Starting phenix.real_space_refine on Sat Mar 16 18:33:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ohy_20074/03_2024/6ohy_20074.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ohy_20074/03_2024/6ohy_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ohy_20074/03_2024/6ohy_20074.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ohy_20074/03_2024/6ohy_20074.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ohy_20074/03_2024/6ohy_20074.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ohy_20074/03_2024/6ohy_20074.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15192 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3547 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 24, 'TRANS': 422} Chain breaks: 2 Chain: "B" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 964 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 3547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3547 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 24, 'TRANS': 422} Chain breaks: 2 Chain: "E" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 964 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'TRANS': 119} Chain breaks: 1 Chain: "D" Number of atoms: 3547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3547 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 24, 'TRANS': 422} Chain breaks: 2 Chain: "F" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 964 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'TRANS': 119} Chain breaks: 1 Chain: "G" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "O" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "c" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "q" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.39, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 7.14 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 1.74 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: 4.41 Time building geometry restraints manager: 7.61 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: 96.54 - 104.05: 199 104.05 - 111.55: 7615 111.55 - 119.05: 5625 119.05 - 126.56: 7290 126.56 - 134.06: 313 Bond angle restraints: 21042 Sorted by residual: angle pdb=" N PHE B 519 " pdb=" CA PHE B 519 " pdb=" C PHE B 519 " ideal model delta sigma weight residual 110.50 118.91 -8.41 1.41e+00 5.03e-01 3.56e+01 angle pdb=" N PHE E 519 " pdb=" CA PHE E 519 " pdb=" C PHE E 519 " ideal model delta sigma weight residual 110.50 118.86 -8.36 1.41e+00 5.03e-01 3.51e+01 angle pdb=" N PHE F 519 " pdb=" CA PHE F 519 " pdb=" C PHE F 519 " ideal model delta sigma weight residual 110.50 118.84 -8.34 1.41e+00 5.03e-01 3.50e+01 angle pdb=" C ASN A 412 " pdb=" N MET A 413 " pdb=" CA MET A 413 " ideal model delta sigma weight residual 121.54 131.45 -9.91 1.91e+00 2.74e-01 2.69e+01 angle pdb=" C ASN D 412 " pdb=" N MET D 413 " pdb=" CA MET D 413 " ideal model delta sigma weight residual 121.54 131.40 -9.86 1.91e+00 2.74e-01 2.66e+01 ... (remaining 21037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.14: 10338 24.14 - 48.28: 442 48.28 - 72.42: 80 72.42 - 96.56: 30 96.56 - 120.70: 27 Dihedral angle restraints: 10917 sinusoidal: 5976 harmonic: 4941 Sorted by residual: dihedral pdb=" CA SER F 534 " pdb=" C SER F 534 " pdb=" N VAL F 535 " pdb=" CA VAL F 535 " ideal model delta harmonic sigma weight residual 180.00 131.35 48.65 0 5.00e+00 4.00e-02 9.47e+01 dihedral pdb=" CA SER B 534 " pdb=" C SER B 534 " pdb=" N VAL B 535 " pdb=" CA VAL B 535 " ideal model delta harmonic sigma weight residual 180.00 131.36 48.64 0 5.00e+00 4.00e-02 9.46e+01 dihedral pdb=" CA SER E 534 " pdb=" C SER E 534 " pdb=" N VAL E 535 " pdb=" CA VAL E 535 " ideal model delta harmonic sigma weight residual 180.00 131.37 48.63 0 5.00e+00 4.00e-02 9.46e+01 ... (remaining 10914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2387 0.095 - 0.189: 322 0.189 - 0.283: 18 0.283 - 0.378: 15 0.378 - 0.472: 9 Chirality restraints: 2751 Sorted by residual: chirality pdb=" C1 NAG u 1 " pdb=" ND2 ASN F 637 " pdb=" C2 NAG u 1 " pdb=" O5 NAG u 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.58e+00 chirality pdb=" CB ILE C 391 " pdb=" CA ILE C 391 " pdb=" CG1 ILE C 391 " pdb=" CG2 ILE C 391 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN B 637 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.94e+00 ... (remaining 2748 not shown) Planarity restraints: 2574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 534 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.18e+00 pdb=" C SER B 534 " 0.046 2.00e-02 2.50e+03 pdb=" O SER B 534 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL B 535 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 534 " 0.013 2.00e-02 2.50e+03 2.68e-02 7.16e+00 pdb=" C SER E 534 " -0.046 2.00e-02 2.50e+03 pdb=" O SER E 534 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL E 535 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 534 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.00e+00 pdb=" C SER F 534 " 0.046 2.00e-02 2.50e+03 pdb=" O SER F 534 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL F 535 " -0.016 2.00e-02 2.50e+03 ... (remaining 2571 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3962 2.81 - 3.33: 13306 3.33 - 3.86: 23997 3.86 - 4.38: 26125 4.38 - 4.90: 44042 Nonbonded interactions: 111432 Sorted by model distance: nonbonded pdb=" NH2 ARG D 503 " pdb=" OD1 ASN F 650 " model vdw 2.288 2.520 nonbonded pdb=" NH2 ARG A 503 " pdb=" OD1 ASN B 650 " model vdw 2.316 2.520 nonbonded pdb=" OH TYR E 586 " pdb=" NE2 GLN F 591 " model vdw 2.316 2.520 nonbonded pdb=" O PHE A 93 " pdb=" OH TYR A 233 " model vdw 2.331 2.440 nonbonded pdb=" O PHE D 93 " pdb=" OH TYR D 233 " model vdw 2.331 2.440 ... (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 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 5.560 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 42.470 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.140 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 15471 Z= 0.465 Angle : 1.113 11.968 21042 Z= 0.547 Chirality : 0.068 0.472 2751 Planarity : 0.007 0.060 2508 Dihedral : 14.531 120.701 7626 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.54 % Allowed : 10.53 % Favored : 88.93 % Rotamer: Outliers : 0.40 % Allowed : 2.39 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.74 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.037 0.004 TRP A 479 HIS 0.007 0.002 HIS C 246 PHE 0.019 0.003 PHE C 53 TYR 0.017 0.003 TYR C 330 ARG 0.005 0.001 ARG D 192 *********************** 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 fitting. rotamer outliers: 6 poor density : 273 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7014 (m-70) cc_final: 0.6581 (m-70) REVERT: A 95 MET cc_start: 0.8705 (ttp) cc_final: 0.8432 (tmm) REVERT: A 98 ASN cc_start: 0.8791 (t0) cc_final: 0.8537 (t0) REVERT: A 104 MET cc_start: 0.8911 (tmm) cc_final: 0.8301 (tmm) REVERT: A 371 VAL cc_start: 0.8629 (m) cc_final: 0.8266 (t) REVERT: B 519 PHE cc_start: 0.7824 (OUTLIER) cc_final: 0.7150 (t80) REVERT: B 611 ASN cc_start: 0.7115 (t0) cc_final: 0.6780 (t0) REVERT: B 612 LYS cc_start: 0.7710 (mttt) cc_final: 0.7354 (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: 0.8205 (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: 0.8369 (mm-30) REVERT: C 66 HIS cc_start: 0.6837 (m-70) cc_final: 0.6571 (m-70) REVERT: C 95 MET cc_start: 0.8853 (ttp) cc_final: 0.8563 (tmm) REVERT: C 98 ASN cc_start: 0.8791 (t0) cc_final: 0.8400 (t0) REVERT: C 104 MET cc_start: 0.8893 (tmm) cc_final: 0.8555 (tmm) REVERT: C 270 THR cc_start: 0.9009 (m) cc_final: 0.8745 (p) REVERT: C 371 VAL cc_start: 0.8591 (m) cc_final: 0.8260 (t) REVERT: C 430 VAL cc_start: 0.5747 (t) cc_final: 0.5387 (t) REVERT: E 611 ASN cc_start: 0.7286 (t0) cc_final: 0.6709 (t0) REVERT: E 612 LYS cc_start: 0.7782 (mttt) cc_final: 0.7531 (ttpp) REVERT: E 633 ARG cc_start: 0.8685 (mtt-85) cc_final: 0.8105 (ptt90) REVERT: E 652 GLN cc_start: 0.8332 (mt0) cc_final: 0.8058 (mt0) REVERT: D 66 HIS cc_start: 0.6786 (m-70) cc_final: 0.6565 (m-70) REVERT: D 95 MET cc_start: 0.8655 (ttp) cc_final: 0.8445 (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: 0.8565 (tmm) REVERT: D 371 VAL cc_start: 0.8631 (m) cc_final: 0.8208 (t) REVERT: F 519 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7374 (t80) REVERT: F 611 ASN cc_start: 0.7198 (t0) cc_final: 0.6823 (t0) REVERT: F 612 LYS cc_start: 0.7657 (mttt) cc_final: 0.7273 (ttpp) REVERT: F 633 ARG cc_start: 0.8303 (mtt-85) cc_final: 0.8045 (ptt90) outliers start: 6 outliers final: 3 residues processed: 279 average time/residue: 0.2833 time to fit residues: 114.1149 Evaluate side-chains 149 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 144 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 2.9990 chunk 127 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 195 ASN A 249 HIS ** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 HIS ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN B 624 ASN ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN C 195 ASN C 249 HIS ** C 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 GLN E 590 GLN E 591 GLN ** E 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 GLN D 195 ASN D 249 HIS ** D 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 492 GLN F 590 GLN F 591 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15471 Z= 0.206 Angle : 0.751 10.020 21042 Z= 0.371 Chirality : 0.052 0.301 2751 Planarity : 0.005 0.062 2508 Dihedral : 13.432 105.336 4386 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.63 % Favored : 90.01 % Rotamer: Outliers : 0.20 % Allowed : 2.79 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.19), residues: 1671 helix: -1.10 (0.24), residues: 345 sheet: -1.31 (0.24), residues: 348 loop : -1.99 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 112 HIS 0.004 0.001 HIS D 374 PHE 0.023 0.002 PHE A 376 TYR 0.027 0.001 TYR F 638 ARG 0.003 0.000 ARG F 585 *********************** 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 211 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 208 time to evaluate : 1.898 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 66 HIS cc_start: 0.7162 (m-70) cc_final: 0.6761 (m-70) REVERT: A 95 MET cc_start: 0.8724 (ttp) cc_final: 0.8505 (tmm) REVERT: A 98 ASN cc_start: 0.8751 (t0) cc_final: 0.8347 (t0) REVERT: A 234 LYS cc_start: 0.9399 (mmtt) cc_final: 0.9066 (tmtt) REVERT: A 370 GLU cc_start: 0.7697 (mp0) cc_final: 0.6532 (tt0) REVERT: B 611 ASN cc_start: 0.7060 (t0) cc_final: 0.6729 (t0) REVERT: B 612 LYS cc_start: 0.7683 (mttt) cc_final: 0.7331 (ttpp) REVERT: B 614 TRP cc_start: 0.7739 (m-10) cc_final: 0.6738 (m-10) REVERT: B 633 ARG cc_start: 0.8608 (mtt-85) cc_final: 0.8145 (ptt90) REVERT: B 659 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8275 (mm-30) REVERT: C 66 HIS cc_start: 0.6921 (m-70) cc_final: 0.6528 (m-70) REVERT: C 95 MET cc_start: 0.8897 (ttp) cc_final: 0.8622 (tmm) REVERT: C 234 LYS cc_start: 0.9320 (mmtt) cc_final: 0.8852 (tmtt) REVERT: C 370 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6567 (tt0) REVERT: C 479 TRP cc_start: 0.8435 (m-10) cc_final: 0.7887 (m-90) REVERT: C 501 CYS cc_start: 0.4105 (p) cc_final: 0.3870 (p) REVERT: E 611 ASN cc_start: 0.7295 (t0) cc_final: 0.6743 (t0) REVERT: E 612 LYS cc_start: 0.7765 (mttt) cc_final: 0.7552 (ttpp) REVERT: E 630 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8224 (mm-40) REVERT: E 633 ARG cc_start: 0.8663 (mtt-85) cc_final: 0.8042 (ptt90) REVERT: D 66 HIS cc_start: 0.6942 (m-70) cc_final: 0.6459 (m-70) REVERT: D 95 MET cc_start: 0.8678 (ttp) cc_final: 0.8394 (tmm) REVERT: D 234 LYS cc_start: 0.9369 (mmtt) cc_final: 0.8975 (tmtt) REVERT: D 370 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6341 (tt0) REVERT: F 523 LEU cc_start: 0.8255 (pp) cc_final: 0.7997 (pp) REVERT: F 614 TRP cc_start: 0.7374 (m-10) cc_final: 0.6502 (m-10) REVERT: F 633 ARG cc_start: 0.8204 (mtt-85) cc_final: 0.7914 (ptt90) REVERT: F 647 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7631 (mm-30) REVERT: F 648 GLU cc_start: 0.8633 (tt0) cc_final: 0.7894 (tp30) REVERT: F 651 THR cc_start: 0.8717 (p) cc_final: 0.7286 (p) REVERT: F 652 GLN cc_start: 0.8066 (mt0) cc_final: 0.7220 (mp10) REVERT: F 659 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8017 (mm-30) outliers start: 3 outliers final: 0 residues processed: 208 average time/residue: 0.2652 time to fit residues: 81.9728 Evaluate side-chains 152 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 150 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 165 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 GLN ** 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** E 590 GLN ** E 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 590 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 15471 Z= 0.438 Angle : 0.873 10.107 21042 Z= 0.423 Chirality : 0.053 0.314 2751 Planarity : 0.005 0.051 2508 Dihedral : 12.754 106.831 4386 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.55 % Favored : 88.27 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.19), residues: 1671 helix: -0.97 (0.25), residues: 345 sheet: -1.19 (0.24), residues: 348 loop : -2.00 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 112 HIS 0.011 0.002 HIS A 374 PHE 0.021 0.003 PHE C 376 TYR 0.023 0.002 TYR F 638 ARG 0.004 0.001 ARG F 585 *********************** 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 180 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.675 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 95 MET cc_start: 0.8779 (ttp) cc_final: 0.8499 (tmm) REVERT: A 98 ASN cc_start: 0.8774 (t0) cc_final: 0.8456 (t0) REVERT: A 370 GLU cc_start: 0.7357 (mp0) cc_final: 0.6638 (tt0) REVERT: A 428 MET cc_start: 0.6875 (mtt) cc_final: 0.6495 (mtt) REVERT: B 579 ARG cc_start: 0.7240 (mtt-85) cc_final: 0.6993 (mtp85) REVERT: B 584 GLU cc_start: 0.8536 (tt0) cc_final: 0.8267 (tm-30) REVERT: B 611 ASN cc_start: 0.7537 (t0) cc_final: 0.7263 (t0) REVERT: B 621 VAL cc_start: 0.8707 (t) cc_final: 0.8451 (t) REVERT: B 633 ARG cc_start: 0.8681 (mtt-85) cc_final: 0.8207 (ptt90) REVERT: B 648 GLU cc_start: 0.8654 (tt0) cc_final: 0.8157 (tp30) REVERT: C 95 MET cc_start: 0.8915 (ttp) cc_final: 0.8599 (tmm) REVERT: C 98 ASN cc_start: 0.8867 (t0) cc_final: 0.8596 (t0) REVERT: C 370 GLU cc_start: 0.7300 (mp0) cc_final: 0.6662 (tt0) REVERT: C 428 MET cc_start: 0.6536 (mtm) cc_final: 0.6093 (mtm) REVERT: E 535 VAL cc_start: 0.6567 (t) cc_final: 0.6334 (t) REVERT: E 579 ARG cc_start: 0.7243 (mtt-85) cc_final: 0.6843 (mtp85) REVERT: E 611 ASN cc_start: 0.7408 (t0) cc_final: 0.6895 (t0) REVERT: E 612 LYS cc_start: 0.7781 (mttt) cc_final: 0.7462 (ttpp) REVERT: E 630 GLN cc_start: 0.9093 (mm-40) cc_final: 0.8803 (mm-40) REVERT: E 633 ARG cc_start: 0.8762 (mtt-85) cc_final: 0.8136 (ptt90) REVERT: E 648 GLU cc_start: 0.8498 (tt0) cc_final: 0.8231 (tp30) REVERT: D 95 MET cc_start: 0.8779 (ttp) cc_final: 0.8528 (tmm) REVERT: D 180 ASP cc_start: 0.8391 (m-30) cc_final: 0.8182 (m-30) REVERT: D 370 GLU cc_start: 0.7227 (mp0) cc_final: 0.6454 (tt0) REVERT: D 423 ILE cc_start: 0.9518 (mt) cc_final: 0.9313 (tp) REVERT: D 428 MET cc_start: 0.6361 (mtm) cc_final: 0.5839 (mtm) REVERT: F 611 ASN cc_start: 0.7572 (t0) cc_final: 0.6949 (t0) REVERT: F 612 LYS cc_start: 0.7885 (mttt) cc_final: 0.7185 (ttpp) REVERT: F 614 TRP cc_start: 0.7690 (m-10) cc_final: 0.6688 (m-10) REVERT: F 621 VAL cc_start: 0.8817 (t) cc_final: 0.8581 (t) REVERT: F 633 ARG cc_start: 0.8470 (mtt-85) cc_final: 0.8084 (ptt90) REVERT: F 651 THR cc_start: 0.8564 (p) cc_final: 0.8015 (p) REVERT: F 652 GLN cc_start: 0.8412 (mt0) cc_final: 0.8125 (mm-40) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2715 time to fit residues: 72.0232 Evaluate side-chains 142 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 102 optimal weight: 0.0970 chunk 153 optimal weight: 0.8980 chunk 162 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 145 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 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** ** E 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15471 Z= 0.175 Angle : 0.724 12.215 21042 Z= 0.345 Chirality : 0.057 0.816 2751 Planarity : 0.004 0.051 2508 Dihedral : 11.441 103.820 4386 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.62 % Favored : 91.32 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.19), residues: 1671 helix: -0.42 (0.27), residues: 348 sheet: -1.13 (0.25), residues: 348 loop : -1.77 (0.19), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 112 HIS 0.007 0.002 HIS A 375 PHE 0.015 0.002 PHE A 376 TYR 0.018 0.001 TYR F 638 ARG 0.003 0.000 ARG A 429 *********************** 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 192 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.757 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 95 MET cc_start: 0.8776 (ttp) cc_final: 0.8447 (tmm) REVERT: A 98 ASN cc_start: 0.8769 (t0) cc_final: 0.8237 (t0) REVERT: A 370 GLU cc_start: 0.7115 (mp0) cc_final: 0.6511 (tt0) REVERT: A 428 MET cc_start: 0.6602 (mtt) cc_final: 0.6111 (mtt) REVERT: A 470 LEU cc_start: 0.7217 (mt) cc_final: 0.6327 (tp) REVERT: B 579 ARG cc_start: 0.7132 (mtt-85) cc_final: 0.6806 (mtp85) REVERT: B 611 ASN cc_start: 0.7413 (t0) cc_final: 0.7049 (t0) REVERT: B 612 LYS cc_start: 0.7812 (mttt) cc_final: 0.7220 (ttpt) REVERT: B 621 VAL cc_start: 0.8680 (t) cc_final: 0.8451 (t) REVERT: B 633 ARG cc_start: 0.8672 (mtt-85) cc_final: 0.8220 (ptt90) REVERT: B 648 GLU cc_start: 0.8577 (tt0) cc_final: 0.8029 (tp30) REVERT: C 95 MET cc_start: 0.8846 (ttp) cc_final: 0.8585 (tmm) REVERT: C 98 ASN cc_start: 0.8675 (t0) cc_final: 0.8449 (t0) REVERT: C 370 GLU cc_start: 0.7019 (mp0) cc_final: 0.6579 (tt0) REVERT: C 428 MET cc_start: 0.6160 (mtm) cc_final: 0.5565 (mtt) REVERT: C 470 LEU cc_start: 0.7433 (mt) cc_final: 0.6402 (tp) REVERT: C 501 CYS cc_start: 0.4116 (p) cc_final: 0.3900 (p) REVERT: E 579 ARG cc_start: 0.7208 (mtt-85) cc_final: 0.6752 (mtp85) REVERT: E 611 ASN cc_start: 0.7242 (t0) cc_final: 0.6701 (t0) REVERT: E 612 LYS cc_start: 0.7863 (mttt) cc_final: 0.7504 (ttpp) REVERT: E 630 GLN cc_start: 0.9006 (mm-40) cc_final: 0.8448 (mm110) REVERT: E 633 ARG cc_start: 0.8775 (mtt-85) cc_final: 0.8115 (ptt90) REVERT: E 648 GLU cc_start: 0.8373 (tt0) cc_final: 0.8116 (tp30) REVERT: D 95 MET cc_start: 0.8842 (ttp) cc_final: 0.8525 (tmm) REVERT: D 370 GLU cc_start: 0.7046 (mp0) cc_final: 0.6236 (tt0) REVERT: D 423 ILE cc_start: 0.9514 (mt) cc_final: 0.9207 (mt) REVERT: D 428 MET cc_start: 0.5819 (mtm) cc_final: 0.5303 (mtt) REVERT: D 470 LEU cc_start: 0.7199 (mt) cc_final: 0.6342 (tp) REVERT: F 611 ASN cc_start: 0.7508 (t0) cc_final: 0.6985 (t0) REVERT: F 612 LYS cc_start: 0.7863 (mttt) cc_final: 0.7261 (ttpt) REVERT: F 614 TRP cc_start: 0.7526 (m-10) cc_final: 0.6580 (m-10) REVERT: F 621 VAL cc_start: 0.8711 (t) cc_final: 0.8508 (t) REVERT: F 633 ARG cc_start: 0.8480 (mtt-85) cc_final: 0.8049 (ptt90) REVERT: F 647 GLU cc_start: 0.7968 (tt0) cc_final: 0.7330 (mm-30) REVERT: F 648 GLU cc_start: 0.8603 (tt0) cc_final: 0.7694 (tp30) REVERT: F 651 THR cc_start: 0.8401 (p) cc_final: 0.7457 (m) REVERT: F 652 GLN cc_start: 0.8192 (mt0) cc_final: 0.7220 (mp10) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.2731 time to fit residues: 77.5018 Evaluate side-chains 144 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.0370 chunk 92 optimal weight: 0.3980 chunk 2 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 overall best weight: 1.8864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 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** ** E 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 624 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15471 Z= 0.251 Angle : 0.744 10.475 21042 Z= 0.357 Chirality : 0.052 0.473 2751 Planarity : 0.004 0.066 2508 Dihedral : 10.717 101.165 4386 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.11 % Favored : 89.71 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.20), residues: 1671 helix: -0.33 (0.27), residues: 351 sheet: -1.01 (0.25), residues: 351 loop : -1.75 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 112 HIS 0.008 0.002 HIS A 374 PHE 0.019 0.002 PHE A 376 TYR 0.012 0.001 TYR F 638 ARG 0.003 0.000 ARG F 585 *********************** 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 175 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.517 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 95 MET cc_start: 0.8807 (ttp) cc_final: 0.8517 (tmm) REVERT: A 98 ASN cc_start: 0.8666 (t0) cc_final: 0.8200 (t0) REVERT: A 370 GLU cc_start: 0.7265 (mp0) cc_final: 0.6811 (tt0) REVERT: A 470 LEU cc_start: 0.7507 (mt) cc_final: 0.6589 (tp) REVERT: B 579 ARG cc_start: 0.7176 (mtt-85) cc_final: 0.6929 (mtp85) REVERT: B 611 ASN cc_start: 0.7399 (t0) cc_final: 0.6944 (t0) REVERT: B 612 LYS cc_start: 0.7752 (mttt) cc_final: 0.7265 (ttpt) REVERT: B 621 VAL cc_start: 0.8689 (t) cc_final: 0.8456 (t) REVERT: B 633 ARG cc_start: 0.8732 (mtt-85) cc_final: 0.8257 (ptt90) REVERT: B 648 GLU cc_start: 0.8629 (tt0) cc_final: 0.7549 (tp30) REVERT: B 652 GLN cc_start: 0.7824 (mp10) cc_final: 0.6635 (mp10) REVERT: C 95 MET cc_start: 0.8901 (ttp) cc_final: 0.8664 (tmm) REVERT: C 104 MET cc_start: 0.8483 (tmm) cc_final: 0.7992 (tmm) REVERT: C 370 GLU cc_start: 0.7057 (mp0) cc_final: 0.6722 (tt0) REVERT: C 428 MET cc_start: 0.6536 (mtm) cc_final: 0.6041 (mtt) REVERT: E 611 ASN cc_start: 0.7360 (t0) cc_final: 0.6880 (t0) REVERT: E 612 LYS cc_start: 0.7880 (mttt) cc_final: 0.7451 (ttpp) REVERT: E 630 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8511 (mm110) REVERT: E 633 ARG cc_start: 0.8821 (mtt-85) cc_final: 0.8151 (ptt90) REVERT: E 648 GLU cc_start: 0.8413 (tt0) cc_final: 0.8137 (tp30) REVERT: D 95 MET cc_start: 0.8819 (ttp) cc_final: 0.8561 (tmm) REVERT: D 180 ASP cc_start: 0.8411 (m-30) cc_final: 0.8195 (m-30) REVERT: D 423 ILE cc_start: 0.9542 (mt) cc_final: 0.9204 (mt) REVERT: D 470 LEU cc_start: 0.7396 (mt) cc_final: 0.6437 (tp) REVERT: F 579 ARG cc_start: 0.7250 (mtt-85) cc_final: 0.6778 (mtp85) REVERT: F 611 ASN cc_start: 0.7517 (t0) cc_final: 0.7195 (t0) REVERT: F 612 LYS cc_start: 0.7869 (mttt) cc_final: 0.7158 (mtpp) REVERT: F 621 VAL cc_start: 0.8729 (t) cc_final: 0.8522 (t) REVERT: F 633 ARG cc_start: 0.8521 (mtt-85) cc_final: 0.8098 (ptt90) REVERT: F 650 ASN cc_start: 0.8452 (t0) cc_final: 0.8206 (t0) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2693 time to fit residues: 69.4590 Evaluate side-chains 133 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 162 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 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** ** E 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15471 Z= 0.188 Angle : 0.703 13.159 21042 Z= 0.335 Chirality : 0.052 0.394 2751 Planarity : 0.004 0.066 2508 Dihedral : 10.194 98.378 4386 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.20), residues: 1671 helix: -0.05 (0.28), residues: 351 sheet: -1.40 (0.24), residues: 378 loop : -1.64 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 112 HIS 0.007 0.001 HIS D 375 PHE 0.015 0.001 PHE D 376 TYR 0.011 0.001 TYR C 217 ARG 0.005 0.000 ARG D 429 *********************** 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 175 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.658 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 95 MET cc_start: 0.8838 (ttp) cc_final: 0.8497 (tmm) REVERT: A 98 ASN cc_start: 0.8764 (t0) cc_final: 0.8307 (t0) REVERT: A 470 LEU cc_start: 0.7065 (mt) cc_final: 0.6678 (tt) REVERT: B 579 ARG cc_start: 0.7212 (mtt-85) cc_final: 0.6850 (mtp85) REVERT: B 611 ASN cc_start: 0.7345 (t0) cc_final: 0.6989 (t0) REVERT: B 612 LYS cc_start: 0.7844 (mttt) cc_final: 0.7304 (ttpt) REVERT: B 621 VAL cc_start: 0.8664 (t) cc_final: 0.8441 (t) REVERT: B 633 ARG cc_start: 0.8713 (mtt-85) cc_final: 0.8225 (ptt90) REVERT: B 648 GLU cc_start: 0.8594 (tt0) cc_final: 0.7487 (tp30) REVERT: B 652 GLN cc_start: 0.7579 (mp10) cc_final: 0.6276 (mp10) REVERT: C 95 MET cc_start: 0.8836 (ttp) cc_final: 0.8635 (tmm) REVERT: C 470 LEU cc_start: 0.7050 (mt) cc_final: 0.6645 (tt) REVERT: E 611 ASN cc_start: 0.7315 (t0) cc_final: 0.6803 (t0) REVERT: E 612 LYS cc_start: 0.7917 (mttt) cc_final: 0.7458 (ttpp) REVERT: E 621 VAL cc_start: 0.8801 (t) cc_final: 0.8498 (t) REVERT: E 630 GLN cc_start: 0.9003 (mm-40) cc_final: 0.8453 (mm-40) REVERT: E 633 ARG cc_start: 0.8836 (mtt-85) cc_final: 0.8197 (ptt90) REVERT: E 648 GLU cc_start: 0.8438 (tt0) cc_final: 0.8123 (tp30) REVERT: D 95 MET cc_start: 0.8837 (ttp) cc_final: 0.8544 (tmm) REVERT: D 423 ILE cc_start: 0.9531 (mt) cc_final: 0.9256 (mt) REVERT: D 458 LYS cc_start: 0.4585 (mmtm) cc_final: 0.4361 (mmtm) REVERT: D 470 LEU cc_start: 0.7062 (mt) cc_final: 0.6614 (tt) REVERT: F 579 ARG cc_start: 0.7240 (mtt-85) cc_final: 0.6722 (mtp85) REVERT: F 611 ASN cc_start: 0.7539 (t0) cc_final: 0.7102 (t0) REVERT: F 612 LYS cc_start: 0.7849 (mttt) cc_final: 0.7167 (mtpp) REVERT: F 633 ARG cc_start: 0.8580 (mtt-85) cc_final: 0.8178 (ptt90) REVERT: F 648 GLU cc_start: 0.8421 (tt0) cc_final: 0.8142 (tp30) REVERT: F 651 THR cc_start: 0.8287 (m) cc_final: 0.7960 (m) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2646 time to fit residues: 68.3643 Evaluate side-chains 141 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 90 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 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** ** E 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 ASN ** D 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15471 Z= 0.319 Angle : 0.773 11.566 21042 Z= 0.371 Chirality : 0.052 0.337 2751 Planarity : 0.005 0.064 2508 Dihedral : 10.194 95.440 4386 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.61 % Favored : 88.33 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.19), residues: 1671 helix: -0.26 (0.27), residues: 351 sheet: -0.92 (0.24), residues: 366 loop : -1.92 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 112 HIS 0.009 0.002 HIS A 374 PHE 0.014 0.002 PHE A 376 TYR 0.015 0.002 TYR C 217 ARG 0.004 0.000 ARG C 429 *********************** 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 172 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.665 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 95 MET cc_start: 0.8834 (ttp) cc_final: 0.8494 (tmm) REVERT: A 104 MET cc_start: 0.8872 (tmm) cc_final: 0.8637 (tmm) REVERT: B 584 GLU cc_start: 0.8426 (tt0) cc_final: 0.8176 (tm-30) REVERT: B 611 ASN cc_start: 0.7527 (t0) cc_final: 0.7070 (t0) REVERT: B 612 LYS cc_start: 0.7773 (mttt) cc_final: 0.7291 (ttpt) REVERT: B 621 VAL cc_start: 0.8650 (t) cc_final: 0.8420 (t) REVERT: B 633 ARG cc_start: 0.8785 (mtt-85) cc_final: 0.8313 (ptt90) REVERT: B 648 GLU cc_start: 0.8643 (tt0) cc_final: 0.8048 (tp30) REVERT: C 47 GLU cc_start: 0.7852 (tp30) cc_final: 0.7637 (mt-10) REVERT: E 584 GLU cc_start: 0.8558 (tt0) cc_final: 0.8283 (tm-30) REVERT: E 611 ASN cc_start: 0.7402 (t0) cc_final: 0.6941 (t0) REVERT: E 612 LYS cc_start: 0.7987 (mttt) cc_final: 0.7539 (ttpt) REVERT: E 621 VAL cc_start: 0.8638 (t) cc_final: 0.8332 (t) REVERT: E 630 GLN cc_start: 0.9109 (mm-40) cc_final: 0.8894 (mm110) REVERT: E 633 ARG cc_start: 0.8883 (mtt-85) cc_final: 0.8334 (ptt90) REVERT: E 648 GLU cc_start: 0.8464 (tt0) cc_final: 0.8135 (tp30) REVERT: D 95 MET cc_start: 0.8855 (ttp) cc_final: 0.8566 (tmm) REVERT: D 180 ASP cc_start: 0.8452 (m-30) cc_final: 0.8201 (m-30) REVERT: D 423 ILE cc_start: 0.9545 (mt) cc_final: 0.9299 (tp) REVERT: D 458 LYS cc_start: 0.4840 (mmtm) cc_final: 0.4491 (mmtm) REVERT: D 470 LEU cc_start: 0.7535 (mt) cc_final: 0.7302 (tp) REVERT: F 611 ASN cc_start: 0.7561 (t0) cc_final: 0.7125 (t0) REVERT: F 612 LYS cc_start: 0.7826 (mttt) cc_final: 0.7199 (mtpp) REVERT: F 633 ARG cc_start: 0.8724 (mtt-85) cc_final: 0.8293 (ptt90) REVERT: F 638 TYR cc_start: 0.7094 (m-80) cc_final: 0.6782 (m-10) REVERT: F 648 GLU cc_start: 0.8637 (tt0) cc_final: 0.8227 (tp30) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.2752 time to fit residues: 69.4742 Evaluate side-chains 129 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 0.3980 chunk 102 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 147 optimal weight: 1.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 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** ** E 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 15471 Z= 0.371 Angle : 0.807 12.442 21042 Z= 0.387 Chirality : 0.052 0.304 2751 Planarity : 0.005 0.062 2508 Dihedral : 10.253 92.649 4386 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.61 % Favored : 88.33 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.19), residues: 1671 helix: -0.43 (0.27), residues: 351 sheet: -0.99 (0.25), residues: 348 loop : -2.11 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 112 HIS 0.012 0.002 HIS A 374 PHE 0.020 0.002 PHE C 376 TYR 0.018 0.002 TYR A 217 ARG 0.008 0.001 ARG D 503 *********************** 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 162 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.703 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: A 95 MET cc_start: 0.8881 (ttp) cc_final: 0.8520 (tmm) REVERT: B 584 GLU cc_start: 0.8614 (tt0) cc_final: 0.8290 (tm-30) REVERT: B 611 ASN cc_start: 0.7621 (t0) cc_final: 0.7283 (t0) REVERT: B 612 LYS cc_start: 0.7836 (mttt) cc_final: 0.7376 (ttpt) REVERT: B 621 VAL cc_start: 0.8679 (t) cc_final: 0.8467 (t) REVERT: B 633 ARG cc_start: 0.8849 (mtt-85) cc_final: 0.8356 (ptt90) REVERT: B 648 GLU cc_start: 0.8701 (tt0) cc_final: 0.8095 (tp30) REVERT: E 584 GLU cc_start: 0.8677 (tt0) cc_final: 0.8321 (tm-30) REVERT: E 611 ASN cc_start: 0.7477 (t0) cc_final: 0.7103 (t0) REVERT: E 612 LYS cc_start: 0.7884 (mttt) cc_final: 0.7378 (ttpt) REVERT: E 621 VAL cc_start: 0.8418 (t) cc_final: 0.8149 (t) REVERT: E 630 GLN cc_start: 0.9186 (mm-40) cc_final: 0.8978 (mm110) REVERT: E 633 ARG cc_start: 0.8900 (mtt-85) cc_final: 0.8373 (ptt90) REVERT: E 648 GLU cc_start: 0.8474 (tt0) cc_final: 0.8093 (tp30) REVERT: D 95 MET cc_start: 0.8891 (ttp) cc_final: 0.8580 (tmm) REVERT: D 180 ASP cc_start: 0.8541 (m-30) cc_final: 0.8302 (m-30) REVERT: D 423 ILE cc_start: 0.9540 (mt) cc_final: 0.9312 (tp) REVERT: D 470 LEU cc_start: 0.7572 (mt) cc_final: 0.7318 (tt) REVERT: F 584 GLU cc_start: 0.8526 (tt0) cc_final: 0.8213 (tm-30) REVERT: F 611 ASN cc_start: 0.7414 (t0) cc_final: 0.7153 (t0) REVERT: F 612 LYS cc_start: 0.7806 (mttt) cc_final: 0.7150 (mtpp) REVERT: F 633 ARG cc_start: 0.8808 (mtt-85) cc_final: 0.8320 (ptt90) REVERT: F 638 TYR cc_start: 0.7080 (m-80) cc_final: 0.6564 (m-10) REVERT: F 648 GLU cc_start: 0.8652 (tt0) cc_final: 0.7814 (tp30) REVERT: F 652 GLN cc_start: 0.7766 (mp10) cc_final: 0.6104 (mp10) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2656 time to fit residues: 64.9687 Evaluate side-chains 122 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 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** ** E 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 15471 Z= 0.365 Angle : 0.809 11.266 21042 Z= 0.388 Chirality : 0.052 0.293 2751 Planarity : 0.005 0.069 2508 Dihedral : 10.177 89.650 4386 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.61 % Favored : 88.33 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.19), residues: 1671 helix: -0.44 (0.27), residues: 351 sheet: -1.08 (0.25), residues: 333 loop : -2.12 (0.18), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP C 427 HIS 0.011 0.002 HIS A 374 PHE 0.018 0.002 PHE A 376 TYR 0.019 0.002 TYR A 191 ARG 0.008 0.001 ARG C 429 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.727 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 95 MET cc_start: 0.8897 (ttp) cc_final: 0.8532 (tmm) REVERT: A 430 VAL cc_start: 0.5955 (t) cc_final: 0.5625 (t) REVERT: B 584 GLU cc_start: 0.8637 (tt0) cc_final: 0.8284 (tm-30) REVERT: B 611 ASN cc_start: 0.7627 (t0) cc_final: 0.7297 (t0) REVERT: B 612 LYS cc_start: 0.7871 (mttt) cc_final: 0.7350 (ttpt) REVERT: B 621 VAL cc_start: 0.8671 (t) cc_final: 0.8468 (t) REVERT: B 633 ARG cc_start: 0.8902 (mtt-85) cc_final: 0.8375 (ptt90) REVERT: B 648 GLU cc_start: 0.8714 (tt0) cc_final: 0.8101 (tp30) REVERT: C 429 ARG cc_start: 0.8158 (mmt180) cc_final: 0.7807 (mmp80) REVERT: E 584 GLU cc_start: 0.8670 (tt0) cc_final: 0.8335 (tm-30) REVERT: E 612 LYS cc_start: 0.7916 (mttt) cc_final: 0.7448 (ttpt) REVERT: E 621 VAL cc_start: 0.8458 (t) cc_final: 0.8204 (t) REVERT: E 630 GLN cc_start: 0.9212 (mm-40) cc_final: 0.8998 (mm110) REVERT: E 633 ARG cc_start: 0.8964 (mtt-85) cc_final: 0.8409 (ptt90) REVERT: E 648 GLU cc_start: 0.8482 (tt0) cc_final: 0.8092 (tp30) REVERT: D 95 MET cc_start: 0.8920 (ttp) cc_final: 0.8588 (tmm) REVERT: D 104 MET cc_start: 0.8915 (tmm) cc_final: 0.8653 (tmm) REVERT: D 154 MET cc_start: 0.9032 (mmm) cc_final: 0.8739 (mmm) REVERT: D 180 ASP cc_start: 0.8531 (m-30) cc_final: 0.8308 (m-30) REVERT: D 423 ILE cc_start: 0.9540 (mt) cc_final: 0.9323 (tp) REVERT: F 584 GLU cc_start: 0.8541 (tt0) cc_final: 0.8232 (tm-30) REVERT: F 611 ASN cc_start: 0.7534 (t0) cc_final: 0.7187 (t0) REVERT: F 612 LYS cc_start: 0.7825 (mttt) cc_final: 0.7155 (mtpp) REVERT: F 633 ARG cc_start: 0.8841 (mtt-85) cc_final: 0.8353 (ptt90) REVERT: F 638 TYR cc_start: 0.7095 (m-80) cc_final: 0.6765 (m-10) REVERT: F 648 GLU cc_start: 0.8644 (tt0) cc_final: 0.8233 (tp30) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2626 time to fit residues: 64.3468 Evaluate side-chains 128 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 167 optimal weight: 7.9990 chunk 154 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 105 optimal weight: 0.6980 chunk 141 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 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** ** E 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 GLN ** D 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15471 Z= 0.191 Angle : 0.726 12.024 21042 Z= 0.349 Chirality : 0.050 0.278 2751 Planarity : 0.005 0.069 2508 Dihedral : 9.316 87.494 4386 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 0.07 % Allowed : 0.40 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.19), residues: 1671 helix: -0.03 (0.28), residues: 351 sheet: -1.31 (0.24), residues: 372 loop : -1.95 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 427 HIS 0.007 0.001 HIS A 374 PHE 0.010 0.001 PHE C 376 TYR 0.023 0.001 TYR C 217 ARG 0.010 0.000 ARG D 480 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 1.656 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: A 95 MET cc_start: 0.8836 (ttp) cc_final: 0.8561 (tmm) REVERT: B 584 GLU cc_start: 0.8519 (tt0) cc_final: 0.8260 (tm-30) REVERT: B 611 ASN cc_start: 0.7585 (t0) cc_final: 0.7160 (t0) REVERT: B 612 LYS cc_start: 0.7786 (mttt) cc_final: 0.7249 (ttpt) REVERT: B 633 ARG cc_start: 0.8827 (mtt-85) cc_final: 0.8319 (ptt90) REVERT: B 652 GLN cc_start: 0.7737 (mp10) cc_final: 0.7235 (mp10) REVERT: C 429 ARG cc_start: 0.7874 (mmt180) cc_final: 0.7418 (mmp80) REVERT: E 584 GLU cc_start: 0.8605 (tt0) cc_final: 0.8271 (tm-30) REVERT: E 611 ASN cc_start: 0.7395 (t0) cc_final: 0.6970 (t0) REVERT: E 612 LYS cc_start: 0.8034 (mttt) cc_final: 0.7480 (ttpt) REVERT: E 621 VAL cc_start: 0.8427 (t) cc_final: 0.8192 (t) REVERT: E 630 GLN cc_start: 0.9112 (mm-40) cc_final: 0.8586 (mm-40) REVERT: E 633 ARG cc_start: 0.8904 (mtt-85) cc_final: 0.8369 (ptt90) REVERT: E 648 GLU cc_start: 0.8473 (tt0) cc_final: 0.8096 (tp30) REVERT: D 95 MET cc_start: 0.8849 (ttp) cc_final: 0.8590 (tmm) REVERT: D 423 ILE cc_start: 0.9530 (mt) cc_final: 0.9240 (mt) REVERT: D 429 ARG cc_start: 0.7847 (mmt180) cc_final: 0.7551 (mmp80) REVERT: F 611 ASN cc_start: 0.7431 (t0) cc_final: 0.7012 (t0) REVERT: F 612 LYS cc_start: 0.7795 (mttt) cc_final: 0.7133 (mtpp) REVERT: F 633 ARG cc_start: 0.8793 (mtt-85) cc_final: 0.8306 (ptt90) REVERT: F 638 TYR cc_start: 0.6721 (m-80) cc_final: 0.6411 (m-10) REVERT: F 648 GLU cc_start: 0.8558 (tt0) cc_final: 0.8078 (tp30) outliers start: 1 outliers final: 0 residues processed: 170 average time/residue: 0.2655 time to fit residues: 67.3843 Evaluate side-chains 132 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 137 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN C 310 GLN ** C 319 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** ** E 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 GLN ** D 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 HIS ** D 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 611 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 = 0.3537 r_free = 0.3537 target = 0.096832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.081610 restraints weight = 43025.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.083276 restraints weight = 31353.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.084451 restraints weight = 25069.104| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15471 Z= 0.239 Angle : 0.725 11.598 21042 Z= 0.347 Chirality : 0.049 0.270 2751 Planarity : 0.005 0.070 2508 Dihedral : 8.824 86.066 4386 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.59 % Favored : 89.35 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.20), residues: 1671 helix: 0.01 (0.28), residues: 351 sheet: -1.33 (0.24), residues: 384 loop : -1.86 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 69 HIS 0.009 0.002 HIS A 374 PHE 0.016 0.002 PHE C 376 TYR 0.019 0.001 TYR D 217 ARG 0.008 0.000 ARG A 429 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2552.29 seconds wall clock time: 47 minutes 37.25 seconds (2857.25 seconds total)