Starting phenix.real_space_refine on Sun Jul 5 09:15:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ybl_33725/07_2026/7ybl_33725.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ybl_33725/07_2026/7ybl_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ybl_33725/07_2026/7ybl_33725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ybl_33725/07_2026/7ybl_33725.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ybl_33725/07_2026/7ybl_33725.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ybl_33725/07_2026/7ybl_33725.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ybl_33725/07_2026/7ybl_33725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ybl_33725/07_2026/7ybl_33725.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 8 Time building chain proxies: 5.19, per 1000 atoms: 0.19 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: 1.97 Conformation dependent library (CDL) restraints added in 913.0 milliseconds 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: 1.03 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: 6.19 Time building geometry restraints manager: 2.52 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 - 17.89: 14183 17.89 - 35.77: 1049 35.77 - 53.66: 193 53.66 - 71.54: 42 71.54 - 89.43: 28 Dihedral angle restraints: 15495 sinusoidal: 6075 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 15492 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 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: 2.840 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: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 24.090 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5005 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 : 13.205 89.429 9309 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 14.01 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.026 0.001 ARG C 237 TYR 0.035 0.002 TYR A 242 PHE 0.053 0.002 PHE C 238 TRP 0.023 0.002 TRP B 353 HIS 0.008 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.33 (27413) covalent geometry : angle 0.95952 / 0.58 (37303) SS BOND : bond 0.00471 / 0.29 ( 42) SS BOND : angle 1.51942 / 1.05 ( 84) hydrogen bonds : bond 0.21963 / 14.15 ( 993) hydrogen bonds : angle 8.29559 / 5.64 ( 2763) link_ALPHA1-4 : bond 0.00470 / 0.29 ( 21) link_ALPHA1-4 : angle 2.14094 / 1.44 ( 63) link_BETA1-4 : bond 0.00639 / 0.38 ( 33) link_BETA1-4 : angle 1.36456 / 0.96 ( 99) link_BETA1-6 : bond 0.00827 / 0.41 ( 3) link_BETA1-6 : angle 1.56760 / 0.86 ( 9) link_NAG-ASN : bond 0.00536 / 0.39 ( 53) link_NAG-ASN : angle 3.32916 / 2.14 ( 159) *********************** 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 : 0.719 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: C 38 TYR cc_start: 0.3668 (m-10) cc_final: 0.3393 (m-80) REVERT: C 380 TYR cc_start: 0.6713 (OUTLIER) cc_final: 0.4412 (m-80) REVERT: C 1094 VAL cc_start: 0.3715 (p) cc_final: 0.3370 (p) outliers start: 17 outliers final: 5 residues processed: 526 average time/residue: 0.1458 time to fit residues: 123.1191 Evaluate side-chains 254 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 248 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 197 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 4.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 HIS A 134 GLN A 207 HIS A 544 ASN A 751 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN A1002 GLN A1083 HIS A1118 HIS B 49 HIS B 388 ASN B 448 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B1002 GLN B1005 GLN B1058 HIS ** 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 655 HIS C 751 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C 955 ASN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5054 r_free = 0.5054 target = 0.255911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4912 r_free = 0.4912 target = 0.237651 restraints weight = 59206.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.236382 restraints weight = 70454.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.233479 restraints weight = 62913.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.232805 restraints weight = 74168.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.232426 restraints weight = 63581.688| |-----------------------------------------------------------------------------| r_work (final): 0.4610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5871 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 27565 Z= 0.276 Angle : 0.962 16.406 37717 Z= 0.478 Chirality : 0.056 0.428 4545 Planarity : 0.007 0.065 4675 Dihedral : 5.740 47.915 3481 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.00 % Favored : 94.90 % Rotamer: Outliers : 2.72 % Allowed : 9.71 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.14), residues: 3198 helix: 0.66 (0.19), residues: 720 sheet: -0.87 (0.19), residues: 711 loop : -1.68 (0.13), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 995 TYR 0.036 0.003 TYR B 904 PHE 0.042 0.004 PHE C 194 TRP 0.034 0.004 TRP C 104 HIS 0.011 0.002 HIS A1118 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.27 (27413) covalent geometry : angle 0.92429 / 0.47 (37303) SS BOND : bond 0.01052 / 0.80 ( 42) SS BOND : angle 2.10848 / 1.43 ( 84) hydrogen bonds : bond 0.07321 / 4.84 ( 993) hydrogen bonds : angle 6.53251 / 4.42 ( 2763) link_ALPHA1-4 : bond 0.00632 / 0.40 ( 21) link_ALPHA1-4 : angle 2.16181 / 1.41 ( 63) link_BETA1-4 : bond 0.00697 / 0.44 ( 33) link_BETA1-4 : angle 2.51773 / 1.62 ( 99) link_BETA1-6 : bond 0.00996 / 0.50 ( 3) link_BETA1-6 : angle 0.76656 / 0.43 ( 9) link_NAG-ASN : bond 0.01529 / 1.19 ( 53) link_NAG-ASN : angle 3.32673 / 2.12 ( 159) *********************** 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 403 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 326 time to evaluate : 0.930 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: B 902 MET cc_start: 0.7887 (tpp) cc_final: 0.7620 (tpt) REVERT: B 1055 SER cc_start: 0.8744 (p) cc_final: 0.8478 (t) REVERT: B 1096 VAL cc_start: 0.7191 (p) cc_final: 0.6955 (m) REVERT: C 51 THR cc_start: 0.5549 (p) cc_final: 0.5164 (p) REVERT: C 776 LYS cc_start: 0.9089 (tptp) cc_final: 0.8824 (tptt) REVERT: C 788 ILE cc_start: 0.6837 (OUTLIER) cc_final: 0.6401 (mt) REVERT: C 1029 MET cc_start: 0.8817 (tpt) cc_final: 0.8372 (tpt) outliers start: 77 outliers final: 45 residues processed: 381 average time/residue: 0.1541 time to fit residues: 96.0853 Evaluate side-chains 261 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 215 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 896 ILE 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 998 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 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 383 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 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 194 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 chunk 163 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 266 optimal weight: 4.9990 chunk 258 optimal weight: 30.0000 chunk 301 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 chunk 221 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 784 GLN B 969 ASN B1054 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN ** C1119 ASN ** 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 = 0.4832 r_free = 0.4832 target = 0.226342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.188919 restraints weight = 51971.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.181107 restraints weight = 64164.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.176990 restraints weight = 60073.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.178067 restraints weight = 42503.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.178406 restraints weight = 30678.594| |-----------------------------------------------------------------------------| r_work (final): 0.4308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27565 Z= 0.161 Angle : 0.732 15.940 37717 Z= 0.356 Chirality : 0.046 0.357 4545 Planarity : 0.005 0.063 4675 Dihedral : 4.885 24.992 3471 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.60 % Favored : 95.28 % Rotamer: Outliers : 2.51 % Allowed : 14.16 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.14), residues: 3198 helix: 1.35 (0.20), residues: 738 sheet: -0.75 (0.19), residues: 723 loop : -1.47 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 346 TYR 0.019 0.002 TYR B1067 PHE 0.030 0.002 PHE A 855 TRP 0.034 0.002 TRP A 104 HIS 0.016 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (27413) covalent geometry : angle 0.70084 / 0.35 (37303) SS BOND : bond 0.00409 / 0.24 ( 42) SS BOND : angle 1.66872 / 1.15 ( 84) hydrogen bonds : bond 0.06173 / 4.04 ( 993) hydrogen bonds : angle 5.84390 / 3.93 ( 2763) link_ALPHA1-4 : bond 0.00662 / 0.44 ( 21) link_ALPHA1-4 : angle 1.71699 / 1.16 ( 63) link_BETA1-4 : bond 0.00421 / 0.27 ( 33) link_BETA1-4 : angle 1.22536 / 0.84 ( 99) link_BETA1-6 : bond 0.00925 / 0.47 ( 3) link_BETA1-6 : angle 1.34726 / 0.77 ( 9) link_NAG-ASN : bond 0.00699 / 0.52 ( 53) link_NAG-ASN : angle 2.87106 / 1.91 ( 159) *********************** 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 338 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 267 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLN cc_start: 0.7081 (mm110) cc_final: 0.6776 (mm-40) REVERT: A 388 ASN cc_start: 0.6261 (OUTLIER) cc_final: 0.5909 (p0) REVERT: A 697 MET cc_start: 0.6046 (OUTLIER) cc_final: 0.5752 (ttp) REVERT: A 900 MET cc_start: 0.7366 (mmt) cc_final: 0.6761 (mmt) REVERT: B 304 LYS cc_start: 0.8427 (mmtt) cc_final: 0.8178 (mmmt) REVERT: B 571 ASP cc_start: 0.6643 (t0) cc_final: 0.6352 (t0) REVERT: B 1096 VAL cc_start: 0.7094 (p) cc_final: 0.6802 (m) REVERT: B 1104 VAL cc_start: 0.6370 (OUTLIER) cc_final: 0.6053 (m) REVERT: B 1115 ILE cc_start: 0.6995 (OUTLIER) cc_final: 0.6668 (tp) REVERT: C 177 MET cc_start: 0.6265 (mpp) cc_final: 0.4805 (ttm) REVERT: C 380 TYR cc_start: 0.6925 (OUTLIER) cc_final: 0.4188 (m-80) REVERT: C 697 MET cc_start: 0.5873 (ptm) cc_final: 0.5566 (ptm) REVERT: C 776 LYS cc_start: 0.9016 (tptp) cc_final: 0.8793 (tptt) REVERT: C 788 ILE cc_start: 0.7058 (OUTLIER) cc_final: 0.6711 (mp) REVERT: C 1029 MET cc_start: 0.8822 (tpt) cc_final: 0.8282 (tpt) REVERT: C 1107 ARG cc_start: 0.7868 (mpt-90) cc_final: 0.7667 (mpt-90) REVERT: C 1115 ILE cc_start: 0.7132 (OUTLIER) cc_final: 0.6599 (tp) outliers start: 71 outliers final: 37 residues processed: 320 average time/residue: 0.1574 time to fit residues: 83.1165 Evaluate side-chains 251 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 207 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain B residue 206 LYS 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 512 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 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 717 ASN Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 1115 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 230 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 206 optimal weight: 6.9990 chunk 176 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 144 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 223 optimal weight: 20.0000 chunk 67 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN A 121 ASN A 164 ASN A 564 GLN A 580 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN A 953 ASN A 992 GLN A1108 ASN B 121 ASN B 625 HIS B 969 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 360 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 955 ASN C1058 HIS C1119 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.207055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.147344 restraints weight = 50260.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.144391 restraints weight = 34374.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.144304 restraints weight = 29125.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.144776 restraints weight = 30209.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.144974 restraints weight = 26537.526| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.7986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 27565 Z= 0.305 Angle : 0.996 15.375 37717 Z= 0.491 Chirality : 0.056 0.435 4545 Planarity : 0.007 0.168 4675 Dihedral : 6.005 26.069 3471 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.19 % Favored : 92.68 % Rotamer: Outliers : 5.40 % Allowed : 16.03 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.14), residues: 3198 helix: 0.63 (0.19), residues: 735 sheet: -1.08 (0.19), residues: 672 loop : -2.01 (0.13), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG B 102 TYR 0.037 0.003 TYR B 904 PHE 0.043 0.003 PHE C 400 TRP 0.047 0.003 TRP B 104 HIS 0.020 0.002 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00692 / 0.30 (27413) covalent geometry : angle 0.95938 / 0.48 (37303) SS BOND : bond 0.00615 / 0.33 ( 42) SS BOND : angle 2.28079 / 1.60 ( 84) hydrogen bonds : bond 0.08407 / 5.55 ( 993) hydrogen bonds : angle 6.51703 / 4.42 ( 2763) link_ALPHA1-4 : bond 0.00676 / 0.46 ( 21) link_ALPHA1-4 : angle 2.07938 / 1.40 ( 63) link_BETA1-4 : bond 0.00580 / 0.39 ( 33) link_BETA1-4 : angle 1.77855 / 1.25 ( 99) link_BETA1-6 : bond 0.00968 / 0.48 ( 3) link_BETA1-6 : angle 1.64370 / 0.93 ( 9) link_NAG-ASN : bond 0.01344 / 0.95 ( 53) link_NAG-ASN : angle 3.55668 / 2.34 ( 159) *********************** 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 376 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 223 time to evaluate : 0.971 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 237 ARG cc_start: 0.5639 (ppt170) cc_final: 0.5363 (ptt-90) REVERT: A 270 LEU cc_start: 0.6665 (OUTLIER) cc_final: 0.6330 (tt) REVERT: A 402 ILE cc_start: 0.6039 (OUTLIER) cc_final: 0.5790 (pp) REVERT: A 619 GLU cc_start: 0.6228 (mm-30) cc_final: 0.5929 (mt-10) REVERT: A 779 GLN cc_start: 0.8011 (tp40) cc_final: 0.7636 (tt0) REVERT: A 977 LEU cc_start: 0.8141 (mp) cc_final: 0.7897 (mt) REVERT: B 552 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6847 (pt) REVERT: B 591 SER cc_start: 0.8026 (m) cc_final: 0.7439 (p) REVERT: B 674 TYR cc_start: 0.5813 (t80) cc_final: 0.5595 (t80) REVERT: B 819 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7778 (mt-10) REVERT: B 984 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7344 (mm) REVERT: C 133 PHE cc_start: 0.2777 (m-80) cc_final: 0.2573 (m-80) REVERT: C 380 TYR cc_start: 0.7380 (OUTLIER) cc_final: 0.5164 (m-80) REVERT: C 779 GLN cc_start: 0.7983 (tp40) cc_final: 0.7641 (tt0) REVERT: C 788 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7178 (mt) REVERT: C 900 MET cc_start: 0.7773 (mmp) cc_final: 0.7566 (mmp) outliers start: 153 outliers final: 83 residues processed: 358 average time/residue: 0.1524 time to fit residues: 90.7888 Evaluate side-chains 245 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 155 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 270 LEU 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 318 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE 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 590 CYS Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 739 THR 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 865 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 644 GLN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1077 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 153 optimal weight: 9.9990 chunk 181 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 307 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 196 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 chunk 248 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN A 564 GLN A 787 GLN A 969 ASN A1058 HIS B 644 GLN B 787 GLN B 953 ASN B 969 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.207954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.146765 restraints weight = 49776.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.147095 restraints weight = 33416.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.146405 restraints weight = 27287.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.146519 restraints weight = 26931.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.147204 restraints weight = 24427.493| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.8495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27565 Z= 0.182 Angle : 0.769 15.041 37717 Z= 0.371 Chirality : 0.047 0.380 4545 Planarity : 0.005 0.061 4675 Dihedral : 5.246 23.924 3471 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.13 % Favored : 94.75 % Rotamer: Outliers : 3.28 % Allowed : 18.75 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.14), residues: 3198 helix: 1.30 (0.19), residues: 747 sheet: -0.97 (0.19), residues: 720 loop : -1.88 (0.13), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 567 TYR 0.021 0.002 TYR B1067 PHE 0.032 0.002 PHE B 86 TRP 0.043 0.002 TRP A 104 HIS 0.005 0.001 HIS C1118 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (27413) covalent geometry : angle 0.73724 / 0.36 (37303) SS BOND : bond 0.00567 / 0.40 ( 42) SS BOND : angle 1.81124 / 1.26 ( 84) hydrogen bonds : bond 0.06438 / 4.22 ( 993) hydrogen bonds : angle 5.88077 / 3.97 ( 2763) link_ALPHA1-4 : bond 0.00691 / 0.47 ( 21) link_ALPHA1-4 : angle 1.88960 / 1.28 ( 63) link_BETA1-4 : bond 0.00439 / 0.29 ( 33) link_BETA1-4 : angle 1.45259 / 1.01 ( 99) link_BETA1-6 : bond 0.00794 / 0.40 ( 3) link_BETA1-6 : angle 1.70666 / 0.96 ( 9) link_NAG-ASN : bond 0.00648 / 0.49 ( 53) link_NAG-ASN : angle 2.86017 / 1.84 ( 159) *********************** 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 277 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 184 time to evaluate : 0.794 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 192 PHE cc_start: 0.6251 (m-80) cc_final: 0.5906 (m-80) REVERT: A 237 ARG cc_start: 0.5488 (ppt170) cc_final: 0.5072 (ppt170) REVERT: A 386 LYS cc_start: 0.6318 (mmtm) cc_final: 0.6071 (mttp) REVERT: A 400 PHE cc_start: 0.6503 (p90) cc_final: 0.5943 (p90) REVERT: A 900 MET cc_start: 0.7507 (mmt) cc_final: 0.7123 (mmt) REVERT: A 977 LEU cc_start: 0.7911 (mp) cc_final: 0.7661 (mt) REVERT: B 552 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6910 (pt) REVERT: B 571 ASP cc_start: 0.6894 (t0) cc_final: 0.6584 (t0) REVERT: B 591 SER cc_start: 0.8255 (m) cc_final: 0.7731 (p) REVERT: B 819 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7749 (mt-10) REVERT: B 984 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7441 (mm) REVERT: B 1115 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.7148 (tp) REVERT: C 118 LEU cc_start: 0.6089 (tp) cc_final: 0.5760 (tp) REVERT: C 133 PHE cc_start: 0.2565 (m-80) cc_final: 0.1866 (m-80) REVERT: C 380 TYR cc_start: 0.7408 (OUTLIER) cc_final: 0.5120 (m-80) REVERT: C 400 PHE cc_start: 0.7348 (p90) cc_final: 0.6964 (p90) REVERT: C 776 LYS cc_start: 0.9148 (tptp) cc_final: 0.8909 (tptt) REVERT: C 779 GLN cc_start: 0.7873 (tp40) cc_final: 0.7537 (tt0) REVERT: C 788 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7500 (mp) outliers start: 93 outliers final: 57 residues processed: 261 average time/residue: 0.1511 time to fit residues: 66.3805 Evaluate side-chains 213 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 150 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 274 THR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 301 CYS 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 515 PHE Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 282 optimal weight: 0.6980 chunk 167 optimal weight: 0.9980 chunk 292 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 44 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 chunk 279 optimal weight: 0.9980 chunk 190 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 163 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 969 ASN C 439 ASN C 787 GLN C1118 HIS ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.209802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.163268 restraints weight = 49700.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.159952 restraints weight = 54230.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.154545 restraints weight = 35850.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.153969 restraints weight = 33871.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.154917 restraints weight = 33002.808| |-----------------------------------------------------------------------------| r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.8728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27565 Z= 0.134 Angle : 0.705 14.227 37717 Z= 0.337 Chirality : 0.046 0.363 4545 Planarity : 0.005 0.078 4675 Dihedral : 4.928 24.503 3471 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.28 % Favored : 94.59 % Rotamer: Outliers : 2.61 % Allowed : 19.99 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.15), residues: 3198 helix: 1.91 (0.20), residues: 717 sheet: -0.83 (0.19), residues: 723 loop : -1.71 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 983 TYR 0.015 0.001 TYR A1138 PHE 0.027 0.002 PHE C 823 TRP 0.039 0.001 TRP A 104 HIS 0.006 0.001 HIS C1118 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (27413) covalent geometry : angle 0.67533 / 0.33 (37303) SS BOND : bond 0.00383 / 0.24 ( 42) SS BOND : angle 1.55441 / 1.08 ( 84) hydrogen bonds : bond 0.05485 / 3.59 ( 993) hydrogen bonds : angle 5.50859 / 3.72 ( 2763) link_ALPHA1-4 : bond 0.00609 / 0.41 ( 21) link_ALPHA1-4 : angle 1.75360 / 1.19 ( 63) link_BETA1-4 : bond 0.00411 / 0.26 ( 33) link_BETA1-4 : angle 1.26686 / 0.87 ( 99) link_BETA1-6 : bond 0.00832 / 0.42 ( 3) link_BETA1-6 : angle 1.50140 / 0.84 ( 9) link_NAG-ASN : bond 0.00589 / 0.44 ( 53) link_NAG-ASN : angle 2.68901 / 1.72 ( 159) *********************** 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 264 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 190 time to evaluate : 1.012 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 237 ARG cc_start: 0.5249 (ppt170) cc_final: 0.4676 (ptt-90) REVERT: A 386 LYS cc_start: 0.6634 (mmtm) cc_final: 0.6354 (mttp) REVERT: A 400 PHE cc_start: 0.6580 (p90) cc_final: 0.6095 (p90) REVERT: A 977 LEU cc_start: 0.7789 (mp) cc_final: 0.7495 (mt) REVERT: B 237 ARG cc_start: 0.6792 (ttt90) cc_final: 0.6411 (mtp-110) REVERT: B 1115 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.7155 (tp) REVERT: C 118 LEU cc_start: 0.6231 (tp) cc_final: 0.6007 (tp) REVERT: C 133 PHE cc_start: 0.1786 (m-80) cc_final: 0.1538 (m-80) REVERT: C 177 MET cc_start: 0.4102 (mmp) cc_final: 0.2591 (mtp) REVERT: C 380 TYR cc_start: 0.7413 (OUTLIER) cc_final: 0.4797 (m-80) REVERT: C 400 PHE cc_start: 0.7388 (p90) cc_final: 0.7113 (p90) REVERT: C 776 LYS cc_start: 0.9173 (tptp) cc_final: 0.8856 (tptt) REVERT: C 779 GLN cc_start: 0.7671 (tp40) cc_final: 0.7367 (tt0) REVERT: C 788 ILE cc_start: 0.7970 (OUTLIER) cc_final: 0.7563 (mp) REVERT: C 819 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7651 (mt-10) outliers start: 74 outliers final: 48 residues processed: 251 average time/residue: 0.1473 time to fit residues: 62.0332 Evaluate side-chains 212 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 160 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 1077 THR 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 274 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 430 THR 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 649 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 301 CYS 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 512 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 61 optimal weight: 0.0570 chunk 304 optimal weight: 0.2980 chunk 301 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 193 optimal weight: 0.6980 chunk 277 optimal weight: 6.9990 chunk 186 optimal weight: 0.6980 chunk 285 optimal weight: 1.9990 chunk 279 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 233 optimal weight: 0.9990 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN B 969 ASN C 658 ASN ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.211107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.171437 restraints weight = 50122.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.168161 restraints weight = 76774.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.170434 restraints weight = 60216.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.170730 restraints weight = 37755.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.171566 restraints weight = 33870.740| |-----------------------------------------------------------------------------| r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.8912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27565 Z= 0.122 Angle : 0.679 13.901 37717 Z= 0.322 Chirality : 0.045 0.511 4545 Planarity : 0.005 0.057 4675 Dihedral : 4.666 24.180 3471 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.57 % Favored : 95.28 % Rotamer: Outliers : 2.51 % Allowed : 20.37 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.15), residues: 3198 helix: 2.13 (0.20), residues: 717 sheet: -0.68 (0.19), residues: 723 loop : -1.60 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 34 TYR 0.015 0.001 TYR B 269 PHE 0.029 0.001 PHE A 192 TRP 0.039 0.001 TRP A 104 HIS 0.004 0.001 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (27413) covalent geometry : angle 0.64981 / 0.32 (37303) SS BOND : bond 0.00336 / 0.22 ( 42) SS BOND : angle 1.35907 / 0.92 ( 84) hydrogen bonds : bond 0.04956 / 3.24 ( 993) hydrogen bonds : angle 5.27488 / 3.57 ( 2763) link_ALPHA1-4 : bond 0.00566 / 0.39 ( 21) link_ALPHA1-4 : angle 1.72379 / 1.20 ( 63) link_BETA1-4 : bond 0.00460 / 0.27 ( 33) link_BETA1-4 : angle 1.18605 / 0.82 ( 99) link_BETA1-6 : bond 0.00798 / 0.40 ( 3) link_BETA1-6 : angle 1.45577 / 0.82 ( 9) link_NAG-ASN : bond 0.00499 / 0.36 ( 53) link_NAG-ASN : angle 2.65707 / 1.68 ( 159) *********************** 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 254 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 183 time to evaluate : 0.937 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 58 PHE cc_start: 0.7451 (OUTLIER) cc_final: 0.6994 (t80) REVERT: A 237 ARG cc_start: 0.4758 (ppt170) cc_final: 0.4534 (ptt90) REVERT: A 900 MET cc_start: 0.7276 (mmt) cc_final: 0.7075 (mmt) REVERT: A 977 LEU cc_start: 0.7908 (mp) cc_final: 0.7655 (mt) REVERT: B 133 PHE cc_start: 0.1026 (m-80) cc_final: 0.0607 (m-80) REVERT: B 190 ARG cc_start: 0.4692 (mpt180) cc_final: 0.4465 (mpt180) REVERT: B 494 SER cc_start: 0.5863 (OUTLIER) cc_final: 0.5502 (t) REVERT: B 552 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6904 (pt) REVERT: B 591 SER cc_start: 0.8090 (m) cc_final: 0.7826 (p) REVERT: B 1115 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.7157 (tp) REVERT: C 118 LEU cc_start: 0.6195 (tp) cc_final: 0.5954 (tt) REVERT: C 177 MET cc_start: 0.2855 (mmp) cc_final: 0.2330 (mpp) REVERT: C 380 TYR cc_start: 0.7410 (OUTLIER) cc_final: 0.4783 (m-80) REVERT: C 776 LYS cc_start: 0.9203 (tptp) cc_final: 0.8917 (tptt) REVERT: C 779 GLN cc_start: 0.7546 (tp40) cc_final: 0.7204 (tt0) REVERT: C 788 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7525 (mp) REVERT: C 819 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7431 (mt-10) outliers start: 71 outliers final: 47 residues processed: 239 average time/residue: 0.1404 time to fit residues: 57.1627 Evaluate side-chains 216 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 162 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 51 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 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 552 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 91 TYR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 274 THR 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 512 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 2 optimal weight: 0.9980 chunk 302 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 251 optimal weight: 3.9990 chunk 241 optimal weight: 0.0670 chunk 308 optimal weight: 0.6980 chunk 265 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN B 969 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN C 954 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.210192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.170469 restraints weight = 50362.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.167438 restraints weight = 76487.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.169849 restraints weight = 58828.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.169788 restraints weight = 37372.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.170759 restraints weight = 33955.345| |-----------------------------------------------------------------------------| r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.9126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27565 Z= 0.124 Angle : 0.665 13.887 37717 Z= 0.319 Chirality : 0.045 0.391 4545 Planarity : 0.005 0.058 4675 Dihedral : 4.593 21.763 3471 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.97 % Favored : 94.87 % Rotamer: Outliers : 2.75 % Allowed : 20.59 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.15), residues: 3198 helix: 2.09 (0.20), residues: 729 sheet: -0.47 (0.19), residues: 711 loop : -1.59 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 237 TYR 0.028 0.001 TYR C 508 PHE 0.025 0.001 PHE B 86 TRP 0.032 0.002 TRP A 104 HIS 0.004 0.001 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (27413) covalent geometry : angle 0.63900 / 0.31 (37303) SS BOND : bond 0.00365 / 0.22 ( 42) SS BOND : angle 1.34473 / 0.90 ( 84) hydrogen bonds : bond 0.04881 / 3.20 ( 993) hydrogen bonds : angle 5.21866 / 3.54 ( 2763) link_ALPHA1-4 : bond 0.00578 / 0.40 ( 21) link_ALPHA1-4 : angle 1.63028 / 1.13 ( 63) link_BETA1-4 : bond 0.00376 / 0.24 ( 33) link_BETA1-4 : angle 1.15012 / 0.79 ( 99) link_BETA1-6 : bond 0.00767 / 0.38 ( 3) link_BETA1-6 : angle 1.40982 / 0.79 ( 9) link_NAG-ASN : bond 0.00489 / 0.36 ( 53) link_NAG-ASN : angle 2.50921 / 1.59 ( 159) *********************** 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 263 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 185 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.7523 (OUTLIER) cc_final: 0.7112 (t80) REVERT: A 237 ARG cc_start: 0.4754 (ppt170) cc_final: 0.4531 (ptt90) REVERT: A 664 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7918 (mt) REVERT: A 977 LEU cc_start: 0.7865 (mp) cc_final: 0.7651 (mt) REVERT: A 1029 MET cc_start: 0.8780 (tpp) cc_final: 0.8384 (tpt) REVERT: B 133 PHE cc_start: 0.1321 (m-80) cc_final: 0.0978 (m-80) REVERT: B 190 ARG cc_start: 0.4999 (mpt180) cc_final: 0.4770 (mpt180) REVERT: B 494 SER cc_start: 0.5888 (OUTLIER) cc_final: 0.5525 (t) REVERT: B 515 PHE cc_start: 0.7733 (OUTLIER) cc_final: 0.6654 (p90) REVERT: B 552 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6940 (pt) REVERT: B 591 SER cc_start: 0.8199 (m) cc_final: 0.7916 (p) REVERT: B 984 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7191 (mm) REVERT: B 1115 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7276 (tp) REVERT: C 133 PHE cc_start: 0.2102 (m-80) cc_final: 0.1208 (m-80) REVERT: C 380 TYR cc_start: 0.7507 (OUTLIER) cc_final: 0.4939 (m-80) REVERT: C 571 ASP cc_start: 0.6545 (t0) cc_final: 0.6267 (t0) REVERT: C 776 LYS cc_start: 0.9222 (tptp) cc_final: 0.8935 (tptt) REVERT: C 779 GLN cc_start: 0.7486 (tp40) cc_final: 0.7262 (tt0) REVERT: C 819 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7468 (mt-10) outliers start: 78 outliers final: 52 residues processed: 250 average time/residue: 0.1477 time to fit residues: 62.8505 Evaluate side-chains 229 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 168 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 274 THR 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 590 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 282 optimal weight: 0.3980 chunk 185 optimal weight: 0.8980 chunk 214 optimal weight: 30.0000 chunk 52 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 73 optimal weight: 0.4980 chunk 187 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 314 optimal weight: 0.9990 chunk 302 optimal weight: 2.9990 chunk 316 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C 787 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.209267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.166644 restraints weight = 48846.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.160762 restraints weight = 49943.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.162299 restraints weight = 47399.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.162587 restraints weight = 30222.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.166691 restraints weight = 28725.384| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.9347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27565 Z= 0.125 Angle : 0.669 13.160 37717 Z= 0.321 Chirality : 0.045 0.355 4545 Planarity : 0.005 0.081 4675 Dihedral : 4.556 22.513 3471 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.78 % Favored : 95.09 % Rotamer: Outliers : 2.26 % Allowed : 21.22 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.15), residues: 3198 helix: 2.14 (0.20), residues: 729 sheet: -0.49 (0.20), residues: 648 loop : -1.59 (0.13), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 237 TYR 0.020 0.001 TYR C 170 PHE 0.030 0.001 PHE B 86 TRP 0.044 0.002 TRP C 104 HIS 0.004 0.001 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (27413) covalent geometry : angle 0.64324 / 0.32 (37303) SS BOND : bond 0.00347 / 0.22 ( 42) SS BOND : angle 1.34687 / 0.91 ( 84) hydrogen bonds : bond 0.04830 / 3.17 ( 993) hydrogen bonds : angle 5.20464 / 3.52 ( 2763) link_ALPHA1-4 : bond 0.00574 / 0.39 ( 21) link_ALPHA1-4 : angle 1.61785 / 1.12 ( 63) link_BETA1-4 : bond 0.00375 / 0.24 ( 33) link_BETA1-4 : angle 1.12907 / 0.78 ( 99) link_BETA1-6 : bond 0.00742 / 0.37 ( 3) link_BETA1-6 : angle 1.41321 / 0.80 ( 9) link_NAG-ASN : bond 0.00483 / 0.36 ( 53) link_NAG-ASN : angle 2.46153 / 1.56 ( 159) *********************** 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 242 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 178 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.7701 (OUTLIER) cc_final: 0.7368 (t80) REVERT: A 237 ARG cc_start: 0.5156 (ppt170) cc_final: 0.4675 (ptt-90) REVERT: A 664 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7867 (mt) REVERT: A 977 LEU cc_start: 0.7831 (mp) cc_final: 0.7610 (mt) REVERT: A 1029 MET cc_start: 0.8744 (tpp) cc_final: 0.8377 (tpt) REVERT: B 133 PHE cc_start: 0.1480 (m-80) cc_final: 0.0946 (m-80) REVERT: B 190 ARG cc_start: 0.5021 (mpt180) cc_final: 0.4660 (mpt180) REVERT: B 237 ARG cc_start: 0.6863 (ttt90) cc_final: 0.6565 (ppt170) REVERT: B 494 SER cc_start: 0.5990 (OUTLIER) cc_final: 0.5608 (t) REVERT: B 515 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.6668 (p90) REVERT: B 552 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7077 (pt) REVERT: B 984 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7241 (mm) REVERT: C 380 TYR cc_start: 0.7509 (OUTLIER) cc_final: 0.5072 (m-80) REVERT: C 571 ASP cc_start: 0.6503 (t0) cc_final: 0.6249 (t0) REVERT: C 779 GLN cc_start: 0.7534 (tp40) cc_final: 0.7318 (tt0) REVERT: C 819 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7415 (mt-10) REVERT: C 896 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.7970 (mm) outliers start: 64 outliers final: 46 residues processed: 229 average time/residue: 0.1539 time to fit residues: 59.3988 Evaluate side-chains 220 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 165 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 127 VAL 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 358 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 278 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 120 optimal weight: 5.9990 chunk 270 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 chunk 211 optimal weight: 0.0570 chunk 139 optimal weight: 8.9990 chunk 316 optimal weight: 0.8980 chunk 197 optimal weight: 0.5980 chunk 169 optimal weight: 4.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 969 ASN B1083 HIS C1088 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.208923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.167072 restraints weight = 48986.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.161132 restraints weight = 49242.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.162316 restraints weight = 49172.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.162655 restraints weight = 31273.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.166816 restraints weight = 29564.293| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.9507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27565 Z= 0.119 Angle : 0.663 13.522 37717 Z= 0.317 Chirality : 0.045 0.413 4545 Planarity : 0.005 0.054 4675 Dihedral : 4.498 21.508 3471 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.00 % Favored : 94.87 % Rotamer: Outliers : 2.12 % Allowed : 21.36 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.15), residues: 3198 helix: 2.18 (0.20), residues: 729 sheet: -0.49 (0.20), residues: 654 loop : -1.55 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 237 TYR 0.018 0.001 TYR A 91 PHE 0.019 0.001 PHE B 86 TRP 0.028 0.002 TRP C 104 HIS 0.004 0.001 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (27413) covalent geometry : angle 0.63846 / 0.31 (37303) SS BOND : bond 0.00335 / 0.21 ( 42) SS BOND : angle 1.33783 / 0.88 ( 84) hydrogen bonds : bond 0.04674 / 3.06 ( 993) hydrogen bonds : angle 5.09509 / 3.45 ( 2763) link_ALPHA1-4 : bond 0.00565 / 0.38 ( 21) link_ALPHA1-4 : angle 1.59417 / 1.10 ( 63) link_BETA1-4 : bond 0.00366 / 0.24 ( 33) link_BETA1-4 : angle 1.11632 / 0.77 ( 99) link_BETA1-6 : bond 0.00741 / 0.37 ( 3) link_BETA1-6 : angle 1.38692 / 0.79 ( 9) link_NAG-ASN : bond 0.00461 / 0.34 ( 53) link_NAG-ASN : angle 2.40977 / 1.52 ( 159) ********************** 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 232 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 172 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.7462 (t80) REVERT: A 237 ARG cc_start: 0.5332 (ppt170) cc_final: 0.4955 (ptt-90) REVERT: A 977 LEU cc_start: 0.7841 (mp) cc_final: 0.7620 (mt) REVERT: A 1029 MET cc_start: 0.8758 (tpp) cc_final: 0.8397 (tpt) REVERT: B 133 PHE cc_start: 0.1635 (m-80) cc_final: 0.1043 (m-80) REVERT: B 237 ARG cc_start: 0.6874 (ttt90) cc_final: 0.6595 (ppt170) REVERT: B 494 SER cc_start: 0.6212 (OUTLIER) cc_final: 0.5810 (t) REVERT: B 984 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7303 (mm) REVERT: C 133 PHE cc_start: 0.1576 (m-80) cc_final: 0.0742 (m-80) REVERT: C 380 TYR cc_start: 0.7495 (OUTLIER) cc_final: 0.5207 (m-80) REVERT: C 400 PHE cc_start: 0.7162 (p90) cc_final: 0.6925 (p90) REVERT: C 571 ASP cc_start: 0.6399 (t0) cc_final: 0.6155 (t0) REVERT: C 779 GLN cc_start: 0.7566 (tp40) cc_final: 0.7335 (tt0) REVERT: C 819 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7454 (mt-10) outliers start: 60 outliers final: 49 residues processed: 223 average time/residue: 0.1504 time to fit residues: 56.9480 Evaluate side-chains 219 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 165 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain B residue 51 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 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 525 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 94 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 257 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 256 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 298 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 969 ASN C 607 GLN C 655 HIS C 690 GLN C 777 ASN C1011 GLN ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.199588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.158683 restraints weight = 48112.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.145914 restraints weight = 62140.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.143636 restraints weight = 48127.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.143142 restraints weight = 41071.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.143764 restraints weight = 34014.085| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 1.0340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27565 Z= 0.194 Angle : 0.782 12.942 37717 Z= 0.380 Chirality : 0.049 0.370 4545 Planarity : 0.005 0.095 4675 Dihedral : 5.150 22.977 3471 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.57 % Favored : 93.31 % Rotamer: Outliers : 2.19 % Allowed : 21.43 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.14), residues: 3198 helix: 1.66 (0.19), residues: 729 sheet: -0.85 (0.20), residues: 663 loop : -1.66 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 190 TYR 0.028 0.002 TYR C 674 PHE 0.029 0.002 PHE A 86 TRP 0.023 0.002 TRP C 104 HIS 0.008 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (27413) covalent geometry : angle 0.75527 / 0.37 (37303) SS BOND : bond 0.00487 / 0.30 ( 42) SS BOND : angle 1.62820 / 1.08 ( 84) hydrogen bonds : bond 0.06812 / 4.50 ( 993) hydrogen bonds : angle 5.63968 / 3.83 ( 2763) link_ALPHA1-4 : bond 0.00693 / 0.48 ( 21) link_ALPHA1-4 : angle 1.79340 / 1.26 ( 63) link_BETA1-4 : bond 0.00372 / 0.25 ( 33) link_BETA1-4 : angle 1.42608 / 1.00 ( 99) link_BETA1-6 : bond 0.00713 / 0.36 ( 3) link_BETA1-6 : angle 1.48996 / 0.85 ( 9) link_NAG-ASN : bond 0.00609 / 0.43 ( 53) link_NAG-ASN : angle 2.71116 / 1.68 ( 159) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4342.53 seconds wall clock time: 91 minutes 44.00 seconds (5504.00 seconds total)