link_NAG-ASN : angle 3.14297 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 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: A 479 TRP cc_start: 0.8210 (m-90) cc_final: 0.7519 (m-90) REVERT: B 621 VAL cc_start: 0.8345 (t) cc_final: 0.8047 (t) REVERT: B 652 GLN cc_start: 0.7312 (mp10) cc_final: 0.6686 (mp10) REVERT: E 652 GLN cc_start: 0.6994 (mp10) cc_final: 0.6425 (mp10) REVERT: F 621 VAL cc_start: 0.8423 (t) cc_final: 0.8176 (t) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1053 time to fit residues: 26.8895 Evaluate side-chains 121 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 43 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 111 optimal weight: 0.0050 chunk 143 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 chunk 162 optimal weight: 0.1980 chunk 153 optimal weight: 5.9990 overall best weight: 3.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 425 ASN D 422 GLN ** F 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.094409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.079429 restraints weight = 43909.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.081083 restraints weight = 31555.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.082245 restraints weight = 25170.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.083010 restraints weight = 21464.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.083518 restraints weight = 19257.537| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 15630 Z= 0.268 Angle : 0.952 13.706 21486 Z= 0.431 Chirality : 0.052 0.293 2751 Planarity : 0.006 0.087 2508 Dihedral : 10.281 92.534 4386 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.07 % Favored : 88.81 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.18 (0.20), residues: 1671 helix: -0.46 (0.27), residues: 351 sheet: -1.40 (0.24), residues: 384 loop : -1.88 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 585 TYR 0.018 0.002 TYR E 586 PHE 0.020 0.003 PHE A 376 TRP 0.018 0.002 TRP C 112 HIS 0.013 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00612 (15471) covalent geometry : angle 0.86977 (21042) SS BOND : bond 0.00332 ( 33) SS BOND : angle 0.74815 ( 66) hydrogen bonds : bond 0.04003 ( 426) hydrogen bonds : angle 5.36506 ( 1215) link_ALPHA1-3 : bond 0.01738 ( 6) link_ALPHA1-3 : angle 3.76449 ( 18) link_ALPHA1-6 : bond 0.00414 ( 6) link_ALPHA1-6 : angle 1.96861 ( 18) link_BETA1-4 : bond 0.00450 ( 33) link_BETA1-4 : angle 2.14417 ( 99) link_BETA1-6 : bond 0.01228 ( 15) link_BETA1-6 : angle 2.65730 ( 45) link_NAG-ASN : bond 0.00652 ( 66) link_NAG-ASN : angle 3.48780 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.409 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 584 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7742 (tm-30) REVERT: B 652 GLN cc_start: 0.7523 (mp10) cc_final: 0.6798 (mp10) REVERT: E 584 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7759 (tm-30) REVERT: E 611 ASN cc_start: 0.7442 (t0) cc_final: 0.7211 (t0) REVERT: E 621 VAL cc_start: 0.8290 (t) cc_final: 0.7914 (t) REVERT: F 611 ASN cc_start: 0.7208 (t0) cc_final: 0.7003 (t0) REVERT: F 648 GLU cc_start: 0.7801 (tp30) cc_final: 0.6588 (tp30) REVERT: F 652 GLN cc_start: 0.7317 (mp10) cc_final: 0.6242 (mp10) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1002 time to fit residues: 25.7778 Evaluate side-chains 116 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 74 optimal weight: 0.7980 chunk 116 optimal weight: 0.0670 chunk 162 optimal weight: 0.5980 chunk 137 optimal weight: 0.9980 chunk 148 optimal weight: 0.7980 chunk 134 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 158 optimal weight: 8.9990 chunk 67 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN ** F 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.098696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.083079 restraints weight = 42302.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.085037 restraints weight = 28726.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.086426 restraints weight = 22051.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.087390 restraints weight = 18307.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.088079 restraints weight = 16019.129| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15630 Z= 0.134 Angle : 0.835 13.826 21486 Z= 0.374 Chirality : 0.051 0.322 2751 Planarity : 0.005 0.090 2508 Dihedral : 9.472 87.824 4386 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.98 (0.20), residues: 1671 helix: -0.15 (0.28), residues: 351 sheet: -1.31 (0.24), residues: 381 loop : -1.79 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 429 TYR 0.022 0.001 TYR A 217 PHE 0.014 0.001 PHE D 376 TRP 0.024 0.001 TRP D 479 HIS 0.005 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00280 (15471) covalent geometry : angle 0.74091 (21042) SS BOND : bond 0.00178 ( 33) SS BOND : angle 0.67546 ( 66) hydrogen bonds : bond 0.03272 ( 426) hydrogen bonds : angle 5.11708 ( 1215) link_ALPHA1-3 : bond 0.01891 ( 6) link_ALPHA1-3 : angle 3.50813 ( 18) link_ALPHA1-6 : bond 0.00500 ( 6) link_ALPHA1-6 : angle 1.72238 ( 18) link_BETA1-4 : bond 0.00411 ( 33) link_BETA1-4 : angle 1.55479 ( 99) link_BETA1-6 : bond 0.01370 ( 15) link_BETA1-6 : angle 2.49186 ( 45) link_NAG-ASN : bond 0.00624 ( 66) link_NAG-ASN : angle 3.61746 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.470 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 621 VAL cc_start: 0.8298 (t) cc_final: 0.8073 (t) REVERT: B 652 GLN cc_start: 0.7238 (mp10) cc_final: 0.6587 (mp10) REVERT: E 621 VAL cc_start: 0.8283 (t) cc_final: 0.7964 (t) REVERT: E 652 GLN cc_start: 0.7163 (mp10) cc_final: 0.6571 (mp10) REVERT: D 154 MET cc_start: 0.8682 (mmm) cc_final: 0.7919 (mtt) REVERT: F 621 VAL cc_start: 0.8415 (t) cc_final: 0.8212 (t) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1021 time to fit residues: 26.2109 Evaluate side-chains 117 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 66 optimal weight: 6.9990 chunk 126 optimal weight: 0.5980 chunk 121 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 162 optimal weight: 0.6980 chunk 138 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 195 ASN D 425 ASN ** F 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.098647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.082905 restraints weight = 42469.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.084839 restraints weight = 28875.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.086210 restraints weight = 22245.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.087182 restraints weight = 18518.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.087880 restraints weight = 16225.330| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15630 Z= 0.141 Angle : 0.813 13.236 21486 Z= 0.367 Chirality : 0.050 0.311 2751 Planarity : 0.005 0.088 2508 Dihedral : 8.534 82.855 4386 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.90 (0.20), residues: 1671 helix: -0.07 (0.28), residues: 351 sheet: -1.14 (0.26), residues: 357 loop : -1.81 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 429 TYR 0.028 0.001 TYR A 217 PHE 0.015 0.002 PHE F 522 TRP 0.021 0.001 TRP D 427 HIS 0.006 0.002 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00306 (15471) covalent geometry : angle 0.72506 (21042) SS BOND : bond 0.00177 ( 33) SS BOND : angle 0.58241 ( 66) hydrogen bonds : bond 0.03150 ( 426) hydrogen bonds : angle 5.03607 ( 1215) link_ALPHA1-3 : bond 0.01939 ( 6) link_ALPHA1-3 : angle 3.64131 ( 18) link_ALPHA1-6 : bond 0.00380 ( 6) link_ALPHA1-6 : angle 1.61928 ( 18) link_BETA1-4 : bond 0.00439 ( 33) link_BETA1-4 : angle 1.59820 ( 99) link_BETA1-6 : bond 0.01299 ( 15) link_BETA1-6 : angle 2.48049 ( 45) link_NAG-ASN : bond 0.00558 ( 66) link_NAG-ASN : angle 3.40185 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.563 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: A 104 MET cc_start: 0.8425 (tpp) cc_final: 0.8225 (tpp) REVERT: A 428 MET cc_start: 0.6126 (mtt) cc_final: 0.5821 (mtm) REVERT: A 475 MET cc_start: 0.7915 (ptm) cc_final: 0.7078 (ttp) REVERT: B 652 GLN cc_start: 0.7143 (mp10) cc_final: 0.6375 (mp10) REVERT: C 95 MET cc_start: 0.9131 (ppp) cc_final: 0.8771 (ppp) REVERT: E 584 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7554 (tm-30) REVERT: E 652 GLN cc_start: 0.7175 (mp10) cc_final: 0.6634 (mp10) REVERT: D 429 ARG cc_start: 0.7743 (mmp80) cc_final: 0.7410 (mmp80) REVERT: F 621 VAL cc_start: 0.8390 (t) cc_final: 0.8189 (t) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.0983 time to fit residues: 25.3563 Evaluate side-chains 121 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 64 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 143 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.097247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.081885 restraints weight = 42320.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.083650 restraints weight = 29917.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.084886 restraints weight = 23577.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.085732 restraints weight = 19947.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.086361 restraints weight = 17727.140| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15630 Z= 0.177 Angle : 0.837 13.041 21486 Z= 0.377 Chirality : 0.050 0.267 2751 Planarity : 0.005 0.089 2508 Dihedral : 8.415 78.280 4386 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.90 (0.20), residues: 1671 helix: -0.11 (0.28), residues: 351 sheet: -1.12 (0.26), residues: 357 loop : -1.80 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 429 TYR 0.025 0.001 TYR A 217 PHE 0.015 0.002 PHE E 522 TRP 0.021 0.001 TRP C 427 HIS 0.010 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00398 (15471) covalent geometry : angle 0.75242 (21042) SS BOND : bond 0.00236 ( 33) SS BOND : angle 0.60844 ( 66) hydrogen bonds : bond 0.03368 ( 426) hydrogen bonds : angle 5.11721 ( 1215) link_ALPHA1-3 : bond 0.01957 ( 6) link_ALPHA1-3 : angle 3.57005 ( 18) link_ALPHA1-6 : bond 0.00264 ( 6) link_ALPHA1-6 : angle 1.72276 ( 18) link_BETA1-4 : bond 0.00403 ( 33) link_BETA1-4 : angle 1.74899 ( 99) link_BETA1-6 : bond 0.01211 ( 15) link_BETA1-6 : angle 2.55031 ( 45) link_NAG-ASN : bond 0.00567 ( 66) link_NAG-ASN : angle 3.35567 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1891.30 seconds wall clock time: 33 minutes 46.15 seconds (2026.15 seconds total)