Starting phenix.real_space_refine on Sun May 25 15:15:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ybl_33725/05_2025/7ybl_33725.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ybl_33725/05_2025/7ybl_33725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ybl_33725/05_2025/7ybl_33725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ybl_33725/05_2025/7ybl_33725.map" model { file = "/net/cci-nas-00/data/ceres_data/7ybl_33725/05_2025/7ybl_33725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ybl_33725/05_2025/7ybl_33725.cif" } resolution = 3.6 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 17018 2.51 5 N 4321 2.21 5 O 5369 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.51s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 26819 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1078, 8442 Classifications: {'peptide': 1078} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 58, 'TRANS': 1019} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 8442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1078, 8442 Classifications: {'peptide': 1078} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 58, 'TRANS': 1019} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 8442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1078, 8442 Classifications: {'peptide': 1078} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 58, 'TRANS': 1019} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "W" 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: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 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: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 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: 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: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 15.25, per 1000 atoms: 0.57 Number of scatterers: 26819 At special positions: 0 Unit cell: (139.1, 141.24, 197.95, 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 111 16.00 O 5369 8.00 N 4321 7.00 C 17018 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG E 2 " - " MAN E 3 " " NAG G 2 " - " MAN G 3 " " NAG H 2 " - " MAN H 3 " " NAG J 2 " - " MAN J 3 " " NAG K 2 " - " MAN K 3 " " NAG M 2 " - " MAN M 3 " " NAG N 2 " - " MAN N 3 " " NAG P 2 " - " MAN P 3 " " NAG R 2 " - " MAN R 3 " " NAG S 2 " - " MAN S 3 " " NAG U 2 " - " MAN U 3 " " NAG V 2 " - " MAN V 3 " " NAG X 2 " - " MAN X 3 " " NAG Y 2 " - " MAN Y 3 " " NAG a 2 " - " MAN a 3 " " NAG c 2 " - " MAN c 3 " " NAG d 2 " - " MAN d 3 " " NAG f 2 " - " MAN f 3 " " NAG g 2 " - " MAN g 3 " " NAG i 2 " - " MAN i 3 " " NAG j 2 " - " MAN j 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG 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 c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " BETA1-6 " NAG L 1 " - " FUC L 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG W 1 " - " FUC W 3 " " NAG h 1 " - " FUC h 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 331 " " NAG A1403 " - " ASN A 343 " " NAG A1404 " - " ASN A 603 " " NAG A1405 " - " ASN A 657 " " NAG A1406 " - " ASN A 709 " " NAG A1407 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 331 " " NAG B1403 " - " ASN B 343 " " NAG B1404 " - " ASN B 603 " " NAG B1405 " - " ASN B 657 " " NAG B1406 " - " ASN B 709 " " NAG B1407 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1403 " - " ASN C 331 " " NAG C1404 " - " ASN C 343 " " NAG C1405 " - " ASN C 603 " " NAG C1406 " - " ASN C 657 " " NAG C1407 " - " ASN C 709 " " NAG C1408 " - " ASN C1158 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 122 " " NAG F 1 " - " ASN A 165 " " NAG G 1 " - " ASN A 234 " " NAG H 1 " - " ASN A 282 " " NAG I 1 " - " ASN A 616 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1074 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 17 " " NAG P 1 " - " ASN B 122 " " NAG Q 1 " - " ASN B 165 " " NAG R 1 " - " ASN B 234 " " NAG T 1 " - " ASN B 616 " " NAG U 1 " - " ASN B 717 " " NAG V 1 " - " ASN B 801 " " NAG W 1 " - " ASN B1074 " " NAG X 1 " - " ASN B1098 " " NAG Y 1 " - " ASN B1134 " " NAG Z 1 " - " ASN C 17 " " NAG a 1 " - " ASN C 122 " " NAG b 1 " - " ASN C 165 " " NAG c 1 " - " ASN C 234 " " NAG d 1 " - " ASN C 282 " " NAG e 1 " - " ASN C 616 " " NAG f 1 " - " ASN C 717 " " NAG g 1 " - " ASN C 801 " " NAG h 1 " - " ASN C1074 " " NAG i 1 " - " ASN C1098 " " NAG j 1 " - " ASN C1134 " Time building additional restraints: 8.32 Conformation dependent library (CDL) restraints added in 3.4 seconds 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6060 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 53 sheets defined 26.3% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.39 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.624A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.255A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 618 through 623 removed outlier: 4.291A pdb=" N VAL A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 639 removed outlier: 3.818A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLY A 639 " --> pdb=" O TYR A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.744A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 853 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.954A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 939 removed outlier: 3.669A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.542A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1140 through 1160 removed outlier: 4.164A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.862A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 406 through 411 removed outlier: 3.556A pdb=" N ILE B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA B 411 " --> pdb=" O VAL B 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 406 through 411' Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 634 through 639 removed outlier: 4.317A pdb=" N GLY B 639 " --> pdb=" O TYR B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.532A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.722A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 853 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 4.051A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 3.819A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.455A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 988 through 1033 removed outlier: 4.136A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1160 removed outlier: 3.878A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.790A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.118A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 3.937A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 634 through 639 removed outlier: 3.528A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLY C 639 " --> pdb=" O TYR C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.734A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.504A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.638A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.098A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.195A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1160 removed outlier: 3.876A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR C1160 " --> pdb=" O PHE C1156 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.628A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.628A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.688A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.623A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 121 removed outlier: 12.174A pdb=" N ALA A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.706A pdb=" N GLU A 169 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 11.627A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 9.126A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.469A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.777A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AB4, first strand: chain 'A' and resid 551 through 554 removed outlier: 3.508A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.608A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.529A pdb=" N LYS C 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.119A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.935A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AC2, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.300A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.693A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC5, first strand: chain 'B' and resid 27 through 28 removed outlier: 3.580A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.772A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.650A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN B 122 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN B 125 " --> pdb=" O ASN B 122 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.967A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.974A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 9.972A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.122A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.317A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL B 595 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.555A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD4, first strand: chain 'B' and resid 542 through 543 removed outlier: 3.718A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.523A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.098A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.761A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AE1, first strand: chain 'B' and resid 787 through 790 removed outlier: 5.343A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.570A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.072A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.878A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.652A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 11.614A pdb=" N ALA C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 10.087A pdb=" N GLU C 169 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 11.266A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.468A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.717A pdb=" N ILE C 326 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.717A pdb=" N ILE C 326 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 587 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.520A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AF2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF4, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.509A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.687A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1047 through 1050 removed outlier: 7.131A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AF8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.478A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) 1027 hydrogen bonds defined for protein. 2763 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: 13.46 Time building geometry restraints manager: 9.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7523 1.33 - 1.46: 6466 1.46 - 1.58: 13285 1.58 - 1.70: 1 1.70 - 1.83: 138 Bond restraints: 27413 Sorted by residual: bond pdb=" C LEU B 977 " pdb=" N ASN B 978 " ideal model delta sigma weight residual 1.335 1.470 -0.135 1.36e-02 5.41e+03 9.83e+01 bond pdb=" C VAL A 83 " pdb=" N LEU A 84 " ideal model delta sigma weight residual 1.329 1.385 -0.056 1.35e-02 5.49e+03 1.73e+01 bond pdb=" N PRO B 986 " pdb=" CD PRO B 986 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.71e+01 bond pdb=" N PRO B 899 " pdb=" CD PRO B 899 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.58e+01 bond pdb=" N PRO C 986 " pdb=" CD PRO C 986 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.51e+01 ... (remaining 27408 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.44: 37142 4.44 - 8.88: 126 8.88 - 13.32: 26 13.32 - 17.76: 4 17.76 - 22.19: 5 Bond angle restraints: 37303 Sorted by residual: angle pdb=" O ILE C 993 " pdb=" C ILE C 993 " pdb=" N ASP C 994 " ideal model delta sigma weight residual 122.06 99.87 22.19 1.14e+00 7.69e-01 3.79e+02 angle pdb=" O ILE B 993 " pdb=" C ILE B 993 " pdb=" N ASP B 994 " ideal model delta sigma weight residual 121.87 104.00 17.87 9.70e-01 1.06e+00 3.39e+02 angle pdb=" CA ILE B 993 " pdb=" C ILE B 993 " pdb=" N ASP B 994 " ideal model delta sigma weight residual 117.15 135.17 -18.02 1.14e+00 7.69e-01 2.50e+02 angle pdb=" CA ILE C 993 " pdb=" C ILE C 993 " pdb=" N ASP C 994 " ideal model delta sigma weight residual 117.87 136.91 -19.04 1.25e+00 6.40e-01 2.32e+02 angle pdb=" C ILE B 993 " pdb=" N ASP B 994 " pdb=" CA ASP B 994 " ideal model delta sigma weight residual 120.44 136.94 -16.50 1.30e+00 5.92e-01 1.61e+02 ... (remaining 37298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.18: 16661 24.18 - 48.35: 889 48.35 - 72.53: 130 72.53 - 96.70: 72 96.70 - 120.88: 41 Dihedral angle restraints: 17793 sinusoidal: 8373 harmonic: 9420 Sorted by residual: dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual 93.00 175.82 -82.82 1 1.00e+01 1.00e-02 8.40e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -4.08 -81.92 1 1.00e+01 1.00e-02 8.25e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -11.90 -74.10 1 1.00e+01 1.00e-02 6.97e+01 ... (remaining 17790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 4465 0.133 - 0.267: 74 0.267 - 0.400: 4 0.400 - 0.534: 1 0.534 - 0.667: 1 Chirality restraints: 4545 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 1.04e+01 chirality pdb=" C1 NAG C1403 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1403 " pdb=" O5 NAG C1403 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.34e+00 ... (remaining 4542 not shown) Planarity restraints: 4728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 985 " -0.131 5.00e-02 4.00e+02 1.85e-01 5.47e+01 pdb=" N PRO C 986 " 0.319 5.00e-02 4.00e+02 pdb=" CA PRO C 986 " -0.105 5.00e-02 4.00e+02 pdb=" CD PRO C 986 " -0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 898 " -0.117 5.00e-02 4.00e+02 1.65e-01 4.34e+01 pdb=" N PRO A 899 " 0.284 5.00e-02 4.00e+02 pdb=" CA PRO A 899 " -0.086 5.00e-02 4.00e+02 pdb=" CD PRO A 899 " -0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 898 " -0.117 5.00e-02 4.00e+02 1.64e-01 4.32e+01 pdb=" N PRO C 899 " 0.284 5.00e-02 4.00e+02 pdb=" CA PRO C 899 " -0.086 5.00e-02 4.00e+02 pdb=" CD PRO C 899 " -0.081 5.00e-02 4.00e+02 ... (remaining 4725 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 92 2.44 - 3.05: 17738 3.05 - 3.67: 38714 3.67 - 4.28: 56401 4.28 - 4.90: 92422 Nonbonded interactions: 205367 Sorted by model distance: nonbonded pdb=" OD1 ASP B 985 " pdb=" CD PRO B 987 " model vdw 1.819 3.440 nonbonded pdb=" OG SER C 816 " pdb=" CD PRO C 817 " model vdw 2.003 3.440 nonbonded pdb=" OG SER B 816 " pdb=" CD PRO B 817 " model vdw 2.022 3.440 nonbonded pdb=" OD2 ASP B 985 " pdb=" CG PRO B 987 " model vdw 2.039 3.440 nonbonded pdb=" OG SER B 31 " pdb=" OG SER B 60 " model vdw 2.119 3.040 ... (remaining 205362 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and (resid 14 through 1162 or resid 1401 through 1407)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'I' selection = chain 'O' selection = chain 'Q' selection = chain 'T' selection = chain 'Z' selection = chain 'b' selection = chain 'e' } ncs_group { reference = (chain 'E' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'H' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'h' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) } 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.100 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 63.690 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.170 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4950 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 : 0.006 0.135 27565 Z= 0.329 Angle : 0.988 22.194 37717 Z= 0.583 Chirality : 0.053 0.667 4545 Planarity : 0.009 0.185 4675 Dihedral : 16.195 120.877 11607 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.85 % Favored : 93.96 % Rotamer: Outliers : 0.60 % Allowed : 0.78 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.98 (0.14), residues: 3198 helix: 1.20 (0.20), residues: 720 sheet: -0.60 (0.19), residues: 669 loop : -1.49 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 353 HIS 0.008 0.001 HIS C 49 PHE 0.053 0.002 PHE C 238 TYR 0.035 0.002 TYR A 242 ARG 0.026 0.001 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00536 ( 53) link_NAG-ASN : angle 3.32916 ( 159) link_ALPHA1-4 : bond 0.00470 ( 21) link_ALPHA1-4 : angle 2.14094 ( 63) link_BETA1-4 : bond 0.00639 ( 33) link_BETA1-4 : angle 1.36456 ( 99) hydrogen bonds : bond 0.21963 ( 993) hydrogen bonds : angle 8.29559 ( 2763) link_BETA1-6 : bond 0.00827 ( 3) link_BETA1-6 : angle 1.56760 ( 9) SS BOND : bond 0.00471 ( 42) SS BOND : angle 1.51942 ( 84) covalent geometry : bond 0.00593 (27413) covalent geometry : angle 0.95952 (37303) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 512 time to evaluate : 2.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 645 THR cc_start: 0.6000 (p) cc_final: 0.5564 (p) REVERT: B 1089 PHE cc_start: 0.7064 (m-80) cc_final: 0.6745 (m-10) REVERT: C 38 TYR cc_start: 0.3668 (m-10) cc_final: 0.3391 (m-80) REVERT: C 380 TYR cc_start: 0.6713 (OUTLIER) cc_final: 0.4421 (m-80) REVERT: C 1094 VAL cc_start: 0.3715 (p) cc_final: 0.3385 (p) outliers start: 17 outliers final: 5 residues processed: 526 average time/residue: 0.3600 time to fit residues: 300.6432 Evaluate side-chains 257 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 251 time to evaluate : 2.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 385 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 0.9990 chunk 243 optimal weight: 0.9990 chunk 135 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 164 optimal weight: 6.9990 chunk 129 optimal weight: 0.8980 chunk 251 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 152 optimal weight: 9.9990 chunk 187 optimal weight: 2.9990 chunk 291 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 544 ASN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1118 HIS ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 388 ASN B 777 ASN B1002 GLN B1005 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 935 GLN C1054 GLN C1119 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4991 r_free = 0.4991 target = 0.246307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.222652 restraints weight = 58367.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.223287 restraints weight = 90967.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.223722 restraints weight = 73124.348| |-----------------------------------------------------------------------------| r_work (final): 0.4718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5296 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 27565 Z= 0.175 Angle : 0.798 13.867 37717 Z= 0.384 Chirality : 0.049 0.485 4545 Planarity : 0.006 0.070 4675 Dihedral : 13.227 105.107 5779 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.85 % Favored : 95.06 % Rotamer: Outliers : 2.08 % Allowed : 8.93 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.82 (0.14), residues: 3198 helix: 1.47 (0.20), residues: 714 sheet: -0.54 (0.19), residues: 717 loop : -1.43 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 104 HIS 0.012 0.001 HIS A1118 PHE 0.033 0.002 PHE A 86 TYR 0.020 0.002 TYR B1067 ARG 0.008 0.001 ARG A 995 Details of bonding type rmsd link_NAG-ASN : bond 0.01627 ( 53) link_NAG-ASN : angle 3.13255 ( 159) link_ALPHA1-4 : bond 0.01124 ( 21) link_ALPHA1-4 : angle 2.77901 ( 63) link_BETA1-4 : bond 0.00492 ( 33) link_BETA1-4 : angle 1.68572 ( 99) hydrogen bonds : bond 0.06093 ( 993) hydrogen bonds : angle 6.24599 ( 2763) link_BETA1-6 : bond 0.01486 ( 3) link_BETA1-6 : angle 1.84495 ( 9) SS BOND : bond 0.00506 ( 42) SS BOND : angle 1.72951 ( 84) covalent geometry : bond 0.00363 (27413) covalent geometry : angle 0.75757 (37303) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 308 time to evaluate : 2.482 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 279 TYR cc_start: 0.3939 (m-10) cc_final: 0.3727 (m-10) REVERT: A 571 ASP cc_start: 0.5653 (t0) cc_final: 0.5403 (t0) REVERT: A 602 THR cc_start: 0.6656 (m) cc_final: 0.6228 (t) REVERT: B 494 SER cc_start: 0.5462 (OUTLIER) cc_final: 0.5132 (t) REVERT: B 740 MET cc_start: 0.7697 (tpp) cc_final: 0.7448 (tpp) REVERT: B 775 ASP cc_start: 0.6235 (m-30) cc_final: 0.5931 (m-30) REVERT: B 902 MET cc_start: 0.7430 (tpp) cc_final: 0.7182 (tpt) REVERT: B 916 LEU cc_start: 0.5702 (tp) cc_final: 0.5380 (tp) REVERT: B 1065 VAL cc_start: 0.7684 (t) cc_final: 0.7478 (p) REVERT: C 289 VAL cc_start: 0.2483 (OUTLIER) cc_final: 0.2223 (p) REVERT: C 380 TYR cc_start: 0.6617 (OUTLIER) cc_final: 0.4001 (m-80) REVERT: C 386 LYS cc_start: 0.6025 (OUTLIER) cc_final: 0.5496 (ttpt) REVERT: C 776 LYS cc_start: 0.8581 (tptp) cc_final: 0.8378 (tptt) REVERT: C 906 PHE cc_start: 0.7718 (OUTLIER) cc_final: 0.6665 (t80) outliers start: 59 outliers final: 32 residues processed: 350 average time/residue: 0.3354 time to fit residues: 194.1427 Evaluate side-chains 261 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 224 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 254 optimal weight: 9.9990 chunk 175 optimal weight: 3.9990 chunk 229 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 263 optimal weight: 5.9990 chunk 155 optimal weight: 0.7980 chunk 158 optimal weight: 0.0040 chunk 28 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 236 optimal weight: 8.9990 overall best weight: 2.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 655 HIS A 751 ASN A 774 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1011 GLN A1083 HIS A1108 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS B1108 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS C 658 ASN C 955 ASN C1005 GLN C1054 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.219658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.164442 restraints weight = 51220.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.160642 restraints weight = 40178.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.161305 restraints weight = 30869.144| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.5768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 27565 Z= 0.275 Angle : 1.019 26.190 37717 Z= 0.482 Chirality : 0.059 0.893 4545 Planarity : 0.006 0.078 4675 Dihedral : 11.475 96.696 5771 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.25 % Favored : 93.62 % Rotamer: Outliers : 3.43 % Allowed : 12.78 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.43 (0.14), residues: 3198 helix: 0.61 (0.19), residues: 738 sheet: -0.79 (0.19), residues: 711 loop : -1.75 (0.13), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP B 104 HIS 0.034 0.002 HIS C 49 PHE 0.056 0.003 PHE A 194 TYR 0.025 0.002 TYR B1067 ARG 0.011 0.001 ARG B 44 Details of bonding type rmsd link_NAG-ASN : bond 0.01012 ( 53) link_NAG-ASN : angle 3.66368 ( 159) link_ALPHA1-4 : bond 0.01552 ( 21) link_ALPHA1-4 : angle 3.42768 ( 63) link_BETA1-4 : bond 0.00981 ( 33) link_BETA1-4 : angle 1.77112 ( 99) hydrogen bonds : bond 0.08109 ( 993) hydrogen bonds : angle 6.49682 ( 2763) link_BETA1-6 : bond 0.01671 ( 3) link_BETA1-6 : angle 2.52194 ( 9) SS BOND : bond 0.01122 ( 42) SS BOND : angle 2.13949 ( 84) covalent geometry : bond 0.00611 (27413) covalent geometry : angle 0.97604 (37303) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 285 time to evaluate : 2.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 PHE cc_start: 0.6101 (m-80) cc_final: 0.5878 (m-80) REVERT: A 321 GLN cc_start: 0.7734 (mm110) cc_final: 0.7277 (mm-40) REVERT: A 388 ASN cc_start: 0.6208 (OUTLIER) cc_final: 0.5898 (p0) REVERT: B 104 TRP cc_start: 0.5754 (m-90) cc_final: 0.5139 (m-90) REVERT: B 133 PHE cc_start: 0.1151 (m-80) cc_final: 0.0777 (m-80) REVERT: B 237 ARG cc_start: 0.7142 (ptm160) cc_final: 0.6787 (mtp-110) REVERT: B 304 LYS cc_start: 0.8544 (mmtt) cc_final: 0.8315 (mmmt) REVERT: B 321 GLN cc_start: 0.7648 (mm110) cc_final: 0.7349 (mm-40) REVERT: B 494 SER cc_start: 0.5836 (OUTLIER) cc_final: 0.5461 (t) REVERT: B 591 SER cc_start: 0.6665 (m) cc_final: 0.6002 (p) REVERT: B 611 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7777 (tp) REVERT: B 740 MET cc_start: 0.7758 (tpp) cc_final: 0.7105 (tpp) REVERT: B 969 ASN cc_start: 0.8473 (m110) cc_final: 0.8264 (m110) REVERT: B 1115 ILE cc_start: 0.7117 (OUTLIER) cc_final: 0.6778 (tp) REVERT: C 177 MET cc_start: 0.6984 (mpp) cc_final: 0.5963 (mtp) REVERT: C 776 LYS cc_start: 0.9240 (tptp) cc_final: 0.8998 (tptt) REVERT: C 788 ILE cc_start: 0.7350 (OUTLIER) cc_final: 0.6369 (mt) REVERT: C 1029 MET cc_start: 0.8776 (tpt) cc_final: 0.8536 (tpt) outliers start: 97 outliers final: 49 residues processed: 365 average time/residue: 0.3527 time to fit residues: 208.8176 Evaluate side-chains 249 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 195 time to evaluate : 2.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 278 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 255 optimal weight: 1.9990 chunk 225 optimal weight: 10.0000 chunk 237 optimal weight: 4.9990 chunk 253 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 191 optimal weight: 0.9980 chunk 264 optimal weight: 6.9990 chunk 287 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 658 ASN A 955 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 954 GLN C1011 GLN C1054 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.219009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.175238 restraints weight = 50528.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.170419 restraints weight = 60611.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.172347 restraints weight = 49152.077| |-----------------------------------------------------------------------------| r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.6367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27565 Z= 0.173 Angle : 0.802 15.121 37717 Z= 0.372 Chirality : 0.048 0.429 4545 Planarity : 0.005 0.100 4675 Dihedral : 9.880 91.173 5769 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.25 % Favored : 95.62 % Rotamer: Outliers : 2.90 % Allowed : 16.28 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.12 (0.14), residues: 3198 helix: 1.25 (0.20), residues: 738 sheet: -0.76 (0.19), residues: 711 loop : -1.68 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 104 HIS 0.005 0.001 HIS B1088 PHE 0.035 0.002 PHE B 86 TYR 0.022 0.001 TYR B1067 ARG 0.010 0.001 ARG A 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00746 ( 53) link_NAG-ASN : angle 3.05912 ( 159) link_ALPHA1-4 : bond 0.01760 ( 21) link_ALPHA1-4 : angle 3.02320 ( 63) link_BETA1-4 : bond 0.00612 ( 33) link_BETA1-4 : angle 1.43139 ( 99) hydrogen bonds : bond 0.06145 ( 993) hydrogen bonds : angle 5.79631 ( 2763) link_BETA1-6 : bond 0.01690 ( 3) link_BETA1-6 : angle 2.62817 ( 9) SS BOND : bond 0.00420 ( 42) SS BOND : angle 1.73546 ( 84) covalent geometry : bond 0.00382 (27413) covalent geometry : angle 0.76192 (37303) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 225 time to evaluate : 2.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.2509 (OUTLIER) cc_final: 0.2133 (p) REVERT: A 321 GLN cc_start: 0.7446 (mm110) cc_final: 0.7054 (mm-40) REVERT: A 388 ASN cc_start: 0.6411 (OUTLIER) cc_final: 0.6119 (p0) REVERT: A 634 ARG cc_start: 0.4716 (OUTLIER) cc_final: 0.3810 (ttt180) REVERT: A 900 MET cc_start: 0.7607 (mmt) cc_final: 0.7173 (mmt) REVERT: B 237 ARG cc_start: 0.6721 (ptm160) cc_final: 0.6460 (mtp-110) REVERT: B 304 LYS cc_start: 0.8608 (mmtt) cc_final: 0.8318 (mmmt) REVERT: B 321 GLN cc_start: 0.7450 (mm110) cc_final: 0.7239 (mm-40) REVERT: B 494 SER cc_start: 0.5824 (OUTLIER) cc_final: 0.5444 (t) REVERT: B 602 THR cc_start: 0.7392 (m) cc_final: 0.7155 (t) REVERT: B 902 MET cc_start: 0.8247 (tpt) cc_final: 0.7586 (tpt) REVERT: B 969 ASN cc_start: 0.8505 (m110) cc_final: 0.8286 (m110) REVERT: B 1111 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.6404 (tt0) REVERT: B 1115 ILE cc_start: 0.7165 (OUTLIER) cc_final: 0.6692 (tp) REVERT: C 48 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6657 (mt) REVERT: C 177 MET cc_start: 0.6705 (mpp) cc_final: 0.6474 (mmp) REVERT: C 380 TYR cc_start: 0.7107 (OUTLIER) cc_final: 0.4594 (m-80) REVERT: C 591 SER cc_start: 0.7208 (m) cc_final: 0.6808 (p) REVERT: C 776 LYS cc_start: 0.9247 (tptp) cc_final: 0.8958 (tptt) REVERT: C 902 MET cc_start: 0.7847 (tpp) cc_final: 0.7053 (tpt) REVERT: C 1029 MET cc_start: 0.8606 (tpt) cc_final: 0.8172 (tpt) outliers start: 82 outliers final: 42 residues processed: 294 average time/residue: 0.3390 time to fit residues: 166.0716 Evaluate side-chains 234 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 184 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 644 GLN Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 223 optimal weight: 8.9990 chunk 289 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 chunk 37 optimal weight: 20.0000 chunk 237 optimal weight: 0.6980 chunk 306 optimal weight: 0.8980 chunk 208 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 234 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN C 81 ASN C 207 HIS C 439 ASN C 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.218756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.171575 restraints weight = 51028.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.170405 restraints weight = 47910.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.166136 restraints weight = 30674.448| |-----------------------------------------------------------------------------| r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.6734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27565 Z= 0.146 Angle : 0.737 12.345 37717 Z= 0.341 Chirality : 0.046 0.599 4545 Planarity : 0.005 0.075 4675 Dihedral : 8.588 85.839 5769 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.82 % Favored : 95.06 % Rotamer: Outliers : 2.82 % Allowed : 17.41 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.96 (0.14), residues: 3198 helix: 1.46 (0.20), residues: 750 sheet: -0.66 (0.19), residues: 717 loop : -1.63 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 104 HIS 0.004 0.001 HIS B1088 PHE 0.036 0.002 PHE A 192 TYR 0.015 0.001 TYR B1067 ARG 0.006 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00732 ( 53) link_NAG-ASN : angle 3.07033 ( 159) link_ALPHA1-4 : bond 0.01788 ( 21) link_ALPHA1-4 : angle 2.92864 ( 63) link_BETA1-4 : bond 0.00398 ( 33) link_BETA1-4 : angle 1.28829 ( 99) hydrogen bonds : bond 0.05481 ( 993) hydrogen bonds : angle 5.47521 ( 2763) link_BETA1-6 : bond 0.01871 ( 3) link_BETA1-6 : angle 2.62368 ( 9) SS BOND : bond 0.00316 ( 42) SS BOND : angle 1.56595 ( 84) covalent geometry : bond 0.00307 (27413) covalent geometry : angle 0.69454 (37303) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 200 time to evaluate : 2.832 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 33 THR cc_start: 0.2542 (OUTLIER) cc_final: 0.2035 (p) REVERT: A 388 ASN cc_start: 0.6290 (OUTLIER) cc_final: 0.6037 (p0) REVERT: A 400 PHE cc_start: 0.6425 (p90) cc_final: 0.6210 (p90) REVERT: A 634 ARG cc_start: 0.4503 (OUTLIER) cc_final: 0.4010 (ttt180) REVERT: B 83 VAL cc_start: 0.4516 (OUTLIER) cc_final: 0.3423 (t) REVERT: B 304 LYS cc_start: 0.8701 (mmtt) cc_final: 0.8359 (mmmt) REVERT: B 321 GLN cc_start: 0.7689 (mm110) cc_final: 0.7352 (mm-40) REVERT: B 494 SER cc_start: 0.5941 (OUTLIER) cc_final: 0.5560 (t) REVERT: B 819 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7559 (mt-10) REVERT: B 902 MET cc_start: 0.8308 (tpt) cc_final: 0.7677 (tpt) REVERT: B 969 ASN cc_start: 0.8574 (m110) cc_final: 0.8335 (m110) REVERT: B 1111 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6649 (tt0) REVERT: B 1115 ILE cc_start: 0.7107 (OUTLIER) cc_final: 0.6718 (tp) REVERT: C 177 MET cc_start: 0.6718 (mpp) cc_final: 0.6439 (mmp) REVERT: C 380 TYR cc_start: 0.7036 (OUTLIER) cc_final: 0.4421 (m-80) REVERT: C 591 SER cc_start: 0.7147 (m) cc_final: 0.6782 (p) REVERT: C 776 LYS cc_start: 0.9178 (tptp) cc_final: 0.8891 (tptt) REVERT: C 1029 MET cc_start: 0.8777 (tpt) cc_final: 0.8571 (tpt) REVERT: C 1092 GLU cc_start: 0.8010 (pm20) cc_final: 0.7781 (pm20) outliers start: 80 outliers final: 52 residues processed: 265 average time/residue: 0.3302 time to fit residues: 146.3706 Evaluate side-chains 235 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 174 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 63 optimal weight: 5.9990 chunk 221 optimal weight: 9.9990 chunk 261 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 212 optimal weight: 0.1980 chunk 138 optimal weight: 7.9990 chunk 273 optimal weight: 0.6980 chunk 307 optimal weight: 3.9990 chunk 314 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 913 GLN A1058 HIS ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 953 ASN C1058 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.213641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.149990 restraints weight = 49058.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.151935 restraints weight = 32225.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.151343 restraints weight = 23296.831| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.7393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 27565 Z= 0.162 Angle : 0.743 12.447 37717 Z= 0.349 Chirality : 0.046 0.431 4545 Planarity : 0.005 0.075 4675 Dihedral : 7.376 70.234 5769 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.00 % Favored : 94.87 % Rotamer: Outliers : 3.21 % Allowed : 18.11 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.95 (0.14), residues: 3198 helix: 1.49 (0.19), residues: 750 sheet: -0.72 (0.19), residues: 741 loop : -1.61 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 104 HIS 0.005 0.001 HIS A1118 PHE 0.030 0.002 PHE B 238 TYR 0.017 0.001 TYR C 674 ARG 0.009 0.001 ARG B 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00532 ( 53) link_NAG-ASN : angle 2.75208 ( 159) link_ALPHA1-4 : bond 0.01925 ( 21) link_ALPHA1-4 : angle 2.98371 ( 63) link_BETA1-4 : bond 0.00445 ( 33) link_BETA1-4 : angle 1.40202 ( 99) hydrogen bonds : bond 0.05499 ( 993) hydrogen bonds : angle 5.38062 ( 2763) link_BETA1-6 : bond 0.01964 ( 3) link_BETA1-6 : angle 2.55013 ( 9) SS BOND : bond 0.00352 ( 42) SS BOND : angle 1.50482 ( 84) covalent geometry : bond 0.00358 (27413) covalent geometry : angle 0.70662 (37303) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 196 time to evaluate : 2.535 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 400 PHE cc_start: 0.6441 (p90) cc_final: 0.6050 (p90) REVERT: A 900 MET cc_start: 0.7528 (mmp) cc_final: 0.6997 (mmt) REVERT: B 304 LYS cc_start: 0.8681 (mmtt) cc_final: 0.8409 (mmmt) REVERT: B 321 GLN cc_start: 0.7860 (mm110) cc_final: 0.7568 (mm-40) REVERT: B 494 SER cc_start: 0.5866 (OUTLIER) cc_final: 0.5528 (t) REVERT: B 619 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7170 (mm-30) REVERT: B 819 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7614 (mp0) REVERT: B 902 MET cc_start: 0.8412 (tpt) cc_final: 0.7777 (tpt) REVERT: B 969 ASN cc_start: 0.8626 (m110) cc_final: 0.8395 (m110) REVERT: B 1111 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6644 (tt0) REVERT: C 48 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.6885 (mt) REVERT: C 270 LEU cc_start: 0.6340 (OUTLIER) cc_final: 0.6088 (tp) REVERT: C 380 TYR cc_start: 0.7160 (OUTLIER) cc_final: 0.6689 (m-80) REVERT: C 400 PHE cc_start: 0.7017 (p90) cc_final: 0.6669 (p90) REVERT: C 776 LYS cc_start: 0.9184 (tptp) cc_final: 0.8908 (tptt) REVERT: C 819 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7705 (mt-10) outliers start: 91 outliers final: 55 residues processed: 267 average time/residue: 0.3355 time to fit residues: 149.4746 Evaluate side-chains 235 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 173 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 1 optimal weight: 0.3980 chunk 134 optimal weight: 20.0000 chunk 41 optimal weight: 20.0000 chunk 128 optimal weight: 9.9990 chunk 277 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 252 optimal weight: 9.9990 chunk 298 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 953 ASN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 HIS B 895 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS C 787 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.208549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.166639 restraints weight = 50213.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.154895 restraints weight = 69349.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.152050 restraints weight = 52422.048| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.8365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 27565 Z= 0.215 Angle : 0.786 11.632 37717 Z= 0.376 Chirality : 0.048 0.432 4545 Planarity : 0.005 0.089 4675 Dihedral : 6.652 54.502 5769 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.04 % Favored : 93.84 % Rotamer: Outliers : 3.21 % Allowed : 19.07 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.97 (0.14), residues: 3198 helix: 1.65 (0.19), residues: 726 sheet: -0.59 (0.19), residues: 696 loop : -1.72 (0.13), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 104 HIS 0.004 0.001 HIS A1118 PHE 0.024 0.002 PHE B1089 TYR 0.023 0.002 TYR B1067 ARG 0.018 0.001 ARG C 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00619 ( 53) link_NAG-ASN : angle 2.81754 ( 159) link_ALPHA1-4 : bond 0.01857 ( 21) link_ALPHA1-4 : angle 2.90983 ( 63) link_BETA1-4 : bond 0.00393 ( 33) link_BETA1-4 : angle 1.53695 ( 99) hydrogen bonds : bond 0.06261 ( 993) hydrogen bonds : angle 5.56487 ( 2763) link_BETA1-6 : bond 0.01979 ( 3) link_BETA1-6 : angle 2.35306 ( 9) SS BOND : bond 0.01207 ( 42) SS BOND : angle 1.74574 ( 84) covalent geometry : bond 0.00485 (27413) covalent geometry : angle 0.75000 (37303) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 189 time to evaluate : 2.593 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 86 PHE cc_start: 0.5006 (OUTLIER) cc_final: 0.3341 (m-10) REVERT: A 386 LYS cc_start: 0.6736 (mmtm) cc_final: 0.6511 (mttp) REVERT: A 400 PHE cc_start: 0.6722 (p90) cc_final: 0.6347 (p90) REVERT: A 900 MET cc_start: 0.7507 (mmp) cc_final: 0.7225 (mmt) REVERT: B 133 PHE cc_start: 0.0954 (m-80) cc_final: 0.0459 (m-80) REVERT: B 494 SER cc_start: 0.5963 (OUTLIER) cc_final: 0.5583 (t) REVERT: B 619 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7262 (mm-30) REVERT: B 819 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7677 (mp0) REVERT: B 902 MET cc_start: 0.8257 (tpt) cc_final: 0.7402 (tpt) REVERT: B 1111 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.7044 (tt0) REVERT: C 48 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8019 (mt) REVERT: C 177 MET cc_start: 0.4220 (mmp) cc_final: 0.2375 (mtt) REVERT: C 380 TYR cc_start: 0.7552 (OUTLIER) cc_final: 0.6864 (m-80) REVERT: C 400 PHE cc_start: 0.7328 (p90) cc_final: 0.7108 (p90) REVERT: C 776 LYS cc_start: 0.9149 (tptp) cc_final: 0.8825 (tptt) REVERT: C 788 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.6976 (mt) REVERT: C 819 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7616 (mt-10) REVERT: C 869 MET cc_start: 0.8274 (mpp) cc_final: 0.7929 (mtt) outliers start: 91 outliers final: 65 residues processed: 265 average time/residue: 0.3359 time to fit residues: 149.6212 Evaluate side-chains 233 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 160 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 132 optimal weight: 2.9990 chunk 253 optimal weight: 20.0000 chunk 217 optimal weight: 2.9990 chunk 144 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 235 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 202 optimal weight: 0.5980 chunk 156 optimal weight: 7.9990 chunk 229 optimal weight: 9.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN B 895 GLN B1083 HIS ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.203805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.156619 restraints weight = 49680.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.152354 restraints weight = 55972.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.145404 restraints weight = 37335.020| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.9466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 27565 Z= 0.220 Angle : 0.819 15.582 37717 Z= 0.393 Chirality : 0.049 0.438 4545 Planarity : 0.005 0.072 4675 Dihedral : 6.505 59.454 5769 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.04 % Favored : 93.84 % Rotamer: Outliers : 2.97 % Allowed : 19.35 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.14 (0.14), residues: 3198 helix: 1.39 (0.19), residues: 747 sheet: -0.72 (0.19), residues: 717 loop : -1.80 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 104 HIS 0.007 0.001 HIS C1118 PHE 0.030 0.002 PHE A 106 TYR 0.027 0.002 TYR A 269 ARG 0.014 0.001 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00600 ( 53) link_NAG-ASN : angle 2.94778 ( 159) link_ALPHA1-4 : bond 0.01834 ( 21) link_ALPHA1-4 : angle 2.88152 ( 63) link_BETA1-4 : bond 0.00410 ( 33) link_BETA1-4 : angle 1.72383 ( 99) hydrogen bonds : bond 0.06534 ( 993) hydrogen bonds : angle 5.69941 ( 2763) link_BETA1-6 : bond 0.01832 ( 3) link_BETA1-6 : angle 2.03947 ( 9) SS BOND : bond 0.00573 ( 42) SS BOND : angle 1.71277 ( 84) covalent geometry : bond 0.00509 (27413) covalent geometry : angle 0.78173 (37303) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 172 time to evaluate : 2.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.6589 (p90) cc_final: 0.6246 (p90) REVERT: A 900 MET cc_start: 0.7568 (mmp) cc_final: 0.7316 (mmt) REVERT: B 133 PHE cc_start: 0.1056 (m-80) cc_final: 0.0437 (m-80) REVERT: B 237 ARG cc_start: 0.5978 (tmm-80) cc_final: 0.5633 (ttp80) REVERT: B 494 SER cc_start: 0.6112 (OUTLIER) cc_final: 0.5734 (t) REVERT: B 819 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7869 (mp0) REVERT: B 1111 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7265 (tt0) REVERT: C 177 MET cc_start: 0.4157 (mmp) cc_final: 0.2292 (mtp) REVERT: C 380 TYR cc_start: 0.7659 (OUTLIER) cc_final: 0.5878 (m-80) REVERT: C 776 LYS cc_start: 0.9124 (tptp) cc_final: 0.8792 (tptt) outliers start: 84 outliers final: 63 residues processed: 244 average time/residue: 0.3227 time to fit residues: 133.1540 Evaluate side-chains 213 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 146 time to evaluate : 2.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 17 optimal weight: 9.9990 chunk 313 optimal weight: 0.0670 chunk 295 optimal weight: 0.4980 chunk 4 optimal weight: 0.6980 chunk 282 optimal weight: 2.9990 chunk 271 optimal weight: 6.9990 chunk 191 optimal weight: 5.9990 chunk 197 optimal weight: 0.0470 chunk 150 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 293 optimal weight: 0.9980 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN B 895 GLN C 49 HIS C1118 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.207510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.154336 restraints weight = 50148.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.149843 restraints weight = 39951.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.149621 restraints weight = 32898.272| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.9588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 27565 Z= 0.135 Angle : 0.715 13.509 37717 Z= 0.339 Chirality : 0.046 0.423 4545 Planarity : 0.005 0.071 4675 Dihedral : 5.952 57.807 5769 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.82 % Favored : 95.06 % Rotamer: Outliers : 2.08 % Allowed : 20.62 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.83 (0.15), residues: 3198 helix: 1.89 (0.20), residues: 729 sheet: -0.51 (0.19), residues: 714 loop : -1.71 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP B 104 HIS 0.007 0.001 HIS C1118 PHE 0.032 0.002 PHE A 58 TYR 0.023 0.001 TYR C 508 ARG 0.012 0.001 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00443 ( 53) link_NAG-ASN : angle 2.60273 ( 159) link_ALPHA1-4 : bond 0.01634 ( 21) link_ALPHA1-4 : angle 2.69703 ( 63) link_BETA1-4 : bond 0.00425 ( 33) link_BETA1-4 : angle 1.47319 ( 99) hydrogen bonds : bond 0.05219 ( 993) hydrogen bonds : angle 5.32716 ( 2763) link_BETA1-6 : bond 0.01526 ( 3) link_BETA1-6 : angle 1.76635 ( 9) SS BOND : bond 0.00451 ( 42) SS BOND : angle 1.66423 ( 84) covalent geometry : bond 0.00283 (27413) covalent geometry : angle 0.67998 (37303) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 189 time to evaluate : 2.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.6372 (ptp90) cc_final: 0.6140 (ptp90) REVERT: A 400 PHE cc_start: 0.6492 (p90) cc_final: 0.6152 (p90) REVERT: A 1029 MET cc_start: 0.8825 (tpp) cc_final: 0.8558 (tpp) REVERT: B 133 PHE cc_start: 0.0729 (m-80) cc_final: 0.0420 (m-80) REVERT: B 237 ARG cc_start: 0.6021 (tmm-80) cc_final: 0.5644 (ttp80) REVERT: B 494 SER cc_start: 0.6251 (OUTLIER) cc_final: 0.5855 (t) REVERT: B 902 MET cc_start: 0.8293 (tpt) cc_final: 0.8007 (tpt) REVERT: B 974 SER cc_start: 0.8799 (t) cc_final: 0.8434 (m) REVERT: B 1111 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.7082 (tt0) REVERT: C 177 MET cc_start: 0.4457 (mmp) cc_final: 0.3469 (mpp) REVERT: C 380 TYR cc_start: 0.7581 (OUTLIER) cc_final: 0.5906 (m-80) REVERT: C 776 LYS cc_start: 0.9125 (tptp) cc_final: 0.8840 (tptt) REVERT: C 819 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7874 (mt-10) outliers start: 59 outliers final: 40 residues processed: 238 average time/residue: 0.3259 time to fit residues: 129.9654 Evaluate side-chains 205 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 10 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 123 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 251 optimal weight: 7.9990 chunk 196 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 223 optimal weight: 0.7980 chunk 278 optimal weight: 4.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN C 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.205204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.146297 restraints weight = 49209.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.143518 restraints weight = 34266.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.144665 restraints weight = 30773.366| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.9943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27565 Z= 0.161 Angle : 0.737 13.168 37717 Z= 0.350 Chirality : 0.046 0.428 4545 Planarity : 0.005 0.067 4675 Dihedral : 5.881 57.240 5769 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.60 % Favored : 94.28 % Rotamer: Outliers : 1.73 % Allowed : 21.22 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.82 (0.15), residues: 3198 helix: 1.91 (0.20), residues: 729 sheet: -0.55 (0.19), residues: 717 loop : -1.69 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 104 HIS 0.004 0.001 HIS C 49 PHE 0.034 0.002 PHE C 192 TYR 0.021 0.002 TYR C 170 ARG 0.014 0.001 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00490 ( 53) link_NAG-ASN : angle 2.68538 ( 159) link_ALPHA1-4 : bond 0.01545 ( 21) link_ALPHA1-4 : angle 2.66139 ( 63) link_BETA1-4 : bond 0.00354 ( 33) link_BETA1-4 : angle 1.52256 ( 99) hydrogen bonds : bond 0.05638 ( 993) hydrogen bonds : angle 5.32210 ( 2763) link_BETA1-6 : bond 0.01400 ( 3) link_BETA1-6 : angle 1.78421 ( 9) SS BOND : bond 0.00398 ( 42) SS BOND : angle 1.60317 ( 84) covalent geometry : bond 0.00365 (27413) covalent geometry : angle 0.70313 (37303) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6396 Ramachandran restraints generated. 3198 Oldfield, 0 Emsley, 3198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 155 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.6602 (ptp90) cc_final: 0.6317 (ptp90) REVERT: A 400 PHE cc_start: 0.6600 (p90) cc_final: 0.6266 (p90) REVERT: B 494 SER cc_start: 0.6335 (OUTLIER) cc_final: 0.5937 (t) REVERT: B 902 MET cc_start: 0.8501 (tpt) cc_final: 0.7763 (tpt) REVERT: B 1111 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.7125 (tt0) REVERT: C 133 PHE cc_start: 0.1372 (m-80) cc_final: 0.1030 (m-80) REVERT: C 177 MET cc_start: 0.4141 (mmp) cc_final: 0.3138 (mpp) REVERT: C 380 TYR cc_start: 0.7568 (OUTLIER) cc_final: 0.6064 (m-10) REVERT: C 776 LYS cc_start: 0.9047 (tptp) cc_final: 0.8797 (tptt) REVERT: C 788 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7454 (mt) outliers start: 49 outliers final: 36 residues processed: 197 average time/residue: 0.3393 time to fit residues: 112.9834 Evaluate side-chains 186 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 146 time to evaluate : 2.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 123 optimal weight: 0.3980 chunk 69 optimal weight: 4.9990 chunk 163 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 236 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 254 optimal weight: 9.9990 chunk 313 optimal weight: 0.3980 chunk 230 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN C 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.205154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.163276 restraints weight = 48655.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.159839 restraints weight = 62621.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.162319 restraints weight = 52561.617| |-----------------------------------------------------------------------------| r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 1.0102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27565 Z= 0.133 Angle : 0.698 13.444 37717 Z= 0.330 Chirality : 0.045 0.424 4545 Planarity : 0.005 0.063 4675 Dihedral : 5.664 58.055 5769 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.85 % Favored : 95.03 % Rotamer: Outliers : 1.84 % Allowed : 21.05 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.71 (0.15), residues: 3198 helix: 2.04 (0.20), residues: 729 sheet: -0.45 (0.19), residues: 744 loop : -1.66 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP C 104 HIS 0.005 0.001 HIS C1048 PHE 0.039 0.002 PHE A 106 TYR 0.017 0.001 TYR A 91 ARG 0.014 0.001 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 53) link_NAG-ASN : angle 2.53195 ( 159) link_ALPHA1-4 : bond 0.01564 ( 21) link_ALPHA1-4 : angle 2.54629 ( 63) link_BETA1-4 : bond 0.00377 ( 33) link_BETA1-4 : angle 1.41940 ( 99) hydrogen bonds : bond 0.05081 ( 993) hydrogen bonds : angle 5.16058 ( 2763) link_BETA1-6 : bond 0.01322 ( 3) link_BETA1-6 : angle 1.65503 ( 9) SS BOND : bond 0.00324 ( 42) SS BOND : angle 1.43676 ( 84) covalent geometry : bond 0.00288 (27413) covalent geometry : angle 0.66594 (37303) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8288.70 seconds wall clock time: 146 minutes 19.10 seconds (8779.10 seconds total)