Starting phenix.real_space_refine on Sun Jul 5 12:41:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sbp_24984/07_2026/7sbp_24984.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sbp_24984/07_2026/7sbp_24984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sbp_24984/07_2026/7sbp_24984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sbp_24984/07_2026/7sbp_24984.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7sbp_24984/07_2026/7sbp_24984.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sbp_24984/07_2026/7sbp_24984.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sbp_24984/07_2026/7sbp_24984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sbp_24984/07_2026/7sbp_24984.map" } resolution = 3.1 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= 0.003 sd= 0.042 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 117 5.16 5 C 17553 2.51 5 N 4461 2.21 5 O 5562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 153 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27693 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 8688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 8688 Classifications: {'peptide': 1110} Link IDs: {'PTRANS': 53, 'TRANS': 1056} Chain breaks: 4 Chain: "B" Number of atoms: 8688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 8688 Classifications: {'peptide': 1110} Link IDs: {'PTRANS': 53, 'TRANS': 1056} Chain breaks: 4 Chain: "C" Number of atoms: 8688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 8688 Classifications: {'peptide': 1110} Link IDs: {'PTRANS': 53, 'TRANS': 1056} Chain breaks: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.25, per 1000 atoms: 0.23 Number of scatterers: 27693 At special positions: 0 Unit cell: (150.162, 146.862, 196.366, 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 117 16.00 O 5562 8.00 N 4461 7.00 C 17553 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 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 A 840 " - pdb=" SG CYS A 851 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.01 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 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=2.02 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=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=1.99 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.05 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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 F 2 " - " MAN F 3 " " NAG G 2 " - " MAN G 3 " " NAG I 2 " - " MAN I 3 " " NAG J 2 " - " MAN J 3 " " NAG L 2 " - " MAN L 3 " " NAG M 2 " - " MAN M 3 " " NAG N 2 " - " MAN N 3 " " NAG O 2 " - " MAN O 3 " " NAG Q 2 " - " MAN Q 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 Z 2 " - " MAN Z 3 " " NAG a 2 " - " MAN a 3 " " NAG c 2 " - " MAN c 3 " " NAG d 2 " - " MAN d 3 " " 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 l 2 " - " MAN l 3 " " NAG m 2 " - " MAN m 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 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " BETA1-6 " NAG K 1 " - " FUC K 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG W 1 " - " FUC W 3 " " NAG i 1 " - " FUC i 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 149 " " NAG A1403 " - " ASN A 331 " " 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 149 " " NAG B1403 " - " ASN B 331 " " 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 C1402 " - " ASN C 149 " " NAG C1403 " - " ASN C 331 " " NAG C1404 " - " ASN C 603 " " NAG C1405 " - " ASN C 657 " " NAG C1406 " - " ASN C 709 " " NAG C1407 " - " ASN C1158 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 122 " " NAG F 1 " - " ASN A 234 " " NAG G 1 " - " ASN A 282 " " NAG H 1 " - " ASN A 616 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1074 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN A 165 " " NAG O 1 " - " ASN A 343 " " NAG P 1 " - " ASN B 17 " " NAG Q 1 " - " ASN B 122 " " NAG R 1 " - " ASN B 234 " " NAG S 1 " - " ASN B 282 " " 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 B 165 " " NAG a 1 " - " ASN B 343 " " NAG b 1 " - " ASN C 17 " " NAG c 1 " - " ASN C 122 " " NAG d 1 " - " ASN C 234 " " NAG e 1 " - " ASN C 282 " " NAG f 1 " - " ASN C 616 " " NAG g 1 " - " ASN C 717 " " NAG h 1 " - " ASN C 801 " " NAG i 1 " - " ASN C1074 " " NAG j 1 " - " ASN C1098 " " NAG k 1 " - " ASN C1134 " " NAG l 1 " - " ASN C 165 " " NAG m 1 " - " ASN C 343 " Time building additional restraints: 2.83 Conformation dependent library (CDL) restraints added in 1.2 seconds 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6240 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 47 sheets defined 27.3% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.861A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.972A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.187A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 634 through 639 removed outlier: 3.580A pdb=" N GLY A 639 " --> pdb=" O TYR A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.510A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) 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: 3.787A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.620A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.714A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 848 removed outlier: 4.425A pdb=" N ARG A 847 " --> pdb=" O ASP A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.532A 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 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.450A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (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 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.800A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1160 removed outlier: 4.242A 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 337 through 343 removed outlier: 3.789A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.839A 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 389 removed outlier: 4.750A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.834A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 618 through 623 removed outlier: 4.473A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 639 removed outlier: 4.118A 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 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: 4.044A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.466A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 843 through 848 removed outlier: 4.282A pdb=" N ARG B 847 " --> pdb=" O ASP B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.647A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.298A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.921A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1160 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.719A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.951A 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 383 through 389 removed outlier: 4.240A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 409 removed outlier: 3.858A 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 616 through 620 Processing helix chain 'C' and resid 635 through 639 removed outlier: 3.977A 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: 3.936A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.631A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.604A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 846 removed outlier: 3.605A pdb=" N ILE C 844 " --> pdb=" O LEU C 841 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA C 846 " --> pdb=" O ASP C 843 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 removed outlier: 3.876A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.574A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.542A pdb=" N ALA C 890 " --> 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 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.793A 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 removed outlier: 3.564A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.083A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1159 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.915A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.901A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.937A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.896A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.509A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.763A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.578A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.302A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.392A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 7.040A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.956A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.661A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.508A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.874A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.953A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.577A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.009A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.843A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.926A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.904A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.685A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.842A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 10.471A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.185A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.146A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.961A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.699A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.229A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.579A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.529A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.945A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.262A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.440A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.005A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.642A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.967A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 134 through 145 removed outlier: 8.054A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.122A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 324 through 328 removed outlier: 7.048A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.045A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.735A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.876A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.233A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.570A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1092 hydrogen bonds defined for protein. 2967 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: 7.20 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4438 1.30 - 1.43: 7441 1.43 - 1.56: 16279 1.56 - 1.69: 0 1.69 - 1.82: 144 Bond restraints: 28302 Sorted by residual: bond pdb=" C PRO C 217 " pdb=" N HIS C 218 " ideal model delta sigma weight residual 1.331 1.245 0.086 1.42e-02 4.96e+03 3.63e+01 bond pdb=" C TYR A 279 " pdb=" O TYR A 279 " ideal model delta sigma weight residual 1.235 1.171 0.064 1.22e-02 6.72e+03 2.78e+01 bond pdb=" C ARG A 328 " pdb=" O ARG A 328 " ideal model delta sigma weight residual 1.234 1.178 0.057 1.11e-02 8.12e+03 2.62e+01 bond pdb=" C ARG B1019 " pdb=" O ARG B1019 " ideal model delta sigma weight residual 1.237 1.179 0.058 1.16e-02 7.43e+03 2.51e+01 bond pdb=" C ARG C1019 " pdb=" O ARG C1019 " ideal model delta sigma weight residual 1.236 1.177 0.059 1.19e-02 7.06e+03 2.45e+01 ... (remaining 28297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 33013 2.61 - 5.22: 5215 5.22 - 7.83: 263 7.83 - 10.44: 15 10.44 - 13.05: 2 Bond angle restraints: 38508 Sorted by residual: angle pdb=" N CYS B 525 " pdb=" CA CYS B 525 " pdb=" C CYS B 525 " ideal model delta sigma weight residual 108.38 121.43 -13.05 1.35e+00 5.49e-01 9.34e+01 angle pdb=" N ARG B1107 " pdb=" CA ARG B1107 " pdb=" C ARG B1107 " ideal model delta sigma weight residual 112.38 122.72 -10.34 1.22e+00 6.72e-01 7.18e+01 angle pdb=" N THR A 618 " pdb=" CA THR A 618 " pdb=" C THR A 618 " ideal model delta sigma weight residual 113.20 102.98 10.22 1.21e+00 6.83e-01 7.14e+01 angle pdb=" C GLY B 526 " pdb=" N PRO B 527 " pdb=" CA PRO B 527 " ideal model delta sigma weight residual 120.83 128.09 -7.26 1.02e+00 9.61e-01 5.06e+01 angle pdb=" N PRO C 217 " pdb=" CA PRO C 217 " pdb=" C PRO C 217 " ideal model delta sigma weight residual 111.15 121.68 -10.53 1.58e+00 4.01e-01 4.44e+01 ... (remaining 38503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 14717 17.89 - 35.79: 948 35.79 - 53.68: 153 53.68 - 71.57: 55 71.57 - 89.47: 36 Dihedral angle restraints: 15909 sinusoidal: 6207 harmonic: 9702 Sorted by residual: dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual -86.00 -168.49 82.49 1 1.00e+01 1.00e-02 8.35e+01 dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual -86.00 -165.22 79.22 1 1.00e+01 1.00e-02 7.80e+01 dihedral pdb=" C LEU C 24 " pdb=" N LEU C 24 " pdb=" CA LEU C 24 " pdb=" CB LEU C 24 " ideal model delta harmonic sigma weight residual -122.60 -143.79 21.19 0 2.50e+00 1.60e-01 7.18e+01 ... (remaining 15906 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.271: 4651 0.271 - 0.542: 56 0.542 - 0.813: 7 0.813 - 1.084: 0 1.084 - 1.355: 2 Chirality restraints: 4716 Sorted by residual: chirality pdb=" C1 MAN F 3 " pdb=" O4 NAG F 2 " pdb=" C2 MAN F 3 " pdb=" O5 MAN F 3 " both_signs ideal model delta sigma weight residual False 2.40 2.16 0.24 2.00e-02 2.50e+03 1.49e+02 chirality pdb=" C1 MAN O 3 " pdb=" O4 NAG O 2 " pdb=" C2 MAN O 3 " pdb=" O5 MAN O 3 " both_signs ideal model delta sigma weight residual False 2.40 2.57 -0.17 2.00e-02 2.50e+03 7.09e+01 chirality pdb=" C1 NAG f 2 " pdb=" O4 NAG f 1 " pdb=" C2 NAG f 2 " pdb=" O5 NAG f 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.66e+01 ... (remaining 4713 not shown) Planarity restraints: 4860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 104 " -0.186 2.00e-02 2.50e+03 9.85e-02 2.43e+02 pdb=" CG TRP C 104 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP C 104 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP C 104 " 0.097 2.00e-02 2.50e+03 pdb=" NE1 TRP C 104 " 0.070 2.00e-02 2.50e+03 pdb=" CE2 TRP C 104 " 0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP C 104 " 0.139 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 104 " -0.112 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 104 " 0.037 2.00e-02 2.50e+03 pdb=" CH2 TRP C 104 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 122 " -0.097 2.00e-02 2.50e+03 1.11e-01 1.54e+02 pdb=" CG ASN B 122 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN B 122 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN B 122 " 0.182 2.00e-02 2.50e+03 pdb=" C1 NAG Q 1 " -0.134 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1134 " 0.099 2.00e-02 2.50e+03 9.98e-02 1.25e+02 pdb=" CG ASN A1134 " -0.061 2.00e-02 2.50e+03 pdb=" OD1 ASN A1134 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A1134 " -0.146 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " 0.121 2.00e-02 2.50e+03 ... (remaining 4857 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 192 2.64 - 3.21: 24650 3.21 - 3.77: 41212 3.77 - 4.34: 58914 4.34 - 4.90: 93951 Nonbonded interactions: 218919 Sorted by model distance: nonbonded pdb=" O ARG C 634 " pdb=" NH1 ARG C 634 " model vdw 2.078 3.120 nonbonded pdb=" NH1 ARG C 905 " pdb=" O LEU C1049 " model vdw 2.214 3.120 nonbonded pdb=" NH1 ARG B 905 " pdb=" O LEU B1049 " model vdw 2.228 3.120 nonbonded pdb=" OG SER C 349 " pdb=" O ARG C 452 " model vdw 2.230 3.040 nonbonded pdb=" O ASN C 439 " pdb=" OG SER C 443 " model vdw 2.247 3.040 ... (remaining 218914 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'P' selection = chain 'T' selection = chain 'b' selection = chain 'f' } ncs_group { reference = (chain 'E' and resid 1 through 2) selection = (chain 'F' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'I' 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 'O' and resid 1 through 2) selection = (chain 'Q' 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 'Z' 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 'e' 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) selection = (chain 'k' and resid 1 through 2) selection = (chain 'l' and resid 1 through 2) selection = (chain 'm' 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 individual isotropic 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: 10.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 28.810 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 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 : 0.015 0.086 28470 Z= 0.802 Angle : 1.838 23.166 38967 Z= 1.173 Chirality : 0.110 1.355 4716 Planarity : 0.012 0.125 4803 Dihedral : 13.392 89.468 9534 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.03 % Favored : 92.30 % Rotamer: Outliers : 1.38 % Allowed : 5.27 % Favored : 93.35 % Cbeta Deviations : 0.48 % 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: -1.85 (0.13), residues: 3300 helix: -1.19 (0.16), residues: 747 sheet: -0.33 (0.18), residues: 738 loop : -1.64 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 44 TYR 0.119 0.021 TYR C 660 PHE 0.105 0.013 PHE C 133 TRP 0.186 0.032 TRP C 104 HIS 0.014 0.003 HIS A1159 Details of bonding type rmsd/Z covalent geometry : bond 0.01453 / 0.80 (28302) covalent geometry : angle 1.78940 / 1.17 (38508) SS BOND : bond 0.01213 / 0.91 ( 45) SS BOND : angle 2.38578 / 1.61 ( 90) hydrogen bonds : bond 0.16351 / 11.11 ( 1092) hydrogen bonds : angle 8.48825 / 5.83 ( 2967) link_ALPHA1-4 : bond 0.02447 / 1.58 ( 27) link_ALPHA1-4 : angle 3.58772 / 2.36 ( 81) link_BETA1-4 : bond 0.02311 / 1.51 ( 36) link_BETA1-4 : angle 3.96410 / 2.71 ( 108) link_BETA1-6 : bond 0.02987 / 1.49 ( 3) link_BETA1-6 : angle 3.20640 / 1.96 ( 9) link_NAG-ASN : bond 0.01132 / 0.76 ( 57) link_NAG-ASN : angle 5.42523 / 3.46 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 787 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8257 (mttt) cc_final: 0.8007 (mtmm) REVERT: A 52 GLN cc_start: 0.8538 (tm-30) cc_final: 0.8268 (tm-30) REVERT: A 81 ASN cc_start: 0.8879 (m-40) cc_final: 0.8380 (m-40) REVERT: A 237 ARG cc_start: 0.7637 (mtm-85) cc_final: 0.7307 (mtm-85) REVERT: A 319 ARG cc_start: 0.8432 (ttp-110) cc_final: 0.8133 (ttm110) REVERT: A 351 TYR cc_start: 0.8303 (p90) cc_final: 0.7986 (p90) REVERT: A 354 ASN cc_start: 0.8222 (t0) cc_final: 0.7963 (t0) REVERT: A 396 TYR cc_start: 0.7840 (m-80) cc_final: 0.7270 (m-80) REVERT: A 421 TYR cc_start: 0.7516 (m-80) cc_final: 0.6958 (m-10) REVERT: A 462 LYS cc_start: 0.8660 (mmmm) cc_final: 0.8334 (mmmm) REVERT: A 495 TYR cc_start: 0.7937 (m-80) cc_final: 0.7706 (m-80) REVERT: A 540 ASN cc_start: 0.8366 (m-40) cc_final: 0.8165 (m-40) REVERT: A 555 SER cc_start: 0.8926 (t) cc_final: 0.8465 (p) REVERT: A 565 PHE cc_start: 0.7475 (m-80) cc_final: 0.7028 (m-80) REVERT: A 574 ASP cc_start: 0.8018 (p0) cc_final: 0.7757 (p0) REVERT: A 578 ASP cc_start: 0.6928 (m-30) cc_final: 0.6305 (m-30) REVERT: A 584 ILE cc_start: 0.9073 (mm) cc_final: 0.8708 (mm) REVERT: A 585 LEU cc_start: 0.7957 (mt) cc_final: 0.7648 (mt) REVERT: A 596 SER cc_start: 0.8827 (m) cc_final: 0.8506 (p) REVERT: A 643 PHE cc_start: 0.8183 (t80) cc_final: 0.7796 (t80) REVERT: A 658 ASN cc_start: 0.8453 (OUTLIER) cc_final: 0.8191 (p0) REVERT: A 663 ASP cc_start: 0.7985 (t0) cc_final: 0.7684 (t0) REVERT: A 702 GLU cc_start: 0.8242 (tp30) cc_final: 0.7922 (tp30) REVERT: A 708 SER cc_start: 0.9022 (t) cc_final: 0.8694 (p) REVERT: A 736 VAL cc_start: 0.9082 (t) cc_final: 0.8865 (m) REVERT: A 758 SER cc_start: 0.8295 (t) cc_final: 0.8079 (t) REVERT: A 788 ILE cc_start: 0.9131 (mm) cc_final: 0.8787 (mm) REVERT: A 796 ASP cc_start: 0.7990 (t0) cc_final: 0.7719 (t0) REVERT: A 912 THR cc_start: 0.9022 (m) cc_final: 0.8714 (p) REVERT: A 986 LYS cc_start: 0.8329 (ttmm) cc_final: 0.8106 (ttpt) REVERT: A 994 ASP cc_start: 0.8035 (t70) cc_final: 0.7704 (t0) REVERT: A 1100 THR cc_start: 0.8987 (m) cc_final: 0.8757 (p) REVERT: B 58 PHE cc_start: 0.9170 (m-10) cc_final: 0.8868 (m-80) REVERT: B 140 PHE cc_start: 0.7779 (p90) cc_final: 0.7560 (p90) REVERT: B 191 GLU cc_start: 0.7542 (pt0) cc_final: 0.7289 (pt0) REVERT: B 287 ASP cc_start: 0.7917 (t0) cc_final: 0.7595 (t0) REVERT: B 298 GLU cc_start: 0.8109 (tt0) cc_final: 0.7562 (tm-30) REVERT: B 301 CYS cc_start: 0.6950 (t) cc_final: 0.6274 (t) REVERT: B 319 ARG cc_start: 0.8463 (ttp-110) cc_final: 0.8196 (ptm-80) REVERT: B 369 TYR cc_start: 0.7030 (t80) cc_final: 0.6821 (t80) REVERT: B 396 TYR cc_start: 0.7965 (m-80) cc_final: 0.7301 (m-10) REVERT: B 462 LYS cc_start: 0.8835 (mmtm) cc_final: 0.8518 (mtmm) REVERT: B 465 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7538 (mt-10) REVERT: B 490 PHE cc_start: 0.8339 (t80) cc_final: 0.8094 (t80) REVERT: B 574 ASP cc_start: 0.7913 (p0) cc_final: 0.7712 (p0) REVERT: B 596 SER cc_start: 0.9078 (m) cc_final: 0.8828 (m) REVERT: B 738 CYS cc_start: 0.5870 (t) cc_final: 0.5534 (t) REVERT: B 762 GLN cc_start: 0.8047 (tt0) cc_final: 0.7819 (tt0) REVERT: B 790 LYS cc_start: 0.8711 (ptpp) cc_final: 0.8433 (ptmt) REVERT: B 796 ASP cc_start: 0.7988 (t0) cc_final: 0.7656 (t0) REVERT: B 808 ASP cc_start: 0.7909 (t0) cc_final: 0.7671 (t0) REVERT: B 814 LYS cc_start: 0.8516 (mmtm) cc_final: 0.8226 (mptt) REVERT: B 985 ASP cc_start: 0.7777 (p0) cc_final: 0.7360 (p0) REVERT: B 994 ASP cc_start: 0.7974 (t70) cc_final: 0.7608 (t0) REVERT: B 1005 GLN cc_start: 0.7636 (mt0) cc_final: 0.7418 (mt0) REVERT: B 1073 LYS cc_start: 0.8591 (mttm) cc_final: 0.8377 (mttm) REVERT: B 1149 LYS cc_start: 0.8777 (tmtt) cc_final: 0.8486 (tppp) REVERT: C 54 LEU cc_start: 0.8753 (mt) cc_final: 0.8537 (mt) REVERT: C 116 SER cc_start: 0.8742 (m) cc_final: 0.8387 (p) REVERT: C 135 PHE cc_start: 0.7065 (m-80) cc_final: 0.6517 (m-80) REVERT: C 191 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7131 (mt-10) REVERT: C 342 PHE cc_start: 0.8438 (m-80) cc_final: 0.8192 (m-80) REVERT: C 360 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.8165 (t0) REVERT: C 402 ILE cc_start: 0.8531 (pt) cc_final: 0.8258 (pt) REVERT: C 420 ASP cc_start: 0.7427 (m-30) cc_final: 0.7085 (m-30) REVERT: C 436 TRP cc_start: 0.8174 (p90) cc_final: 0.7850 (p90) REVERT: C 455 LEU cc_start: 0.8249 (tp) cc_final: 0.8012 (mt) REVERT: C 462 LYS cc_start: 0.8745 (mmmt) cc_final: 0.8511 (mmmm) REVERT: C 512 VAL cc_start: 0.9320 (t) cc_final: 0.9007 (m) REVERT: C 563 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8163 (mm-40) REVERT: C 581 THR cc_start: 0.8922 (p) cc_final: 0.8606 (t) REVERT: C 583 GLU cc_start: 0.7315 (mp0) cc_final: 0.7114 (mp0) REVERT: C 586 ASP cc_start: 0.8194 (t70) cc_final: 0.7860 (t0) REVERT: C 737 ASP cc_start: 0.7512 (t0) cc_final: 0.7232 (t0) REVERT: C 776 LYS cc_start: 0.8624 (tttm) cc_final: 0.8245 (tttm) REVERT: C 780 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7470 (mm-30) REVERT: C 796 ASP cc_start: 0.7974 (t0) cc_final: 0.7495 (t0) REVERT: C 817 PHE cc_start: 0.8715 (t80) cc_final: 0.8341 (t80) REVERT: C 907 ASN cc_start: 0.8692 (t0) cc_final: 0.8409 (t0) REVERT: C 912 THR cc_start: 0.8784 (m) cc_final: 0.8435 (p) REVERT: C 935 GLN cc_start: 0.8630 (tp-100) cc_final: 0.7797 (tp-100) REVERT: C 985 ASP cc_start: 0.7585 (p0) cc_final: 0.7353 (p0) REVERT: C 994 ASP cc_start: 0.7905 (t70) cc_final: 0.7607 (t0) REVERT: C 1101 ASP cc_start: 0.7425 (m-30) cc_final: 0.7195 (m-30) outliers start: 40 outliers final: 13 residues processed: 814 average time/residue: 0.2070 time to fit residues: 257.2793 Evaluate side-chains 668 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 652 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 1014 ARG Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 843 ASP Chi-restraints excluded: chain C residue 1014 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1119 ASN B 125 ASN B 450 ASN B 658 ASN B 955 ASN B 969 ASN B1002 GLN B1010 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 HIS C 370 ASN C 394 ASN C 580 GLN C 675 GLN C 960 ASN C1005 GLN C1108 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.111228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.088543 restraints weight = 61317.173| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.60 r_work: 0.3188 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 28470 Z= 0.183 Angle : 0.806 10.481 38967 Z= 0.399 Chirality : 0.048 0.243 4716 Planarity : 0.004 0.049 4803 Dihedral : 6.825 53.700 3612 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.64 % Favored : 96.15 % Rotamer: Outliers : 2.21 % Allowed : 9.86 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.06 % 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: -0.87 (0.14), residues: 3300 helix: 0.62 (0.18), residues: 771 sheet: -0.20 (0.18), residues: 762 loop : -1.30 (0.13), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 452 TYR 0.021 0.002 TYR C 495 PHE 0.022 0.002 PHE A1148 TRP 0.021 0.002 TRP B 64 HIS 0.010 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (28302) covalent geometry : angle 0.76279 / 0.39 (38508) SS BOND : bond 0.00507 / 0.32 ( 45) SS BOND : angle 2.42719 / 1.62 ( 90) hydrogen bonds : bond 0.04991 / 3.36 ( 1092) hydrogen bonds : angle 6.30418 / 4.32 ( 2967) link_ALPHA1-4 : bond 0.00955 / 0.61 ( 27) link_ALPHA1-4 : angle 2.45847 / 1.71 ( 81) link_BETA1-4 : bond 0.00406 / 0.25 ( 36) link_BETA1-4 : angle 1.67765 / 1.13 ( 108) link_BETA1-6 : bond 0.00741 / 0.37 ( 3) link_BETA1-6 : angle 1.51335 / 0.87 ( 9) link_NAG-ASN : bond 0.00548 / 0.36 ( 57) link_NAG-ASN : angle 3.01829 / 1.96 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 657 time to evaluate : 1.020 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 29 THR cc_start: 0.8137 (m) cc_final: 0.7913 (m) REVERT: A 32 PHE cc_start: 0.8227 (m-80) cc_final: 0.7963 (m-80) REVERT: A 41 LYS cc_start: 0.8342 (mttt) cc_final: 0.7990 (mtmm) REVERT: A 190 ARG cc_start: 0.7527 (tpp80) cc_final: 0.7060 (tpp80) REVERT: A 207 HIS cc_start: 0.7970 (p90) cc_final: 0.7255 (p-80) REVERT: A 237 ARG cc_start: 0.8319 (mtm-85) cc_final: 0.8102 (mtm-85) REVERT: A 242 LEU cc_start: 0.8164 (mt) cc_final: 0.7927 (mt) REVERT: A 271 GLN cc_start: 0.8174 (mp10) cc_final: 0.7671 (mp10) REVERT: A 287 ASP cc_start: 0.8358 (t0) cc_final: 0.8077 (m-30) REVERT: A 317 ASN cc_start: 0.8690 (p0) cc_final: 0.8171 (p0) REVERT: A 319 ARG cc_start: 0.8668 (ttp-110) cc_final: 0.8393 (ttm110) REVERT: A 351 TYR cc_start: 0.8668 (p90) cc_final: 0.8246 (p90) REVERT: A 408 ARG cc_start: 0.8509 (ptm-80) cc_final: 0.8217 (ptm-80) REVERT: A 565 PHE cc_start: 0.7683 (m-80) cc_final: 0.7330 (m-80) REVERT: A 591 SER cc_start: 0.7865 (t) cc_final: 0.7485 (t) REVERT: A 643 PHE cc_start: 0.8317 (t80) cc_final: 0.7953 (t80) REVERT: A 658 ASN cc_start: 0.8454 (OUTLIER) cc_final: 0.8230 (p0) REVERT: A 663 ASP cc_start: 0.8356 (t0) cc_final: 0.8053 (t0) REVERT: A 736 VAL cc_start: 0.9124 (t) cc_final: 0.8787 (m) REVERT: A 737 ASP cc_start: 0.7993 (p0) cc_final: 0.7628 (p0) REVERT: A 796 ASP cc_start: 0.8450 (t0) cc_final: 0.8167 (t0) REVERT: A 804 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8496 (tp40) REVERT: A 994 ASP cc_start: 0.8616 (t70) cc_final: 0.8291 (t0) REVERT: A 1072 GLU cc_start: 0.8351 (pm20) cc_final: 0.8107 (pm20) REVERT: A 1119 ASN cc_start: 0.8582 (m110) cc_final: 0.8304 (m-40) REVERT: B 140 PHE cc_start: 0.8539 (p90) cc_final: 0.8155 (p90) REVERT: B 187 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7656 (mmtt) REVERT: B 281 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8273 (pp20) REVERT: B 287 ASP cc_start: 0.8340 (t0) cc_final: 0.8038 (m-30) REVERT: B 319 ARG cc_start: 0.8772 (ttp-110) cc_final: 0.8354 (ptm-80) REVERT: B 351 TYR cc_start: 0.8750 (p90) cc_final: 0.8300 (p90) REVERT: B 369 TYR cc_start: 0.7615 (t80) cc_final: 0.7290 (t80) REVERT: B 389 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7678 (t0) REVERT: B 396 TYR cc_start: 0.8193 (m-80) cc_final: 0.7951 (m-10) REVERT: B 455 LEU cc_start: 0.8759 (tp) cc_final: 0.8558 (mt) REVERT: B 462 LYS cc_start: 0.8938 (mmtm) cc_final: 0.8557 (mttp) REVERT: B 465 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8058 (mt-10) REVERT: B 490 PHE cc_start: 0.8311 (t80) cc_final: 0.7896 (t80) REVERT: B 523 THR cc_start: 0.8238 (p) cc_final: 0.7716 (t) REVERT: B 568 ASP cc_start: 0.8455 (t0) cc_final: 0.8204 (t0) REVERT: B 578 ASP cc_start: 0.8380 (t0) cc_final: 0.8040 (t70) REVERT: B 661 GLU cc_start: 0.7703 (pm20) cc_final: 0.7471 (pm20) REVERT: B 796 ASP cc_start: 0.8482 (t0) cc_final: 0.8081 (t0) REVERT: B 808 ASP cc_start: 0.8082 (t0) cc_final: 0.7727 (t0) REVERT: B 994 ASP cc_start: 0.8607 (t70) cc_final: 0.8336 (t0) REVERT: B 1072 GLU cc_start: 0.8580 (pm20) cc_final: 0.8120 (pm20) REVERT: C 52 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8568 (tm-30) REVERT: C 65 PHE cc_start: 0.8697 (m-80) cc_final: 0.8237 (m-80) REVERT: C 132 GLU cc_start: 0.7182 (tp30) cc_final: 0.6882 (tp30) REVERT: C 278 LYS cc_start: 0.8719 (tttt) cc_final: 0.8388 (ttpt) REVERT: C 360 ASN cc_start: 0.8538 (OUTLIER) cc_final: 0.8333 (t0) REVERT: C 374 PHE cc_start: 0.8237 (m-80) cc_final: 0.7946 (m-80) REVERT: C 402 ILE cc_start: 0.8490 (pt) cc_final: 0.7557 (pt) REVERT: C 406 GLU cc_start: 0.7550 (pm20) cc_final: 0.7201 (pm20) REVERT: C 448 ASN cc_start: 0.8086 (t0) cc_final: 0.7629 (t0) REVERT: C 450 ASN cc_start: 0.8859 (m110) cc_final: 0.8434 (p0) REVERT: C 462 LYS cc_start: 0.8920 (mmmt) cc_final: 0.8437 (mmmm) REVERT: C 466 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7901 (ptp90) REVERT: C 563 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.7988 (mm-40) REVERT: C 564 GLN cc_start: 0.8393 (tp40) cc_final: 0.7973 (tp40) REVERT: C 584 ILE cc_start: 0.9126 (mm) cc_final: 0.8924 (mm) REVERT: C 586 ASP cc_start: 0.8559 (t70) cc_final: 0.8353 (t0) REVERT: C 643 PHE cc_start: 0.8312 (t80) cc_final: 0.7991 (t80) REVERT: C 758 SER cc_start: 0.8350 (t) cc_final: 0.8090 (t) REVERT: C 776 LYS cc_start: 0.8943 (tttm) cc_final: 0.8641 (tttm) REVERT: C 780 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8125 (mm-30) REVERT: C 787 GLN cc_start: 0.8591 (mt0) cc_final: 0.8337 (mp10) REVERT: C 796 ASP cc_start: 0.8397 (t0) cc_final: 0.7991 (t0) REVERT: C 912 THR cc_start: 0.8770 (m) cc_final: 0.8481 (p) REVERT: C 935 GLN cc_start: 0.8698 (tp-100) cc_final: 0.7927 (tp-100) REVERT: C 994 ASP cc_start: 0.8631 (t70) cc_final: 0.8244 (t0) REVERT: C 1119 ASN cc_start: 0.8873 (m-40) cc_final: 0.8573 (m-40) outliers start: 64 outliers final: 32 residues processed: 695 average time/residue: 0.1881 time to fit residues: 204.1341 Evaluate side-chains 625 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 586 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 975 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 215 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 257 optimal weight: 0.5980 chunk 280 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 0.0970 chunk 299 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 238 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN A 360 ASN A 519 HIS A 613 GLN A 658 ASN A 804 GLN A1005 GLN B 66 HIS B 207 HIS B 388 ASN B 658 ASN B 919 ASN B1010 GLN C 66 HIS C 563 GLN C1002 GLN C1159 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.111589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.089004 restraints weight = 61181.618| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.58 r_work: 0.3226 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28470 Z= 0.152 Angle : 0.724 11.012 38967 Z= 0.358 Chirality : 0.046 0.274 4716 Planarity : 0.004 0.060 4803 Dihedral : 6.096 46.900 3596 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.12 % Favored : 95.67 % Rotamer: Outliers : 2.48 % Allowed : 12.31 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.03 % 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: -0.48 (0.14), residues: 3300 helix: 1.44 (0.19), residues: 747 sheet: -0.29 (0.18), residues: 753 loop : -1.11 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 102 TYR 0.020 0.002 TYR C1067 PHE 0.024 0.002 PHE B 643 TRP 0.035 0.001 TRP B 64 HIS 0.011 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (28302) covalent geometry : angle 0.68950 / 0.35 (38508) SS BOND : bond 0.00566 / 0.34 ( 45) SS BOND : angle 2.32805 / 1.78 ( 90) hydrogen bonds : bond 0.04272 / 2.87 ( 1092) hydrogen bonds : angle 5.94078 / 4.05 ( 2967) link_ALPHA1-4 : bond 0.00875 / 0.56 ( 27) link_ALPHA1-4 : angle 1.99132 / 1.38 ( 81) link_BETA1-4 : bond 0.00364 / 0.23 ( 36) link_BETA1-4 : angle 1.38658 / 0.94 ( 108) link_BETA1-6 : bond 0.00827 / 0.41 ( 3) link_BETA1-6 : angle 1.08835 / 0.61 ( 9) link_NAG-ASN : bond 0.00390 / 0.26 ( 57) link_NAG-ASN : angle 2.52118 / 1.59 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 614 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8316 (mttt) cc_final: 0.8018 (mtmm) REVERT: A 158 ARG cc_start: 0.7287 (mmt-90) cc_final: 0.7012 (mmt-90) REVERT: A 190 ARG cc_start: 0.7508 (tpp80) cc_final: 0.6978 (tpp80) REVERT: A 237 ARG cc_start: 0.8288 (mtm-85) cc_final: 0.8053 (mtm-85) REVERT: A 242 LEU cc_start: 0.8115 (mt) cc_final: 0.7797 (mt) REVERT: A 271 GLN cc_start: 0.8144 (mp10) cc_final: 0.7925 (mp10) REVERT: A 319 ARG cc_start: 0.8634 (ttp-110) cc_final: 0.8355 (ttm110) REVERT: A 351 TYR cc_start: 0.8693 (p90) cc_final: 0.8265 (p90) REVERT: A 398 ASP cc_start: 0.7272 (m-30) cc_final: 0.6882 (m-30) REVERT: A 408 ARG cc_start: 0.8553 (ptm-80) cc_final: 0.8331 (ptm-80) REVERT: A 473 TYR cc_start: 0.7866 (t80) cc_final: 0.7636 (t80) REVERT: A 505 TYR cc_start: 0.8060 (OUTLIER) cc_final: 0.7830 (m-80) REVERT: A 565 PHE cc_start: 0.7699 (m-80) cc_final: 0.7381 (m-80) REVERT: A 643 PHE cc_start: 0.8390 (t80) cc_final: 0.7911 (t80) REVERT: A 663 ASP cc_start: 0.8360 (t0) cc_final: 0.8069 (t0) REVERT: A 790 LYS cc_start: 0.8998 (ptpp) cc_final: 0.8621 (ptpp) REVERT: A 796 ASP cc_start: 0.8504 (t0) cc_final: 0.8247 (t0) REVERT: A 994 ASP cc_start: 0.8619 (t70) cc_final: 0.8297 (t0) REVERT: A 995 ARG cc_start: 0.8765 (mtt-85) cc_final: 0.8532 (mtp180) REVERT: A 1119 ASN cc_start: 0.8560 (m110) cc_final: 0.8286 (m-40) REVERT: B 140 PHE cc_start: 0.8457 (p90) cc_final: 0.8121 (p90) REVERT: B 281 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8243 (pp20) REVERT: B 287 ASP cc_start: 0.8356 (t0) cc_final: 0.8071 (m-30) REVERT: B 319 ARG cc_start: 0.8791 (ttp-110) cc_final: 0.8307 (ptm-80) REVERT: B 351 TYR cc_start: 0.8725 (p90) cc_final: 0.8248 (p90) REVERT: B 389 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7702 (t0) REVERT: B 460 ASN cc_start: 0.8327 (m-40) cc_final: 0.8063 (m-40) REVERT: B 490 PHE cc_start: 0.8264 (t80) cc_final: 0.7882 (t80) REVERT: B 523 THR cc_start: 0.8358 (p) cc_final: 0.7801 (t) REVERT: B 578 ASP cc_start: 0.8393 (t0) cc_final: 0.8019 (t70) REVERT: B 591 SER cc_start: 0.8953 (t) cc_final: 0.8629 (p) REVERT: B 661 GLU cc_start: 0.7641 (pm20) cc_final: 0.7304 (pm20) REVERT: B 776 LYS cc_start: 0.8943 (ttmm) cc_final: 0.8675 (tttt) REVERT: B 796 ASP cc_start: 0.8558 (t0) cc_final: 0.8120 (t0) REVERT: B 994 ASP cc_start: 0.8637 (t70) cc_final: 0.8349 (t0) REVERT: B 1073 LYS cc_start: 0.8776 (mtpp) cc_final: 0.8376 (mttm) REVERT: C 146 HIS cc_start: 0.6420 (m-70) cc_final: 0.6143 (m170) REVERT: C 191 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7684 (mp0) REVERT: C 200 TYR cc_start: 0.6194 (m-10) cc_final: 0.5974 (m-10) REVERT: C 278 LYS cc_start: 0.8744 (tttt) cc_final: 0.8455 (ttpt) REVERT: C 298 GLU cc_start: 0.8764 (tp30) cc_final: 0.8548 (tp30) REVERT: C 351 TYR cc_start: 0.8821 (OUTLIER) cc_final: 0.8559 (p90) REVERT: C 360 ASN cc_start: 0.8732 (t0) cc_final: 0.8393 (t0) REVERT: C 368 LEU cc_start: 0.9065 (pp) cc_final: 0.8759 (pp) REVERT: C 402 ILE cc_start: 0.8464 (pt) cc_final: 0.7453 (pt) REVERT: C 462 LYS cc_start: 0.8940 (mmmt) cc_final: 0.8493 (mmmm) REVERT: C 516 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7664 (tm-30) REVERT: C 564 GLN cc_start: 0.8395 (tp40) cc_final: 0.8054 (tp40) REVERT: C 578 ASP cc_start: 0.8073 (t0) cc_final: 0.7775 (t70) REVERT: C 584 ILE cc_start: 0.9068 (mm) cc_final: 0.8846 (mm) REVERT: C 643 PHE cc_start: 0.8286 (t80) cc_final: 0.7997 (t80) REVERT: C 776 LYS cc_start: 0.8901 (tttm) cc_final: 0.8574 (tttm) REVERT: C 780 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8135 (mm-30) REVERT: C 787 GLN cc_start: 0.8576 (mt0) cc_final: 0.8358 (mp10) REVERT: C 796 ASP cc_start: 0.8445 (t0) cc_final: 0.8089 (t0) REVERT: C 817 PHE cc_start: 0.8540 (t80) cc_final: 0.8307 (t80) REVERT: C 912 THR cc_start: 0.8781 (m) cc_final: 0.8496 (p) REVERT: C 935 GLN cc_start: 0.8736 (tp-100) cc_final: 0.8416 (tt0) REVERT: C 994 ASP cc_start: 0.8616 (t70) cc_final: 0.8198 (t0) REVERT: C 1119 ASN cc_start: 0.8873 (m-40) cc_final: 0.8542 (m-40) outliers start: 72 outliers final: 38 residues processed: 651 average time/residue: 0.1892 time to fit residues: 191.6655 Evaluate side-chains 611 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 568 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 975 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 260 optimal weight: 1.9990 chunk 303 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 149 optimal weight: 0.6980 chunk 188 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 314 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 327 optimal weight: 0.8980 chunk 257 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN A 388 ASN A 784 GLN A1005 GLN B 66 HIS B 655 HIS B 658 ASN B 804 GLN B1088 HIS C 66 HIS C 960 ASN C1002 GLN C1159 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.109445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.086804 restraints weight = 60952.880| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.59 r_work: 0.3202 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 28470 Z= 0.217 Angle : 0.736 11.489 38967 Z= 0.361 Chirality : 0.046 0.271 4716 Planarity : 0.004 0.091 4803 Dihedral : 5.780 44.838 3582 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.97 % Favored : 94.82 % Rotamer: Outliers : 3.03 % Allowed : 12.82 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.39 (0.14), residues: 3300 helix: 1.62 (0.19), residues: 750 sheet: -0.11 (0.19), residues: 708 loop : -1.14 (0.13), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 577 TYR 0.021 0.002 TYR C1067 PHE 0.026 0.002 PHE A1148 TRP 0.022 0.002 TRP B 64 HIS 0.023 0.002 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.22 (28302) covalent geometry : angle 0.70181 / 0.35 (38508) SS BOND : bond 0.00523 / 0.29 ( 45) SS BOND : angle 2.55749 / 1.90 ( 90) hydrogen bonds : bond 0.04295 / 2.89 ( 1092) hydrogen bonds : angle 5.83743 / 3.99 ( 2967) link_ALPHA1-4 : bond 0.00866 / 0.55 ( 27) link_ALPHA1-4 : angle 1.92201 / 1.34 ( 81) link_BETA1-4 : bond 0.00260 / 0.16 ( 36) link_BETA1-4 : angle 1.37738 / 0.93 ( 108) link_BETA1-6 : bond 0.00577 / 0.29 ( 3) link_BETA1-6 : angle 1.16309 / 0.65 ( 9) link_NAG-ASN : bond 0.00394 / 0.26 ( 57) link_NAG-ASN : angle 2.45245 / 1.55 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 591 time to evaluate : 0.774 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 41 LYS cc_start: 0.8308 (mttt) cc_final: 0.8081 (mtmm) REVERT: A 102 ARG cc_start: 0.6826 (mtt-85) cc_final: 0.6605 (mtt-85) REVERT: A 190 ARG cc_start: 0.7491 (tpp80) cc_final: 0.7158 (tpp80) REVERT: A 220 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.8112 (t80) REVERT: A 237 ARG cc_start: 0.8323 (mtm-85) cc_final: 0.7986 (mtm-85) REVERT: A 271 GLN cc_start: 0.8275 (mp10) cc_final: 0.7651 (mp10) REVERT: A 319 ARG cc_start: 0.8658 (ttp-110) cc_final: 0.8362 (ttm110) REVERT: A 351 TYR cc_start: 0.8734 (p90) cc_final: 0.8321 (p90) REVERT: A 473 TYR cc_start: 0.7924 (t80) cc_final: 0.7675 (t80) REVERT: A 565 PHE cc_start: 0.7746 (m-80) cc_final: 0.7474 (m-80) REVERT: A 574 ASP cc_start: 0.8328 (p0) cc_final: 0.8056 (p0) REVERT: A 586 ASP cc_start: 0.8707 (t70) cc_final: 0.8480 (t0) REVERT: A 643 PHE cc_start: 0.8399 (t80) cc_final: 0.7918 (t80) REVERT: A 790 LYS cc_start: 0.8955 (ptpp) cc_final: 0.8483 (ptpp) REVERT: A 796 ASP cc_start: 0.8561 (t0) cc_final: 0.8330 (t0) REVERT: A 804 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8669 (mp10) REVERT: A 994 ASP cc_start: 0.8671 (t70) cc_final: 0.8350 (t0) REVERT: A 1119 ASN cc_start: 0.8603 (m110) cc_final: 0.8348 (m-40) REVERT: B 65 PHE cc_start: 0.8838 (m-80) cc_final: 0.8599 (m-80) REVERT: B 140 PHE cc_start: 0.8463 (p90) cc_final: 0.8150 (p90) REVERT: B 187 LYS cc_start: 0.8155 (tppt) cc_final: 0.7764 (tppt) REVERT: B 191 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7575 (mp0) REVERT: B 207 HIS cc_start: 0.8273 (t-90) cc_final: 0.7527 (t-90) REVERT: B 287 ASP cc_start: 0.8330 (t0) cc_final: 0.8016 (m-30) REVERT: B 319 ARG cc_start: 0.8813 (ttp-110) cc_final: 0.8430 (ttm110) REVERT: B 351 TYR cc_start: 0.8738 (p90) cc_final: 0.8277 (p90) REVERT: B 389 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7722 (t0) REVERT: B 465 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7636 (mt-10) REVERT: B 490 PHE cc_start: 0.8366 (t80) cc_final: 0.8018 (t80) REVERT: B 523 THR cc_start: 0.8422 (p) cc_final: 0.7889 (t) REVERT: B 578 ASP cc_start: 0.8446 (t0) cc_final: 0.8118 (t70) REVERT: B 661 GLU cc_start: 0.7717 (pm20) cc_final: 0.7334 (pm20) REVERT: B 796 ASP cc_start: 0.8609 (t0) cc_final: 0.8210 (t0) REVERT: B 808 ASP cc_start: 0.8143 (t0) cc_final: 0.7761 (t0) REVERT: B 819 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8209 (mt-10) REVERT: B 994 ASP cc_start: 0.8675 (t70) cc_final: 0.8385 (t0) REVERT: B 1073 LYS cc_start: 0.8784 (mtpp) cc_final: 0.8342 (mttm) REVERT: C 52 GLN cc_start: 0.8913 (tm-30) cc_final: 0.8613 (tm-30) REVERT: C 146 HIS cc_start: 0.6566 (m-70) cc_final: 0.6289 (m170) REVERT: C 158 ARG cc_start: 0.7036 (mtt180) cc_final: 0.6497 (mtt180) REVERT: C 191 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7544 (mp0) REVERT: C 278 LYS cc_start: 0.8823 (tttt) cc_final: 0.8447 (ttpt) REVERT: C 347 PHE cc_start: 0.7629 (OUTLIER) cc_final: 0.6599 (m-80) REVERT: C 360 ASN cc_start: 0.8795 (t0) cc_final: 0.8469 (t0) REVERT: C 368 LEU cc_start: 0.9092 (pp) cc_final: 0.8774 (pp) REVERT: C 462 LYS cc_start: 0.9043 (mmmt) cc_final: 0.8687 (mmmm) REVERT: C 516 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7584 (tm-30) REVERT: C 564 GLN cc_start: 0.8458 (tp40) cc_final: 0.8093 (tp40) REVERT: C 584 ILE cc_start: 0.9120 (mm) cc_final: 0.8882 (mm) REVERT: C 643 PHE cc_start: 0.8300 (t80) cc_final: 0.7960 (t80) REVERT: C 776 LYS cc_start: 0.8899 (tttm) cc_final: 0.8547 (tttm) REVERT: C 780 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8119 (mm-30) REVERT: C 787 GLN cc_start: 0.8662 (mt0) cc_final: 0.8456 (mt0) REVERT: C 796 ASP cc_start: 0.8480 (t0) cc_final: 0.8160 (t0) REVERT: C 935 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8353 (tt0) REVERT: C 994 ASP cc_start: 0.8665 (t70) cc_final: 0.8229 (t0) REVERT: C 1072 GLU cc_start: 0.8418 (pm20) cc_final: 0.8174 (pm20) REVERT: C 1119 ASN cc_start: 0.8876 (m-40) cc_final: 0.8556 (m-40) outliers start: 88 outliers final: 48 residues processed: 644 average time/residue: 0.1866 time to fit residues: 186.1215 Evaluate side-chains 606 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 551 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 975 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 293 optimal weight: 0.9990 chunk 239 optimal weight: 2.9990 chunk 287 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 314 optimal weight: 0.2980 chunk 197 optimal weight: 0.8980 chunk 249 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN A1005 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN C 66 HIS C1159 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.110315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.087732 restraints weight = 60953.125| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.60 r_work: 0.3215 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 28470 Z= 0.155 Angle : 0.695 11.477 38967 Z= 0.341 Chirality : 0.045 0.264 4716 Planarity : 0.004 0.070 4803 Dihedral : 5.547 45.068 3582 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.42 % Favored : 95.39 % Rotamer: Outliers : 2.69 % Allowed : 14.10 % Favored : 83.21 % 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: -0.31 (0.14), residues: 3300 helix: 1.74 (0.20), residues: 750 sheet: -0.22 (0.18), residues: 732 loop : -1.05 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 408 TYR 0.023 0.001 TYR C 495 PHE 0.020 0.001 PHE C 392 TRP 0.021 0.001 TRP A 104 HIS 0.012 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (28302) covalent geometry : angle 0.66296 / 0.33 (38508) SS BOND : bond 0.00431 / 0.24 ( 45) SS BOND : angle 2.53106 / 1.85 ( 90) hydrogen bonds : bond 0.03996 / 2.70 ( 1092) hydrogen bonds : angle 5.70628 / 3.89 ( 2967) link_ALPHA1-4 : bond 0.00791 / 0.50 ( 27) link_ALPHA1-4 : angle 1.77681 / 1.24 ( 81) link_BETA1-4 : bond 0.00312 / 0.19 ( 36) link_BETA1-4 : angle 1.25885 / 0.85 ( 108) link_BETA1-6 : bond 0.00604 / 0.30 ( 3) link_BETA1-6 : angle 1.14434 / 0.63 ( 9) link_NAG-ASN : bond 0.00356 / 0.24 ( 57) link_NAG-ASN : angle 2.28417 / 1.42 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 580 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8287 (mttt) cc_final: 0.8042 (mtmm) REVERT: A 102 ARG cc_start: 0.6809 (OUTLIER) cc_final: 0.6516 (mtt-85) REVERT: A 158 ARG cc_start: 0.7219 (mmt-90) cc_final: 0.6974 (mmt-90) REVERT: A 190 ARG cc_start: 0.7496 (tpp80) cc_final: 0.7168 (tpp80) REVERT: A 220 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.8089 (t80) REVERT: A 237 ARG cc_start: 0.8320 (mtm-85) cc_final: 0.8102 (mtm-85) REVERT: A 271 GLN cc_start: 0.8221 (mp10) cc_final: 0.7828 (mp10) REVERT: A 298 GLU cc_start: 0.8765 (tp30) cc_final: 0.8465 (tp30) REVERT: A 319 ARG cc_start: 0.8641 (ttp-110) cc_final: 0.8401 (ttm110) REVERT: A 351 TYR cc_start: 0.8731 (p90) cc_final: 0.8352 (p90) REVERT: A 473 TYR cc_start: 0.7994 (t80) cc_final: 0.7722 (t80) REVERT: A 490 PHE cc_start: 0.8364 (t80) cc_final: 0.7866 (t80) REVERT: A 505 TYR cc_start: 0.8015 (OUTLIER) cc_final: 0.7756 (m-80) REVERT: A 565 PHE cc_start: 0.7733 (m-80) cc_final: 0.7461 (m-80) REVERT: A 790 LYS cc_start: 0.8988 (ptpp) cc_final: 0.8614 (ptpp) REVERT: A 796 ASP cc_start: 0.8549 (t0) cc_final: 0.8337 (t0) REVERT: A 804 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8656 (mp10) REVERT: A 994 ASP cc_start: 0.8624 (t70) cc_final: 0.8310 (t0) REVERT: A 1119 ASN cc_start: 0.8578 (m110) cc_final: 0.8323 (m-40) REVERT: B 65 PHE cc_start: 0.8775 (m-80) cc_final: 0.8557 (m-80) REVERT: B 140 PHE cc_start: 0.8427 (p90) cc_final: 0.8105 (p90) REVERT: B 191 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7704 (mp0) REVERT: B 207 HIS cc_start: 0.8258 (t-90) cc_final: 0.7683 (t-90) REVERT: B 287 ASP cc_start: 0.8333 (t0) cc_final: 0.8034 (m-30) REVERT: B 298 GLU cc_start: 0.8693 (tt0) cc_final: 0.8192 (tm-30) REVERT: B 319 ARG cc_start: 0.8735 (ttp-110) cc_final: 0.8504 (ttm110) REVERT: B 351 TYR cc_start: 0.8737 (p90) cc_final: 0.8285 (p90) REVERT: B 389 ASP cc_start: 0.7992 (t0) cc_final: 0.7655 (t0) REVERT: B 462 LYS cc_start: 0.9043 (mmmm) cc_final: 0.8393 (mmmm) REVERT: B 465 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7551 (mt-10) REVERT: B 490 PHE cc_start: 0.8391 (t80) cc_final: 0.8055 (t80) REVERT: B 523 THR cc_start: 0.8479 (p) cc_final: 0.7943 (t) REVERT: B 578 ASP cc_start: 0.8440 (t0) cc_final: 0.8104 (t70) REVERT: B 633 TRP cc_start: 0.8565 (p-90) cc_final: 0.7344 (p-90) REVERT: B 661 GLU cc_start: 0.7683 (pm20) cc_final: 0.7303 (pm20) REVERT: B 693 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8930 (pp) REVERT: B 796 ASP cc_start: 0.8589 (t0) cc_final: 0.8203 (t0) REVERT: B 808 ASP cc_start: 0.8148 (t0) cc_final: 0.7787 (t0) REVERT: B 819 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8187 (mt-10) REVERT: B 994 ASP cc_start: 0.8655 (t70) cc_final: 0.8334 (t0) REVERT: B 1073 LYS cc_start: 0.8774 (mtpp) cc_final: 0.8307 (mttm) REVERT: C 52 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8617 (tm-30) REVERT: C 146 HIS cc_start: 0.6472 (m-70) cc_final: 0.6193 (m170) REVERT: C 158 ARG cc_start: 0.7042 (mtt180) cc_final: 0.6345 (mmm-85) REVERT: C 191 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7600 (mp0) REVERT: C 278 LYS cc_start: 0.8824 (tttt) cc_final: 0.8491 (ttpt) REVERT: C 298 GLU cc_start: 0.8787 (tp30) cc_final: 0.8542 (tp30) REVERT: C 347 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.6654 (m-80) REVERT: C 360 ASN cc_start: 0.8786 (t0) cc_final: 0.8475 (t0) REVERT: C 368 LEU cc_start: 0.9069 (pp) cc_final: 0.8737 (pp) REVERT: C 408 ARG cc_start: 0.8576 (ptm-80) cc_final: 0.8326 (ptm-80) REVERT: C 462 LYS cc_start: 0.9070 (mmmt) cc_final: 0.8702 (mmmm) REVERT: C 516 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7520 (tm-30) REVERT: C 564 GLN cc_start: 0.8457 (tp40) cc_final: 0.8117 (tp40) REVERT: C 578 ASP cc_start: 0.8128 (t0) cc_final: 0.7834 (t70) REVERT: C 584 ILE cc_start: 0.9113 (mm) cc_final: 0.8875 (mm) REVERT: C 643 PHE cc_start: 0.8248 (t80) cc_final: 0.7971 (t80) REVERT: C 776 LYS cc_start: 0.8887 (tttm) cc_final: 0.8532 (tttm) REVERT: C 780 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8028 (mm-30) REVERT: C 787 GLN cc_start: 0.8656 (mt0) cc_final: 0.8238 (mt0) REVERT: C 794 ILE cc_start: 0.9043 (mm) cc_final: 0.8831 (tp) REVERT: C 796 ASP cc_start: 0.8478 (t0) cc_final: 0.8202 (t0) REVERT: C 935 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8339 (tt0) REVERT: C 994 ASP cc_start: 0.8631 (t70) cc_final: 0.8215 (t0) REVERT: C 1072 GLU cc_start: 0.8395 (pm20) cc_final: 0.8143 (pm20) REVERT: C 1119 ASN cc_start: 0.8844 (m-40) cc_final: 0.8527 (m-40) outliers start: 78 outliers final: 46 residues processed: 627 average time/residue: 0.1943 time to fit residues: 190.5951 Evaluate side-chains 603 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 548 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 281 optimal weight: 0.9990 chunk 144 optimal weight: 0.6980 chunk 206 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 277 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 240 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 291 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN A 388 ASN A1005 GLN A1088 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 658 ASN C1002 GLN C1159 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.109971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.087486 restraints weight = 60944.000| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.60 r_work: 0.3218 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 28470 Z= 0.166 Angle : 0.687 11.784 38967 Z= 0.336 Chirality : 0.045 0.273 4716 Planarity : 0.004 0.068 4803 Dihedral : 5.423 45.381 3581 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.58 % Favored : 95.21 % Rotamer: Outliers : 3.10 % Allowed : 14.51 % Favored : 82.39 % 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: -0.22 (0.14), residues: 3300 helix: 1.98 (0.20), residues: 732 sheet: -0.12 (0.19), residues: 717 loop : -1.06 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 567 TYR 0.020 0.001 TYR C1067 PHE 0.021 0.001 PHE C 392 TRP 0.027 0.001 TRP A 104 HIS 0.013 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (28302) covalent geometry : angle 0.65835 / 0.33 (38508) SS BOND : bond 0.00421 / 0.25 ( 45) SS BOND : angle 2.20178 / 1.57 ( 90) hydrogen bonds : bond 0.03958 / 2.69 ( 1092) hydrogen bonds : angle 5.64016 / 3.85 ( 2967) link_ALPHA1-4 : bond 0.00750 / 0.47 ( 27) link_ALPHA1-4 : angle 1.71408 / 1.19 ( 81) link_BETA1-4 : bond 0.00279 / 0.17 ( 36) link_BETA1-4 : angle 1.21964 / 0.83 ( 108) link_BETA1-6 : bond 0.00620 / 0.31 ( 3) link_BETA1-6 : angle 1.18851 / 0.66 ( 9) link_NAG-ASN : bond 0.00349 / 0.23 ( 57) link_NAG-ASN : angle 2.24491 / 1.39 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 581 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7989 (mtt-85) cc_final: 0.7479 (mtt90) REVERT: A 102 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.6545 (mtt-85) REVERT: A 158 ARG cc_start: 0.7255 (mmt-90) cc_final: 0.6995 (mmt-90) REVERT: A 191 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7441 (mp0) REVERT: A 237 ARG cc_start: 0.8314 (mtm-85) cc_final: 0.8031 (mtm-85) REVERT: A 269 TYR cc_start: 0.7602 (m-10) cc_final: 0.7289 (m-10) REVERT: A 271 GLN cc_start: 0.8277 (mp10) cc_final: 0.7566 (mp10) REVERT: A 298 GLU cc_start: 0.8786 (tp30) cc_final: 0.8477 (tp30) REVERT: A 319 ARG cc_start: 0.8679 (ttp-110) cc_final: 0.8365 (ttm110) REVERT: A 351 TYR cc_start: 0.8736 (p90) cc_final: 0.8383 (p90) REVERT: A 421 TYR cc_start: 0.7952 (m-80) cc_final: 0.7504 (m-10) REVERT: A 473 TYR cc_start: 0.7991 (t80) cc_final: 0.7714 (t80) REVERT: A 490 PHE cc_start: 0.8482 (t80) cc_final: 0.7964 (t80) REVERT: A 505 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.7707 (m-80) REVERT: A 523 THR cc_start: 0.8527 (p) cc_final: 0.8199 (t) REVERT: A 565 PHE cc_start: 0.7748 (m-80) cc_final: 0.7485 (m-80) REVERT: A 586 ASP cc_start: 0.8610 (t70) cc_final: 0.8399 (t0) REVERT: A 804 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8647 (mp10) REVERT: A 994 ASP cc_start: 0.8611 (t70) cc_final: 0.8317 (t0) REVERT: A 995 ARG cc_start: 0.8823 (mtt-85) cc_final: 0.8580 (mtp180) REVERT: A 1119 ASN cc_start: 0.8595 (m110) cc_final: 0.8361 (m-40) REVERT: B 65 PHE cc_start: 0.8785 (m-80) cc_final: 0.8527 (m-80) REVERT: B 140 PHE cc_start: 0.8408 (p90) cc_final: 0.8084 (p90) REVERT: B 191 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7585 (mt-10) REVERT: B 207 HIS cc_start: 0.8332 (t-90) cc_final: 0.7746 (t-90) REVERT: B 287 ASP cc_start: 0.8338 (t0) cc_final: 0.8009 (m-30) REVERT: B 298 GLU cc_start: 0.8694 (tt0) cc_final: 0.8007 (tm-30) REVERT: B 319 ARG cc_start: 0.8736 (ttp-110) cc_final: 0.8525 (ttm110) REVERT: B 351 TYR cc_start: 0.8759 (p90) cc_final: 0.8260 (p90) REVERT: B 389 ASP cc_start: 0.7998 (t0) cc_final: 0.7642 (t0) REVERT: B 462 LYS cc_start: 0.9068 (mmmm) cc_final: 0.8394 (mmmm) REVERT: B 465 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7638 (mt-10) REVERT: B 490 PHE cc_start: 0.8444 (t80) cc_final: 0.8127 (t80) REVERT: B 523 THR cc_start: 0.8542 (p) cc_final: 0.8007 (t) REVERT: B 578 ASP cc_start: 0.8449 (t0) cc_final: 0.8138 (t70) REVERT: B 661 GLU cc_start: 0.7747 (pm20) cc_final: 0.7415 (pm20) REVERT: B 693 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8906 (pp) REVERT: B 796 ASP cc_start: 0.8581 (t0) cc_final: 0.8220 (t0) REVERT: B 808 ASP cc_start: 0.8157 (t0) cc_final: 0.7781 (t0) REVERT: B 819 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8227 (mt-10) REVERT: B 986 LYS cc_start: 0.8551 (mmmt) cc_final: 0.8312 (mmmt) REVERT: B 994 ASP cc_start: 0.8639 (t70) cc_final: 0.8220 (t0) REVERT: B 1072 GLU cc_start: 0.8621 (pm20) cc_final: 0.8238 (pm20) REVERT: B 1073 LYS cc_start: 0.8792 (mtpp) cc_final: 0.8332 (mttm) REVERT: B 1082 CYS cc_start: 0.7221 (t) cc_final: 0.6938 (t) REVERT: B 1123 SER cc_start: 0.9294 (OUTLIER) cc_final: 0.8905 (t) REVERT: C 191 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7530 (mp0) REVERT: C 278 LYS cc_start: 0.8864 (tttt) cc_final: 0.8517 (ttpt) REVERT: C 347 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.6726 (m-80) REVERT: C 360 ASN cc_start: 0.8799 (t0) cc_final: 0.8505 (t0) REVERT: C 368 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8712 (pp) REVERT: C 403 ARG cc_start: 0.7758 (mtm110) cc_final: 0.7424 (mtm110) REVERT: C 408 ARG cc_start: 0.8564 (ptm-80) cc_final: 0.8278 (ptm-80) REVERT: C 462 LYS cc_start: 0.9068 (mmmt) cc_final: 0.8795 (mmmm) REVERT: C 516 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7480 (tm-30) REVERT: C 564 GLN cc_start: 0.8492 (tp40) cc_final: 0.8139 (tp40) REVERT: C 578 ASP cc_start: 0.8216 (t0) cc_final: 0.7693 (t70) REVERT: C 584 ILE cc_start: 0.9158 (mm) cc_final: 0.8916 (mm) REVERT: C 643 PHE cc_start: 0.8200 (t80) cc_final: 0.7910 (t80) REVERT: C 710 ASN cc_start: 0.9107 (p0) cc_final: 0.8867 (p0) REVERT: C 776 LYS cc_start: 0.8882 (tttm) cc_final: 0.8434 (tttm) REVERT: C 780 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8009 (mm-30) REVERT: C 787 GLN cc_start: 0.8669 (mt0) cc_final: 0.8257 (mt0) REVERT: C 794 ILE cc_start: 0.9045 (mm) cc_final: 0.8830 (tp) REVERT: C 796 ASP cc_start: 0.8495 (t0) cc_final: 0.8234 (t0) REVERT: C 935 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8322 (tt0) REVERT: C 994 ASP cc_start: 0.8649 (t70) cc_final: 0.8197 (t0) REVERT: C 1072 GLU cc_start: 0.8423 (pm20) cc_final: 0.8173 (pm20) REVERT: C 1119 ASN cc_start: 0.8846 (m-40) cc_final: 0.8534 (m-40) outliers start: 90 outliers final: 60 residues processed: 637 average time/residue: 0.1922 time to fit residues: 191.9306 Evaluate side-chains 632 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 562 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 60 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 chunk 138 optimal weight: 0.0980 chunk 131 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 253 optimal weight: 3.9990 chunk 266 optimal weight: 0.2980 chunk 178 optimal weight: 0.7980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN A 954 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN C 188 ASN C 394 ASN C1159 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.110641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.088241 restraints weight = 60380.473| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 3.58 r_work: 0.3225 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 28470 Z= 0.141 Angle : 0.685 11.237 38967 Z= 0.334 Chirality : 0.045 0.270 4716 Planarity : 0.004 0.063 4803 Dihedral : 5.310 45.495 3581 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.03 % Favored : 95.79 % Rotamer: Outliers : 2.96 % Allowed : 15.55 % Favored : 81.49 % 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: -0.16 (0.14), residues: 3300 helix: 2.03 (0.20), residues: 732 sheet: -0.15 (0.19), residues: 717 loop : -0.98 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 567 TYR 0.025 0.001 TYR A1138 PHE 0.022 0.001 PHE C 392 TRP 0.030 0.001 TRP A 104 HIS 0.012 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (28302) covalent geometry : angle 0.65708 / 0.33 (38508) SS BOND : bond 0.00407 / 0.25 ( 45) SS BOND : angle 2.27644 / 1.58 ( 90) hydrogen bonds : bond 0.03753 / 2.55 ( 1092) hydrogen bonds : angle 5.59464 / 3.82 ( 2967) link_ALPHA1-4 : bond 0.00743 / 0.47 ( 27) link_ALPHA1-4 : angle 1.66250 / 1.15 ( 81) link_BETA1-4 : bond 0.00323 / 0.20 ( 36) link_BETA1-4 : angle 1.16517 / 0.79 ( 108) link_BETA1-6 : bond 0.00626 / 0.31 ( 3) link_BETA1-6 : angle 1.17221 / 0.65 ( 9) link_NAG-ASN : bond 0.00338 / 0.23 ( 57) link_NAG-ASN : angle 2.15208 / 1.32 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 594 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8286 (p) cc_final: 0.8070 (p) REVERT: A 34 ARG cc_start: 0.7981 (mtt-85) cc_final: 0.7480 (mtt90) REVERT: A 102 ARG cc_start: 0.6809 (OUTLIER) cc_final: 0.6503 (mtt-85) REVERT: A 191 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7433 (mp0) REVERT: A 269 TYR cc_start: 0.7516 (m-10) cc_final: 0.7155 (m-10) REVERT: A 271 GLN cc_start: 0.8298 (mp10) cc_final: 0.7546 (mp10) REVERT: A 298 GLU cc_start: 0.8793 (tp30) cc_final: 0.8469 (tp30) REVERT: A 319 ARG cc_start: 0.8653 (ttp-110) cc_final: 0.8394 (ttm110) REVERT: A 351 TYR cc_start: 0.8719 (p90) cc_final: 0.8366 (p90) REVERT: A 353 TRP cc_start: 0.8436 (p-90) cc_final: 0.8091 (p-90) REVERT: A 421 TYR cc_start: 0.7919 (m-80) cc_final: 0.7411 (m-10) REVERT: A 490 PHE cc_start: 0.8526 (t80) cc_final: 0.7996 (t80) REVERT: A 505 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.7707 (m-80) REVERT: A 523 THR cc_start: 0.8581 (p) cc_final: 0.8275 (t) REVERT: A 565 PHE cc_start: 0.7749 (m-80) cc_final: 0.7455 (m-80) REVERT: A 607 GLN cc_start: 0.8589 (mt0) cc_final: 0.8358 (mt0) REVERT: A 804 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8640 (mp10) REVERT: A 808 ASP cc_start: 0.8084 (t0) cc_final: 0.7788 (t0) REVERT: A 994 ASP cc_start: 0.8602 (t70) cc_final: 0.8308 (t0) REVERT: A 1107 ARG cc_start: 0.8461 (mtt90) cc_final: 0.8115 (mtt90) REVERT: A 1119 ASN cc_start: 0.8580 (m110) cc_final: 0.8334 (m-40) REVERT: B 65 PHE cc_start: 0.8769 (m-80) cc_final: 0.8521 (m-80) REVERT: B 140 PHE cc_start: 0.8347 (p90) cc_final: 0.8029 (p90) REVERT: B 191 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7821 (mt-10) REVERT: B 207 HIS cc_start: 0.8351 (t-90) cc_final: 0.7720 (t-90) REVERT: B 236 THR cc_start: 0.8337 (OUTLIER) cc_final: 0.8102 (p) REVERT: B 287 ASP cc_start: 0.8343 (t0) cc_final: 0.7907 (m-30) REVERT: B 298 GLU cc_start: 0.8685 (tt0) cc_final: 0.7994 (tm-30) REVERT: B 319 ARG cc_start: 0.8729 (ttp-110) cc_final: 0.8502 (ttm110) REVERT: B 351 TYR cc_start: 0.8762 (p90) cc_final: 0.8253 (p90) REVERT: B 389 ASP cc_start: 0.7998 (t0) cc_final: 0.7627 (t0) REVERT: B 462 LYS cc_start: 0.9074 (mmmm) cc_final: 0.8833 (mmmm) REVERT: B 490 PHE cc_start: 0.8480 (t80) cc_final: 0.8163 (t80) REVERT: B 505 TYR cc_start: 0.8064 (OUTLIER) cc_final: 0.7813 (m-80) REVERT: B 523 THR cc_start: 0.8581 (p) cc_final: 0.8059 (t) REVERT: B 578 ASP cc_start: 0.8470 (t0) cc_final: 0.8151 (t70) REVERT: B 646 ARG cc_start: 0.9094 (mmm-85) cc_final: 0.8826 (mtt90) REVERT: B 661 GLU cc_start: 0.7760 (pm20) cc_final: 0.7430 (pm20) REVERT: B 693 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8951 (pp) REVERT: B 796 ASP cc_start: 0.8590 (t0) cc_final: 0.8233 (t0) REVERT: B 808 ASP cc_start: 0.8124 (t0) cc_final: 0.7768 (t0) REVERT: B 817 PHE cc_start: 0.8719 (t80) cc_final: 0.8415 (t80) REVERT: B 819 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8239 (mt-10) REVERT: B 823 PHE cc_start: 0.8566 (t80) cc_final: 0.8019 (t80) REVERT: B 986 LYS cc_start: 0.8536 (mmmt) cc_final: 0.8253 (mmmt) REVERT: B 994 ASP cc_start: 0.8586 (t70) cc_final: 0.8296 (t0) REVERT: B 1072 GLU cc_start: 0.8579 (pm20) cc_final: 0.8206 (pm20) REVERT: B 1073 LYS cc_start: 0.8771 (mtpp) cc_final: 0.8308 (mttm) REVERT: B 1082 CYS cc_start: 0.7210 (t) cc_final: 0.6904 (t) REVERT: C 191 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7794 (mp0) REVERT: C 278 LYS cc_start: 0.8888 (tttt) cc_final: 0.8543 (ttpt) REVERT: C 347 PHE cc_start: 0.7543 (OUTLIER) cc_final: 0.6763 (m-80) REVERT: C 360 ASN cc_start: 0.8786 (t0) cc_final: 0.8501 (t0) REVERT: C 368 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8694 (pp) REVERT: C 408 ARG cc_start: 0.8592 (ptm-80) cc_final: 0.8241 (ptm-80) REVERT: C 516 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7483 (tm-30) REVERT: C 564 GLN cc_start: 0.8514 (tp40) cc_final: 0.8148 (tp40) REVERT: C 578 ASP cc_start: 0.8141 (t0) cc_final: 0.7831 (t70) REVERT: C 643 PHE cc_start: 0.8161 (t80) cc_final: 0.7873 (t80) REVERT: C 710 ASN cc_start: 0.9082 (p0) cc_final: 0.8855 (p0) REVERT: C 776 LYS cc_start: 0.8875 (tttm) cc_final: 0.8418 (tttm) REVERT: C 780 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8036 (mm-30) REVERT: C 787 GLN cc_start: 0.8662 (mt0) cc_final: 0.8251 (mt0) REVERT: C 796 ASP cc_start: 0.8473 (t0) cc_final: 0.8252 (t0) REVERT: C 935 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8346 (tt0) REVERT: C 994 ASP cc_start: 0.8630 (t70) cc_final: 0.8177 (t0) REVERT: C 1002 GLN cc_start: 0.8689 (tt0) cc_final: 0.8357 (tt0) REVERT: C 1119 ASN cc_start: 0.8828 (m-40) cc_final: 0.8426 (m-40) outliers start: 86 outliers final: 58 residues processed: 646 average time/residue: 0.1926 time to fit residues: 194.4994 Evaluate side-chains 631 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 562 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 38 optimal weight: 0.9990 chunk 193 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 142 optimal weight: 1.9990 chunk 268 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 25 optimal weight: 0.0980 chunk 266 optimal weight: 0.0470 chunk 262 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 overall best weight: 0.4682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN A 954 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN C 188 ASN C 394 ASN C 969 ASN C1159 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.111365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.088930 restraints weight = 60978.001| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 3.59 r_work: 0.3244 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28470 Z= 0.129 Angle : 0.684 14.282 38967 Z= 0.334 Chirality : 0.045 0.272 4716 Planarity : 0.004 0.067 4803 Dihedral : 5.195 45.110 3581 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.24 % Favored : 95.58 % Rotamer: Outliers : 2.72 % Allowed : 16.61 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.14), residues: 3300 helix: 2.10 (0.19), residues: 732 sheet: -0.09 (0.19), residues: 693 loop : -0.96 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 102 TYR 0.018 0.001 TYR C1067 PHE 0.029 0.001 PHE C 817 TRP 0.035 0.001 TRP A 436 HIS 0.011 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (28302) covalent geometry : angle 0.65944 / 0.33 (38508) SS BOND : bond 0.00466 / 0.27 ( 45) SS BOND : angle 2.03035 / 1.43 ( 90) hydrogen bonds : bond 0.03644 / 2.48 ( 1092) hydrogen bonds : angle 5.53938 / 3.79 ( 2967) link_ALPHA1-4 : bond 0.00718 / 0.45 ( 27) link_ALPHA1-4 : angle 1.62947 / 1.12 ( 81) link_BETA1-4 : bond 0.00328 / 0.21 ( 36) link_BETA1-4 : angle 1.11437 / 0.76 ( 108) link_BETA1-6 : bond 0.00634 / 0.32 ( 3) link_BETA1-6 : angle 1.18146 / 0.66 ( 9) link_NAG-ASN : bond 0.00348 / 0.23 ( 57) link_NAG-ASN : angle 2.09720 / 1.28 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 573 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8340 (p) cc_final: 0.7932 (p) REVERT: A 34 ARG cc_start: 0.7925 (mtt-85) cc_final: 0.7452 (mtt90) REVERT: A 102 ARG cc_start: 0.6777 (OUTLIER) cc_final: 0.6483 (mtt-85) REVERT: A 153 MET cc_start: 0.7101 (mpp) cc_final: 0.6723 (mpp) REVERT: A 191 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7349 (mp0) REVERT: A 220 PHE cc_start: 0.8207 (t80) cc_final: 0.7952 (t80) REVERT: A 269 TYR cc_start: 0.7453 (m-10) cc_final: 0.7092 (m-80) REVERT: A 271 GLN cc_start: 0.8273 (mp10) cc_final: 0.7551 (mp10) REVERT: A 278 LYS cc_start: 0.8984 (tttt) cc_final: 0.8729 (ttmt) REVERT: A 298 GLU cc_start: 0.8764 (tp30) cc_final: 0.8445 (tp30) REVERT: A 319 ARG cc_start: 0.8667 (ttp-110) cc_final: 0.8413 (ttm110) REVERT: A 351 TYR cc_start: 0.8692 (p90) cc_final: 0.8350 (p90) REVERT: A 353 TRP cc_start: 0.8396 (p-90) cc_final: 0.8011 (p-90) REVERT: A 421 TYR cc_start: 0.7935 (m-80) cc_final: 0.7464 (m-10) REVERT: A 505 TYR cc_start: 0.7955 (OUTLIER) cc_final: 0.7680 (m-80) REVERT: A 523 THR cc_start: 0.8707 (p) cc_final: 0.8344 (t) REVERT: A 565 PHE cc_start: 0.7730 (m-80) cc_final: 0.7417 (m-80) REVERT: A 607 GLN cc_start: 0.8585 (mt0) cc_final: 0.8373 (mt0) REVERT: A 740 MET cc_start: 0.8552 (ttt) cc_final: 0.8258 (ttm) REVERT: A 804 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8634 (mp10) REVERT: A 808 ASP cc_start: 0.8057 (t0) cc_final: 0.7760 (t0) REVERT: A 994 ASP cc_start: 0.8606 (t70) cc_final: 0.8298 (t0) REVERT: A 1119 ASN cc_start: 0.8579 (m110) cc_final: 0.8357 (m-40) REVERT: A 1142 GLN cc_start: 0.8840 (tp40) cc_final: 0.8632 (tp40) REVERT: B 65 PHE cc_start: 0.8755 (m-80) cc_final: 0.8524 (m-80) REVERT: B 108 THR cc_start: 0.7220 (OUTLIER) cc_final: 0.6289 (m) REVERT: B 140 PHE cc_start: 0.8287 (p90) cc_final: 0.7981 (p90) REVERT: B 191 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7838 (mt-10) REVERT: B 207 HIS cc_start: 0.8366 (t-90) cc_final: 0.7648 (t-90) REVERT: B 236 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.7872 (p) REVERT: B 298 GLU cc_start: 0.8660 (tt0) cc_final: 0.8239 (tm-30) REVERT: B 319 ARG cc_start: 0.8741 (ttp-110) cc_final: 0.8509 (ttm110) REVERT: B 351 TYR cc_start: 0.8742 (p90) cc_final: 0.8239 (p90) REVERT: B 389 ASP cc_start: 0.7919 (t0) cc_final: 0.7560 (t0) REVERT: B 462 LYS cc_start: 0.9096 (mmmm) cc_final: 0.8782 (mmtm) REVERT: B 490 PHE cc_start: 0.8470 (t80) cc_final: 0.8158 (t80) REVERT: B 505 TYR cc_start: 0.8059 (OUTLIER) cc_final: 0.7809 (m-80) REVERT: B 523 THR cc_start: 0.8594 (p) cc_final: 0.8067 (t) REVERT: B 534 VAL cc_start: 0.9130 (p) cc_final: 0.8908 (m) REVERT: B 578 ASP cc_start: 0.8462 (t0) cc_final: 0.8153 (t70) REVERT: B 646 ARG cc_start: 0.9055 (mmm-85) cc_final: 0.8780 (mtt90) REVERT: B 661 GLU cc_start: 0.7713 (pm20) cc_final: 0.7387 (pm20) REVERT: B 693 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8940 (pp) REVERT: B 776 LYS cc_start: 0.8884 (ttmm) cc_final: 0.8618 (tttt) REVERT: B 796 ASP cc_start: 0.8572 (t0) cc_final: 0.8232 (t0) REVERT: B 808 ASP cc_start: 0.8048 (t0) cc_final: 0.7693 (t0) REVERT: B 817 PHE cc_start: 0.8713 (t80) cc_final: 0.8398 (t80) REVERT: B 819 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8249 (mt-10) REVERT: B 823 PHE cc_start: 0.8536 (t80) cc_final: 0.8004 (t80) REVERT: B 986 LYS cc_start: 0.8484 (mmmt) cc_final: 0.8241 (mmmt) REVERT: B 994 ASP cc_start: 0.8534 (t70) cc_final: 0.8223 (t0) REVERT: B 1072 GLU cc_start: 0.8589 (pm20) cc_final: 0.8230 (pm20) REVERT: B 1073 LYS cc_start: 0.8796 (mtpp) cc_final: 0.8338 (mttm) REVERT: B 1082 CYS cc_start: 0.7243 (t) cc_final: 0.6925 (t) REVERT: B 1123 SER cc_start: 0.9274 (OUTLIER) cc_final: 0.9061 (t) REVERT: C 191 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7774 (mp0) REVERT: C 278 LYS cc_start: 0.8880 (tttt) cc_final: 0.8551 (ttpt) REVERT: C 347 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.6765 (m-80) REVERT: C 360 ASN cc_start: 0.8788 (t0) cc_final: 0.8513 (t0) REVERT: C 368 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8670 (pp) REVERT: C 408 ARG cc_start: 0.8578 (ptm-80) cc_final: 0.8225 (ptm-80) REVERT: C 564 GLN cc_start: 0.8506 (tp40) cc_final: 0.8140 (tp40) REVERT: C 578 ASP cc_start: 0.8190 (t0) cc_final: 0.7902 (t70) REVERT: C 643 PHE cc_start: 0.8153 (t80) cc_final: 0.7868 (t80) REVERT: C 658 ASN cc_start: 0.8860 (p0) cc_final: 0.8562 (p0) REVERT: C 710 ASN cc_start: 0.9054 (p0) cc_final: 0.8826 (p0) REVERT: C 776 LYS cc_start: 0.8866 (tttm) cc_final: 0.8470 (tttm) REVERT: C 780 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8026 (mm-30) REVERT: C 787 GLN cc_start: 0.8664 (mt0) cc_final: 0.8257 (mt0) REVERT: C 796 ASP cc_start: 0.8476 (t0) cc_final: 0.8248 (t0) REVERT: C 994 ASP cc_start: 0.8623 (t70) cc_final: 0.8170 (t0) REVERT: C 1002 GLN cc_start: 0.8660 (tt0) cc_final: 0.8315 (tt0) REVERT: C 1092 GLU cc_start: 0.8248 (pm20) cc_final: 0.7892 (pm20) REVERT: C 1119 ASN cc_start: 0.8795 (m-40) cc_final: 0.8419 (m-40) outliers start: 79 outliers final: 55 residues processed: 621 average time/residue: 0.1865 time to fit residues: 180.8837 Evaluate side-chains 611 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 545 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 218 optimal weight: 0.9990 chunk 29 optimal weight: 0.0370 chunk 212 optimal weight: 2.9990 chunk 187 optimal weight: 0.5980 chunk 198 optimal weight: 0.9990 chunk 313 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 242 optimal weight: 0.5980 chunk 207 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 271 optimal weight: 4.9990 overall best weight: 0.6462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN A 954 GLN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN C 188 ASN C 969 ASN C1088 HIS C1159 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.111352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.089304 restraints weight = 60750.546| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.54 r_work: 0.3237 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28470 Z= 0.144 Angle : 0.693 18.616 38967 Z= 0.338 Chirality : 0.045 0.280 4716 Planarity : 0.004 0.058 4803 Dihedral : 5.172 44.901 3581 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.24 % Favored : 95.58 % Rotamer: Outliers : 2.59 % Allowed : 17.10 % Favored : 80.32 % 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: -0.11 (0.14), residues: 3300 helix: 2.09 (0.19), residues: 732 sheet: -0.12 (0.19), residues: 693 loop : -0.95 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 34 TYR 0.024 0.001 TYR A1138 PHE 0.032 0.001 PHE A 490 TRP 0.036 0.001 TRP A 104 HIS 0.011 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (28302) covalent geometry : angle 0.66871 / 0.33 (38508) SS BOND : bond 0.00439 / 0.29 ( 45) SS BOND : angle 2.05818 / 1.46 ( 90) hydrogen bonds : bond 0.03682 / 2.51 ( 1092) hydrogen bonds : angle 5.54126 / 3.80 ( 2967) link_ALPHA1-4 : bond 0.00727 / 0.46 ( 27) link_ALPHA1-4 : angle 1.62162 / 1.12 ( 81) link_BETA1-4 : bond 0.00292 / 0.19 ( 36) link_BETA1-4 : angle 1.11319 / 0.76 ( 108) link_BETA1-6 : bond 0.00643 / 0.32 ( 3) link_BETA1-6 : angle 1.19228 / 0.67 ( 9) link_NAG-ASN : bond 0.00337 / 0.23 ( 57) link_NAG-ASN : angle 2.09003 / 1.28 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 559 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8341 (p) cc_final: 0.7967 (p) REVERT: A 34 ARG cc_start: 0.7939 (mtt-85) cc_final: 0.7612 (mtt90) REVERT: A 102 ARG cc_start: 0.6819 (mtt-85) cc_final: 0.6480 (mtt-85) REVERT: A 153 MET cc_start: 0.7082 (mpp) cc_final: 0.6754 (mpp) REVERT: A 158 ARG cc_start: 0.7138 (mmt-90) cc_final: 0.6666 (mmm160) REVERT: A 190 ARG cc_start: 0.7414 (tpp80) cc_final: 0.7206 (tpp80) REVERT: A 220 PHE cc_start: 0.8195 (t80) cc_final: 0.7919 (t80) REVERT: A 242 LEU cc_start: 0.7791 (mt) cc_final: 0.7037 (mt) REVERT: A 269 TYR cc_start: 0.7519 (m-10) cc_final: 0.7219 (m-10) REVERT: A 271 GLN cc_start: 0.8296 (mp10) cc_final: 0.7563 (mp10) REVERT: A 278 LYS cc_start: 0.9000 (tttt) cc_final: 0.8753 (ttmt) REVERT: A 298 GLU cc_start: 0.8757 (tp30) cc_final: 0.8434 (tp30) REVERT: A 319 ARG cc_start: 0.8654 (ttp-110) cc_final: 0.8395 (ttm110) REVERT: A 353 TRP cc_start: 0.8423 (p-90) cc_final: 0.8123 (p-90) REVERT: A 421 TYR cc_start: 0.7830 (m-80) cc_final: 0.7200 (m-10) REVERT: A 490 PHE cc_start: 0.8654 (t80) cc_final: 0.8333 (t80) REVERT: A 505 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.7671 (m-80) REVERT: A 523 THR cc_start: 0.8766 (p) cc_final: 0.8413 (t) REVERT: A 565 PHE cc_start: 0.7728 (m-80) cc_final: 0.7402 (m-80) REVERT: A 808 ASP cc_start: 0.8040 (t0) cc_final: 0.7743 (t0) REVERT: A 994 ASP cc_start: 0.8615 (t70) cc_final: 0.8302 (t0) REVERT: A 1119 ASN cc_start: 0.8596 (m110) cc_final: 0.8378 (m-40) REVERT: A 1142 GLN cc_start: 0.8827 (tp40) cc_final: 0.8623 (tp40) REVERT: B 65 PHE cc_start: 0.8756 (m-80) cc_final: 0.8526 (m-80) REVERT: B 108 THR cc_start: 0.7168 (OUTLIER) cc_final: 0.6230 (m) REVERT: B 140 PHE cc_start: 0.8305 (p90) cc_final: 0.7999 (p90) REVERT: B 191 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7822 (mt-10) REVERT: B 207 HIS cc_start: 0.8376 (t-90) cc_final: 0.7574 (t-90) REVERT: B 236 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.7852 (p) REVERT: B 287 ASP cc_start: 0.8127 (t0) cc_final: 0.7620 (t0) REVERT: B 298 GLU cc_start: 0.8671 (tt0) cc_final: 0.8238 (tm-30) REVERT: B 306 PHE cc_start: 0.8926 (m-10) cc_final: 0.8001 (m-10) REVERT: B 319 ARG cc_start: 0.8727 (ttp-110) cc_final: 0.8487 (ttm110) REVERT: B 351 TYR cc_start: 0.8771 (p90) cc_final: 0.8258 (p90) REVERT: B 389 ASP cc_start: 0.7921 (t0) cc_final: 0.7570 (t0) REVERT: B 490 PHE cc_start: 0.8489 (t80) cc_final: 0.8175 (t80) REVERT: B 505 TYR cc_start: 0.8014 (OUTLIER) cc_final: 0.7785 (m-80) REVERT: B 523 THR cc_start: 0.8604 (p) cc_final: 0.8077 (t) REVERT: B 578 ASP cc_start: 0.8465 (t0) cc_final: 0.8149 (t70) REVERT: B 646 ARG cc_start: 0.9047 (mmm-85) cc_final: 0.8777 (mtt90) REVERT: B 661 GLU cc_start: 0.7773 (pm20) cc_final: 0.7448 (pm20) REVERT: B 693 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8929 (pp) REVERT: B 776 LYS cc_start: 0.8896 (ttmm) cc_final: 0.8635 (tttt) REVERT: B 796 ASP cc_start: 0.8565 (t0) cc_final: 0.8231 (t0) REVERT: B 808 ASP cc_start: 0.8015 (t0) cc_final: 0.7670 (t0) REVERT: B 817 PHE cc_start: 0.8688 (t80) cc_final: 0.8380 (t80) REVERT: B 819 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8244 (mt-10) REVERT: B 823 PHE cc_start: 0.8543 (t80) cc_final: 0.8009 (t80) REVERT: B 986 LYS cc_start: 0.8496 (mmmt) cc_final: 0.8279 (mmmt) REVERT: B 994 ASP cc_start: 0.8534 (t70) cc_final: 0.8222 (t0) REVERT: B 1072 GLU cc_start: 0.8571 (pm20) cc_final: 0.8215 (pm20) REVERT: B 1073 LYS cc_start: 0.8787 (mtpp) cc_final: 0.8324 (mttm) REVERT: B 1082 CYS cc_start: 0.7195 (t) cc_final: 0.6863 (t) REVERT: B 1123 SER cc_start: 0.9276 (OUTLIER) cc_final: 0.9062 (t) REVERT: C 191 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7800 (mp0) REVERT: C 278 LYS cc_start: 0.8905 (tttt) cc_final: 0.8569 (ttpt) REVERT: C 347 PHE cc_start: 0.7447 (OUTLIER) cc_final: 0.6713 (m-80) REVERT: C 357 ARG cc_start: 0.8448 (tmm-80) cc_final: 0.8070 (tmm-80) REVERT: C 360 ASN cc_start: 0.8750 (t0) cc_final: 0.8488 (t0) REVERT: C 368 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8722 (pp) REVERT: C 408 ARG cc_start: 0.8608 (ptm-80) cc_final: 0.8256 (ptm-80) REVERT: C 455 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8393 (mt) REVERT: C 564 GLN cc_start: 0.8468 (tp40) cc_final: 0.8139 (tp40) REVERT: C 578 ASP cc_start: 0.8185 (t0) cc_final: 0.7889 (t70) REVERT: C 643 PHE cc_start: 0.8125 (t80) cc_final: 0.7818 (t80) REVERT: C 710 ASN cc_start: 0.9063 (p0) cc_final: 0.8834 (p0) REVERT: C 776 LYS cc_start: 0.8875 (tttm) cc_final: 0.8438 (ttpp) REVERT: C 780 GLU cc_start: 0.8665 (mm-30) cc_final: 0.7976 (mm-30) REVERT: C 787 GLN cc_start: 0.8667 (mt0) cc_final: 0.8270 (mt0) REVERT: C 796 ASP cc_start: 0.8464 (t0) cc_final: 0.8239 (t0) REVERT: C 994 ASP cc_start: 0.8657 (t70) cc_final: 0.8217 (t0) REVERT: C 1002 GLN cc_start: 0.8665 (tt0) cc_final: 0.8326 (tt0) REVERT: C 1092 GLU cc_start: 0.8237 (pm20) cc_final: 0.7882 (pm20) REVERT: C 1119 ASN cc_start: 0.8789 (m-40) cc_final: 0.8429 (m-40) outliers start: 75 outliers final: 59 residues processed: 608 average time/residue: 0.1990 time to fit residues: 188.2231 Evaluate side-chains 617 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 548 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 212 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 315 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 197 optimal weight: 1.9990 chunk 264 optimal weight: 0.2980 chunk 145 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 330 optimal weight: 0.3980 chunk 151 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS C 188 ASN C 804 GLN C 969 ASN C1159 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.111390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.089179 restraints weight = 60958.936| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.56 r_work: 0.3239 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28470 Z= 0.146 Angle : 0.696 17.239 38967 Z= 0.338 Chirality : 0.045 0.300 4716 Planarity : 0.004 0.061 4803 Dihedral : 5.080 27.617 3577 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.30 % Favored : 95.52 % Rotamer: Outliers : 2.45 % Allowed : 17.44 % Favored : 80.11 % 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: -0.09 (0.14), residues: 3300 helix: 2.10 (0.20), residues: 732 sheet: -0.12 (0.19), residues: 693 loop : -0.94 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 567 TYR 0.019 0.001 TYR C1067 PHE 0.026 0.001 PHE C 817 TRP 0.034 0.001 TRP A 104 HIS 0.012 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (28302) covalent geometry : angle 0.67273 / 0.33 (38508) SS BOND : bond 0.00402 / 0.25 ( 45) SS BOND : angle 1.99632 / 1.42 ( 90) hydrogen bonds : bond 0.03645 / 2.48 ( 1092) hydrogen bonds : angle 5.56350 / 3.81 ( 2967) link_ALPHA1-4 : bond 0.00713 / 0.45 ( 27) link_ALPHA1-4 : angle 1.61256 / 1.11 ( 81) link_BETA1-4 : bond 0.00299 / 0.19 ( 36) link_BETA1-4 : angle 1.10724 / 0.75 ( 108) link_BETA1-6 : bond 0.00564 / 0.28 ( 3) link_BETA1-6 : angle 1.18351 / 0.67 ( 9) link_NAG-ASN : bond 0.00331 / 0.22 ( 57) link_NAG-ASN : angle 2.08464 / 1.28 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 556 time to evaluate : 1.072 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 33 THR cc_start: 0.8323 (p) cc_final: 0.7961 (p) REVERT: A 34 ARG cc_start: 0.7869 (mtt-85) cc_final: 0.7459 (mtt90) REVERT: A 102 ARG cc_start: 0.6867 (mtt-85) cc_final: 0.6524 (mtt-85) REVERT: A 153 MET cc_start: 0.7071 (mpp) cc_final: 0.6771 (mpp) REVERT: A 158 ARG cc_start: 0.7137 (mmt-90) cc_final: 0.6907 (mmm160) REVERT: A 191 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7312 (mp0) REVERT: A 220 PHE cc_start: 0.8171 (t80) cc_final: 0.7884 (t80) REVERT: A 242 LEU cc_start: 0.7782 (mt) cc_final: 0.7021 (mt) REVERT: A 269 TYR cc_start: 0.7532 (m-10) cc_final: 0.7233 (m-10) REVERT: A 271 GLN cc_start: 0.8296 (mp10) cc_final: 0.7565 (mp10) REVERT: A 278 LYS cc_start: 0.8987 (tttt) cc_final: 0.8740 (ttmt) REVERT: A 298 GLU cc_start: 0.8757 (tp30) cc_final: 0.8438 (tp30) REVERT: A 319 ARG cc_start: 0.8656 (ttp-110) cc_final: 0.8394 (ttm110) REVERT: A 353 TRP cc_start: 0.8417 (p-90) cc_final: 0.8198 (p-90) REVERT: A 421 TYR cc_start: 0.7779 (m-80) cc_final: 0.7352 (m-10) REVERT: A 505 TYR cc_start: 0.7946 (OUTLIER) cc_final: 0.7678 (m-80) REVERT: A 523 THR cc_start: 0.8797 (p) cc_final: 0.8454 (t) REVERT: A 565 PHE cc_start: 0.7763 (m-80) cc_final: 0.7447 (m-80) REVERT: A 790 LYS cc_start: 0.8815 (ptpp) cc_final: 0.8608 (mtmt) REVERT: A 808 ASP cc_start: 0.8043 (t0) cc_final: 0.7765 (t0) REVERT: A 994 ASP cc_start: 0.8616 (t70) cc_final: 0.8303 (t0) REVERT: A 1119 ASN cc_start: 0.8599 (m110) cc_final: 0.8365 (m-40) REVERT: A 1138 TYR cc_start: 0.8640 (t80) cc_final: 0.8384 (t80) REVERT: B 65 PHE cc_start: 0.8750 (m-80) cc_final: 0.8516 (m-80) REVERT: B 108 THR cc_start: 0.7179 (OUTLIER) cc_final: 0.6237 (m) REVERT: B 140 PHE cc_start: 0.8307 (p90) cc_final: 0.7995 (p90) REVERT: B 191 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: B 207 HIS cc_start: 0.8164 (t70) cc_final: 0.7518 (t-90) REVERT: B 236 THR cc_start: 0.8312 (OUTLIER) cc_final: 0.7846 (p) REVERT: B 287 ASP cc_start: 0.8134 (t0) cc_final: 0.7594 (t0) REVERT: B 298 GLU cc_start: 0.8669 (tt0) cc_final: 0.8238 (tm-30) REVERT: B 306 PHE cc_start: 0.8928 (m-10) cc_final: 0.8028 (m-10) REVERT: B 319 ARG cc_start: 0.8723 (ttp-110) cc_final: 0.8453 (ttm110) REVERT: B 351 TYR cc_start: 0.8763 (p90) cc_final: 0.8256 (p90) REVERT: B 389 ASP cc_start: 0.7945 (t0) cc_final: 0.7589 (t0) REVERT: B 490 PHE cc_start: 0.8440 (t80) cc_final: 0.8131 (t80) REVERT: B 505 TYR cc_start: 0.8029 (OUTLIER) cc_final: 0.7794 (m-80) REVERT: B 523 THR cc_start: 0.8628 (p) cc_final: 0.8104 (t) REVERT: B 578 ASP cc_start: 0.8478 (t0) cc_final: 0.8148 (t70) REVERT: B 646 ARG cc_start: 0.9053 (mmm-85) cc_final: 0.8786 (mtt90) REVERT: B 693 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8922 (pp) REVERT: B 776 LYS cc_start: 0.8886 (ttmm) cc_final: 0.8623 (tttt) REVERT: B 796 ASP cc_start: 0.8570 (t0) cc_final: 0.8239 (t0) REVERT: B 808 ASP cc_start: 0.8028 (t0) cc_final: 0.7735 (t0) REVERT: B 817 PHE cc_start: 0.8742 (t80) cc_final: 0.8400 (t80) REVERT: B 819 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8258 (mt-10) REVERT: B 823 PHE cc_start: 0.8542 (t80) cc_final: 0.8010 (t80) REVERT: B 986 LYS cc_start: 0.8467 (mmmt) cc_final: 0.8266 (mmmt) REVERT: B 994 ASP cc_start: 0.8544 (t70) cc_final: 0.8231 (t0) REVERT: B 1072 GLU cc_start: 0.8572 (pm20) cc_final: 0.8220 (pm20) REVERT: B 1073 LYS cc_start: 0.8789 (mtpp) cc_final: 0.8326 (mttm) REVERT: B 1082 CYS cc_start: 0.7198 (t) cc_final: 0.6867 (t) REVERT: B 1123 SER cc_start: 0.9270 (OUTLIER) cc_final: 0.8922 (t) REVERT: C 191 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7759 (mp0) REVERT: C 278 LYS cc_start: 0.8901 (tttt) cc_final: 0.8563 (ttpt) REVERT: C 347 PHE cc_start: 0.7395 (OUTLIER) cc_final: 0.6807 (m-80) REVERT: C 357 ARG cc_start: 0.8472 (tmm-80) cc_final: 0.8100 (tmm-80) REVERT: C 360 ASN cc_start: 0.8797 (t0) cc_final: 0.8537 (t0) REVERT: C 368 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8724 (pp) REVERT: C 408 ARG cc_start: 0.8591 (ptm-80) cc_final: 0.8244 (ptm-80) REVERT: C 455 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8397 (mt) REVERT: C 564 GLN cc_start: 0.8490 (tp40) cc_final: 0.8164 (tp40) REVERT: C 578 ASP cc_start: 0.8191 (t0) cc_final: 0.7815 (t70) REVERT: C 643 PHE cc_start: 0.8143 (t80) cc_final: 0.7821 (t80) REVERT: C 710 ASN cc_start: 0.9061 (p0) cc_final: 0.8834 (p0) REVERT: C 776 LYS cc_start: 0.8876 (tttm) cc_final: 0.8462 (ttpp) REVERT: C 780 GLU cc_start: 0.8660 (mm-30) cc_final: 0.7982 (mm-30) REVERT: C 787 GLN cc_start: 0.8666 (mt0) cc_final: 0.8264 (mt0) REVERT: C 796 ASP cc_start: 0.8464 (t0) cc_final: 0.8244 (t0) REVERT: C 804 GLN cc_start: 0.8965 (mm110) cc_final: 0.8731 (mm110) REVERT: C 935 GLN cc_start: 0.8550 (tp40) cc_final: 0.8212 (tt0) REVERT: C 994 ASP cc_start: 0.8643 (t70) cc_final: 0.8193 (t0) REVERT: C 1002 GLN cc_start: 0.8656 (tt0) cc_final: 0.8309 (tt0) REVERT: C 1092 GLU cc_start: 0.8230 (pm20) cc_final: 0.7877 (pm20) REVERT: C 1119 ASN cc_start: 0.8790 (m-40) cc_final: 0.8442 (m-40) outliers start: 71 outliers final: 57 residues processed: 603 average time/residue: 0.2021 time to fit residues: 189.1499 Evaluate side-chains 616 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 549 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1086 LYS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 157 optimal weight: 0.0970 chunk 280 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 279 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 258 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 283 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN A 360 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 954 GLN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN C 188 ASN C 969 ASN C1159 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.111252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.088938 restraints weight = 60868.472| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 3.57 r_work: 0.3247 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 28470 Z= 0.141 Angle : 0.701 18.198 38967 Z= 0.339 Chirality : 0.045 0.281 4716 Planarity : 0.004 0.052 4803 Dihedral : 5.050 27.554 3577 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.30 % Favored : 95.52 % Rotamer: Outliers : 2.45 % Allowed : 17.65 % Favored : 79.90 % 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: -0.09 (0.14), residues: 3300 helix: 2.14 (0.20), residues: 732 sheet: -0.19 (0.18), residues: 738 loop : -0.94 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 567 TYR 0.019 0.001 TYR C1067 PHE 0.041 0.001 PHE C 817 TRP 0.032 0.001 TRP A 104 HIS 0.012 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (28302) covalent geometry : angle 0.67872 / 0.33 (38508) SS BOND : bond 0.00396 / 0.25 ( 45) SS BOND : angle 1.91652 / 1.37 ( 90) hydrogen bonds : bond 0.03591 / 2.44 ( 1092) hydrogen bonds : angle 5.54954 / 3.80 ( 2967) link_ALPHA1-4 : bond 0.00707 / 0.44 ( 27) link_ALPHA1-4 : angle 1.60468 / 1.10 ( 81) link_BETA1-4 : bond 0.00302 / 0.19 ( 36) link_BETA1-4 : angle 1.08743 / 0.74 ( 108) link_BETA1-6 : bond 0.00606 / 0.30 ( 3) link_BETA1-6 : angle 1.21544 / 0.69 ( 9) link_NAG-ASN : bond 0.00326 / 0.22 ( 57) link_NAG-ASN : angle 2.05909 / 1.26 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7214.79 seconds wall clock time: 124 minutes 37.29 seconds (7477.29 seconds total)