Starting phenix.real_space_refine on Fri Mar 6 01:27:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ybl_33725/03_2026/7ybl_33725.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ybl_33725/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ybl_33725/03_2026/7ybl_33725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ybl_33725/03_2026/7ybl_33725.map" model { file = "/net/cci-nas-00/data/ceres_data/7ybl_33725/03_2026/7ybl_33725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ybl_33725/03_2026/7ybl_33725.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.26, per 1000 atoms: 0.23 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: 2.21 Conformation dependent library (CDL) restraints added in 927.5 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: 1.31 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: 6.18 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7523 1.33 - 1.46: 6466 1.46 - 1.58: 13285 1.58 - 1.70: 1 1.70 - 1.83: 138 Bond restraints: 27413 Sorted by residual: bond pdb=" C LEU B 977 " pdb=" N ASN B 978 " ideal model delta sigma weight residual 1.335 1.470 -0.135 1.36e-02 5.41e+03 9.83e+01 bond pdb=" C VAL A 83 " pdb=" N LEU A 84 " ideal model delta sigma weight residual 1.329 1.385 -0.056 1.35e-02 5.49e+03 1.73e+01 bond pdb=" N PRO B 986 " pdb=" CD PRO B 986 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.71e+01 bond pdb=" N PRO B 899 " pdb=" CD PRO B 899 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.58e+01 bond pdb=" N PRO C 986 " pdb=" CD PRO C 986 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.51e+01 ... (remaining 27408 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.44: 37142 4.44 - 8.88: 126 8.88 - 13.32: 26 13.32 - 17.76: 4 17.76 - 22.19: 5 Bond angle restraints: 37303 Sorted by residual: angle pdb=" O ILE C 993 " pdb=" C ILE C 993 " pdb=" N ASP C 994 " ideal model delta sigma weight residual 122.06 99.87 22.19 1.14e+00 7.69e-01 3.79e+02 angle pdb=" O ILE B 993 " pdb=" C ILE B 993 " pdb=" N ASP B 994 " ideal model delta sigma weight residual 121.87 104.00 17.87 9.70e-01 1.06e+00 3.39e+02 angle pdb=" CA ILE B 993 " pdb=" C ILE B 993 " pdb=" N ASP B 994 " ideal model delta sigma weight residual 117.15 135.17 -18.02 1.14e+00 7.69e-01 2.50e+02 angle pdb=" CA ILE C 993 " pdb=" C ILE C 993 " pdb=" N ASP C 994 " ideal model delta sigma weight residual 117.87 136.91 -19.04 1.25e+00 6.40e-01 2.32e+02 angle pdb=" C ILE B 993 " pdb=" N ASP B 994 " pdb=" CA ASP B 994 " ideal model delta sigma weight residual 120.44 136.94 -16.50 1.30e+00 5.92e-01 1.61e+02 ... (remaining 37298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.18: 16661 24.18 - 48.35: 889 48.35 - 72.53: 130 72.53 - 96.70: 72 96.70 - 120.88: 41 Dihedral angle restraints: 17793 sinusoidal: 8373 harmonic: 9420 Sorted by residual: dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual 93.00 175.82 -82.82 1 1.00e+01 1.00e-02 8.40e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -4.08 -81.92 1 1.00e+01 1.00e-02 8.25e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -11.90 -74.10 1 1.00e+01 1.00e-02 6.97e+01 ... (remaining 17790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 4465 0.133 - 0.267: 74 0.267 - 0.400: 4 0.400 - 0.534: 1 0.534 - 0.667: 1 Chirality restraints: 4545 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 1.04e+01 chirality pdb=" C1 NAG C1403 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1403 " pdb=" O5 NAG C1403 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.34e+00 ... (remaining 4542 not shown) Planarity restraints: 4728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 985 " -0.131 5.00e-02 4.00e+02 1.85e-01 5.47e+01 pdb=" N PRO C 986 " 0.319 5.00e-02 4.00e+02 pdb=" CA PRO C 986 " -0.105 5.00e-02 4.00e+02 pdb=" CD PRO C 986 " -0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 898 " -0.117 5.00e-02 4.00e+02 1.65e-01 4.34e+01 pdb=" N PRO A 899 " 0.284 5.00e-02 4.00e+02 pdb=" CA PRO A 899 " -0.086 5.00e-02 4.00e+02 pdb=" CD PRO A 899 " -0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 898 " -0.117 5.00e-02 4.00e+02 1.64e-01 4.32e+01 pdb=" N PRO C 899 " 0.284 5.00e-02 4.00e+02 pdb=" CA PRO C 899 " -0.086 5.00e-02 4.00e+02 pdb=" CD PRO C 899 " -0.081 5.00e-02 4.00e+02 ... (remaining 4725 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 92 2.44 - 3.05: 17738 3.05 - 3.67: 38714 3.67 - 4.28: 56401 4.28 - 4.90: 92422 Nonbonded interactions: 205367 Sorted by model distance: nonbonded pdb=" OD1 ASP B 985 " pdb=" CD PRO B 987 " model vdw 1.819 3.440 nonbonded pdb=" OG SER C 816 " pdb=" CD PRO C 817 " model vdw 2.003 3.440 nonbonded pdb=" OG SER B 816 " pdb=" CD PRO B 817 " model vdw 2.022 3.440 nonbonded pdb=" OD2 ASP B 985 " pdb=" CG PRO B 987 " model vdw 2.039 3.440 nonbonded pdb=" OG SER B 31 " pdb=" OG SER B 60 " model vdw 2.119 3.040 ... (remaining 205362 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and resid 14 through 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: 3.020 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: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.300 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4950 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.135 27565 Z= 0.329 Angle : 0.988 22.194 37717 Z= 0.583 Chirality : 0.053 0.667 4545 Planarity : 0.009 0.185 4675 Dihedral : 16.195 120.877 11607 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 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 covalent geometry : bond 0.00593 (27413) covalent geometry : angle 0.95952 (37303) SS BOND : bond 0.00471 ( 42) SS BOND : angle 1.51942 ( 84) hydrogen bonds : bond 0.21963 ( 993) hydrogen bonds : angle 8.29559 ( 2763) link_ALPHA1-4 : bond 0.00470 ( 21) link_ALPHA1-4 : angle 2.14094 ( 63) link_BETA1-4 : bond 0.00639 ( 33) link_BETA1-4 : angle 1.36456 ( 99) link_BETA1-6 : bond 0.00827 ( 3) link_BETA1-6 : angle 1.56760 ( 9) link_NAG-ASN : bond 0.00536 ( 53) link_NAG-ASN : angle 3.32916 ( 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 : 0.891 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: 0.1674 time to fit residues: 141.4349 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 : 1.133 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 544 ASN A 751 ASN ** 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 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 935 GLN C 955 ASN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5070 r_free = 0.5070 target = 0.257693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4930 r_free = 0.4930 target = 0.239608 restraints weight = 59677.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4928 r_free = 0.4928 target = 0.238394 restraints weight = 71266.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4910 r_free = 0.4910 target = 0.236054 restraints weight = 61584.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.235028 restraints weight = 75844.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.234043 restraints weight = 72117.834| |-----------------------------------------------------------------------------| r_work (final): 0.4627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5698 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.165 27565 Z= 0.266 Angle : 0.939 14.861 37717 Z= 0.455 Chirality : 0.053 0.470 4545 Planarity : 0.007 0.068 4675 Dihedral : 12.796 100.510 5779 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.03 % Favored : 94.87 % Rotamer: Outliers : 2.58 % Allowed : 9.18 % Favored : 88.24 % 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: -1.20 (0.14), residues: 3198 helix: 0.92 (0.19), residues: 720 sheet: -0.73 (0.19), residues: 711 loop : -1.59 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 190 TYR 0.030 0.002 TYR B 904 PHE 0.043 0.003 PHE A 194 TRP 0.032 0.003 TRP A 104 HIS 0.011 0.002 HIS A1118 Details of bonding type rmsd covalent geometry : bond 0.00586 (27413) covalent geometry : angle 0.89396 (37303) SS BOND : bond 0.00619 ( 42) SS BOND : angle 2.01019 ( 84) hydrogen bonds : bond 0.07192 ( 993) hydrogen bonds : angle 6.47384 ( 2763) link_ALPHA1-4 : bond 0.01243 ( 21) link_ALPHA1-4 : angle 3.09906 ( 63) link_BETA1-4 : bond 0.00707 ( 33) link_BETA1-4 : angle 2.44548 ( 99) link_BETA1-6 : bond 0.01608 ( 3) link_BETA1-6 : angle 1.89395 ( 9) link_NAG-ASN : bond 0.01796 ( 53) link_NAG-ASN : angle 3.45586 ( 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 399 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 326 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TYR cc_start: 0.3614 (m-10) cc_final: 0.3397 (m-80) REVERT: A 279 TYR cc_start: 0.5629 (m-10) cc_final: 0.5357 (m-80) REVERT: A 571 ASP cc_start: 0.5702 (t0) cc_final: 0.5478 (t0) REVERT: A 602 THR cc_start: 0.6683 (m) cc_final: 0.6448 (t) REVERT: B 740 MET cc_start: 0.7832 (tpp) cc_final: 0.7622 (tpp) REVERT: B 902 MET cc_start: 0.7920 (tpp) cc_final: 0.7579 (tpt) REVERT: B 1055 SER cc_start: 0.8533 (p) cc_final: 0.8287 (t) REVERT: C 51 THR cc_start: 0.4815 (p) cc_final: 0.4213 (p) REVERT: C 386 LYS cc_start: 0.6222 (OUTLIER) cc_final: 0.6008 (ttpt) REVERT: C 776 LYS cc_start: 0.9040 (tptp) cc_final: 0.8791 (tptt) REVERT: C 788 ILE cc_start: 0.6461 (OUTLIER) cc_final: 0.6050 (mp) REVERT: C 896 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7616 (mm) REVERT: C 900 MET cc_start: 0.7306 (mpp) cc_final: 0.6770 (mmt) REVERT: C 1029 MET cc_start: 0.8843 (tpt) cc_final: 0.8441 (tpt) REVERT: C 1107 ARG cc_start: 0.7874 (mpt-90) cc_final: 0.7619 (mpt-90) outliers start: 73 outliers final: 43 residues processed: 377 average time/residue: 0.1569 time to fit residues: 97.7533 Evaluate side-chains 268 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 222 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 610 VAL 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 1120 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1096 VAL 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: 0.9980 chunk 140 optimal weight: 0.9990 chunk 163 optimal weight: 0.0770 chunk 99 optimal weight: 2.9990 chunk 266 optimal weight: 5.9990 chunk 258 optimal weight: 20.0000 chunk 301 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 221 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 overall best weight: 1.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 580 GLN A 955 ASN ** B 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN 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** C 955 ASN C1011 GLN C1054 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.228563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.180291 restraints weight = 53332.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.175094 restraints weight = 42287.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.175853 restraints weight = 33381.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.176234 restraints weight = 30300.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.176343 restraints weight = 27633.858| |-----------------------------------------------------------------------------| r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 27565 Z= 0.168 Angle : 0.784 14.323 37717 Z= 0.365 Chirality : 0.048 0.417 4545 Planarity : 0.005 0.060 4675 Dihedral : 11.453 101.712 5769 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.85 % Favored : 95.03 % Rotamer: Outliers : 2.22 % Allowed : 12.89 % Favored : 84.89 % 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: -0.90 (0.14), residues: 3198 helix: 1.29 (0.20), residues: 741 sheet: -0.65 (0.19), residues: 738 loop : -1.45 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 983 TYR 0.019 0.001 TYR B1067 PHE 0.029 0.002 PHE A 855 TRP 0.036 0.002 TRP A 104 HIS 0.012 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00360 (27413) covalent geometry : angle 0.73954 (37303) SS BOND : bond 0.00928 ( 42) SS BOND : angle 1.54467 ( 84) hydrogen bonds : bond 0.06109 ( 993) hydrogen bonds : angle 5.88549 ( 2763) link_ALPHA1-4 : bond 0.01623 ( 21) link_ALPHA1-4 : angle 3.09663 ( 63) link_BETA1-4 : bond 0.00613 ( 33) link_BETA1-4 : angle 1.41429 ( 99) link_BETA1-6 : bond 0.01693 ( 3) link_BETA1-6 : angle 2.25113 ( 9) link_NAG-ASN : bond 0.00661 ( 53) link_NAG-ASN : angle 3.29867 ( 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 324 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 261 time to evaluate : 0.799 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 38 TYR cc_start: 0.3839 (m-10) cc_final: 0.3327 (m-10) REVERT: A 602 THR cc_start: 0.7122 (m) cc_final: 0.6833 (t) REVERT: A 717 ASN cc_start: 0.6346 (OUTLIER) cc_final: 0.5962 (m-40) REVERT: B 571 ASP cc_start: 0.6522 (t0) cc_final: 0.6238 (t0) REVERT: B 740 MET cc_start: 0.7598 (tpp) cc_final: 0.7355 (tpp) REVERT: B 895 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.7398 (pp30) REVERT: B 1055 SER cc_start: 0.8737 (p) cc_final: 0.8524 (t) REVERT: C 177 MET cc_start: 0.6635 (mpp) cc_final: 0.5322 (ttm) REVERT: C 380 TYR cc_start: 0.6867 (OUTLIER) cc_final: 0.4578 (m-80) REVERT: C 788 ILE cc_start: 0.6735 (OUTLIER) cc_final: 0.6427 (mp) REVERT: C 1029 MET cc_start: 0.8878 (tpt) cc_final: 0.8650 (tpp) REVERT: C 1115 ILE cc_start: 0.7016 (OUTLIER) cc_final: 0.6616 (tp) outliers start: 63 outliers final: 39 residues processed: 312 average time/residue: 0.1607 time to fit residues: 83.2034 Evaluate side-chains 252 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 208 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 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 717 ASN Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 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 883 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 127 VAL 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 512 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 894 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 979 ASP 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: 9.9990 chunk 98 optimal weight: 0.9980 chunk 206 optimal weight: 0.6980 chunk 176 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 144 optimal weight: 40.0000 chunk 63 optimal weight: 0.8980 chunk 189 optimal weight: 4.9990 chunk 223 optimal weight: 20.0000 chunk 67 optimal weight: 0.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN ** B1083 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** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.220463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.164674 restraints weight = 51076.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.161980 restraints weight = 37064.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.161648 restraints weight = 32315.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.162224 restraints weight = 30637.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.162349 restraints weight = 27831.322| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.6026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 27565 Z= 0.201 Angle : 0.830 15.106 37717 Z= 0.389 Chirality : 0.049 0.425 4545 Planarity : 0.005 0.079 4675 Dihedral : 9.479 92.058 5769 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.22 % Favored : 94.65 % Rotamer: Outliers : 3.14 % Allowed : 15.32 % Favored : 81.53 % 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: -0.99 (0.14), residues: 3198 helix: 1.31 (0.20), residues: 741 sheet: -0.79 (0.19), residues: 747 loop : -1.51 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 509 TYR 0.028 0.002 TYR B 904 PHE 0.047 0.002 PHE A 194 TRP 0.032 0.003 TRP B 104 HIS 0.009 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00446 (27413) covalent geometry : angle 0.78793 (37303) SS BOND : bond 0.00612 ( 42) SS BOND : angle 2.30047 ( 84) hydrogen bonds : bond 0.06171 ( 993) hydrogen bonds : angle 5.73583 ( 2763) link_ALPHA1-4 : bond 0.01832 ( 21) link_ALPHA1-4 : angle 3.08080 ( 63) link_BETA1-4 : bond 0.00483 ( 33) link_BETA1-4 : angle 1.48886 ( 99) link_BETA1-6 : bond 0.01864 ( 3) link_BETA1-6 : angle 2.48734 ( 9) link_NAG-ASN : bond 0.00678 ( 53) link_NAG-ASN : angle 3.06008 ( 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 338 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 249 time to evaluate : 0.881 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 270 LEU cc_start: 0.6514 (OUTLIER) cc_final: 0.6270 (tt) REVERT: A 321 GLN cc_start: 0.7669 (mm110) cc_final: 0.7259 (mm-40) REVERT: A 619 GLU cc_start: 0.6350 (mm-30) cc_final: 0.6128 (mt-10) REVERT: A 634 ARG cc_start: 0.4660 (OUTLIER) cc_final: 0.3843 (ttt180) REVERT: A 697 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.6636 (ttp) REVERT: A 900 MET cc_start: 0.7833 (mmt) cc_final: 0.7590 (mmt) REVERT: B 304 LYS cc_start: 0.8650 (mmtt) cc_final: 0.8361 (mmmt) REVERT: B 740 MET cc_start: 0.7682 (tpp) cc_final: 0.7046 (tpp) REVERT: B 819 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7517 (mp0) REVERT: B 1104 VAL cc_start: 0.6694 (OUTLIER) cc_final: 0.6459 (m) REVERT: C 177 MET cc_start: 0.6644 (mpp) cc_final: 0.5141 (ttm) REVERT: C 380 TYR cc_start: 0.6919 (OUTLIER) cc_final: 0.4602 (m-80) REVERT: C 752 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8634 (mp) REVERT: C 869 MET cc_start: 0.7900 (mpp) cc_final: 0.7501 (mpp) REVERT: C 900 MET cc_start: 0.7291 (OUTLIER) cc_final: 0.6870 (mpp) REVERT: C 1050 MET cc_start: 0.8112 (ptp) cc_final: 0.7836 (ptt) outliers start: 89 outliers final: 50 residues processed: 318 average time/residue: 0.1530 time to fit residues: 79.8904 Evaluate side-chains 247 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 189 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 270 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 634 ARG 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 865 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 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 819 GLU Chi-restraints excluded: chain B residue 883 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 33 THR 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 285 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 432 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 979 ASP 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 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: 0.0370 chunk 3 optimal weight: 8.9990 chunk 307 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 196 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 overall best weight: 1.1260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN A1058 HIS B 121 ASN B 644 GLN B 784 GLN C 49 HIS C 81 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** 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 = 0.4762 r_free = 0.4762 target = 0.220661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.176810 restraints weight = 50949.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.171306 restraints weight = 56302.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.173231 restraints weight = 46416.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.173332 restraints weight = 31748.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.175066 restraints weight = 30576.564| |-----------------------------------------------------------------------------| r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.6696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27565 Z= 0.159 Angle : 0.751 11.376 37717 Z= 0.351 Chirality : 0.046 0.414 4545 Planarity : 0.005 0.056 4675 Dihedral : 8.256 84.766 5769 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.72 % Favored : 95.15 % Rotamer: Outliers : 3.21 % Allowed : 17.23 % Favored : 79.56 % 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: -0.88 (0.15), residues: 3198 helix: 1.52 (0.20), residues: 750 sheet: -0.72 (0.19), residues: 726 loop : -1.52 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 567 TYR 0.018 0.001 TYR B1067 PHE 0.023 0.002 PHE B 106 TRP 0.048 0.002 TRP A 104 HIS 0.005 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00344 (27413) covalent geometry : angle 0.71337 (37303) SS BOND : bond 0.00420 ( 42) SS BOND : angle 1.72896 ( 84) hydrogen bonds : bond 0.05588 ( 993) hydrogen bonds : angle 5.54454 ( 2763) link_ALPHA1-4 : bond 0.01894 ( 21) link_ALPHA1-4 : angle 2.97009 ( 63) link_BETA1-4 : bond 0.00409 ( 33) link_BETA1-4 : angle 1.43155 ( 99) link_BETA1-6 : bond 0.01951 ( 3) link_BETA1-6 : angle 2.59208 ( 9) link_NAG-ASN : bond 0.00552 ( 53) link_NAG-ASN : angle 2.74431 ( 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 302 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 211 time to evaluate : 0.652 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 33 THR cc_start: 0.2697 (OUTLIER) cc_final: 0.2414 (p) REVERT: A 400 PHE cc_start: 0.6611 (p90) cc_final: 0.6319 (p90) REVERT: A 697 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.6901 (ttp) REVERT: A 859 THR cc_start: 0.7636 (t) cc_final: 0.7082 (m) REVERT: B 83 VAL cc_start: 0.4857 (OUTLIER) cc_final: 0.4642 (t) REVERT: B 304 LYS cc_start: 0.8695 (mmtt) cc_final: 0.8398 (mmmt) REVERT: B 494 SER cc_start: 0.5930 (OUTLIER) cc_final: 0.5547 (t) REVERT: B 984 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7228 (mm) REVERT: C 380 TYR cc_start: 0.7002 (OUTLIER) cc_final: 0.4425 (m-80) REVERT: C 752 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8599 (mp) REVERT: C 869 MET cc_start: 0.7856 (mpp) cc_final: 0.7387 (mpp) REVERT: C 900 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.6731 (mpp) outliers start: 91 outliers final: 51 residues processed: 288 average time/residue: 0.1484 time to fit residues: 71.2635 Evaluate side-chains 237 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 178 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 512 VAL 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 697 MET Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 33 THR 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 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 642 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 752 LEU 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 900 MET Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 282 optimal weight: 0.9990 chunk 167 optimal weight: 6.9990 chunk 292 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 44 optimal weight: 0.0010 chunk 74 optimal weight: 0.9990 chunk 279 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 163 optimal weight: 0.5980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 953 ASN B 969 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN C 787 GLN C1054 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.216565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.158689 restraints weight = 49620.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.156668 restraints weight = 33328.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.156219 restraints weight = 28394.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.156745 restraints weight = 26823.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.156821 restraints weight = 25114.709| |-----------------------------------------------------------------------------| r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.7028 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= 0.139 Angle : 0.724 13.216 37717 Z= 0.335 Chirality : 0.046 0.426 4545 Planarity : 0.004 0.058 4675 Dihedral : 7.312 75.008 5769 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.78 % Favored : 95.09 % Rotamer: Outliers : 3.21 % Allowed : 18.01 % Favored : 78.78 % 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: -0.72 (0.15), residues: 3198 helix: 1.73 (0.20), residues: 750 sheet: -0.61 (0.19), residues: 726 loop : -1.47 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 237 TYR 0.015 0.001 TYR B1067 PHE 0.019 0.001 PHE C 823 TRP 0.032 0.001 TRP A 104 HIS 0.004 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00292 (27413) covalent geometry : angle 0.68578 (37303) SS BOND : bond 0.00329 ( 42) SS BOND : angle 1.45510 ( 84) hydrogen bonds : bond 0.05142 ( 993) hydrogen bonds : angle 5.33090 ( 2763) link_ALPHA1-4 : bond 0.01813 ( 21) link_ALPHA1-4 : angle 2.85596 ( 63) link_BETA1-4 : bond 0.00398 ( 33) link_BETA1-4 : angle 1.27824 ( 99) link_BETA1-6 : bond 0.01986 ( 3) link_BETA1-6 : angle 2.47062 ( 9) link_NAG-ASN : bond 0.00544 ( 53) link_NAG-ASN : angle 2.90847 ( 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 292 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 201 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.2622 (OUTLIER) cc_final: 0.2265 (p) REVERT: A 270 LEU cc_start: 0.6452 (OUTLIER) cc_final: 0.6042 (tt) REVERT: A 402 ILE cc_start: 0.5606 (OUTLIER) cc_final: 0.4958 (pp) REVERT: A 697 MET cc_start: 0.7344 (ptm) cc_final: 0.7108 (ttp) REVERT: A 859 THR cc_start: 0.7758 (t) cc_final: 0.7166 (m) REVERT: B 83 VAL cc_start: 0.5155 (OUTLIER) cc_final: 0.4785 (t) REVERT: B 304 LYS cc_start: 0.8697 (mmtt) cc_final: 0.8456 (mmmt) REVERT: B 494 SER cc_start: 0.5902 (OUTLIER) cc_final: 0.5543 (t) REVERT: B 1115 ILE cc_start: 0.7259 (OUTLIER) cc_final: 0.6579 (mt) REVERT: C 51 THR cc_start: 0.7019 (p) cc_final: 0.6670 (p) REVERT: C 55 PHE cc_start: 0.6916 (OUTLIER) cc_final: 0.6199 (m-80) REVERT: C 118 LEU cc_start: 0.5317 (tp) cc_final: 0.5104 (mt) REVERT: C 285 ILE cc_start: 0.6933 (OUTLIER) cc_final: 0.6712 (mt) REVERT: C 380 TYR cc_start: 0.6895 (OUTLIER) cc_final: 0.4624 (m-80) REVERT: C 400 PHE cc_start: 0.6778 (p90) cc_final: 0.5943 (p90) REVERT: C 752 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8601 (mp) REVERT: C 819 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7604 (mt-10) REVERT: C 869 MET cc_start: 0.7994 (mpp) cc_final: 0.7409 (mpp) outliers start: 91 outliers final: 54 residues processed: 273 average time/residue: 0.1445 time to fit residues: 66.4869 Evaluate side-chains 248 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 183 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 94 SER 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 432 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 61 optimal weight: 0.0050 chunk 304 optimal weight: 1.9990 chunk 301 optimal weight: 3.9990 chunk 99 optimal weight: 0.2980 chunk 193 optimal weight: 0.8980 chunk 277 optimal weight: 0.7980 chunk 186 optimal weight: 3.9990 chunk 285 optimal weight: 1.9990 chunk 279 optimal weight: 0.9980 chunk 189 optimal weight: 4.9990 chunk 233 optimal weight: 0.6980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 895 GLN B 969 ASN C 954 GLN C1058 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.216480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.154267 restraints weight = 49575.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.155566 restraints weight = 31826.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.155033 restraints weight = 23569.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.155533 restraints weight = 24222.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.155720 restraints weight = 22700.100| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.7278 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= 0.131 Angle : 0.696 13.093 37717 Z= 0.323 Chirality : 0.045 0.417 4545 Planarity : 0.004 0.055 4675 Dihedral : 6.516 59.986 5769 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.82 % Favored : 95.06 % Rotamer: Outliers : 3.04 % Allowed : 18.61 % Favored : 78.35 % 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: -0.60 (0.15), residues: 3198 helix: 1.86 (0.20), residues: 750 sheet: -0.47 (0.19), residues: 714 loop : -1.43 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 567 TYR 0.014 0.001 TYR B1067 PHE 0.017 0.001 PHE B 238 TRP 0.028 0.001 TRP B 104 HIS 0.004 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00275 (27413) covalent geometry : angle 0.66165 (37303) SS BOND : bond 0.00295 ( 42) SS BOND : angle 1.35726 ( 84) hydrogen bonds : bond 0.04804 ( 993) hydrogen bonds : angle 5.18458 ( 2763) link_ALPHA1-4 : bond 0.01840 ( 21) link_ALPHA1-4 : angle 2.83361 ( 63) link_BETA1-4 : bond 0.00378 ( 33) link_BETA1-4 : angle 1.25976 ( 99) link_BETA1-6 : bond 0.01930 ( 3) link_BETA1-6 : angle 2.23773 ( 9) link_NAG-ASN : bond 0.00451 ( 53) link_NAG-ASN : angle 2.59038 ( 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 282 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 196 time to evaluate : 0.737 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 400 PHE cc_start: 0.6327 (p90) cc_final: 0.5987 (p90) REVERT: A 402 ILE cc_start: 0.5892 (OUTLIER) cc_final: 0.5486 (pp) REVERT: A 634 ARG cc_start: 0.4218 (OUTLIER) cc_final: 0.3846 (tpt170) REVERT: A 697 MET cc_start: 0.7381 (ptm) cc_final: 0.7150 (ttp) REVERT: B 83 VAL cc_start: 0.5142 (OUTLIER) cc_final: 0.4788 (t) REVERT: B 304 LYS cc_start: 0.8716 (mmtt) cc_final: 0.8474 (mmmt) REVERT: B 494 SER cc_start: 0.5961 (OUTLIER) cc_final: 0.5632 (t) REVERT: B 619 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7131 (mm-30) REVERT: C 33 THR cc_start: 0.2094 (OUTLIER) cc_final: 0.1887 (p) REVERT: C 51 THR cc_start: 0.7159 (p) cc_final: 0.6768 (p) REVERT: C 55 PHE cc_start: 0.6817 (OUTLIER) cc_final: 0.6141 (m-80) REVERT: C 285 ILE cc_start: 0.7018 (OUTLIER) cc_final: 0.6802 (mt) REVERT: C 380 TYR cc_start: 0.6922 (OUTLIER) cc_final: 0.4897 (m-80) REVERT: C 400 PHE cc_start: 0.6689 (p90) cc_final: 0.6296 (p90) REVERT: C 752 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8521 (mp) REVERT: C 819 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7589 (mt-10) REVERT: C 868 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6904 (mp0) REVERT: C 869 MET cc_start: 0.8033 (mpp) cc_final: 0.7379 (mpp) outliers start: 86 outliers final: 55 residues processed: 264 average time/residue: 0.1507 time to fit residues: 66.7189 Evaluate side-chains 246 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 181 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 274 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 395 VAL Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 94 SER 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 432 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 2 optimal weight: 1.9990 chunk 302 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 chunk 251 optimal weight: 8.9990 chunk 241 optimal weight: 1.9990 chunk 308 optimal weight: 3.9990 chunk 265 optimal weight: 0.5980 chunk 138 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN B 969 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.212088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.158037 restraints weight = 50607.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.154283 restraints weight = 38891.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.153882 restraints weight = 33545.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.154142 restraints weight = 31175.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.154428 restraints weight = 29430.039| |-----------------------------------------------------------------------------| r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.8047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 27565 Z= 0.162 Angle : 0.735 11.328 37717 Z= 0.347 Chirality : 0.046 0.423 4545 Planarity : 0.005 0.050 4675 Dihedral : 5.866 53.989 5769 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.00 % Favored : 94.87 % Rotamer: Outliers : 3.04 % Allowed : 18.89 % Favored : 78.07 % 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: 1.80 (0.20), residues: 747 sheet: -0.57 (0.19), residues: 735 loop : -1.43 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 646 TYR 0.018 0.001 TYR B1067 PHE 0.031 0.002 PHE A 86 TRP 0.024 0.001 TRP B 104 HIS 0.006 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00364 (27413) covalent geometry : angle 0.70115 (37303) SS BOND : bond 0.00363 ( 42) SS BOND : angle 1.49742 ( 84) hydrogen bonds : bond 0.05483 ( 993) hydrogen bonds : angle 5.31145 ( 2763) link_ALPHA1-4 : bond 0.01821 ( 21) link_ALPHA1-4 : angle 2.78581 ( 63) link_BETA1-4 : bond 0.00378 ( 33) link_BETA1-4 : angle 1.42039 ( 99) link_BETA1-6 : bond 0.01651 ( 3) link_BETA1-6 : angle 2.27069 ( 9) link_NAG-ASN : bond 0.00544 ( 53) link_NAG-ASN : angle 2.63328 ( 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 287 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 201 time to evaluate : 0.890 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 402 ILE cc_start: 0.5421 (OUTLIER) cc_final: 0.5134 (pp) REVERT: A 731 MET cc_start: 0.8670 (ptp) cc_final: 0.8435 (ptp) REVERT: A 900 MET cc_start: 0.7455 (mmp) cc_final: 0.7088 (mmt) REVERT: B 83 VAL cc_start: 0.5465 (OUTLIER) cc_final: 0.5127 (t) REVERT: B 494 SER cc_start: 0.6086 (OUTLIER) cc_final: 0.5724 (t) REVERT: C 33 THR cc_start: 0.3047 (OUTLIER) cc_final: 0.2586 (p) REVERT: C 51 THR cc_start: 0.7349 (p) cc_final: 0.6913 (p) REVERT: C 55 PHE cc_start: 0.7016 (OUTLIER) cc_final: 0.6049 (m-80) REVERT: C 270 LEU cc_start: 0.6223 (OUTLIER) cc_final: 0.5998 (tp) REVERT: C 380 TYR cc_start: 0.7324 (OUTLIER) cc_final: 0.4886 (m-80) REVERT: C 400 PHE cc_start: 0.6981 (p90) cc_final: 0.6575 (p90) REVERT: C 752 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8586 (mp) REVERT: C 819 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7523 (mt-10) REVERT: C 869 MET cc_start: 0.8152 (mpp) cc_final: 0.7742 (mtt) REVERT: C 900 MET cc_start: 0.7690 (mmt) cc_final: 0.7433 (mmt) outliers start: 86 outliers final: 59 residues processed: 273 average time/residue: 0.1375 time to fit residues: 64.2521 Evaluate side-chains 238 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 170 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 664 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 941 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 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 395 VAL Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 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 432 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 282 optimal weight: 0.8980 chunk 185 optimal weight: 0.6980 chunk 214 optimal weight: 30.0000 chunk 52 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 73 optimal weight: 0.0040 chunk 187 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 314 optimal weight: 1.9990 chunk 302 optimal weight: 3.9990 chunk 316 optimal weight: 0.6980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 895 GLN B 969 ASN B1083 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.214242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.172101 restraints weight = 49297.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.168776 restraints weight = 60543.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.171182 restraints weight = 51560.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.170857 restraints weight = 34446.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.173598 restraints weight = 30091.257| |-----------------------------------------------------------------------------| r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.8291 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= 0.131 Angle : 0.706 13.198 37717 Z= 0.331 Chirality : 0.045 0.417 4545 Planarity : 0.005 0.092 4675 Dihedral : 5.621 58.182 5769 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.60 % Favored : 95.28 % Rotamer: Outliers : 2.51 % Allowed : 19.84 % Favored : 77.65 % 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: -0.50 (0.15), residues: 3198 helix: 2.07 (0.20), residues: 732 sheet: -0.30 (0.20), residues: 693 loop : -1.45 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 567 TYR 0.015 0.001 TYR A 91 PHE 0.020 0.001 PHE B 135 TRP 0.044 0.001 TRP B 104 HIS 0.005 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00279 (27413) covalent geometry : angle 0.67504 (37303) SS BOND : bond 0.00307 ( 42) SS BOND : angle 1.30457 ( 84) hydrogen bonds : bond 0.04875 ( 993) hydrogen bonds : angle 5.18124 ( 2763) link_ALPHA1-4 : bond 0.01694 ( 21) link_ALPHA1-4 : angle 2.65474 ( 63) link_BETA1-4 : bond 0.00372 ( 33) link_BETA1-4 : angle 1.35549 ( 99) link_BETA1-6 : bond 0.01659 ( 3) link_BETA1-6 : angle 1.77270 ( 9) link_NAG-ASN : bond 0.00447 ( 53) link_NAG-ASN : angle 2.54451 ( 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 255 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 184 time to evaluate : 0.729 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 400 PHE cc_start: 0.6720 (p90) cc_final: 0.6492 (p90) REVERT: A 402 ILE cc_start: 0.4973 (OUTLIER) cc_final: 0.4670 (pp) REVERT: A 731 MET cc_start: 0.8760 (ptp) cc_final: 0.8498 (ptp) REVERT: B 83 VAL cc_start: 0.5445 (OUTLIER) cc_final: 0.5033 (t) REVERT: B 133 PHE cc_start: 0.0875 (m-80) cc_final: 0.0664 (m-80) REVERT: B 494 SER cc_start: 0.5956 (OUTLIER) cc_final: 0.5598 (t) REVERT: B 571 ASP cc_start: 0.7149 (t0) cc_final: 0.6808 (t0) REVERT: C 51 THR cc_start: 0.7144 (p) cc_final: 0.6881 (p) REVERT: C 55 PHE cc_start: 0.6849 (OUTLIER) cc_final: 0.6094 (m-80) REVERT: C 177 MET cc_start: 0.3343 (mmp) cc_final: 0.2346 (mtp) REVERT: C 380 TYR cc_start: 0.7244 (OUTLIER) cc_final: 0.4570 (m-80) REVERT: C 400 PHE cc_start: 0.7177 (p90) cc_final: 0.6847 (p90) REVERT: C 752 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8480 (mp) REVERT: C 819 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7340 (mt-10) REVERT: C 869 MET cc_start: 0.7986 (mpp) cc_final: 0.7697 (mtt) REVERT: C 900 MET cc_start: 0.7531 (mmt) cc_final: 0.6887 (mmt) outliers start: 71 outliers final: 50 residues processed: 244 average time/residue: 0.1470 time to fit residues: 60.1692 Evaluate side-chains 225 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 168 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE 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 664 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 941 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 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 395 VAL Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1116 THR 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 274 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 278 optimal weight: 3.9990 chunk 102 optimal weight: 0.0870 chunk 96 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 270 optimal weight: 1.9990 chunk 232 optimal weight: 8.9990 chunk 211 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 chunk 316 optimal weight: 0.5980 chunk 197 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 164 ASN B 625 HIS B 895 GLN B 954 GLN B 969 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.209953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.4099 r_free = 0.4099 target = 0.158155 restraints weight = 48986.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.154058 restraints weight = 39105.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.153732 restraints weight = 33204.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.154063 restraints weight = 31832.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.154251 restraints weight = 30163.670| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.8952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27565 Z= 0.161 Angle : 0.739 14.096 37717 Z= 0.351 Chirality : 0.047 0.425 4545 Planarity : 0.005 0.100 4675 Dihedral : 5.683 56.888 5769 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.78 % Favored : 94.09 % Rotamer: Outliers : 2.65 % Allowed : 19.95 % 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: -0.59 (0.15), residues: 3198 helix: 2.04 (0.20), residues: 729 sheet: -0.36 (0.20), residues: 669 loop : -1.51 (0.13), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 237 TYR 0.022 0.002 TYR A 91 PHE 0.033 0.002 PHE A 106 TRP 0.036 0.002 TRP B 104 HIS 0.006 0.001 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00365 (27413) covalent geometry : angle 0.70643 (37303) SS BOND : bond 0.00360 ( 42) SS BOND : angle 1.54149 ( 84) hydrogen bonds : bond 0.05498 ( 993) hydrogen bonds : angle 5.27584 ( 2763) link_ALPHA1-4 : bond 0.01613 ( 21) link_ALPHA1-4 : angle 2.65003 ( 63) link_BETA1-4 : bond 0.00351 ( 33) link_BETA1-4 : angle 1.43392 ( 99) link_BETA1-6 : bond 0.01324 ( 3) link_BETA1-6 : angle 1.83204 ( 9) link_NAG-ASN : bond 0.00520 ( 53) link_NAG-ASN : angle 2.61536 ( 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 259 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 184 time to evaluate : 0.951 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 36 VAL cc_start: 0.6002 (t) cc_final: 0.5709 (t) REVERT: A 386 LYS cc_start: 0.6556 (mmtm) cc_final: 0.6328 (mttp) REVERT: A 400 PHE cc_start: 0.6546 (p90) cc_final: 0.6266 (p90) REVERT: A 402 ILE cc_start: 0.5357 (OUTLIER) cc_final: 0.5079 (pp) REVERT: A 900 MET cc_start: 0.7282 (mmp) cc_final: 0.6953 (mmt) REVERT: A 1106 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8143 (pt0) REVERT: B 83 VAL cc_start: 0.5659 (OUTLIER) cc_final: 0.5231 (t) REVERT: B 133 PHE cc_start: 0.1756 (m-80) cc_final: 0.1325 (m-80) REVERT: B 494 SER cc_start: 0.6029 (OUTLIER) cc_final: 0.5672 (t) REVERT: C 380 TYR cc_start: 0.7580 (OUTLIER) cc_final: 0.6807 (m-80) REVERT: C 400 PHE cc_start: 0.7168 (p90) cc_final: 0.6678 (p90) REVERT: C 779 GLN cc_start: 0.7826 (tp40) cc_final: 0.7353 (tt0) REVERT: C 788 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7231 (mt) REVERT: C 819 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7610 (mt-10) outliers start: 75 outliers final: 56 residues processed: 246 average time/residue: 0.1500 time to fit residues: 62.2654 Evaluate side-chains 226 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 163 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 664 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 941 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 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 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1120 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 94 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 257 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 248 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 256 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 298 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 969 ASN C 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.209146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.167152 restraints weight = 48421.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.160482 restraints weight = 66777.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.156178 restraints weight = 47422.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.155615 restraints weight = 43303.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.156437 restraints weight = 33894.357| |-----------------------------------------------------------------------------| r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.9253 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= 0.138 Angle : 0.705 13.303 37717 Z= 0.332 Chirality : 0.045 0.418 4545 Planarity : 0.005 0.089 4675 Dihedral : 5.543 57.734 5769 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.72 % Favored : 95.15 % Rotamer: Outliers : 2.12 % Allowed : 20.97 % Favored : 76.91 % 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: -0.58 (0.15), residues: 3198 helix: 2.11 (0.20), residues: 729 sheet: -0.46 (0.19), residues: 708 loop : -1.49 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 237 TYR 0.019 0.001 TYR A 91 PHE 0.021 0.002 PHE C 133 TRP 0.042 0.001 TRP B 104 HIS 0.005 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00304 (27413) covalent geometry : angle 0.67576 (37303) SS BOND : bond 0.00305 ( 42) SS BOND : angle 1.30393 ( 84) hydrogen bonds : bond 0.05084 ( 993) hydrogen bonds : angle 5.15932 ( 2763) link_ALPHA1-4 : bond 0.01558 ( 21) link_ALPHA1-4 : angle 2.49020 ( 63) link_BETA1-4 : bond 0.00375 ( 33) link_BETA1-4 : angle 1.36301 ( 99) link_BETA1-6 : bond 0.01332 ( 3) link_BETA1-6 : angle 1.62089 ( 9) link_NAG-ASN : bond 0.00453 ( 53) link_NAG-ASN : angle 2.49102 ( 159) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4555.70 seconds wall clock time: 79 minutes 30.19 seconds (4770.19 seconds total)