Starting phenix.real_space_refine on Fri Jul 3 18:45:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ohy_20074/07_2026/6ohy_20074.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ohy_20074/07_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_20074/07_2026/6ohy_20074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ohy_20074/07_2026/6ohy_20074.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6ohy_20074/07_2026/6ohy_20074.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ohy_20074/07_2026/6ohy_20074.cif" model { file = "/net/cci-nas-00/data/ceres_data/6ohy_20074/07_2026/6ohy_20074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ohy_20074/07_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-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 3.52, per 1000 atoms: 0.23 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: 1.59 Conformation dependent library (CDL) restraints added in 449.4 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: 0.48 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: 2.41 Time building geometry restraints manager: 1.96 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 - 14.16: 7699 14.16 - 28.32: 461 28.32 - 42.48: 161 42.48 - 56.64: 31 56.64 - 70.80: 9 Dihedral angle restraints: 8361 sinusoidal: 3420 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 8358 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: 0.04 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.060 Find NCS groups from input model: 0.560 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: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 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 : 10.700 70.803 5070 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/Z covalent geometry : bond 0.00767 / 0.37 (15471) covalent geometry : angle 1.11281 / 0.55 (21042) SS BOND : bond 0.00944 / 0.74 ( 33) SS BOND : angle 1.60203 / 1.13 ( 66) hydrogen bonds : bond 0.18170 / 11.58 ( 426) hydrogen bonds : angle 7.82737 / 5.66 ( 1215) link_ALPHA1-3 : bond 0.00943 / 0.44 ( 6) link_ALPHA1-3 : angle 2.11802 / 1.55 ( 18) link_ALPHA1-6 : bond 0.00068 / 0.03 ( 6) link_ALPHA1-6 : angle 1.81258 / 1.10 ( 18) link_BETA1-4 : bond 0.00759 / 0.46 ( 33) link_BETA1-4 : angle 2.40452 / 1.83 ( 99) link_BETA1-6 : bond 0.00620 / 0.39 ( 15) link_BETA1-6 : angle 1.78914 / 1.28 ( 45) link_NAG-ASN : bond 0.00927 / 0.60 ( 66) link_NAG-ASN : angle 4.65807 / 3.21 ( 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 : 0.558 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: 0.1266 time to fit residues: 51.6780 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 : 0.471 ------------------------------------------------------------------------------- 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... 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 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.097194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.080637 restraints weight = 41467.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.082577 restraints weight = 28371.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.083942 restraints weight = 22002.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.084926 restraints weight = 18359.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.085446 restraints weight = 16120.213| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15630 Z= 0.179 Angle : 0.865 14.281 21486 Z= 0.410 Chirality : 0.050 0.293 2751 Planarity : 0.005 0.068 2508 Dihedral : 7.110 38.291 1830 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.46 % Favored : 90.25 % Rotamer: Outliers : 0.27 % Allowed : 2.52 % Favored : 97.21 % 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: -2.54 (0.19), residues: 1671 helix: -1.10 (0.25), 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 C 192 TYR 0.028 0.001 TYR F 638 PHE 0.024 0.002 PHE A 376 TRP 0.020 0.002 TRP C 112 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (15471) covalent geometry : angle 0.78396 / 0.39 (21042) SS BOND : bond 0.00326 / 0.19 ( 33) SS BOND : angle 0.84312 / 0.62 ( 66) hydrogen bonds : bond 0.04256 / 2.71 ( 426) hydrogen bonds : angle 5.67685 / 4.09 ( 1215) link_ALPHA1-3 : bond 0.01019 / 0.54 ( 6) link_ALPHA1-3 : angle 2.06131 / 1.37 ( 18) link_ALPHA1-6 : bond 0.00235 / 0.13 ( 6) link_ALPHA1-6 : angle 1.80432 / 1.11 ( 18) link_BETA1-4 : bond 0.00436 / 0.26 ( 33) link_BETA1-4 : angle 1.49728 / 1.10 ( 99) link_BETA1-6 : bond 0.00312 / 0.19 ( 15) link_BETA1-6 : angle 1.26635 / 0.90 ( 45) link_NAG-ASN : bond 0.00676 / 0.43 ( 66) link_NAG-ASN : angle 3.66416 / 2.53 ( 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 201 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 197 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: A 98 ASN cc_start: 0.8720 (t0) cc_final: 0.8515 (t0) REVERT: A 370 GLU cc_start: 0.7277 (mp0) cc_final: 0.6550 (tt0) REVERT: B 614 TRP cc_start: 0.7487 (m-10) cc_final: 0.6954 (m-10) REVERT: C 66 HIS cc_start: 0.6710 (m-70) cc_final: 0.6444 (m-70) REVERT: C 370 GLU cc_start: 0.7268 (mp0) cc_final: 0.6720 (tt0) REVERT: C 479 TRP cc_start: 0.8255 (m-10) cc_final: 0.7308 (m-90) REVERT: E 651 THR cc_start: 0.8590 (p) cc_final: 0.7752 (t) REVERT: D 370 GLU cc_start: 0.6927 (mp0) cc_final: 0.6358 (tt0) REVERT: F 523 LEU cc_start: 0.8178 (pp) cc_final: 0.7977 (pp) REVERT: F 614 TRP cc_start: 0.7232 (m-10) cc_final: 0.6810 (m-10) REVERT: F 648 GLU cc_start: 0.8265 (tt0) cc_final: 0.7899 (tp30) REVERT: F 651 THR cc_start: 0.8671 (p) cc_final: 0.7610 (p) REVERT: F 652 GLN cc_start: 0.7256 (mt0) cc_final: 0.6915 (mp10) outliers start: 4 outliers final: 0 residues processed: 200 average time/residue: 0.1090 time to fit residues: 32.9856 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 : 0.522 ------------------------------------------------------------------------------- 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: 5.9990 chunk 69 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 160 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.098096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.082491 restraints weight = 42807.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.084176 restraints weight = 30885.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.085391 restraints weight = 24686.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.086249 restraints weight = 21021.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.086851 restraints weight = 18700.557| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15630 Z= 0.178 Angle : 0.831 13.829 21486 Z= 0.387 Chirality : 0.050 0.255 2751 Planarity : 0.005 0.060 2508 Dihedral : 6.659 36.183 1830 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.40 % Favored : 90.42 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % 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: -2.33 (0.19), residues: 1671 helix: -0.76 (0.26), residues: 342 sheet: -1.33 (0.24), residues: 360 loop : -1.97 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 633 TYR 0.022 0.001 TYR F 638 PHE 0.021 0.002 PHE A 376 TRP 0.017 0.001 TRP D 112 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (15471) covalent geometry : angle 0.74365 / 0.37 (21042) SS BOND : bond 0.00324 / 0.18 ( 33) SS BOND : angle 0.96981 / 0.65 ( 66) hydrogen bonds : bond 0.03812 / 2.47 ( 426) hydrogen bonds : angle 5.35690 / 3.87 ( 1215) link_ALPHA1-3 : bond 0.01030 / 0.52 ( 6) link_ALPHA1-3 : angle 2.10962 / 1.39 ( 18) link_ALPHA1-6 : bond 0.00240 / 0.13 ( 6) link_ALPHA1-6 : angle 1.60879 / 0.95 ( 18) link_BETA1-4 : bond 0.00391 / 0.24 ( 33) link_BETA1-4 : angle 1.59814 / 1.17 ( 99) link_BETA1-6 : bond 0.00538 / 0.32 ( 15) link_BETA1-6 : angle 1.27462 / 0.89 ( 45) link_NAG-ASN : bond 0.00534 / 0.33 ( 66) link_NAG-ASN : angle 3.68912 / 2.57 ( 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 178 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.580 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: B 614 TRP cc_start: 0.7405 (m-10) cc_final: 0.7031 (m-10) REVERT: B 621 VAL cc_start: 0.8311 (t) cc_final: 0.8040 (t) REVERT: E 579 ARG cc_start: 0.7183 (mtt-85) cc_final: 0.6911 (mtm180) REVERT: E 614 TRP cc_start: 0.7548 (m-10) cc_final: 0.7216 (m-10) REVERT: E 621 VAL cc_start: 0.8506 (t) cc_final: 0.8268 (t) REVERT: D 423 ILE cc_start: 0.9518 (mt) cc_final: 0.9176 (mt) REVERT: F 612 LYS cc_start: 0.7055 (mttt) cc_final: 0.6628 (ttpp) REVERT: F 614 TRP cc_start: 0.7253 (m-10) cc_final: 0.6804 (m-10) REVERT: F 621 VAL cc_start: 0.8588 (t) cc_final: 0.8301 (t) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1144 time to fit residues: 31.6256 Evaluate side-chains 139 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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: 6.9990 chunk 150 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN B 591 GLN C 195 ASN C 425 ASN E 591 GLN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 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 = 0.3474 r_free = 0.3474 target = 0.092961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.077762 restraints weight = 43835.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.079273 restraints weight = 32562.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.080324 restraints weight = 26426.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.080922 restraints weight = 22885.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.081565 restraints weight = 20773.848| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 15630 Z= 0.338 Angle : 1.034 13.165 21486 Z= 0.478 Chirality : 0.060 0.794 2751 Planarity : 0.006 0.073 2508 Dihedral : 7.050 36.593 1830 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.49 % Favored : 88.33 % Rotamer: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % 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: -2.61 (0.19), residues: 1671 helix: -1.17 (0.25), residues: 348 sheet: -1.68 (0.23), residues: 372 loop : -1.99 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 503 TYR 0.018 0.003 TYR E 586 PHE 0.025 0.004 PHE C 376 TRP 0.026 0.002 TRP D 112 HIS 0.012 0.003 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00775 / 0.34 (15471) covalent geometry : angle 0.95263 / 0.46 (21042) SS BOND : bond 0.00427 / 0.25 ( 33) SS BOND : angle 0.95725 / 0.71 ( 66) hydrogen bonds : bond 0.04788 / 3.12 ( 426) hydrogen bonds : angle 5.82486 / 4.20 ( 1215) link_ALPHA1-3 : bond 0.00917 / 0.44 ( 6) link_ALPHA1-3 : angle 2.43140 / 1.62 ( 18) link_ALPHA1-6 : bond 0.00062 / 0.04 ( 6) link_ALPHA1-6 : angle 1.69470 / 1.01 ( 18) link_BETA1-4 : bond 0.00523 / 0.31 ( 33) link_BETA1-4 : angle 2.39960 / 1.72 ( 99) link_BETA1-6 : bond 0.00308 / 0.18 ( 15) link_BETA1-6 : angle 1.47353 / 1.06 ( 45) link_NAG-ASN : bond 0.00863 / 0.57 ( 66) link_NAG-ASN : angle 3.88012 / 2.70 ( 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 169 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8990 (tmm) cc_final: 0.8657 (tmm) REVERT: B 621 VAL cc_start: 0.8348 (t) cc_final: 0.8071 (t) REVERT: C 104 MET cc_start: 0.9006 (tmm) cc_final: 0.8723 (tmm) REVERT: C 381 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7708 (mm-30) REVERT: E 621 VAL cc_start: 0.8488 (t) cc_final: 0.8215 (t) REVERT: F 611 ASN cc_start: 0.7324 (t0) cc_final: 0.7058 (t0) REVERT: F 612 LYS cc_start: 0.7044 (mttt) cc_final: 0.6641 (ttpp) REVERT: F 621 VAL cc_start: 0.8484 (t) cc_final: 0.8174 (t) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1104 time to fit residues: 28.7150 Evaluate side-chains 126 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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: 3.9990 chunk 73 optimal weight: 0.0980 chunk 17 optimal weight: 0.0570 chunk 27 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 164 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 611 ASN ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 611 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 = 0.3568 r_free = 0.3568 target = 0.098774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.083601 restraints weight = 42876.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.085427 restraints weight = 29716.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.086747 restraints weight = 23100.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.087669 restraints weight = 19244.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.088276 restraints weight = 16879.535| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15630 Z= 0.132 Angle : 0.816 13.424 21486 Z= 0.374 Chirality : 0.053 0.471 2751 Planarity : 0.005 0.081 2508 Dihedral : 6.405 37.096 1830 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.26 % Favored : 91.68 % Rotamer: Outliers : 0.07 % Allowed : 2.12 % 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: -2.23 (0.19), residues: 1671 helix: -0.53 (0.27), residues: 351 sheet: -1.34 (0.25), residues: 348 loop : -1.95 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 585 TYR 0.008 0.001 TYR F 638 PHE 0.015 0.001 PHE C 376 TRP 0.022 0.001 TRP C 427 HIS 0.007 0.002 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (15471) covalent geometry : angle 0.73430 / 0.36 (21042) SS BOND : bond 0.00212 / 0.13 ( 33) SS BOND : angle 0.73865 / 0.53 ( 66) hydrogen bonds : bond 0.03407 / 2.19 ( 426) hydrogen bonds : angle 5.28492 / 3.84 ( 1215) link_ALPHA1-3 : bond 0.00989 / 0.48 ( 6) link_ALPHA1-3 : angle 1.85459 / 1.22 ( 18) link_ALPHA1-6 : bond 0.00189 / 0.10 ( 6) link_ALPHA1-6 : angle 1.57253 / 0.91 ( 18) link_BETA1-4 : bond 0.00444 / 0.28 ( 33) link_BETA1-4 : angle 1.45067 / 1.05 ( 99) link_BETA1-6 : bond 0.00626 / 0.37 ( 15) link_BETA1-6 : angle 1.23885 / 0.86 ( 45) link_NAG-ASN : bond 0.00690 / 0.44 ( 66) link_NAG-ASN : angle 3.58606 / 2.48 ( 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 182 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 0.616 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: A 104 MET cc_start: 0.8705 (tmm) cc_final: 0.8421 (tmm) REVERT: B 584 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7550 (tm-30) REVERT: B 585 ARG cc_start: 0.8838 (ttm-80) cc_final: 0.8580 (ttm-80) REVERT: B 621 VAL cc_start: 0.8252 (t) cc_final: 0.7949 (t) REVERT: C 104 MET cc_start: 0.8824 (tmm) cc_final: 0.8621 (tmm) REVERT: E 614 TRP cc_start: 0.7512 (m-10) cc_final: 0.7272 (m-10) REVERT: E 621 VAL cc_start: 0.8469 (t) cc_final: 0.8203 (t) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.0996 time to fit residues: 28.3658 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 : 0.520 ------------------------------------------------------------------------------- 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: 0.9990 chunk 161 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 650 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.097146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.081677 restraints weight = 43313.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.083467 restraints weight = 30495.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.084727 restraints weight = 23909.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.085618 restraints weight = 20164.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.086160 restraints weight = 17820.862| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15630 Z= 0.159 Angle : 0.801 13.110 21486 Z= 0.371 Chirality : 0.050 0.379 2751 Planarity : 0.005 0.087 2508 Dihedral : 6.185 37.351 1830 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.04 % Favored : 90.90 % Rotamer: Outliers : 0.07 % Allowed : 1.06 % 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: -2.16 (0.19), residues: 1671 helix: -0.46 (0.27), residues: 357 sheet: -1.52 (0.24), residues: 378 loop : -1.81 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 503 TYR 0.014 0.001 TYR B 586 PHE 0.014 0.002 PHE F 522 TRP 0.012 0.001 TRP C 427 HIS 0.007 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (15471) covalent geometry : angle 0.73064 / 0.36 (21042) SS BOND : bond 0.00264 / 0.16 ( 33) SS BOND : angle 0.60785 / 0.46 ( 66) hydrogen bonds : bond 0.03381 / 2.18 ( 426) hydrogen bonds : angle 5.15763 / 3.73 ( 1215) link_ALPHA1-3 : bond 0.00986 / 0.49 ( 6) link_ALPHA1-3 : angle 2.03158 / 1.37 ( 18) link_ALPHA1-6 : bond 0.00201 / 0.11 ( 6) link_ALPHA1-6 : angle 1.55596 / 0.92 ( 18) link_BETA1-4 : bond 0.00378 / 0.23 ( 33) link_BETA1-4 : angle 1.58921 / 1.16 ( 99) link_BETA1-6 : bond 0.00447 / 0.28 ( 15) link_BETA1-6 : angle 1.24674 / 0.88 ( 45) link_NAG-ASN : bond 0.00523 / 0.34 ( 66) link_NAG-ASN : angle 3.24459 / 2.22 ( 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 167 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 584 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7580 (tm-30) REVERT: B 621 VAL cc_start: 0.8235 (t) cc_final: 0.7935 (t) REVERT: B 652 GLN cc_start: 0.7371 (mp10) cc_final: 0.6826 (mp10) REVERT: E 614 TRP cc_start: 0.7701 (m-10) cc_final: 0.7261 (m-10) REVERT: E 621 VAL cc_start: 0.8482 (t) cc_final: 0.8134 (t) REVERT: F 621 VAL cc_start: 0.8461 (t) cc_final: 0.8216 (t) REVERT: F 648 GLU cc_start: 0.7833 (tp30) cc_final: 0.7607 (tp30) outliers start: 1 outliers final: 0 residues processed: 166 average time/residue: 0.0898 time to fit residues: 23.6901 Evaluate side-chains 120 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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: 2.9990 chunk 90 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 78 optimal weight: 0.0050 chunk 153 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 95 optimal weight: 0.1980 chunk 125 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.096851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.081347 restraints weight = 43112.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.083078 restraints weight = 30802.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.084310 restraints weight = 24412.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.085170 restraints weight = 20688.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.085721 restraints weight = 18405.149| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15630 Z= 0.162 Angle : 0.795 12.834 21486 Z= 0.368 Chirality : 0.050 0.353 2751 Planarity : 0.005 0.091 2508 Dihedral : 6.108 37.537 1830 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % 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 : 0.25 % 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: -2.08 (0.19), residues: 1671 helix: -0.35 (0.27), residues: 357 sheet: -1.47 (0.24), residues: 381 loop : -1.77 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 503 TYR 0.017 0.001 TYR E 626 PHE 0.016 0.002 PHE C 376 TRP 0.013 0.001 TRP E 631 HIS 0.008 0.002 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (15471) covalent geometry : angle 0.72962 / 0.35 (21042) SS BOND : bond 0.00227 / 0.13 ( 33) SS BOND : angle 0.56971 / 0.43 ( 66) hydrogen bonds : bond 0.03329 / 2.15 ( 426) hydrogen bonds : angle 5.16821 / 3.74 ( 1215) link_ALPHA1-3 : bond 0.00996 / 0.49 ( 6) link_ALPHA1-3 : angle 2.04376 / 1.37 ( 18) link_ALPHA1-6 : bond 0.00186 / 0.10 ( 6) link_ALPHA1-6 : angle 1.56920 / 0.93 ( 18) link_BETA1-4 : bond 0.00367 / 0.22 ( 33) link_BETA1-4 : angle 1.57889 / 1.15 ( 99) link_BETA1-6 : bond 0.00461 / 0.28 ( 15) link_BETA1-6 : angle 1.26667 / 0.89 ( 45) link_NAG-ASN : bond 0.00479 / 0.32 ( 66) link_NAG-ASN : angle 3.10386 / 2.12 ( 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 161 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.553 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 381 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7433 (mm-30) REVERT: B 584 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7542 (tm-30) REVERT: B 621 VAL cc_start: 0.8275 (t) cc_final: 0.7967 (t) REVERT: B 652 GLN cc_start: 0.7303 (mp10) cc_final: 0.6678 (mp10) REVERT: E 614 TRP cc_start: 0.7658 (m-10) cc_final: 0.7387 (m-10) REVERT: F 648 GLU cc_start: 0.7687 (tp30) cc_final: 0.7387 (tp30) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1058 time to fit residues: 26.9389 Evaluate side-chains 123 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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: 8.9990 chunk 40 optimal weight: 8.9990 chunk 135 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 137 optimal weight: 7.9990 chunk 162 optimal weight: 0.7980 chunk 153 optimal weight: 6.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN C 425 ASN ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.093550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.078062 restraints weight = 44001.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.079765 restraints weight = 31429.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.080975 restraints weight = 24959.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.081811 restraints weight = 21193.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.082322 restraints weight = 18902.661| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 15630 Z= 0.269 Angle : 0.921 12.497 21486 Z= 0.427 Chirality : 0.052 0.314 2751 Planarity : 0.006 0.088 2508 Dihedral : 6.490 37.210 1830 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.83 % Favored : 89.05 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -2.43 (0.19), residues: 1671 helix: -0.71 (0.26), residues: 357 sheet: -1.52 (0.24), residues: 363 loop : -2.05 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 503 TYR 0.021 0.002 TYR D 217 PHE 0.016 0.002 PHE A 376 TRP 0.022 0.002 TRP C 479 HIS 0.013 0.002 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.27 (15471) covalent geometry : angle 0.85753 / 0.41 (21042) SS BOND : bond 0.00348 / 0.20 ( 33) SS BOND : angle 0.77173 / 0.59 ( 66) hydrogen bonds : bond 0.04140 / 2.69 ( 426) hydrogen bonds : angle 5.50523 / 3.98 ( 1215) link_ALPHA1-3 : bond 0.00960 / 0.46 ( 6) link_ALPHA1-3 : angle 2.31197 / 1.56 ( 18) link_ALPHA1-6 : bond 0.00085 / 0.04 ( 6) link_ALPHA1-6 : angle 1.64818 / 0.98 ( 18) link_BETA1-4 : bond 0.00437 / 0.27 ( 33) link_BETA1-4 : angle 2.12747 / 1.52 ( 99) link_BETA1-6 : bond 0.00418 / 0.26 ( 15) link_BETA1-6 : angle 1.40204 / 1.00 ( 45) link_NAG-ASN : bond 0.00691 / 0.46 ( 66) link_NAG-ASN : angle 3.19232 / 2.19 ( 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 164 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.572 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 104 MET cc_start: 0.8940 (tmm) cc_final: 0.8650 (tmm) REVERT: B 584 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7623 (tm-30) REVERT: B 652 GLN cc_start: 0.7551 (mp10) cc_final: 0.6855 (mp10) REVERT: C 95 MET cc_start: 0.9163 (ppp) cc_final: 0.8947 (ppp) REVERT: E 584 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7743 (tm-30) REVERT: E 611 ASN cc_start: 0.7426 (t0) cc_final: 0.7219 (t0) REVERT: E 621 VAL cc_start: 0.8234 (t) cc_final: 0.7880 (t) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.0944 time to fit residues: 25.0906 Evaluate side-chains 123 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.4626 > 50: distance: 29 - 33: 21.396 distance: 33 - 34: 6.954 distance: 34 - 35: 19.353 distance: 34 - 37: 8.697 distance: 35 - 36: 44.883 distance: 35 - 40: 11.969 distance: 37 - 38: 25.733 distance: 37 - 39: 35.813 distance: 40 - 41: 27.850 distance: 40 - 46: 11.105 distance: 41 - 42: 26.178 distance: 41 - 44: 15.265 distance: 42 - 43: 11.347 distance: 42 - 47: 45.752 distance: 44 - 45: 3.657 distance: 45 - 46: 35.121 distance: 47 - 48: 6.687 distance: 48 - 49: 16.479 distance: 48 - 51: 16.504 distance: 49 - 50: 40.345 distance: 49 - 54: 5.672 distance: 51 - 52: 6.194 distance: 51 - 53: 43.590 distance: 54 - 55: 8.412 distance: 55 - 56: 9.177 distance: 55 - 58: 24.324 distance: 56 - 57: 7.691 distance: 56 - 62: 31.034 distance: 58 - 59: 27.792 distance: 59 - 60: 29.489 distance: 59 - 61: 16.363 distance: 62 - 63: 15.957 distance: 62 - 68: 17.725 distance: 63 - 64: 33.325 distance: 63 - 66: 24.816 distance: 64 - 65: 20.886 distance: 64 - 69: 19.722 distance: 66 - 67: 17.273 distance: 67 - 68: 17.714 distance: 69 - 70: 12.557 distance: 70 - 71: 12.014 distance: 70 - 73: 9.999 distance: 71 - 72: 7.042 distance: 71 - 76: 19.632 distance: 73 - 74: 14.211 distance: 73 - 75: 19.596 distance: 76 - 77: 40.432 distance: 76 - 82: 16.852 distance: 77 - 78: 16.701 distance: 77 - 80: 19.095 distance: 78 - 79: 26.740 distance: 78 - 83: 35.682 distance: 80 - 81: 8.505 distance: 81 - 82: 29.553 distance: 83 - 84: 18.210 distance: 84 - 85: 6.509 distance: 84 - 87: 14.518 distance: 85 - 86: 17.032 distance: 85 - 92: 19.537 distance: 87 - 88: 18.735 distance: 88 - 89: 8.360 distance: 89 - 90: 7.953 distance: 89 - 91: 14.843 distance: 92 - 93: 4.393 distance: 93 - 94: 7.487 distance: 93 - 96: 9.699 distance: 94 - 95: 13.087 distance: 94 - 101: 4.090 distance: 97 - 98: 8.163 distance: 98 - 99: 5.953 distance: 98 - 100: 10.622 distance: 101 - 102: 7.944 distance: 101 - 136: 9.565 distance: 102 - 105: 9.228 distance: 103 - 108: 9.291 distance: 104 - 133: 7.960 distance: 105 - 106: 8.198 distance: 105 - 107: 6.594