Starting phenix.real_space_refine on Mon Jun 23 09:15:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ybl_33725/06_2025/7ybl_33725.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ybl_33725/06_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_33725/06_2025/7ybl_33725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ybl_33725/06_2025/7ybl_33725.map" model { file = "/net/cci-nas-00/data/ceres_data/7ybl_33725/06_2025/7ybl_33725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ybl_33725/06_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): 0.74s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 16.80, per 1000 atoms: 0.63 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: 8.79 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: 4.30 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: 17.34 Time building geometry restraints manager: 10.16 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: 2.110 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: 0.030 Extract box with map and model: 1.070 Check model and map are aligned: 0.180 Set scattering table: 0.290 Process input model: 73.120 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.070 ------------------------------------------------------------------------------- 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 : 2.541 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: 0.4122 time to fit residues: 349.8897 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 : 3.076 ------------------------------------------------------------------------------- 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 = 58367.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.223294 restraints weight = 90942.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.223721 restraints weight = 73138.717| |-----------------------------------------------------------------------------| r_work (final): 0.4722 ------------------------------------------------------------------------------- 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 : 2.979 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: 0.3936 (m-10) cc_final: 0.3727 (m-10) REVERT: A 571 ASP cc_start: 0.5651 (t0) cc_final: 0.5401 (t0) REVERT: A 602 THR cc_start: 0.6654 (m) cc_final: 0.6227 (t) REVERT: B 494 SER cc_start: 0.5459 (OUTLIER) cc_final: 0.5130 (t) REVERT: B 740 MET cc_start: 0.7692 (tpp) cc_final: 0.7442 (tpp) REVERT: B 775 ASP cc_start: 0.6231 (m-30) cc_final: 0.5927 (m-30) REVERT: B 902 MET cc_start: 0.7428 (tpp) cc_final: 0.7182 (tpt) REVERT: B 916 LEU cc_start: 0.5704 (tp) cc_final: 0.5382 (tp) REVERT: B 1065 VAL cc_start: 0.7686 (t) cc_final: 0.7480 (p) REVERT: C 289 VAL cc_start: 0.2481 (OUTLIER) cc_final: 0.2223 (p) REVERT: C 380 TYR cc_start: 0.6615 (OUTLIER) cc_final: 0.3998 (m-80) REVERT: C 386 LYS cc_start: 0.6025 (OUTLIER) cc_final: 0.5497 (ttpt) REVERT: C 776 LYS cc_start: 0.8583 (tptp) cc_final: 0.8380 (tptt) REVERT: C 906 PHE cc_start: 0.7720 (OUTLIER) cc_final: 0.6668 (t80) outliers start: 59 outliers final: 32 residues processed: 350 average time/residue: 0.3548 time to fit residues: 206.6175 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 : 2.685 ------------------------------------------------------------------------------- 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: 4.9990 chunk 229 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 263 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 158 optimal weight: 0.9980 chunk 28 optimal weight: 0.0030 chunk 76 optimal weight: 5.9990 chunk 236 optimal weight: 8.9990 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 751 ASN A 774 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1011 GLN A1083 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 954 GLN C1005 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.227655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.178187 restraints weight = 52785.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.173576 restraints weight = 38191.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.173626 restraints weight = 34560.185| |-----------------------------------------------------------------------------| r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 27565 Z= 0.215 Angle : 0.872 21.034 37717 Z= 0.409 Chirality : 0.052 0.503 4545 Planarity : 0.006 0.097 4675 Dihedral : 11.313 98.832 5771 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.28 % Favored : 94.59 % Rotamer: Outliers : 2.79 % Allowed : 12.29 % Favored : 84.92 % 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: -0.99 (0.14), residues: 3198 helix: 1.09 (0.19), residues: 741 sheet: -0.62 (0.19), residues: 744 loop : -1.49 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 104 HIS 0.022 0.001 HIS C 49 PHE 0.031 0.003 PHE A 194 TYR 0.020 0.002 TYR B1067 ARG 0.020 0.001 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.01052 ( 53) link_NAG-ASN : angle 3.31997 ( 159) link_ALPHA1-4 : bond 0.01549 ( 21) link_ALPHA1-4 : angle 3.28059 ( 63) link_BETA1-4 : bond 0.01035 ( 33) link_BETA1-4 : angle 1.53498 ( 99) hydrogen bonds : bond 0.06729 ( 993) hydrogen bonds : angle 6.04501 ( 2763) link_BETA1-6 : bond 0.01620 ( 3) link_BETA1-6 : angle 2.50629 ( 9) SS BOND : bond 0.00492 ( 42) SS BOND : angle 1.72240 ( 84) covalent geometry : bond 0.00464 (27413) covalent geometry : angle 0.82994 (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 379 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 300 time to evaluate : 2.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TYR cc_start: 0.3806 (m-10) cc_final: 0.3217 (m-10) REVERT: A 602 THR cc_start: 0.7168 (m) cc_final: 0.6910 (t) REVERT: B 104 TRP cc_start: 0.5228 (m-90) cc_final: 0.4848 (m-90) REVERT: B 237 ARG cc_start: 0.7041 (ptm160) cc_final: 0.6702 (mtp-110) REVERT: B 494 SER cc_start: 0.5805 (OUTLIER) cc_final: 0.5445 (t) REVERT: B 740 MET cc_start: 0.7734 (tpp) cc_final: 0.7452 (tpp) REVERT: B 775 ASP cc_start: 0.7598 (m-30) cc_final: 0.7375 (m-30) REVERT: B 1115 ILE cc_start: 0.6988 (OUTLIER) cc_final: 0.6575 (tp) REVERT: C 48 LEU cc_start: 0.5199 (OUTLIER) cc_final: 0.4932 (mt) REVERT: C 177 MET cc_start: 0.6945 (mpp) cc_final: 0.5931 (mtp) REVERT: C 380 TYR cc_start: 0.7092 (OUTLIER) cc_final: 0.4757 (m-80) REVERT: C 902 MET cc_start: 0.7749 (tpp) cc_final: 0.7547 (tpp) REVERT: C 1029 MET cc_start: 0.8915 (tpt) cc_final: 0.8659 (tpp) REVERT: C 1115 ILE cc_start: 0.7039 (OUTLIER) cc_final: 0.6691 (tp) outliers start: 79 outliers final: 37 residues processed: 357 average time/residue: 0.3600 time to fit residues: 211.2245 Evaluate side-chains 248 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 206 time to evaluate : 2.604 ------------------------------------------------------------------------------- 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 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 819 GLU Chi-restraints excluded: chain A residue 865 LEU 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 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 610 VAL Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 127 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 395 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 642 VAL 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 1030 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 278 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 255 optimal weight: 8.9990 chunk 225 optimal weight: 0.6980 chunk 237 optimal weight: 0.2980 chunk 253 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 191 optimal weight: 4.9990 chunk 264 optimal weight: 0.9980 chunk 287 optimal weight: 3.9990 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 134 GLN A 955 ASN B 644 GLN B 784 GLN B1058 HIS C 49 HIS C 81 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.224977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.182310 restraints weight = 52290.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.181756 restraints weight = 51847.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.178383 restraints weight = 37736.218| |-----------------------------------------------------------------------------| r_work (final): 0.4308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6456 moved from start: 0.5482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 27565 Z= 0.172 Angle : 0.783 17.649 37717 Z= 0.363 Chirality : 0.047 0.430 4545 Planarity : 0.005 0.080 4675 Dihedral : 9.708 93.950 5771 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.44 % Favored : 95.47 % Rotamer: Outliers : 2.47 % Allowed : 15.93 % Favored : 81.60 % 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: -0.84 (0.15), residues: 3198 helix: 1.46 (0.19), residues: 741 sheet: -0.64 (0.19), residues: 744 loop : -1.47 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 104 HIS 0.004 0.001 HIS B1088 PHE 0.037 0.002 PHE A 192 TYR 0.019 0.001 TYR B1067 ARG 0.009 0.001 ARG B 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00620 ( 53) link_NAG-ASN : angle 3.04532 ( 159) link_ALPHA1-4 : bond 0.01689 ( 21) link_ALPHA1-4 : angle 2.90579 ( 63) link_BETA1-4 : bond 0.00515 ( 33) link_BETA1-4 : angle 1.28593 ( 99) hydrogen bonds : bond 0.05726 ( 993) hydrogen bonds : angle 5.64386 ( 2763) link_BETA1-6 : bond 0.01779 ( 3) link_BETA1-6 : angle 2.42097 ( 9) SS BOND : bond 0.00390 ( 42) SS BOND : angle 1.55937 ( 84) covalent geometry : bond 0.00382 (27413) covalent geometry : angle 0.74521 (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 303 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 233 time to evaluate : 2.660 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 38 TYR cc_start: 0.4007 (m-10) cc_final: 0.3457 (m-10) REVERT: A 321 GLN cc_start: 0.7103 (mm110) cc_final: 0.6835 (mm-40) REVERT: A 400 PHE cc_start: 0.6751 (p90) cc_final: 0.6529 (p90) REVERT: B 304 LYS cc_start: 0.8407 (mmtt) cc_final: 0.8124 (mmmt) REVERT: B 494 SER cc_start: 0.5707 (OUTLIER) cc_final: 0.5357 (t) REVERT: B 602 THR cc_start: 0.7211 (m) cc_final: 0.6927 (t) REVERT: B 819 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7302 (mt-10) REVERT: B 869 MET cc_start: 0.7294 (mtt) cc_final: 0.6999 (mtp) REVERT: B 902 MET cc_start: 0.8326 (tpt) cc_final: 0.7740 (tpt) REVERT: B 1096 VAL cc_start: 0.7092 (p) cc_final: 0.6831 (m) REVERT: B 1115 ILE cc_start: 0.7046 (OUTLIER) cc_final: 0.6650 (tp) REVERT: C 177 MET cc_start: 0.6555 (mpp) cc_final: 0.6155 (mmp) REVERT: C 380 TYR cc_start: 0.6982 (OUTLIER) cc_final: 0.4198 (m-80) REVERT: C 869 MET cc_start: 0.7757 (mpp) cc_final: 0.7319 (mpp) REVERT: C 902 MET cc_start: 0.8173 (tpp) cc_final: 0.7433 (tpt) REVERT: C 1050 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7786 (ptm) REVERT: C 1115 ILE cc_start: 0.7279 (OUTLIER) cc_final: 0.6721 (tp) outliers start: 70 outliers final: 44 residues processed: 288 average time/residue: 0.3291 time to fit residues: 157.2183 Evaluate side-chains 242 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 192 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 383 SER 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 551 VAL Chi-restraints excluded: chain A residue 697 MET 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 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 276 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 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 819 GLU Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 170 TYR Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 274 THR 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 642 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 223 optimal weight: 20.0000 chunk 289 optimal weight: 0.0370 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 0.0870 chunk 237 optimal weight: 1.9990 chunk 306 optimal weight: 1.9990 chunk 208 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 192 optimal weight: 0.0770 chunk 26 optimal weight: 0.9980 chunk 234 optimal weight: 0.8980 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN B 239 GLN B 787 GLN B 953 ASN B1054 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.226066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.184233 restraints weight = 52025.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.179846 restraints weight = 61368.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.181923 restraints weight = 47084.284| |-----------------------------------------------------------------------------| r_work (final): 0.4332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 0.5764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27565 Z= 0.135 Angle : 0.728 15.080 37717 Z= 0.334 Chirality : 0.045 0.428 4545 Planarity : 0.005 0.093 4675 Dihedral : 8.502 88.549 5771 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.72 % Favored : 95.15 % Rotamer: Outliers : 2.22 % Allowed : 17.27 % Favored : 80.51 % 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: -0.57 (0.15), residues: 3198 helix: 1.78 (0.20), residues: 738 sheet: -0.45 (0.19), residues: 744 loop : -1.35 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 104 HIS 0.005 0.001 HIS C 49 PHE 0.037 0.001 PHE A 192 TYR 0.014 0.001 TYR B 28 ARG 0.009 0.000 ARG B 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00495 ( 53) link_NAG-ASN : angle 2.95468 ( 159) link_ALPHA1-4 : bond 0.01785 ( 21) link_ALPHA1-4 : angle 3.01722 ( 63) link_BETA1-4 : bond 0.00437 ( 33) link_BETA1-4 : angle 1.26943 ( 99) hydrogen bonds : bond 0.05011 ( 993) hydrogen bonds : angle 5.37638 ( 2763) link_BETA1-6 : bond 0.01873 ( 3) link_BETA1-6 : angle 2.47535 ( 9) SS BOND : bond 0.00306 ( 42) SS BOND : angle 1.58002 ( 84) covalent geometry : bond 0.00274 (27413) covalent geometry : angle 0.68680 (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 278 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 215 time to evaluate : 3.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TYR cc_start: 0.4152 (m-10) cc_final: 0.3386 (m-80) REVERT: A 321 GLN cc_start: 0.7131 (mm110) cc_final: 0.6802 (mm-40) REVERT: A 634 ARG cc_start: 0.4470 (OUTLIER) cc_final: 0.3751 (tpt170) REVERT: B 304 LYS cc_start: 0.8397 (mmtt) cc_final: 0.8103 (mmmt) REVERT: B 494 SER cc_start: 0.5843 (OUTLIER) cc_final: 0.5465 (t) REVERT: B 602 THR cc_start: 0.7271 (m) cc_final: 0.6936 (t) REVERT: B 619 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6802 (mm-30) REVERT: B 902 MET cc_start: 0.8102 (tpt) cc_final: 0.7684 (tpt) REVERT: B 931 ILE cc_start: 0.7747 (mp) cc_final: 0.7408 (mt) REVERT: B 1104 VAL cc_start: 0.6323 (OUTLIER) cc_final: 0.6022 (m) REVERT: B 1115 ILE cc_start: 0.7080 (OUTLIER) cc_final: 0.6551 (tp) REVERT: C 177 MET cc_start: 0.6656 (mpp) cc_final: 0.6340 (mmp) REVERT: C 380 TYR cc_start: 0.7003 (OUTLIER) cc_final: 0.4376 (m-80) REVERT: C 788 ILE cc_start: 0.7285 (OUTLIER) cc_final: 0.6840 (mp) REVERT: C 869 MET cc_start: 0.7690 (mpp) cc_final: 0.7260 (mpp) outliers start: 63 outliers final: 31 residues processed: 268 average time/residue: 0.3465 time to fit residues: 154.8415 Evaluate side-chains 225 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 2.585 ------------------------------------------------------------------------------- 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 308 VAL Chi-restraints excluded: chain A residue 358 ILE 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 941 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 276 LEU 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 512 VAL 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 724 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 274 THR 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 642 VAL Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 963 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 63 optimal weight: 6.9990 chunk 221 optimal weight: 0.7980 chunk 261 optimal weight: 0.9990 chunk 175 optimal weight: 4.9990 chunk 212 optimal weight: 0.0970 chunk 138 optimal weight: 1.9990 chunk 273 optimal weight: 0.6980 chunk 307 optimal weight: 3.9990 chunk 314 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN C 439 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.223422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.180802 restraints weight = 51667.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.176767 restraints weight = 58166.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.178382 restraints weight = 47376.175| |-----------------------------------------------------------------------------| r_work (final): 0.4288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.6204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27565 Z= 0.137 Angle : 0.716 14.556 37717 Z= 0.331 Chirality : 0.045 0.431 4545 Planarity : 0.005 0.074 4675 Dihedral : 7.356 78.450 5771 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.53 % Favored : 95.37 % Rotamer: Outliers : 2.61 % Allowed : 17.55 % Favored : 79.84 % 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: -0.52 (0.15), residues: 3198 helix: 1.79 (0.20), residues: 750 sheet: -0.47 (0.19), residues: 741 loop : -1.30 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 104 HIS 0.005 0.001 HIS C 49 PHE 0.029 0.001 PHE A 192 TYR 0.016 0.001 TYR B1067 ARG 0.007 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00463 ( 53) link_NAG-ASN : angle 2.87671 ( 159) link_ALPHA1-4 : bond 0.01839 ( 21) link_ALPHA1-4 : angle 2.93534 ( 63) link_BETA1-4 : bond 0.00371 ( 33) link_BETA1-4 : angle 1.21256 ( 99) hydrogen bonds : bond 0.04903 ( 993) hydrogen bonds : angle 5.20822 ( 2763) link_BETA1-6 : bond 0.01923 ( 3) link_BETA1-6 : angle 2.38328 ( 9) SS BOND : bond 0.00375 ( 42) SS BOND : angle 1.52719 ( 84) covalent geometry : bond 0.00293 (27413) covalent geometry : angle 0.67719 (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 283 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 209 time to evaluate : 2.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TYR cc_start: 0.4633 (m-10) cc_final: 0.4032 (m-80) REVERT: A 591 SER cc_start: 0.7656 (m) cc_final: 0.7421 (m) REVERT: A 634 ARG cc_start: 0.4304 (OUTLIER) cc_final: 0.3854 (ttt180) REVERT: A 900 MET cc_start: 0.6969 (mmp) cc_final: 0.6518 (mmt) REVERT: B 83 VAL cc_start: 0.4940 (OUTLIER) cc_final: 0.4533 (t) REVERT: B 304 LYS cc_start: 0.8539 (mmtt) cc_final: 0.8185 (mmmt) REVERT: B 494 SER cc_start: 0.5871 (OUTLIER) cc_final: 0.5495 (t) REVERT: B 552 LEU cc_start: 0.5831 (OUTLIER) cc_final: 0.5478 (pt) REVERT: B 602 THR cc_start: 0.7332 (m) cc_final: 0.6999 (t) REVERT: B 619 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6896 (mm-30) REVERT: B 869 MET cc_start: 0.7462 (mtt) cc_final: 0.7217 (mtp) REVERT: B 902 MET cc_start: 0.8064 (tpt) cc_final: 0.7629 (tpt) REVERT: B 1115 ILE cc_start: 0.7174 (OUTLIER) cc_final: 0.6725 (tp) REVERT: C 55 PHE cc_start: 0.5516 (m-80) cc_final: 0.4618 (m-80) REVERT: C 380 TYR cc_start: 0.7081 (OUTLIER) cc_final: 0.4451 (m-80) REVERT: C 400 PHE cc_start: 0.7028 (p90) cc_final: 0.6303 (p90) REVERT: C 788 ILE cc_start: 0.7412 (OUTLIER) cc_final: 0.6928 (mp) REVERT: C 869 MET cc_start: 0.7730 (mpp) cc_final: 0.7199 (mpp) outliers start: 74 outliers final: 44 residues processed: 267 average time/residue: 0.3519 time to fit residues: 156.4222 Evaluate side-chains 240 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 189 time to evaluate : 2.729 ------------------------------------------------------------------------------- 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 208 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 512 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 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 83 VAL 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 276 LEU 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 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 1096 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 274 THR Chi-restraints excluded: chain C residue 296 LEU 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 610 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 806 LEU Chi-restraints excluded: chain C residue 819 GLU 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 1116 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: 2.9990 chunk 41 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 277 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 252 optimal weight: 1.9990 chunk 298 optimal weight: 5.9990 chunk 155 optimal weight: 0.0020 chunk 56 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.221379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.179179 restraints weight = 49903.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.174105 restraints weight = 57226.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.176007 restraints weight = 46619.353| |-----------------------------------------------------------------------------| r_work (final): 0.4284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.6680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27565 Z= 0.141 Angle : 0.707 13.723 37717 Z= 0.329 Chirality : 0.045 0.429 4545 Planarity : 0.005 0.110 4675 Dihedral : 6.196 57.294 5771 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.66 % Favored : 95.22 % Rotamer: Outliers : 2.30 % Allowed : 18.08 % Favored : 79.63 % 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: -0.48 (0.15), residues: 3198 helix: 1.85 (0.20), residues: 750 sheet: -0.40 (0.19), residues: 720 loop : -1.31 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 104 HIS 0.005 0.001 HIS C 49 PHE 0.040 0.002 PHE B 106 TYR 0.017 0.001 TYR B1067 ARG 0.015 0.001 ARG B 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 53) link_NAG-ASN : angle 2.68617 ( 159) link_ALPHA1-4 : bond 0.01922 ( 21) link_ALPHA1-4 : angle 2.86600 ( 63) link_BETA1-4 : bond 0.00384 ( 33) link_BETA1-4 : angle 1.29444 ( 99) hydrogen bonds : bond 0.04879 ( 993) hydrogen bonds : angle 5.12365 ( 2763) link_BETA1-6 : bond 0.01993 ( 3) link_BETA1-6 : angle 2.20243 ( 9) SS BOND : bond 0.00824 ( 42) SS BOND : angle 1.37009 ( 84) covalent geometry : bond 0.00301 (27413) covalent geometry : angle 0.67195 (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 273 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 208 time to evaluate : 4.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 591 SER cc_start: 0.8103 (m) cc_final: 0.7673 (p) REVERT: A 634 ARG cc_start: 0.4161 (OUTLIER) cc_final: 0.3873 (ttt180) REVERT: A 697 MET cc_start: 0.6845 (ptm) cc_final: 0.6586 (ttp) REVERT: B 304 LYS cc_start: 0.8524 (mmtt) cc_final: 0.8304 (mmmt) REVERT: B 494 SER cc_start: 0.5867 (OUTLIER) cc_final: 0.5513 (t) REVERT: B 602 THR cc_start: 0.7485 (m) cc_final: 0.7195 (t) REVERT: B 619 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6916 (mm-30) REVERT: B 902 MET cc_start: 0.8133 (tpt) cc_final: 0.7729 (tpt) REVERT: B 1104 VAL cc_start: 0.6638 (OUTLIER) cc_final: 0.6421 (m) REVERT: B 1115 ILE cc_start: 0.7257 (OUTLIER) cc_final: 0.6687 (tp) REVERT: C 380 TYR cc_start: 0.7001 (OUTLIER) cc_final: 0.4370 (m-80) REVERT: C 400 PHE cc_start: 0.7143 (p90) cc_final: 0.6649 (p90) REVERT: C 869 MET cc_start: 0.7734 (mpp) cc_final: 0.7249 (mpp) outliers start: 65 outliers final: 47 residues processed: 260 average time/residue: 0.5860 time to fit residues: 255.8367 Evaluate side-chains 236 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 184 time to evaluate : 3.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 301 CYS 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 512 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 819 GLU Chi-restraints excluded: chain A residue 855 PHE 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 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 276 LEU 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 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 296 LEU 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 610 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 806 LEU 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 1116 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: 0.3980 chunk 253 optimal weight: 20.0000 chunk 217 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 235 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 202 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 229 optimal weight: 9.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 164 ASN A 580 GLN A 655 HIS A 953 ASN A 955 ASN A 992 GLN A1058 HIS A1108 ASN B 625 HIS B 895 GLN B 969 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.205334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.141203 restraints weight = 48255.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.141315 restraints weight = 30943.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.141514 restraints weight = 28878.326| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.8574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 27565 Z= 0.257 Angle : 0.908 11.673 37717 Z= 0.444 Chirality : 0.053 0.446 4545 Planarity : 0.006 0.093 4675 Dihedral : 6.635 53.338 5771 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.88 % Favored : 93.00 % Rotamer: Outliers : 3.04 % Allowed : 18.36 % Favored : 78.60 % 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: -1.18 (0.14), residues: 3198 helix: 1.12 (0.19), residues: 744 sheet: -0.59 (0.20), residues: 660 loop : -1.76 (0.13), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.003 TRP C 104 HIS 0.007 0.002 HIS C1048 PHE 0.041 0.003 PHE B 186 TYR 0.027 0.003 TYR B1067 ARG 0.012 0.001 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00832 ( 53) link_NAG-ASN : angle 3.16516 ( 159) link_ALPHA1-4 : bond 0.01794 ( 21) link_ALPHA1-4 : angle 3.00096 ( 63) link_BETA1-4 : bond 0.00537 ( 33) link_BETA1-4 : angle 1.77377 ( 99) hydrogen bonds : bond 0.07750 ( 993) hydrogen bonds : angle 6.03230 ( 2763) link_BETA1-6 : bond 0.01768 ( 3) link_BETA1-6 : angle 2.40678 ( 9) SS BOND : bond 0.00917 ( 42) SS BOND : angle 2.05150 ( 84) covalent geometry : bond 0.00585 (27413) covalent geometry : angle 0.86985 (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 291 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 205 time to evaluate : 2.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.6372 (mmtm) cc_final: 0.6164 (mttp) REVERT: A 402 ILE cc_start: 0.6423 (OUTLIER) cc_final: 0.6176 (pp) REVERT: A 591 SER cc_start: 0.8954 (m) cc_final: 0.8605 (p) REVERT: A 634 ARG cc_start: 0.4281 (OUTLIER) cc_final: 0.3939 (ttt180) REVERT: A 779 GLN cc_start: 0.8030 (tp40) cc_final: 0.7577 (tt0) REVERT: A 900 MET cc_start: 0.7683 (mmp) cc_final: 0.7367 (mmt) REVERT: B 237 ARG cc_start: 0.7058 (ttt-90) cc_final: 0.6271 (mtp-110) REVERT: B 494 SER cc_start: 0.5862 (OUTLIER) cc_final: 0.5539 (t) REVERT: B 591 SER cc_start: 0.8422 (m) cc_final: 0.7760 (p) REVERT: B 869 MET cc_start: 0.8607 (mtt) cc_final: 0.8350 (mtp) REVERT: C 55 PHE cc_start: 0.7503 (OUTLIER) cc_final: 0.5714 (m-80) REVERT: C 104 TRP cc_start: 0.5676 (m-10) cc_final: 0.5416 (m-10) REVERT: C 177 MET cc_start: 0.4233 (mmp) cc_final: 0.3315 (mtp) REVERT: C 189 LEU cc_start: 0.7856 (tt) cc_final: 0.7579 (pp) REVERT: C 270 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6419 (tt) REVERT: C 400 PHE cc_start: 0.6767 (p90) cc_final: 0.6350 (p90) REVERT: C 869 MET cc_start: 0.8327 (mpp) cc_final: 0.8052 (mtt) outliers start: 86 outliers final: 52 residues processed: 279 average time/residue: 0.3434 time to fit residues: 159.8893 Evaluate side-chains 210 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 153 time to evaluate : 3.190 ------------------------------------------------------------------------------- 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 208 THR Chi-restraints excluded: chain A residue 301 CYS 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 402 ILE 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 551 VAL Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 1077 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 276 LEU 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 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 791 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 270 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 382 VAL 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 664 ILE Chi-restraints excluded: chain C residue 722 VAL 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 977 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1030 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 17 optimal weight: 10.0000 chunk 313 optimal weight: 3.9990 chunk 295 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 282 optimal weight: 0.7980 chunk 271 optimal weight: 0.7980 chunk 191 optimal weight: 0.6980 chunk 197 optimal weight: 0.9980 chunk 150 optimal weight: 0.3980 chunk 63 optimal weight: 0.9990 chunk 293 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** B 613 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN C 49 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.210468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.167666 restraints weight = 48926.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.164475 restraints weight = 60604.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.166840 restraints weight = 50812.892| |-----------------------------------------------------------------------------| r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.8761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27565 Z= 0.142 Angle : 0.727 12.182 37717 Z= 0.347 Chirality : 0.045 0.427 4545 Planarity : 0.005 0.084 4675 Dihedral : 5.856 57.971 5769 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.07 % Favored : 95.81 % Rotamer: Outliers : 1.80 % Allowed : 19.39 % Favored : 78.81 % 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: -0.80 (0.15), residues: 3198 helix: 1.64 (0.20), residues: 747 sheet: -0.48 (0.19), residues: 690 loop : -1.58 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 104 HIS 0.005 0.001 HIS A1118 PHE 0.028 0.002 PHE B 106 TYR 0.019 0.001 TYR B 160 ARG 0.017 0.001 ARG B 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 53) link_NAG-ASN : angle 2.71675 ( 159) link_ALPHA1-4 : bond 0.01739 ( 21) link_ALPHA1-4 : angle 2.68620 ( 63) link_BETA1-4 : bond 0.00412 ( 33) link_BETA1-4 : angle 1.48129 ( 99) hydrogen bonds : bond 0.05490 ( 993) hydrogen bonds : angle 5.42906 ( 2763) link_BETA1-6 : bond 0.01767 ( 3) link_BETA1-6 : angle 1.69032 ( 9) SS BOND : bond 0.00526 ( 42) SS BOND : angle 1.54382 ( 84) covalent geometry : bond 0.00301 (27413) covalent geometry : angle 0.69222 (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 235 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 184 time to evaluate : 2.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.6321 (p90) cc_final: 0.6099 (p90) REVERT: A 402 ILE cc_start: 0.4908 (OUTLIER) cc_final: 0.4540 (pp) REVERT: A 931 ILE cc_start: 0.7833 (mp) cc_final: 0.7563 (mt) REVERT: A 1106 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8206 (pt0) REVERT: B 237 ARG cc_start: 0.6262 (ttt-90) cc_final: 0.5852 (mtp-110) REVERT: B 494 SER cc_start: 0.5938 (OUTLIER) cc_final: 0.5589 (t) REVERT: B 775 ASP cc_start: 0.8127 (m-30) cc_final: 0.7905 (m-30) REVERT: B 902 MET cc_start: 0.8277 (tpt) cc_final: 0.7437 (tpt) REVERT: B 974 SER cc_start: 0.8641 (t) cc_final: 0.8344 (m) REVERT: C 177 MET cc_start: 0.3353 (mmp) cc_final: 0.2943 (mpp) REVERT: C 380 TYR cc_start: 0.7405 (OUTLIER) cc_final: 0.4926 (m-80) REVERT: C 400 PHE cc_start: 0.7229 (p90) cc_final: 0.6826 (p90) REVERT: C 664 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7895 (mt) REVERT: C 819 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7377 (mt-10) outliers start: 51 outliers final: 32 residues processed: 227 average time/residue: 0.3361 time to fit residues: 129.6653 Evaluate side-chains 199 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 301 CYS 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 402 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 1106 GLN 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 238 PHE Chi-restraints excluded: chain B residue 306 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 620 VAL Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 10 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 251 optimal weight: 20.0000 chunk 196 optimal weight: 6.9990 chunk 167 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 223 optimal weight: 5.9990 chunk 278 optimal weight: 1.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 655 HIS A 913 GLN A1005 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN B1002 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 GLN C 360 ASN C 658 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.198102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.142951 restraints weight = 48918.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.139210 restraints weight = 34387.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.138523 restraints weight = 32289.447| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 1.0226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 27565 Z= 0.320 Angle : 1.014 13.794 37717 Z= 0.500 Chirality : 0.057 0.461 4545 Planarity : 0.007 0.095 4675 Dihedral : 7.202 58.957 5769 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.79 % Favored : 92.09 % Rotamer: Outliers : 2.15 % Allowed : 19.70 % Favored : 78.14 % 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: -1.62 (0.14), residues: 3198 helix: 0.81 (0.19), residues: 741 sheet: -0.92 (0.19), residues: 684 loop : -2.05 (0.13), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 64 HIS 0.011 0.002 HIS C 207 PHE 0.035 0.004 PHE C 133 TYR 0.031 0.003 TYR A1067 ARG 0.016 0.001 ARG B 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00898 ( 53) link_NAG-ASN : angle 3.39893 ( 159) link_ALPHA1-4 : bond 0.01717 ( 21) link_ALPHA1-4 : angle 2.89132 ( 63) link_BETA1-4 : bond 0.00506 ( 33) link_BETA1-4 : angle 2.07486 ( 99) hydrogen bonds : bond 0.08589 ( 993) hydrogen bonds : angle 6.32828 ( 2763) link_BETA1-6 : bond 0.01370 ( 3) link_BETA1-6 : angle 2.12407 ( 9) SS BOND : bond 0.00854 ( 42) SS BOND : angle 2.26438 ( 84) covalent geometry : bond 0.00751 (27413) covalent geometry : angle 0.97549 (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 223 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 162 time to evaluate : 2.826 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 386 LYS cc_start: 0.6614 (mmtm) cc_final: 0.6364 (mttp) REVERT: A 400 PHE cc_start: 0.6475 (p90) cc_final: 0.6194 (p90) REVERT: A 402 ILE cc_start: 0.5759 (OUTLIER) cc_final: 0.5036 (pp) REVERT: A 820 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7353 (t70) REVERT: B 494 SER cc_start: 0.6096 (OUTLIER) cc_final: 0.5731 (t) REVERT: B 902 MET cc_start: 0.8507 (tpt) cc_final: 0.7966 (tpt) REVERT: B 1116 THR cc_start: 0.7392 (OUTLIER) cc_final: 0.7102 (p) REVERT: C 380 TYR cc_start: 0.7471 (OUTLIER) cc_final: 0.5928 (m-80) REVERT: C 788 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7352 (mt) outliers start: 61 outliers final: 41 residues processed: 214 average time/residue: 0.3678 time to fit residues: 132.4410 Evaluate side-chains 177 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 130 time to evaluate : 2.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 CYS 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 402 ILE 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 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 882 ILE Chi-restraints excluded: chain A residue 941 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 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 306 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 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 791 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 127 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 515 PHE Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 590 CYS 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 1030 SER Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 123 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 236 optimal weight: 0.8980 chunk 118 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 313 optimal weight: 10.0000 chunk 230 optimal weight: 6.9990 chunk 4 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A1005 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN B1002 GLN B1083 HIS C 30 ASN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.202283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.146351 restraints weight = 49032.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.142882 restraints weight = 35443.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.142654 restraints weight = 28908.424| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 1.0367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 27565 Z= 0.154 Angle : 0.767 12.395 37717 Z= 0.369 Chirality : 0.047 0.447 4545 Planarity : 0.005 0.075 4675 Dihedral : 6.292 57.679 5769 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.50 % Favored : 95.37 % Rotamer: Outliers : 1.77 % Allowed : 20.23 % Favored : 78.00 % 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: -1.13 (0.14), residues: 3198 helix: 1.62 (0.19), residues: 726 sheet: -0.90 (0.19), residues: 729 loop : -1.79 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 104 HIS 0.006 0.001 HIS C 207 PHE 0.021 0.002 PHE A 201 TYR 0.023 0.002 TYR C 37 ARG 0.012 0.001 ARG B 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00464 ( 53) link_NAG-ASN : angle 2.79843 ( 159) link_ALPHA1-4 : bond 0.01657 ( 21) link_ALPHA1-4 : angle 2.49539 ( 63) link_BETA1-4 : bond 0.00429 ( 33) link_BETA1-4 : angle 1.55893 ( 99) hydrogen bonds : bond 0.06019 ( 993) hydrogen bonds : angle 5.62560 ( 2763) link_BETA1-6 : bond 0.01523 ( 3) link_BETA1-6 : angle 1.63546 ( 9) SS BOND : bond 0.00426 ( 42) SS BOND : angle 1.58601 ( 84) covalent geometry : bond 0.00336 (27413) covalent geometry : angle 0.73320 (37303) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9338.89 seconds wall clock time: 167 minutes 17.67 seconds (10037.67 seconds total)