Starting phenix.real_space_refine on Sun May 25 10:31:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wq0_37732/05_2025/8wq0_37732.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wq0_37732/05_2025/8wq0_37732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wq0_37732/05_2025/8wq0_37732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wq0_37732/05_2025/8wq0_37732.map" model { file = "/net/cci-nas-00/data/ceres_data/8wq0_37732/05_2025/8wq0_37732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wq0_37732/05_2025/8wq0_37732.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 132 5.16 5 C 16968 2.51 5 N 4329 2.21 5 O 5321 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 26750 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8485 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 59, 'TRANS': 1028} Chain breaks: 1 Chain: "B" Number of atoms: 8485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8485 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 59, 'TRANS': 1028} Chain breaks: 1 Chain: "C" Number of atoms: 8485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8485 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 59, 'TRANS': 1028} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 15.23, per 1000 atoms: 0.57 Number of scatterers: 26750 At special positions: 0 Unit cell: (147.165, 140.72, 174.02, 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 132 16.00 O 5321 8.00 N 4329 7.00 C 16968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 134 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 160 " distance=2.04 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 349 " distance=2.03 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 420 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 512 " distance=2.03 Simple disulfide: pdb=" SG CYS A 468 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 577 " distance=2.03 Simple disulfide: pdb=" SG CYS A 604 " - pdb=" SG CYS A 636 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 658 " distance=2.03 Simple disulfide: pdb=" SG CYS A 721 " - pdb=" SG CYS A 743 " distance=2.02 Simple disulfide: pdb=" SG CYS A 726 " - pdb=" SG CYS A 732 " distance=2.03 Simple disulfide: pdb=" SG CYS A 823 " - pdb=" SG CYS A 834 " distance=2.03 Simple disulfide: pdb=" SG CYS A1015 " - pdb=" SG CYS A1026 " distance=2.03 Simple disulfide: pdb=" SG CYS A1065 " - pdb=" SG CYS A1109 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 160 " distance=2.03 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 349 " distance=2.04 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 420 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 512 " distance=2.03 Simple disulfide: pdb=" SG CYS B 468 " - pdb=" SG CYS B 475 " distance=2.03 Simple disulfide: pdb=" SG CYS B 525 " - pdb=" SG CYS B 577 " distance=2.03 Simple disulfide: pdb=" SG CYS B 604 " - pdb=" SG CYS B 636 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 658 " distance=2.03 Simple disulfide: pdb=" SG CYS B 721 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 726 " - pdb=" SG CYS B 732 " distance=2.03 Simple disulfide: pdb=" SG CYS B 823 " - pdb=" SG CYS B 834 " distance=2.03 Simple disulfide: pdb=" SG CYS B1015 " - pdb=" SG CYS B1026 " distance=2.03 Simple disulfide: pdb=" SG CYS B1065 " - pdb=" SG CYS B1109 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 160 " distance=2.04 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 324 " - pdb=" SG CYS C 349 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 420 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 512 " distance=2.03 Simple disulfide: pdb=" SG CYS C 468 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 525 " - pdb=" SG CYS C 577 " distance=2.03 Simple disulfide: pdb=" SG CYS C 604 " - pdb=" SG CYS C 636 " distance=2.03 Simple disulfide: pdb=" SG CYS C 649 " - pdb=" SG CYS C 658 " distance=2.03 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 726 " - pdb=" SG CYS C 732 " distance=2.03 Simple disulfide: pdb=" SG CYS C 823 " - pdb=" SG CYS C 834 " distance=2.03 Simple disulfide: pdb=" SG CYS C1015 " - pdb=" SG CYS C1026 " distance=2.03 Simple disulfide: pdb=" SG CYS C1065 " - pdb=" SG CYS C1109 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " 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 I 2 " - " BMA I 3 " " 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 Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " 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 a 2 " - " BMA a 3 " " 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 f 2 " - " BMA f 3 " " 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 j 2 " - " BMA j 3 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 590 " " NAG A1303 " - " ASN A 358 " " NAG A1304 " - " ASN A 145 " " NAG A1305 " - " ASN A 692 " " NAG A1306 " - " ASN A1057 " " NAG A1307 " - " ASN A 159 " " NAG B1301 " - " ASN B 145 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 590 " " NAG B1304 " - " ASN B 358 " " NAG B1305 " - " ASN B 692 " " NAG B1306 " - " ASN B1057 " " NAG B1307 " - " ASN B 159 " " NAG B1308 " - " ASN B1081 " " NAG C1301 " - " ASN C 145 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 590 " " NAG C1304 " - " ASN C 358 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 159 " " NAG D 1 " - " ASN A 66 " " NAG E 1 " - " ASN A 120 " " NAG F 1 " - " ASN A 603 " " NAG G 1 " - " ASN A1081 " " NAG H 1 " - " ASN A1117 " " NAG I 1 " - " ASN A 784 " " NAG J 1 " - " ASN A 110 " " NAG K 1 " - " ASN A 228 " " NAG L 1 " - " ASN A 270 " " NAG M 1 " - " ASN A 700 " " NAG N 1 " - " ASN A 319 " " NAG O 1 " - " ASN B 66 " " NAG P 1 " - " ASN B 110 " " NAG Q 1 " - " ASN B 120 " " NAG R 1 " - " ASN B 319 " " NAG S 1 " - " ASN B 700 " " NAG T 1 " - " ASN B1117 " " NAG U 1 " - " ASN B 784 " " NAG V 1 " - " ASN B 228 " " NAG W 1 " - " ASN B 270 " " NAG X 1 " - " ASN B 603 " " NAG Y 1 " - " ASN C 66 " " NAG Z 1 " - " ASN C 110 " " NAG a 1 " - " ASN C 120 " " NAG b 1 " - " ASN C 228 " " NAG c 1 " - " ASN C 270 " " NAG d 1 " - " ASN C 319 " " NAG e 1 " - " ASN C 692 " " NAG f 1 " - " ASN C 700 " " NAG g 1 " - " ASN C1057 " " NAG h 1 " - " ASN C1081 " " NAG i 1 " - " ASN C1117 " " NAG j 1 " - " ASN C 784 " Time building additional restraints: 6.81 Conformation dependent library (CDL) restraints added in 3.1 seconds 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6120 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 49 sheets defined 24.6% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.73 Creating SS restraints... Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.550A pdb=" N VAL A 355 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 377 Processing helix chain 'A' and resid 393 through 398 removed outlier: 4.354A pdb=" N ARG A 396 " --> pdb=" O ASP A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 489 through 492 Processing helix chain 'A' and resid 720 through 726 Processing helix chain 'A' and resid 729 through 739 Processing helix chain 'A' and resid 743 through 766 Processing helix chain 'A' and resid 799 through 809 removed outlier: 3.610A pdb=" N VAL A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 826 Processing helix chain 'A' and resid 831 through 838 Processing helix chain 'A' and resid 849 through 867 Processing helix chain 'A' and resid 869 through 873 Processing helix chain 'A' and resid 880 through 892 Processing helix chain 'A' and resid 895 through 902 removed outlier: 3.819A pdb=" N LEU A 899 " --> pdb=" O THR A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 923 Processing helix chain 'A' and resid 928 through 949 removed outlier: 3.850A pdb=" N LEU A 945 " --> pdb=" O ALA A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 967 Processing helix chain 'A' and resid 968 through 1016 removed outlier: 4.137A pdb=" N VAL A 974 " --> pdb=" O PRO A 970 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLN A 975 " --> pdb=" O GLU A 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 292 Processing helix chain 'B' and resid 325 through 331 Processing helix chain 'B' and resid 352 through 357 removed outlier: 3.640A pdb=" N VAL B 355 " --> pdb=" O ASP B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 377 Processing helix chain 'B' and resid 393 through 398 removed outlier: 4.395A pdb=" N ARG B 396 " --> pdb=" O ASP B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 426 through 431 Processing helix chain 'B' and resid 489 through 492 Processing helix chain 'B' and resid 720 through 726 Processing helix chain 'B' and resid 729 through 739 Processing helix chain 'B' and resid 742 through 766 removed outlier: 3.617A pdb=" N LEU B 746 " --> pdb=" O PHE B 742 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR B 761 " --> pdb=" O GLN B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 809 removed outlier: 3.628A pdb=" N VAL B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 826 Processing helix chain 'B' and resid 831 through 838 Processing helix chain 'B' and resid 849 through 868 Processing helix chain 'B' and resid 869 through 873 Processing helix chain 'B' and resid 880 through 892 Processing helix chain 'B' and resid 895 through 902 removed outlier: 4.006A pdb=" N LEU B 899 " --> pdb=" O THR B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 923 Processing helix chain 'B' and resid 928 through 948 Processing helix chain 'B' and resid 949 through 951 No H-bonds generated for 'chain 'B' and resid 949 through 951' Processing helix chain 'B' and resid 959 through 965 Processing helix chain 'B' and resid 968 through 1015 removed outlier: 3.868A pdb=" N VAL B 974 " --> pdb=" O PRO B 970 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN B 975 " --> pdb=" O GLU B 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 292 Processing helix chain 'C' and resid 325 through 331 Processing helix chain 'C' and resid 352 through 357 removed outlier: 3.570A pdb=" N VAL C 355 " --> pdb=" O ASP C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 377 Processing helix chain 'C' and resid 393 through 398 removed outlier: 4.321A pdb=" N ARG C 396 " --> pdb=" O ASP C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 Processing helix chain 'C' and resid 426 through 431 Processing helix chain 'C' and resid 489 through 492 Processing helix chain 'C' and resid 720 through 726 Processing helix chain 'C' and resid 729 through 739 Processing helix chain 'C' and resid 742 through 766 removed outlier: 3.669A pdb=" N LEU C 746 " --> pdb=" O PHE C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 799 through 809 removed outlier: 3.684A pdb=" N VAL C 809 " --> pdb=" O LEU C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 826 Processing helix chain 'C' and resid 831 through 838 Processing helix chain 'C' and resid 849 through 868 Processing helix chain 'C' and resid 869 through 873 Processing helix chain 'C' and resid 880 through 892 Processing helix chain 'C' and resid 895 through 902 removed outlier: 4.004A pdb=" N LEU C 899 " --> pdb=" O THR C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 923 Processing helix chain 'C' and resid 928 through 948 Processing helix chain 'C' and resid 949 through 951 No H-bonds generated for 'chain 'C' and resid 949 through 951' Processing helix chain 'C' and resid 959 through 965 Processing helix chain 'C' and resid 968 through 1015 removed outlier: 3.836A pdb=" N VAL C 974 " --> pdb=" O PRO C 970 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN C 975 " --> pdb=" O GLU C 971 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35 removed outlier: 4.029A pdb=" N THR A 32 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASN A 66 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TYR A 257 " --> pdb=" O ASN A 66 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LEU A 195 " --> pdb=" O LYS A 222 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS A 222 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL A 197 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 201 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ALA A 216 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL A 41 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 35 removed outlier: 4.029A pdb=" N THR A 32 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE A 73 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN A 76 " --> pdb=" O PHE A 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 60 removed outlier: 3.978A pdb=" N ASP A 275 " --> pdb=" O LYS A 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 82 through 83 removed outlier: 6.293A pdb=" N PHE A 139 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL A 140 " --> pdb=" O ILE A 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 82 through 83 removed outlier: 6.826A pdb=" N ASN A 231 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE A 104 " --> pdb=" O ASN A 231 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG A 233 " --> pdb=" O TRP A 102 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TRP A 102 " --> pdb=" O ARG A 233 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU A 235 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN A 130 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N CYS A 160 " --> pdb=" O ASN A 130 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N GLU A 132 " --> pdb=" O PHE A 158 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N PHE A 158 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 299 through 302 Processing sheet with id=AA7, first strand: chain 'A' and resid 312 through 316 removed outlier: 4.384A pdb=" N LYS A 312 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ASP A 561 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N PHE A 552 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 342 through 346 removed outlier: 4.323A pdb=" N VAL A 383 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 511 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N CYS A 349 " --> pdb=" O CYS A 512 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 342 through 346 removed outlier: 4.323A pdb=" N VAL A 383 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ASN A 382 " --> pdb=" O GLU A 503 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLU A 503 " --> pdb=" O ASN A 382 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 440 through 442 Processing sheet with id=AB2, first strand: chain 'A' and resid 641 through 642 removed outlier: 6.236A pdb=" N GLU A 641 " --> pdb=" O ALA A 677 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N THR A 679 " --> pdb=" O GLU A 641 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN A 672 " --> pdb=" O VAL A 664 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA A 659 " --> pdb=" O PRO A 652 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 684 through 686 removed outlier: 6.630A pdb=" N ALA A 684 " --> pdb=" O MET B 771 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 694 through 711 removed outlier: 6.559A pdb=" N THR A 694 " --> pdb=" O THR A1059 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR A1059 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA A 696 " --> pdb=" O ASN A1057 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASN A1057 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLU A1055 " --> pdb=" O PRO A 698 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLY A1042 " --> pdb=" O ALA A1038 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ALA A1038 " --> pdb=" O GLY A1042 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL A1044 " --> pdb=" O PRO A1036 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU A1046 " --> pdb=" O SER A1034 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER A1034 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL A1048 " --> pdb=" O LEU A1032 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 694 through 711 removed outlier: 6.559A pdb=" N THR A 694 " --> pdb=" O THR A1059 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR A1059 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA A 696 " --> pdb=" O ASN A1057 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASN A1057 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLU A1055 " --> pdb=" O PRO A 698 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR A1059 " --> pdb=" O PHE A1080 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A1061 " --> pdb=" O PHE A1078 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N PHE A1078 " --> pdb=" O ALA A1061 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 716 through 719 removed outlier: 4.450A pdb=" N LYS A 716 " --> pdb=" O LEU A 844 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 770 through 772 Processing sheet with id=AB8, first strand: chain 'A' and resid 779 through 780 Processing sheet with id=AB9, first strand: chain 'A' and resid 1103 through 1108 removed outlier: 4.085A pdb=" N ALA A1070 " --> pdb=" O SER A1106 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 32 through 35 removed outlier: 3.978A pdb=" N THR B 32 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASN B 66 " --> pdb=" O TYR B 257 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N TYR B 257 " --> pdb=" O ASN B 66 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N LEU B 195 " --> pdb=" O LYS B 222 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS B 222 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B 197 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TYR B 201 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ALA B 216 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL B 41 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 53 through 60 removed outlier: 4.083A pdb=" N ASP B 275 " --> pdb=" O LYS B 266 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 82 through 83 removed outlier: 6.353A pdb=" N PHE B 139 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL B 140 " --> pdb=" O ILE B 149 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.513A pdb=" N GLY B 101 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR B 237 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE B 99 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ASN B 130 " --> pdb=" O CYS B 160 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N CYS B 160 " --> pdb=" O ASN B 130 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N GLU B 132 " --> pdb=" O PHE B 158 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N PHE B 158 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 299 through 302 Processing sheet with id=AC6, first strand: chain 'B' and resid 312 through 316 removed outlier: 4.366A pdb=" N LYS B 312 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ASP B 561 " --> pdb=" O ILE B 574 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 342 through 346 removed outlier: 4.266A pdb=" N VAL B 383 " --> pdb=" O ILE B 346 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 511 " --> pdb=" O PHE B 380 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N CYS B 349 " --> pdb=" O CYS B 512 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 342 through 346 removed outlier: 4.266A pdb=" N VAL B 383 " --> pdb=" O ILE B 346 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ASN B 382 " --> pdb=" O GLU B 503 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLU B 503 " --> pdb=" O ASN B 382 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 440 through 442 Processing sheet with id=AD1, first strand: chain 'B' and resid 641 through 642 removed outlier: 6.174A pdb=" N GLU B 641 " --> pdb=" O ALA B 677 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N THR B 679 " --> pdb=" O GLU B 641 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLN B 672 " --> pdb=" O VAL B 664 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE B 657 " --> pdb=" O ILE B 653 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 684 through 686 removed outlier: 6.552A pdb=" N ALA B 684 " --> pdb=" O MET C 771 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 694 through 711 removed outlier: 6.737A pdb=" N THR B 694 " --> pdb=" O THR B1059 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N THR B1059 " --> pdb=" O THR B 694 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA B 696 " --> pdb=" O ASN B1057 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN B1057 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU B1055 " --> pdb=" O PRO B 698 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TYR B1050 " --> pdb=" O HIS B1031 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N HIS B1031 " --> pdb=" O TYR B1050 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 694 through 711 removed outlier: 6.737A pdb=" N THR B 694 " --> pdb=" O THR B1059 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N THR B1059 " --> pdb=" O THR B 694 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA B 696 " --> pdb=" O ASN B1057 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN B1057 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU B1055 " --> pdb=" O PRO B 698 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA B1061 " --> pdb=" O PHE B1078 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE B1078 " --> pdb=" O ALA B1061 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 716 through 719 removed outlier: 4.353A pdb=" N LYS B 716 " --> pdb=" O LEU B 844 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 779 through 780 Processing sheet with id=AD7, first strand: chain 'B' and resid 1103 through 1105 Processing sheet with id=AD8, first strand: chain 'C' and resid 32 through 35 removed outlier: 3.979A pdb=" N THR C 32 " --> pdb=" O ARG C 69 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ASN C 66 " --> pdb=" O TYR C 257 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N TYR C 257 " --> pdb=" O ASN C 66 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU C 195 " --> pdb=" O LYS C 222 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS C 222 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL C 197 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR C 201 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ALA C 216 " --> pdb=" O TYR C 201 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL C 41 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 53 through 60 removed outlier: 3.975A pdb=" N ASP C 275 " --> pdb=" O LYS C 266 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 82 through 83 removed outlier: 6.371A pdb=" N PHE C 139 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL C 140 " --> pdb=" O ILE C 149 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 82 through 83 removed outlier: 7.061A pdb=" N ASN C 231 " --> pdb=" O PHE C 104 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N PHE C 104 " --> pdb=" O ASN C 231 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ARG C 233 " --> pdb=" O TRP C 102 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N TRP C 102 " --> pdb=" O ARG C 233 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU C 235 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ASN C 130 " --> pdb=" O CYS C 160 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N CYS C 160 " --> pdb=" O ASN C 130 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N GLU C 132 " --> pdb=" O PHE C 158 " (cutoff:3.500A) removed outlier: 9.358A pdb=" N PHE C 158 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 299 through 302 Processing sheet with id=AE4, first strand: chain 'C' and resid 312 through 316 removed outlier: 4.357A pdb=" N LYS C 312 " --> pdb=" O CYS C 525 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ASP C 561 " --> pdb=" O ILE C 574 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 342 through 346 removed outlier: 4.093A pdb=" N VAL C 383 " --> pdb=" O ILE C 346 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N CYS C 349 " --> pdb=" O CYS C 512 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 342 through 346 removed outlier: 4.093A pdb=" N VAL C 383 " --> pdb=" O ILE C 346 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASN C 382 " --> pdb=" O GLU C 503 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLU C 503 " --> pdb=" O ASN C 382 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 440 through 442 Processing sheet with id=AE8, first strand: chain 'C' and resid 641 through 642 removed outlier: 6.255A pdb=" N GLU C 641 " --> pdb=" O ALA C 677 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N THR C 679 " --> pdb=" O GLU C 641 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN C 672 " --> pdb=" O VAL C 664 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE C 657 " --> pdb=" O ILE C 653 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 694 through 711 removed outlier: 6.732A pdb=" N THR C 694 " --> pdb=" O THR C1059 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N THR C1059 " --> pdb=" O THR C 694 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA C 696 " --> pdb=" O ASN C1057 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN C1057 " --> pdb=" O ALA C 696 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLU C1055 " --> pdb=" O PRO C 698 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N TYR C1050 " --> pdb=" O HIS C1031 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N HIS C1031 " --> pdb=" O TYR C1050 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 694 through 711 removed outlier: 6.732A pdb=" N THR C 694 " --> pdb=" O THR C1059 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N THR C1059 " --> pdb=" O THR C 694 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA C 696 " --> pdb=" O ASN C1057 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN C1057 " --> pdb=" O ALA C 696 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLU C1055 " --> pdb=" O PRO C 698 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR C1059 " --> pdb=" O PHE C1080 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA C1061 " --> pdb=" O PHE C1078 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE C1078 " --> pdb=" O ALA C1061 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 716 through 719 removed outlier: 4.383A pdb=" N LYS C 716 " --> pdb=" O LEU C 844 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 779 through 780 Processing sheet with id=AF4, first strand: chain 'C' and resid 1103 through 1105 1088 hydrogen bonds defined for protein. 2997 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: 12.04 Time building geometry restraints manager: 7.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8444 1.34 - 1.47: 7117 1.47 - 1.60: 11627 1.60 - 1.73: 0 1.73 - 1.85: 174 Bond restraints: 27362 Sorted by residual: bond pdb=" CA ASN A 159 " pdb=" C ASN A 159 " ideal model delta sigma weight residual 1.523 1.445 0.078 1.34e-02 5.57e+03 3.39e+01 bond pdb=" C LEU B 413 " pdb=" N PRO B 414 " ideal model delta sigma weight residual 1.330 1.368 -0.038 1.22e-02 6.72e+03 9.45e+00 bond pdb=" C ARG C 450 " pdb=" N PRO C 451 " ideal model delta sigma weight residual 1.331 1.362 -0.031 1.20e-02 6.94e+03 6.78e+00 bond pdb=" C PHE A 317 " pdb=" N PRO A 318 " ideal model delta sigma weight residual 1.330 1.361 -0.031 1.25e-02 6.40e+03 6.19e+00 bond pdb=" C1 NAG g 1 " pdb=" O5 NAG g 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.13e+00 ... (remaining 27357 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 36574 2.32 - 4.65: 595 4.65 - 6.97: 66 6.97 - 9.30: 3 9.30 - 11.62: 4 Bond angle restraints: 37242 Sorted by residual: angle pdb=" C ASN A 159 " pdb=" N CYS A 160 " pdb=" CA CYS A 160 " ideal model delta sigma weight residual 122.73 111.11 11.62 1.62e+00 3.81e-01 5.15e+01 angle pdb=" C PHE A 317 " pdb=" N PRO A 318 " pdb=" CA PRO A 318 " ideal model delta sigma weight residual 120.21 114.26 5.95 9.60e-01 1.09e+00 3.84e+01 angle pdb=" C PHE C 317 " pdb=" N PRO C 318 " pdb=" CA PRO C 318 " ideal model delta sigma weight residual 120.03 114.11 5.92 9.90e-01 1.02e+00 3.58e+01 angle pdb=" N SER A 106 " pdb=" CA SER A 106 " pdb=" C SER A 106 " ideal model delta sigma weight residual 111.36 117.74 -6.38 1.09e+00 8.42e-01 3.43e+01 angle pdb=" C ASP A1122 " pdb=" N PRO A1123 " pdb=" CA PRO A1123 " ideal model delta sigma weight residual 119.56 114.45 5.11 1.01e+00 9.80e-01 2.56e+01 ... (remaining 37237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.48: 16225 21.48 - 42.96: 1058 42.96 - 64.44: 190 64.44 - 85.92: 62 85.92 - 107.40: 28 Dihedral angle restraints: 17563 sinusoidal: 8053 harmonic: 9510 Sorted by residual: dihedral pdb=" CB CYS A 129 " pdb=" SG CYS A 129 " pdb=" SG CYS A 160 " pdb=" CB CYS A 160 " ideal model delta sinusoidal sigma weight residual 93.00 20.66 72.34 1 1.00e+01 1.00e-02 6.69e+01 dihedral pdb=" CB CYS A 721 " pdb=" SG CYS A 721 " pdb=" SG CYS A 743 " pdb=" CB CYS A 743 " ideal model delta sinusoidal sigma weight residual -86.00 -149.40 63.40 1 1.00e+01 1.00e-02 5.30e+01 dihedral pdb=" CB CYS B 604 " pdb=" SG CYS B 604 " pdb=" SG CYS B 636 " pdb=" CB CYS B 636 " ideal model delta sinusoidal sigma weight residual 93.00 135.79 -42.79 1 1.00e+01 1.00e-02 2.56e+01 ... (remaining 17560 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.195: 4403 0.195 - 0.389: 46 0.389 - 0.584: 6 0.584 - 0.778: 0 0.778 - 0.973: 2 Chirality restraints: 4457 Sorted by residual: 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 -2.68 0.28 2.00e-02 2.50e+03 1.98e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.20e+01 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 6.89e+01 ... (remaining 4454 not shown) Planarity restraints: 4785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1306 " 0.334 2.00e-02 2.50e+03 2.85e-01 1.01e+03 pdb=" C7 NAG A1306 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG A1306 " 0.176 2.00e-02 2.50e+03 pdb=" N2 NAG A1306 " -0.500 2.00e-02 2.50e+03 pdb=" O7 NAG A1306 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1308 " 0.308 2.00e-02 2.50e+03 2.65e-01 8.81e+02 pdb=" C7 NAG B1308 " -0.070 2.00e-02 2.50e+03 pdb=" C8 NAG B1308 " 0.159 2.00e-02 2.50e+03 pdb=" N2 NAG B1308 " -0.471 2.00e-02 2.50e+03 pdb=" O7 NAG B1308 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1305 " -0.300 2.00e-02 2.50e+03 2.59e-01 8.39e+02 pdb=" C7 NAG B1305 " 0.066 2.00e-02 2.50e+03 pdb=" C8 NAG B1305 " -0.004 2.00e-02 2.50e+03 pdb=" N2 NAG B1305 " 0.446 2.00e-02 2.50e+03 pdb=" O7 NAG B1305 " -0.207 2.00e-02 2.50e+03 ... (remaining 4782 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4029 2.76 - 3.30: 24133 3.30 - 3.83: 44407 3.83 - 4.37: 54764 4.37 - 4.90: 92581 Nonbonded interactions: 219914 Sorted by model distance: nonbonded pdb=" OH TYR B 42 " pdb=" O HIS B 59 " model vdw 2.226 3.040 nonbonded pdb=" OH TYR A 42 " pdb=" O HIS A 59 " model vdw 2.229 3.040 nonbonded pdb=" OH TYR C 42 " pdb=" O HIS C 59 " model vdw 2.236 3.040 nonbonded pdb=" OG SER B 371 " pdb=" OD1 ASP C 968 " model vdw 2.253 3.040 nonbonded pdb=" OD1 ASP A 968 " pdb=" OG SER C 371 " model vdw 2.257 3.040 ... (remaining 219909 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 1127 or resid 1301 through 1306)) selection = (chain 'B' and (resid 19 through 1127 or resid 1301 through 1306)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'i' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'Q' selection = chain 'S' selection = chain 'a' selection = chain 'f' selection = chain 'j' } 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: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.020 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 59.140 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 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 : 0.004 0.078 27501 Z= 0.223 Angle : 0.705 15.367 37614 Z= 0.360 Chirality : 0.059 0.973 4457 Planarity : 0.018 0.285 4731 Dihedral : 15.232 107.399 11308 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.26 % Allowed : 15.08 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3252 helix: 0.83 (0.19), residues: 675 sheet: 0.70 (0.18), residues: 765 loop : -0.58 (0.13), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 869 HIS 0.002 0.001 HIS A1031 PHE 0.017 0.001 PHE A 104 TYR 0.031 0.001 TYR C1121 ARG 0.004 0.000 ARG B 545 Details of bonding type rmsd link_NAG-ASN : bond 0.00671 ( 54) link_NAG-ASN : angle 2.96359 ( 162) link_BETA1-4 : bond 0.00393 ( 40) link_BETA1-4 : angle 1.70569 ( 120) hydrogen bonds : bond 0.18054 ( 1028) hydrogen bonds : angle 7.86190 ( 2997) SS BOND : bond 0.00288 ( 45) SS BOND : angle 1.78361 ( 90) covalent geometry : bond 0.00425 (27362) covalent geometry : angle 0.66836 (37242) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 399 time to evaluate : 2.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8217 (mmm) cc_final: 0.7680 (mmm) REVERT: A 118 MET cc_start: 0.7802 (pp-130) cc_final: 0.7461 (ptt) REVERT: A 135 ASP cc_start: 0.7088 (m-30) cc_final: 0.6494 (m-30) REVERT: A 163 GLU cc_start: 0.7678 (tp30) cc_final: 0.7477 (mp0) REVERT: A 201 TYR cc_start: 0.8017 (t80) cc_final: 0.7549 (t80) REVERT: A 307 ARG cc_start: 0.7609 (mtm180) cc_final: 0.7356 (mtm180) REVERT: A 383 VAL cc_start: 0.8751 (OUTLIER) cc_final: 0.8391 (t) REVERT: A 467 PRO cc_start: 0.7603 (Cg_exo) cc_final: 0.7302 (Cg_endo) REVERT: A 693 ASN cc_start: 0.8548 (p0) cc_final: 0.8054 (p0) REVERT: A 777 LEU cc_start: 0.7800 (pp) cc_final: 0.7478 (mm) REVERT: A 831 ASP cc_start: 0.6972 (t0) cc_final: 0.6567 (t0) REVERT: A 832 LEU cc_start: 0.8167 (mt) cc_final: 0.7779 (mp) REVERT: A 878 GLN cc_start: 0.8334 (pt0) cc_final: 0.7767 (tm130) REVERT: A 916 GLN cc_start: 0.8168 (mt0) cc_final: 0.7945 (mt0) REVERT: A 997 ARG cc_start: 0.8639 (mtt90) cc_final: 0.8302 (mtt90) REVERT: A 1026 CYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8663 (m) REVERT: A 1091 ASN cc_start: 0.8473 (m-40) cc_final: 0.8169 (m-40) REVERT: B 46 ASP cc_start: 0.8111 (m-30) cc_final: 0.7811 (m-30) REVERT: B 82 ILE cc_start: 0.8482 (mt) cc_final: 0.8234 (mt) REVERT: B 108 MET cc_start: 0.8179 (mmm) cc_final: 0.7840 (mmm) REVERT: B 135 ASP cc_start: 0.7032 (m-30) cc_final: 0.6268 (m-30) REVERT: B 181 LYS cc_start: 0.5851 (tptm) cc_final: 0.5586 (ttmt) REVERT: B 191 LYS cc_start: 0.8332 (tptm) cc_final: 0.8097 (ttpp) REVERT: B 201 TYR cc_start: 0.7808 (t80) cc_final: 0.7349 (t80) REVERT: B 307 ARG cc_start: 0.7360 (mtm180) cc_final: 0.6517 (mtp180) REVERT: B 312 LYS cc_start: 0.7150 (mttt) cc_final: 0.6890 (mttm) REVERT: B 382 ASN cc_start: 0.7903 (m-40) cc_final: 0.7605 (m-40) REVERT: B 467 PRO cc_start: 0.7642 (Cg_exo) cc_final: 0.7329 (Cg_endo) REVERT: B 569 SER cc_start: 0.7349 (m) cc_final: 0.7133 (t) REVERT: B 601 ASP cc_start: 0.7713 (m-30) cc_final: 0.7463 (m-30) REVERT: B 730 THR cc_start: 0.8489 (m) cc_final: 0.8174 (p) REVERT: B 737 LEU cc_start: 0.8050 (tt) cc_final: 0.7833 (mp) REVERT: B 777 LEU cc_start: 0.7836 (pp) cc_final: 0.7302 (mm) REVERT: B 831 ASP cc_start: 0.7108 (t0) cc_final: 0.6764 (t0) REVERT: B 832 LEU cc_start: 0.8361 (mt) cc_final: 0.8002 (mt) REVERT: B 878 GLN cc_start: 0.8177 (pt0) cc_final: 0.7499 (tm130) REVERT: B 1084 SER cc_start: 0.8052 (p) cc_final: 0.7754 (t) REVERT: B 1091 ASN cc_start: 0.8224 (m-40) cc_final: 0.7972 (m-40) REVERT: B 1119 THR cc_start: 0.8499 (OUTLIER) cc_final: 0.8246 (t) REVERT: C 135 ASP cc_start: 0.7216 (m-30) cc_final: 0.6562 (m-30) REVERT: C 201 TYR cc_start: 0.7727 (t80) cc_final: 0.7376 (t80) REVERT: C 307 ARG cc_start: 0.7618 (mtm180) cc_final: 0.6654 (mtp-110) REVERT: C 467 PRO cc_start: 0.7419 (Cg_exo) cc_final: 0.7153 (Cg_endo) REVERT: C 501 SER cc_start: 0.9154 (OUTLIER) cc_final: 0.8950 (m) REVERT: C 633 GLN cc_start: 0.7830 (mm-40) cc_final: 0.7478 (tm-30) REVERT: C 693 ASN cc_start: 0.8489 (p0) cc_final: 0.8251 (p0) REVERT: C 731 GLU cc_start: 0.7851 (mp0) cc_final: 0.7547 (mt-10) REVERT: C 747 ASN cc_start: 0.8719 (m-40) cc_final: 0.8487 (m-40) REVERT: C 777 LEU cc_start: 0.7856 (pp) cc_final: 0.7443 (mm) REVERT: C 824 LEU cc_start: 0.7522 (mp) cc_final: 0.7287 (mp) REVERT: C 831 ASP cc_start: 0.6889 (t0) cc_final: 0.6520 (t0) REVERT: C 878 GLN cc_start: 0.8190 (pt0) cc_final: 0.7939 (tm-30) REVERT: C 935 VAL cc_start: 0.8865 (OUTLIER) cc_final: 0.8662 (p) REVERT: C 985 GLN cc_start: 0.8522 (tm-30) cc_final: 0.8246 (tm-30) REVERT: C 1091 ASN cc_start: 0.8373 (m-40) cc_final: 0.8172 (m-40) outliers start: 64 outliers final: 26 residues processed: 449 average time/residue: 1.2831 time to fit residues: 675.7354 Evaluate side-chains 281 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 250 time to evaluate : 2.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 672 GLN Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 1026 CYS Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 1026 CYS Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1119 THR Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 935 VAL Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1105 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 3.9990 chunk 245 optimal weight: 0.9980 chunk 136 optimal weight: 0.4980 chunk 83 optimal weight: 5.9990 chunk 165 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 253 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 chunk 189 optimal weight: 2.9990 chunk 294 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 627 ASN A 672 GLN A 884 GLN A 938 ASN B 97 ASN B 113 GLN B 155 ASN B 348 ASN B 506 ASN B 884 GLN B 896 GLN B 916 GLN B 938 ASN C 97 ASN C 113 GLN C 155 ASN C 600 GLN C 896 GLN C 937 GLN C 938 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.131402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.099590 restraints weight = 32471.145| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.06 r_work: 0.2821 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 27501 Z= 0.187 Angle : 0.690 10.741 37614 Z= 0.343 Chirality : 0.048 0.253 4457 Planarity : 0.005 0.057 4731 Dihedral : 8.576 64.410 5507 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.49 % Allowed : 14.02 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.14), residues: 3252 helix: 1.24 (0.19), residues: 726 sheet: 0.67 (0.18), residues: 771 loop : -0.74 (0.13), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 869 HIS 0.006 0.002 HIS C1047 PHE 0.018 0.002 PHE A 630 TYR 0.029 0.002 TYR B1050 ARG 0.006 0.001 ARG B1022 Details of bonding type rmsd link_NAG-ASN : bond 0.00356 ( 54) link_NAG-ASN : angle 2.39085 ( 162) link_BETA1-4 : bond 0.00494 ( 40) link_BETA1-4 : angle 1.81565 ( 120) hydrogen bonds : bond 0.05846 ( 1028) hydrogen bonds : angle 5.91626 ( 2997) SS BOND : bond 0.00487 ( 45) SS BOND : angle 1.84037 ( 90) covalent geometry : bond 0.00427 (27362) covalent geometry : angle 0.66110 (37242) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 255 time to evaluate : 3.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8399 (mmm) cc_final: 0.7943 (mmm) REVERT: A 118 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7789 (ptt) REVERT: A 135 ASP cc_start: 0.7420 (m-30) cc_final: 0.6756 (m-30) REVERT: A 201 TYR cc_start: 0.8239 (t80) cc_final: 0.7720 (t80) REVERT: A 307 ARG cc_start: 0.7845 (mtm180) cc_final: 0.7489 (mtm180) REVERT: A 383 VAL cc_start: 0.9035 (OUTLIER) cc_final: 0.8811 (t) REVERT: A 440 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8629 (mttp) REVERT: A 467 PRO cc_start: 0.7628 (Cg_exo) cc_final: 0.7362 (Cg_endo) REVERT: A 648 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7927 (mm-30) REVERT: A 777 LEU cc_start: 0.7916 (pp) cc_final: 0.7609 (mm) REVERT: A 831 ASP cc_start: 0.7002 (t0) cc_final: 0.6695 (t0) REVERT: A 832 LEU cc_start: 0.8366 (mt) cc_final: 0.7996 (mp) REVERT: A 878 GLN cc_start: 0.8568 (pt0) cc_final: 0.8031 (tm-30) REVERT: A 884 GLN cc_start: 0.8779 (tt0) cc_final: 0.8553 (tt0) REVERT: A 973 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7885 (mt-10) REVERT: A 1091 ASN cc_start: 0.8574 (m-40) cc_final: 0.8334 (m-40) REVERT: B 46 ASP cc_start: 0.8303 (m-30) cc_final: 0.8016 (m-30) REVERT: B 127 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7551 (ttt90) REVERT: B 135 ASP cc_start: 0.7188 (m-30) cc_final: 0.6399 (m-30) REVERT: B 181 LYS cc_start: 0.5959 (tptm) cc_final: 0.5652 (ttmt) REVERT: B 201 TYR cc_start: 0.8196 (t80) cc_final: 0.7808 (t80) REVERT: B 236 LEU cc_start: 0.6445 (OUTLIER) cc_final: 0.6223 (mt) REVERT: B 307 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.6765 (mtp180) REVERT: B 345 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8539 (ttt-90) REVERT: B 467 PRO cc_start: 0.7688 (Cg_exo) cc_final: 0.7361 (Cg_endo) REVERT: B 601 ASP cc_start: 0.7906 (m-30) cc_final: 0.7414 (m-30) REVERT: B 737 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8142 (tp) REVERT: B 777 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7622 (mm) REVERT: B 831 ASP cc_start: 0.7233 (t0) cc_final: 0.6857 (t0) REVERT: B 940 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8482 (tt0) REVERT: B 966 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7564 (ttp80) REVERT: B 1091 ASN cc_start: 0.8448 (m-40) cc_final: 0.8175 (m-40) REVERT: C 135 ASP cc_start: 0.7398 (m-30) cc_final: 0.6667 (m-30) REVERT: C 201 TYR cc_start: 0.8113 (t80) cc_final: 0.7789 (t80) REVERT: C 307 ARG cc_start: 0.7823 (mtm180) cc_final: 0.6909 (mtp-110) REVERT: C 467 PRO cc_start: 0.7451 (Cg_exo) cc_final: 0.7203 (Cg_endo) REVERT: C 731 GLU cc_start: 0.8166 (mp0) cc_final: 0.7940 (mt-10) REVERT: C 737 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7848 (tt) REVERT: C 777 LEU cc_start: 0.7973 (pp) cc_final: 0.7634 (mm) REVERT: C 807 ASN cc_start: 0.8167 (m-40) cc_final: 0.7932 (m-40) REVERT: C 831 ASP cc_start: 0.7139 (t0) cc_final: 0.6874 (t0) REVERT: C 878 GLN cc_start: 0.8495 (pt0) cc_final: 0.8177 (tm-30) REVERT: C 940 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8268 (tt0) REVERT: C 1091 ASN cc_start: 0.8614 (m-40) cc_final: 0.8388 (m-40) outliers start: 99 outliers final: 47 residues processed: 328 average time/residue: 1.2022 time to fit residues: 468.8268 Evaluate side-chains 289 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 228 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 968 ASP Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain B residue 345 ARG Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 450 ARG Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 558 ASP Chi-restraints excluded: chain B residue 589 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 686 SER Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 940 GLN Chi-restraints excluded: chain B residue 966 ARG Chi-restraints excluded: chain B residue 968 ASP Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 912 LYS Chi-restraints excluded: chain C residue 940 GLN Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 968 ASP Chi-restraints excluded: chain C residue 1105 VAL Chi-restraints excluded: chain C residue 1106 SER Chi-restraints excluded: chain C residue 1119 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 43 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 227 optimal weight: 0.9980 chunk 288 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 318 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 247 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 938 ASN B 97 ASN B 506 ASN B 738 GLN B 916 GLN B 918 GLN B1102 ASN C 97 ASN C 918 GLN C 938 ASN C1102 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.129757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.098201 restraints weight = 32241.801| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.06 r_work: 0.2801 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 27501 Z= 0.227 Angle : 0.710 11.972 37614 Z= 0.361 Chirality : 0.049 0.260 4457 Planarity : 0.005 0.057 4731 Dihedral : 7.203 59.787 5491 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.83 % Favored : 97.08 % Rotamer: Outliers : 4.58 % Allowed : 12.83 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.14), residues: 3252 helix: 1.19 (0.19), residues: 732 sheet: 0.50 (0.18), residues: 792 loop : -0.83 (0.13), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP C 869 HIS 0.006 0.002 HIS A 196 PHE 0.020 0.002 PHE C 77 TYR 0.026 0.002 TYR B1050 ARG 0.006 0.001 ARG B1056 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 54) link_NAG-ASN : angle 2.38813 ( 162) link_BETA1-4 : bond 0.00524 ( 40) link_BETA1-4 : angle 1.85312 ( 120) hydrogen bonds : bond 0.06480 ( 1028) hydrogen bonds : angle 5.94752 ( 2997) SS BOND : bond 0.00493 ( 45) SS BOND : angle 2.46818 ( 90) covalent geometry : bond 0.00531 (27362) covalent geometry : angle 0.67758 (37242) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 225 time to evaluate : 3.036 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 25 ASP cc_start: 0.5942 (OUTLIER) cc_final: 0.5391 (p0) REVERT: A 119 ASN cc_start: 0.8439 (OUTLIER) cc_final: 0.8225 (t0) REVERT: A 201 TYR cc_start: 0.8190 (t80) cc_final: 0.7761 (t80) REVERT: A 307 ARG cc_start: 0.7861 (mtm180) cc_final: 0.6687 (mtp180) REVERT: A 440 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8668 (mttp) REVERT: A 648 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7920 (mm-30) REVERT: A 777 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7624 (mm) REVERT: A 794 LYS cc_start: 0.6487 (ttmt) cc_final: 0.6146 (ptmt) REVERT: A 831 ASP cc_start: 0.7059 (t0) cc_final: 0.6713 (t0) REVERT: A 832 LEU cc_start: 0.8283 (mt) cc_final: 0.7895 (mp) REVERT: A 973 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8015 (mt-10) REVERT: A 1091 ASN cc_start: 0.8709 (m-40) cc_final: 0.8334 (m-40) REVERT: B 25 ASP cc_start: 0.5707 (OUTLIER) cc_final: 0.5403 (p0) REVERT: B 46 ASP cc_start: 0.8337 (m-30) cc_final: 0.7999 (m-30) REVERT: B 127 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7691 (ttt90) REVERT: B 135 ASP cc_start: 0.7125 (m-30) cc_final: 0.6314 (m-30) REVERT: B 181 LYS cc_start: 0.5990 (OUTLIER) cc_final: 0.5477 (ttpt) REVERT: B 201 TYR cc_start: 0.8093 (t80) cc_final: 0.7767 (t80) REVERT: B 236 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.6175 (mt) REVERT: B 307 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.6790 (mtp180) REVERT: B 382 ASN cc_start: 0.7962 (m-40) cc_final: 0.7704 (t0) REVERT: B 467 PRO cc_start: 0.7548 (Cg_exo) cc_final: 0.7244 (Cg_endo) REVERT: B 594 GLU cc_start: 0.7500 (tp30) cc_final: 0.7202 (tp30) REVERT: B 737 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8095 (tt) REVERT: B 777 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7644 (mm) REVERT: B 831 ASP cc_start: 0.7297 (t0) cc_final: 0.6864 (t0) REVERT: B 926 THR cc_start: 0.7616 (OUTLIER) cc_final: 0.7217 (t) REVERT: B 940 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8437 (tt0) REVERT: B 966 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7668 (ttp80) REVERT: B 997 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8495 (mtt-85) REVERT: C 201 TYR cc_start: 0.8198 (t80) cc_final: 0.7786 (t80) REVERT: C 307 ARG cc_start: 0.7710 (mtm180) cc_final: 0.6834 (mtp180) REVERT: C 633 GLN cc_start: 0.8290 (mm-40) cc_final: 0.8057 (mm-40) REVERT: C 702 SER cc_start: 0.9209 (OUTLIER) cc_final: 0.8973 (t) REVERT: C 731 GLU cc_start: 0.8167 (mp0) cc_final: 0.7865 (mt-10) REVERT: C 737 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7983 (tt) REVERT: C 777 LEU cc_start: 0.8111 (pp) cc_final: 0.7842 (pt) REVERT: C 807 ASN cc_start: 0.8228 (m-40) cc_final: 0.7981 (m-40) REVERT: C 831 ASP cc_start: 0.7099 (t0) cc_final: 0.6724 (t0) REVERT: C 940 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8330 (tt0) REVERT: C 1033 MET cc_start: 0.9313 (ptm) cc_final: 0.9094 (ptm) outliers start: 130 outliers final: 67 residues processed: 328 average time/residue: 1.1978 time to fit residues: 468.4210 Evaluate side-chains 294 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 208 time to evaluate : 2.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 450 ARG Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 558 ASP Chi-restraints excluded: chain B residue 589 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 686 SER Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 819 GLN Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 940 GLN Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 966 ARG Chi-restraints excluded: chain B residue 997 ARG Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 702 SER Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain C residue 940 GLN Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 968 ASP Chi-restraints excluded: chain C residue 1105 VAL Chi-restraints excluded: chain C residue 1106 SER Chi-restraints excluded: chain C residue 1119 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 244 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 295 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 258 optimal weight: 5.9990 chunk 164 optimal weight: 0.7980 chunk 163 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 190 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 916 GLN B1102 ASN C 97 ASN C 938 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.131611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.099902 restraints weight = 32514.464| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.08 r_work: 0.2827 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 27501 Z= 0.129 Angle : 0.599 12.603 37614 Z= 0.303 Chirality : 0.044 0.255 4457 Planarity : 0.004 0.053 4731 Dihedral : 6.367 59.797 5491 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.55 % Favored : 97.36 % Rotamer: Outliers : 3.28 % Allowed : 14.16 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.14), residues: 3252 helix: 1.43 (0.19), residues: 732 sheet: 0.57 (0.17), residues: 771 loop : -0.79 (0.13), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 424 HIS 0.002 0.001 HIS B 196 PHE 0.016 0.001 PHE C 630 TYR 0.023 0.001 TYR B1050 ARG 0.003 0.000 ARG C 127 Details of bonding type rmsd link_NAG-ASN : bond 0.00198 ( 54) link_NAG-ASN : angle 2.19127 ( 162) link_BETA1-4 : bond 0.00414 ( 40) link_BETA1-4 : angle 1.63509 ( 120) hydrogen bonds : bond 0.05117 ( 1028) hydrogen bonds : angle 5.62355 ( 2997) SS BOND : bond 0.00338 ( 45) SS BOND : angle 2.13493 ( 90) covalent geometry : bond 0.00290 (27362) covalent geometry : angle 0.56731 (37242) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 225 time to evaluate : 2.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.7368 (OUTLIER) cc_final: 0.7017 (mm) REVERT: A 201 TYR cc_start: 0.8209 (t80) cc_final: 0.7938 (t80) REVERT: A 307 ARG cc_start: 0.7844 (mtm180) cc_final: 0.7614 (mtm-85) REVERT: A 313 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7322 (mm-30) REVERT: A 648 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7880 (mm-30) REVERT: A 777 LEU cc_start: 0.8017 (pp) cc_final: 0.7686 (mm) REVERT: A 831 ASP cc_start: 0.7021 (t0) cc_final: 0.6709 (t0) REVERT: A 832 LEU cc_start: 0.8320 (mt) cc_final: 0.7951 (mp) REVERT: A 866 THR cc_start: 0.8996 (m) cc_final: 0.8754 (p) REVERT: A 878 GLN cc_start: 0.8523 (pt0) cc_final: 0.7972 (tm-30) REVERT: A 973 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7916 (mt-10) REVERT: A 1033 MET cc_start: 0.9479 (ptm) cc_final: 0.9258 (ptp) REVERT: A 1091 ASN cc_start: 0.8714 (m-40) cc_final: 0.8412 (m-40) REVERT: B 46 ASP cc_start: 0.8340 (m-30) cc_final: 0.8005 (m-30) REVERT: B 55 LEU cc_start: 0.8797 (tp) cc_final: 0.8503 (mt) REVERT: B 135 ASP cc_start: 0.7133 (m-30) cc_final: 0.6361 (m-30) REVERT: B 181 LYS cc_start: 0.5999 (tptm) cc_final: 0.5590 (ttpt) REVERT: B 201 TYR cc_start: 0.8089 (t80) cc_final: 0.7790 (t80) REVERT: B 307 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.6765 (mtp180) REVERT: B 467 PRO cc_start: 0.7675 (Cg_exo) cc_final: 0.7408 (Cg_endo) REVERT: B 702 SER cc_start: 0.9291 (OUTLIER) cc_final: 0.8938 (p) REVERT: B 737 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8200 (tp) REVERT: B 777 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7722 (mm) REVERT: B 831 ASP cc_start: 0.7258 (t0) cc_final: 0.6884 (t0) REVERT: B 926 THR cc_start: 0.7658 (OUTLIER) cc_final: 0.7311 (t) REVERT: B 940 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8493 (tt0) REVERT: B 966 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7541 (ttp80) REVERT: C 201 TYR cc_start: 0.8177 (t80) cc_final: 0.7769 (t80) REVERT: C 307 ARG cc_start: 0.7699 (mtm180) cc_final: 0.6794 (mtp-110) REVERT: C 633 GLN cc_start: 0.8314 (mm-40) cc_final: 0.8054 (mm-40) REVERT: C 731 GLU cc_start: 0.8141 (mp0) cc_final: 0.7913 (mt-10) REVERT: C 777 LEU cc_start: 0.8117 (pp) cc_final: 0.7856 (pt) REVERT: C 807 ASN cc_start: 0.8164 (m-40) cc_final: 0.7917 (m-40) REVERT: C 831 ASP cc_start: 0.6945 (t0) cc_final: 0.6571 (t0) REVERT: C 940 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8338 (tt0) outliers start: 93 outliers final: 47 residues processed: 298 average time/residue: 1.2671 time to fit residues: 446.9168 Evaluate side-chains 274 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 216 time to evaluate : 2.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 968 ASP Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 558 ASP Chi-restraints excluded: chain B residue 589 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 819 GLN Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 940 GLN Chi-restraints excluded: chain B residue 966 ARG Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain C residue 940 GLN Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 968 ASP Chi-restraints excluded: chain C residue 1026 CYS Chi-restraints excluded: chain C residue 1105 VAL Chi-restraints excluded: chain C residue 1106 SER Chi-restraints excluded: chain C residue 1119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 274 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 143 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 192 optimal weight: 0.6980 chunk 157 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 167 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 916 GLN B 988 GLN C 97 ASN C 938 ASN C1091 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.131869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.100311 restraints weight = 32425.678| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.06 r_work: 0.2845 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 27501 Z= 0.137 Angle : 0.590 13.586 37614 Z= 0.299 Chirality : 0.044 0.256 4457 Planarity : 0.004 0.051 4731 Dihedral : 5.975 59.675 5487 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.68 % Favored : 97.23 % Rotamer: Outliers : 3.45 % Allowed : 14.27 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.14), residues: 3252 helix: 1.54 (0.19), residues: 732 sheet: 0.58 (0.18), residues: 765 loop : -0.77 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 424 HIS 0.003 0.001 HIS B1047 PHE 0.013 0.001 PHE A 630 TYR 0.023 0.001 TYR B1050 ARG 0.003 0.000 ARG C 127 Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 54) link_NAG-ASN : angle 2.26663 ( 162) link_BETA1-4 : bond 0.00433 ( 40) link_BETA1-4 : angle 1.49800 ( 120) hydrogen bonds : bond 0.05027 ( 1028) hydrogen bonds : angle 5.51104 ( 2997) SS BOND : bond 0.00332 ( 45) SS BOND : angle 2.09503 ( 90) covalent geometry : bond 0.00312 (27362) covalent geometry : angle 0.55791 (37242) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 217 time to evaluate : 2.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.7341 (OUTLIER) cc_final: 0.7001 (mm) REVERT: A 201 TYR cc_start: 0.8209 (t80) cc_final: 0.7939 (t80) REVERT: A 307 ARG cc_start: 0.7857 (mtm180) cc_final: 0.7642 (mtm-85) REVERT: A 313 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7318 (mm-30) REVERT: A 476 TYR cc_start: 0.8637 (OUTLIER) cc_final: 0.8112 (m-80) REVERT: A 777 LEU cc_start: 0.8021 (pp) cc_final: 0.7684 (mm) REVERT: A 794 LYS cc_start: 0.6298 (ttmt) cc_final: 0.5907 (ptmt) REVERT: A 831 ASP cc_start: 0.7005 (t0) cc_final: 0.6727 (t0) REVERT: A 832 LEU cc_start: 0.8301 (mt) cc_final: 0.7961 (mp) REVERT: A 878 GLN cc_start: 0.8485 (pt0) cc_final: 0.7944 (tm-30) REVERT: A 971 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8039 (tm-30) REVERT: A 973 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7921 (mt-10) REVERT: A 1033 MET cc_start: 0.9451 (ptm) cc_final: 0.9230 (ptp) REVERT: A 1091 ASN cc_start: 0.8684 (m-40) cc_final: 0.8368 (m-40) REVERT: B 46 ASP cc_start: 0.8326 (m-30) cc_final: 0.8059 (m-30) REVERT: B 55 LEU cc_start: 0.8819 (tp) cc_final: 0.8540 (mt) REVERT: B 135 ASP cc_start: 0.7191 (m-30) cc_final: 0.6438 (m-30) REVERT: B 181 LYS cc_start: 0.6073 (tptm) cc_final: 0.5578 (ttpp) REVERT: B 201 TYR cc_start: 0.8087 (t80) cc_final: 0.7813 (t80) REVERT: B 307 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7251 (mtm-85) REVERT: B 467 PRO cc_start: 0.7594 (Cg_exo) cc_final: 0.7307 (Cg_endo) REVERT: B 476 TYR cc_start: 0.8676 (OUTLIER) cc_final: 0.8093 (m-80) REVERT: B 702 SER cc_start: 0.9249 (OUTLIER) cc_final: 0.8915 (p) REVERT: B 737 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8197 (tp) REVERT: B 777 LEU cc_start: 0.8111 (pp) cc_final: 0.7719 (mm) REVERT: B 831 ASP cc_start: 0.7240 (t0) cc_final: 0.6869 (t0) REVERT: B 926 THR cc_start: 0.7763 (OUTLIER) cc_final: 0.7410 (t) REVERT: B 940 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8504 (tt0) REVERT: C 201 TYR cc_start: 0.8072 (t80) cc_final: 0.7700 (t80) REVERT: C 307 ARG cc_start: 0.7694 (mtm180) cc_final: 0.6820 (mtp-110) REVERT: C 633 GLN cc_start: 0.8356 (mm-40) cc_final: 0.8113 (mm-40) REVERT: C 663 THR cc_start: 0.7737 (OUTLIER) cc_final: 0.7428 (p) REVERT: C 731 GLU cc_start: 0.8137 (mp0) cc_final: 0.7879 (mt-10) REVERT: C 737 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7909 (tt) REVERT: C 777 LEU cc_start: 0.8131 (pp) cc_final: 0.7881 (pt) REVERT: C 794 LYS cc_start: 0.6300 (ttpp) cc_final: 0.5896 (ptmt) REVERT: C 807 ASN cc_start: 0.8153 (m-40) cc_final: 0.7912 (m-40) REVERT: C 831 ASP cc_start: 0.6923 (t0) cc_final: 0.6533 (t0) REVERT: C 940 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8319 (tt0) outliers start: 98 outliers final: 59 residues processed: 294 average time/residue: 1.1688 time to fit residues: 407.9987 Evaluate side-chains 285 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 213 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 476 TYR Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 968 ASP Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 476 TYR Chi-restraints excluded: chain B residue 558 ASP Chi-restraints excluded: chain B residue 589 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 940 GLN Chi-restraints excluded: chain B residue 966 ARG Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1106 SER Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain C residue 940 GLN Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 968 ASP Chi-restraints excluded: chain C residue 1026 CYS Chi-restraints excluded: chain C residue 1105 VAL Chi-restraints excluded: chain C residue 1106 SER Chi-restraints excluded: chain C residue 1112 VAL Chi-restraints excluded: chain C residue 1119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 167 optimal weight: 8.9990 chunk 165 optimal weight: 10.0000 chunk 285 optimal weight: 6.9990 chunk 222 optimal weight: 2.9990 chunk 246 optimal weight: 0.0470 chunk 16 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 320 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 overall best weight: 1.7084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN A 938 ASN B 425 ASN B 916 GLN C 97 ASN C 884 GLN C 938 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.130909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.100384 restraints weight = 32322.143| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.99 r_work: 0.2836 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 27501 Z= 0.167 Angle : 0.618 14.806 37614 Z= 0.315 Chirality : 0.045 0.264 4457 Planarity : 0.005 0.051 4731 Dihedral : 6.136 59.349 5487 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.92 % Favored : 96.99 % Rotamer: Outliers : 3.95 % Allowed : 14.09 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3252 helix: 1.47 (0.19), residues: 732 sheet: 0.48 (0.17), residues: 771 loop : -0.79 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 424 HIS 0.003 0.001 HIS B1047 PHE 0.016 0.002 PHE C 630 TYR 0.023 0.001 TYR B1050 ARG 0.003 0.000 ARG B1022 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 54) link_NAG-ASN : angle 2.23728 ( 162) link_BETA1-4 : bond 0.00439 ( 40) link_BETA1-4 : angle 1.49544 ( 120) hydrogen bonds : bond 0.05466 ( 1028) hydrogen bonds : angle 5.60115 ( 2997) SS BOND : bond 0.00447 ( 45) SS BOND : angle 2.26035 ( 90) covalent geometry : bond 0.00388 (27362) covalent geometry : angle 0.58707 (37242) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 216 time to evaluate : 3.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.7377 (OUTLIER) cc_final: 0.6990 (mm) REVERT: A 201 TYR cc_start: 0.8154 (t80) cc_final: 0.7775 (t80) REVERT: A 307 ARG cc_start: 0.7875 (mtm180) cc_final: 0.6727 (mtp180) REVERT: A 313 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7321 (mm-30) REVERT: A 648 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7843 (mm-30) REVERT: A 777 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7678 (mm) REVERT: A 831 ASP cc_start: 0.7007 (t0) cc_final: 0.6727 (t0) REVERT: A 832 LEU cc_start: 0.8294 (mt) cc_final: 0.7967 (mp) REVERT: A 973 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: A 1033 MET cc_start: 0.9448 (ptm) cc_final: 0.9218 (ptp) REVERT: A 1091 ASN cc_start: 0.8685 (m-40) cc_final: 0.8330 (m-40) REVERT: B 46 ASP cc_start: 0.8331 (m-30) cc_final: 0.7982 (m-30) REVERT: B 55 LEU cc_start: 0.8849 (tp) cc_final: 0.8513 (mt) REVERT: B 181 LYS cc_start: 0.6047 (OUTLIER) cc_final: 0.5580 (ttpp) REVERT: B 201 TYR cc_start: 0.8056 (t80) cc_final: 0.7720 (t80) REVERT: B 307 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.6884 (mtp180) REVERT: B 467 PRO cc_start: 0.7582 (Cg_exo) cc_final: 0.7306 (Cg_endo) REVERT: B 476 TYR cc_start: 0.8640 (OUTLIER) cc_final: 0.8077 (m-80) REVERT: B 702 SER cc_start: 0.9263 (OUTLIER) cc_final: 0.8908 (p) REVERT: B 737 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8129 (tt) REVERT: B 777 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7712 (mm) REVERT: B 831 ASP cc_start: 0.7253 (t0) cc_final: 0.6874 (t0) REVERT: B 926 THR cc_start: 0.7830 (OUTLIER) cc_final: 0.7531 (t) REVERT: B 940 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8468 (tt0) REVERT: B 966 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7504 (ttp80) REVERT: C 99 ILE cc_start: 0.7318 (OUTLIER) cc_final: 0.7104 (mm) REVERT: C 201 TYR cc_start: 0.8070 (t80) cc_final: 0.7702 (t80) REVERT: C 307 ARG cc_start: 0.7687 (mtm180) cc_final: 0.6823 (mtp-110) REVERT: C 633 GLN cc_start: 0.8380 (mm-40) cc_final: 0.8125 (mm-40) REVERT: C 731 GLU cc_start: 0.8127 (mp0) cc_final: 0.7870 (mt-10) REVERT: C 737 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7951 (tt) REVERT: C 777 LEU cc_start: 0.8134 (pp) cc_final: 0.7891 (pt) REVERT: C 794 LYS cc_start: 0.6443 (ttpp) cc_final: 0.6039 (ptmt) REVERT: C 807 ASN cc_start: 0.8171 (m-40) cc_final: 0.7921 (m-40) REVERT: C 831 ASP cc_start: 0.6916 (t0) cc_final: 0.6533 (t0) REVERT: C 940 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8319 (tt0) outliers start: 112 outliers final: 71 residues processed: 303 average time/residue: 1.1741 time to fit residues: 425.4436 Evaluate side-chains 293 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 206 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 968 ASP Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 476 TYR Chi-restraints excluded: chain B residue 519 ASP Chi-restraints excluded: chain B residue 558 ASP Chi-restraints excluded: chain B residue 589 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 935 VAL Chi-restraints excluded: chain B residue 940 GLN Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 966 ARG Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1106 SER Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 723 MET Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain C residue 940 GLN Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 968 ASP Chi-restraints excluded: chain C residue 1026 CYS Chi-restraints excluded: chain C residue 1105 VAL Chi-restraints excluded: chain C residue 1106 SER Chi-restraints excluded: chain C residue 1119 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 313 optimal weight: 3.9990 chunk 203 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 224 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 285 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 302 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 819 GLN A 938 ASN B 916 GLN B1102 ASN ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.130042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.098614 restraints weight = 32257.718| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.07 r_work: 0.2813 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 27501 Z= 0.206 Angle : 0.667 15.428 37614 Z= 0.340 Chirality : 0.047 0.271 4457 Planarity : 0.005 0.052 4731 Dihedral : 6.420 59.799 5487 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.29 % Favored : 96.62 % Rotamer: Outliers : 4.02 % Allowed : 14.13 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.14), residues: 3252 helix: 1.37 (0.19), residues: 732 sheet: 0.44 (0.17), residues: 768 loop : -0.84 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 424 HIS 0.005 0.001 HIS B1047 PHE 0.014 0.002 PHE A 630 TYR 0.024 0.002 TYR B1050 ARG 0.005 0.001 ARG B1022 Details of bonding type rmsd link_NAG-ASN : bond 0.00420 ( 54) link_NAG-ASN : angle 2.45991 ( 162) link_BETA1-4 : bond 0.00461 ( 40) link_BETA1-4 : angle 1.54373 ( 120) hydrogen bonds : bond 0.05881 ( 1028) hydrogen bonds : angle 5.70865 ( 2997) SS BOND : bond 0.00502 ( 45) SS BOND : angle 2.48390 ( 90) covalent geometry : bond 0.00484 (27362) covalent geometry : angle 0.63248 (37242) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 213 time to evaluate : 2.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.7368 (OUTLIER) cc_final: 0.6934 (mm) REVERT: A 201 TYR cc_start: 0.8163 (t80) cc_final: 0.7766 (t80) REVERT: A 307 ARG cc_start: 0.7882 (mtm180) cc_final: 0.6744 (mtp180) REVERT: A 313 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7342 (mm-30) REVERT: A 440 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8567 (mttp) REVERT: A 648 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7801 (mm-30) REVERT: A 777 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7673 (mm) REVERT: A 794 LYS cc_start: 0.6452 (ttmt) cc_final: 0.6179 (ptpt) REVERT: A 831 ASP cc_start: 0.7022 (t0) cc_final: 0.6818 (t0) REVERT: A 832 LEU cc_start: 0.8263 (mt) cc_final: 0.7934 (mp) REVERT: A 973 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7908 (mt-10) REVERT: A 1033 MET cc_start: 0.9448 (ptm) cc_final: 0.9223 (ptp) REVERT: B 181 LYS cc_start: 0.6102 (tptm) cc_final: 0.5593 (ttpp) REVERT: B 201 TYR cc_start: 0.8067 (t80) cc_final: 0.7735 (t80) REVERT: B 307 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.6854 (mtp180) REVERT: B 467 PRO cc_start: 0.7515 (Cg_exo) cc_final: 0.7240 (Cg_endo) REVERT: B 476 TYR cc_start: 0.8652 (OUTLIER) cc_final: 0.8093 (m-80) REVERT: B 702 SER cc_start: 0.9306 (OUTLIER) cc_final: 0.8941 (p) REVERT: B 737 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8104 (tt) REVERT: B 777 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7753 (mm) REVERT: B 831 ASP cc_start: 0.7352 (t0) cc_final: 0.7078 (t0) REVERT: B 926 THR cc_start: 0.7955 (OUTLIER) cc_final: 0.7692 (t) REVERT: B 940 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8460 (tt0) REVERT: B 966 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7494 (ttp80) REVERT: C 135 ASP cc_start: 0.6939 (m-30) cc_final: 0.6112 (m-30) REVERT: C 163 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7718 (mp0) REVERT: C 201 TYR cc_start: 0.8078 (t80) cc_final: 0.7720 (t80) REVERT: C 307 ARG cc_start: 0.7712 (mtm180) cc_final: 0.6855 (mtp-110) REVERT: C 633 GLN cc_start: 0.8374 (mm-40) cc_final: 0.8134 (mm-40) REVERT: C 663 THR cc_start: 0.7673 (OUTLIER) cc_final: 0.7404 (p) REVERT: C 731 GLU cc_start: 0.8136 (mp0) cc_final: 0.7880 (mt-10) REVERT: C 737 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7970 (tt) REVERT: C 777 LEU cc_start: 0.8152 (pp) cc_final: 0.7915 (pt) REVERT: C 794 LYS cc_start: 0.6461 (ttpp) cc_final: 0.6052 (ptmt) REVERT: C 807 ASN cc_start: 0.8187 (m-40) cc_final: 0.7939 (m-40) REVERT: C 831 ASP cc_start: 0.6931 (t0) cc_final: 0.6535 (t0) REVERT: C 940 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8330 (tt0) outliers start: 114 outliers final: 77 residues processed: 304 average time/residue: 1.1783 time to fit residues: 426.1888 Evaluate side-chains 301 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 207 time to evaluate : 3.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 476 TYR Chi-restraints excluded: chain B residue 519 ASP Chi-restraints excluded: chain B residue 558 ASP Chi-restraints excluded: chain B residue 589 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 777 LEU Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 819 GLN Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 940 GLN Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 966 ARG Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1106 SER Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 702 SER Chi-restraints excluded: chain C residue 723 MET Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain C residue 940 GLN Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 968 ASP Chi-restraints excluded: chain C residue 1026 CYS Chi-restraints excluded: chain C residue 1105 VAL Chi-restraints excluded: chain C residue 1106 SER Chi-restraints excluded: chain C residue 1119 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 251 optimal weight: 4.9990 chunk 70 optimal weight: 0.4980 chunk 220 optimal weight: 1.9990 chunk 277 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 288 optimal weight: 3.9990 chunk 164 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 261 optimal weight: 0.3980 chunk 158 optimal weight: 4.9990 chunk 290 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 938 ASN A1091 ASN B 113 GLN B 890 ASN B 916 GLN C 97 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.132123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.100627 restraints weight = 32457.223| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.07 r_work: 0.2843 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 27501 Z= 0.121 Angle : 0.576 12.543 37614 Z= 0.293 Chirality : 0.043 0.260 4457 Planarity : 0.004 0.050 4731 Dihedral : 5.979 59.623 5487 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.58 % Favored : 97.32 % Rotamer: Outliers : 3.38 % Allowed : 15.19 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.14), residues: 3252 helix: 1.73 (0.19), residues: 711 sheet: 0.46 (0.18), residues: 756 loop : -0.70 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 424 HIS 0.002 0.001 HIS C1031 PHE 0.015 0.001 PHE C 630 TYR 0.022 0.001 TYR B1050 ARG 0.003 0.000 ARG B 966 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 54) link_NAG-ASN : angle 2.15229 ( 162) link_BETA1-4 : bond 0.00423 ( 40) link_BETA1-4 : angle 1.40177 ( 120) hydrogen bonds : bond 0.04790 ( 1028) hydrogen bonds : angle 5.46206 ( 2997) SS BOND : bond 0.00349 ( 45) SS BOND : angle 1.92401 ( 90) covalent geometry : bond 0.00272 (27362) covalent geometry : angle 0.54770 (37242) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 217 time to evaluate : 2.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 TYR cc_start: 0.8156 (t80) cc_final: 0.7770 (t80) REVERT: A 307 ARG cc_start: 0.7889 (mtm180) cc_final: 0.7605 (mtm180) REVERT: A 474 ASN cc_start: 0.7483 (OUTLIER) cc_final: 0.6762 (t0) REVERT: A 777 LEU cc_start: 0.8019 (pp) cc_final: 0.7679 (mm) REVERT: A 831 ASP cc_start: 0.6995 (t0) cc_final: 0.6734 (t0) REVERT: A 832 LEU cc_start: 0.8281 (mt) cc_final: 0.7934 (mp) REVERT: A 878 GLN cc_start: 0.8523 (pt0) cc_final: 0.7968 (tm-30) REVERT: A 973 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: A 1033 MET cc_start: 0.9443 (ptm) cc_final: 0.9230 (ptp) REVERT: B 55 LEU cc_start: 0.8753 (tp) cc_final: 0.8516 (mt) REVERT: B 181 LYS cc_start: 0.6115 (tptm) cc_final: 0.5627 (ttpp) REVERT: B 201 TYR cc_start: 0.8063 (t80) cc_final: 0.7797 (t80) REVERT: B 307 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.6876 (mtp180) REVERT: B 467 PRO cc_start: 0.7471 (Cg_exo) cc_final: 0.7195 (Cg_endo) REVERT: B 476 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.8045 (m-80) REVERT: B 702 SER cc_start: 0.9216 (OUTLIER) cc_final: 0.8867 (t) REVERT: B 737 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8179 (tp) REVERT: B 777 LEU cc_start: 0.8158 (pp) cc_final: 0.7757 (mm) REVERT: B 831 ASP cc_start: 0.7277 (t0) cc_final: 0.6805 (t0) REVERT: B 926 THR cc_start: 0.7986 (OUTLIER) cc_final: 0.7710 (t) REVERT: B 940 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8487 (tt0) REVERT: B 966 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7614 (ttp80) REVERT: C 135 ASP cc_start: 0.6911 (m-30) cc_final: 0.6128 (m-30) REVERT: C 201 TYR cc_start: 0.8061 (t80) cc_final: 0.7704 (t80) REVERT: C 307 ARG cc_start: 0.7753 (mtm180) cc_final: 0.6849 (mtp-110) REVERT: C 633 GLN cc_start: 0.8326 (mm-40) cc_final: 0.8087 (mm-40) REVERT: C 663 THR cc_start: 0.7733 (OUTLIER) cc_final: 0.7469 (p) REVERT: C 731 GLU cc_start: 0.8139 (mp0) cc_final: 0.7912 (mt-10) REVERT: C 777 LEU cc_start: 0.8151 (pp) cc_final: 0.7906 (pt) REVERT: C 807 ASN cc_start: 0.8174 (m-40) cc_final: 0.7934 (m-40) REVERT: C 831 ASP cc_start: 0.6882 (t0) cc_final: 0.6469 (t0) REVERT: C 940 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8329 (tt0) REVERT: C 1002 ARG cc_start: 0.8676 (tpt170) cc_final: 0.7918 (ttm110) outliers start: 96 outliers final: 63 residues processed: 289 average time/residue: 1.1580 time to fit residues: 398.9001 Evaluate side-chains 285 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 211 time to evaluate : 2.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 476 TYR Chi-restraints excluded: chain B residue 519 ASP Chi-restraints excluded: chain B residue 558 ASP Chi-restraints excluded: chain B residue 589 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 940 GLN Chi-restraints excluded: chain B residue 966 ARG Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1106 SER Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 702 SER Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain C residue 940 GLN Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 968 ASP Chi-restraints excluded: chain C residue 1026 CYS Chi-restraints excluded: chain C residue 1105 VAL Chi-restraints excluded: chain C residue 1106 SER Chi-restraints excluded: chain C residue 1119 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 69 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 255 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 246 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 307 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 382 ASN A 938 ASN B 916 GLN B1102 ASN C 97 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.131702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.100054 restraints weight = 32487.225| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.11 r_work: 0.2829 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 27501 Z= 0.139 Angle : 0.587 12.108 37614 Z= 0.299 Chirality : 0.044 0.267 4457 Planarity : 0.004 0.050 4731 Dihedral : 5.950 59.617 5487 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.08 % Favored : 96.83 % Rotamer: Outliers : 3.31 % Allowed : 15.29 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.14), residues: 3252 helix: 1.73 (0.19), residues: 711 sheet: 0.49 (0.18), residues: 753 loop : -0.70 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 424 HIS 0.003 0.001 HIS B1047 PHE 0.013 0.001 PHE A 630 TYR 0.022 0.001 TYR B1050 ARG 0.003 0.000 ARG C 127 Details of bonding type rmsd link_NAG-ASN : bond 0.00316 ( 54) link_NAG-ASN : angle 2.17295 ( 162) link_BETA1-4 : bond 0.00427 ( 40) link_BETA1-4 : angle 1.42285 ( 120) hydrogen bonds : bond 0.05011 ( 1028) hydrogen bonds : angle 5.46847 ( 2997) SS BOND : bond 0.00385 ( 45) SS BOND : angle 1.89816 ( 90) covalent geometry : bond 0.00317 (27362) covalent geometry : angle 0.55922 (37242) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 209 time to evaluate : 2.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 TYR cc_start: 0.8157 (t80) cc_final: 0.7775 (t80) REVERT: A 307 ARG cc_start: 0.7896 (mtm180) cc_final: 0.7621 (mtm180) REVERT: A 474 ASN cc_start: 0.7524 (OUTLIER) cc_final: 0.6817 (t0) REVERT: A 777 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7677 (mm) REVERT: A 794 LYS cc_start: 0.6279 (ttmt) cc_final: 0.5899 (ptpt) REVERT: A 831 ASP cc_start: 0.7006 (t0) cc_final: 0.6738 (t0) REVERT: A 832 LEU cc_start: 0.8288 (mt) cc_final: 0.7948 (mp) REVERT: A 973 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: A 1033 MET cc_start: 0.9437 (ptm) cc_final: 0.9232 (ptp) REVERT: B 55 LEU cc_start: 0.8772 (tp) cc_final: 0.8506 (mt) REVERT: B 181 LYS cc_start: 0.6168 (tptm) cc_final: 0.5656 (ttpp) REVERT: B 201 TYR cc_start: 0.8078 (t80) cc_final: 0.7821 (t80) REVERT: B 307 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.6884 (mtp180) REVERT: B 467 PRO cc_start: 0.7460 (Cg_exo) cc_final: 0.7190 (Cg_endo) REVERT: B 476 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: B 702 SER cc_start: 0.9231 (OUTLIER) cc_final: 0.8903 (p) REVERT: B 737 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8217 (tp) REVERT: B 777 LEU cc_start: 0.8169 (pp) cc_final: 0.7765 (mm) REVERT: B 831 ASP cc_start: 0.7345 (t0) cc_final: 0.7044 (t0) REVERT: B 926 THR cc_start: 0.7983 (OUTLIER) cc_final: 0.7721 (t) REVERT: B 940 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8485 (tt0) REVERT: B 966 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7645 (ttp80) REVERT: C 135 ASP cc_start: 0.6903 (m-30) cc_final: 0.6132 (m-30) REVERT: C 163 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7685 (mp0) REVERT: C 201 TYR cc_start: 0.8069 (t80) cc_final: 0.7718 (t80) REVERT: C 307 ARG cc_start: 0.7764 (mtm180) cc_final: 0.6858 (mtp-110) REVERT: C 633 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8108 (mm-40) REVERT: C 663 THR cc_start: 0.7692 (OUTLIER) cc_final: 0.7427 (p) REVERT: C 731 GLU cc_start: 0.8132 (mp0) cc_final: 0.7889 (mt-10) REVERT: C 777 LEU cc_start: 0.8167 (pp) cc_final: 0.7931 (pt) REVERT: C 807 ASN cc_start: 0.8188 (m-40) cc_final: 0.7949 (m-40) REVERT: C 831 ASP cc_start: 0.6904 (t0) cc_final: 0.6479 (t0) REVERT: C 940 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8342 (tt0) REVERT: C 1002 ARG cc_start: 0.8689 (tpt170) cc_final: 0.7926 (ttm110) REVERT: C 1033 MET cc_start: 0.9150 (ptm) cc_final: 0.8846 (ptm) outliers start: 94 outliers final: 70 residues processed: 284 average time/residue: 1.1442 time to fit residues: 387.6808 Evaluate side-chains 292 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 209 time to evaluate : 2.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1110 ASP Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 476 TYR Chi-restraints excluded: chain B residue 519 ASP Chi-restraints excluded: chain B residue 558 ASP Chi-restraints excluded: chain B residue 589 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 940 GLN Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 966 ARG Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1106 SER Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 702 SER Chi-restraints excluded: chain C residue 723 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain C residue 940 GLN Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 968 ASP Chi-restraints excluded: chain C residue 1026 CYS Chi-restraints excluded: chain C residue 1105 VAL Chi-restraints excluded: chain C residue 1106 SER Chi-restraints excluded: chain C residue 1119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 93 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 210 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 226 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 254 optimal weight: 1.9990 chunk 288 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 382 ASN A 938 ASN B 916 GLN C 97 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.130918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.099533 restraints weight = 32227.562| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.08 r_work: 0.2824 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 27501 Z= 0.179 Angle : 0.630 12.529 37614 Z= 0.322 Chirality : 0.046 0.275 4457 Planarity : 0.005 0.050 4731 Dihedral : 6.133 59.927 5487 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.14 % Favored : 96.77 % Rotamer: Outliers : 3.24 % Allowed : 15.33 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3252 helix: 1.48 (0.19), residues: 732 sheet: 0.45 (0.18), residues: 759 loop : -0.79 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 424 HIS 0.004 0.001 HIS B1047 PHE 0.014 0.002 PHE A 630 TYR 0.023 0.002 TYR B1050 ARG 0.004 0.000 ARG B1022 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 54) link_NAG-ASN : angle 2.22422 ( 162) link_BETA1-4 : bond 0.00436 ( 40) link_BETA1-4 : angle 1.45006 ( 120) hydrogen bonds : bond 0.05467 ( 1028) hydrogen bonds : angle 5.58521 ( 2997) SS BOND : bond 0.00449 ( 45) SS BOND : angle 2.08808 ( 90) covalent geometry : bond 0.00419 (27362) covalent geometry : angle 0.60170 (37242) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 208 time to evaluate : 2.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 TYR cc_start: 0.8156 (t80) cc_final: 0.7764 (t80) REVERT: A 307 ARG cc_start: 0.7894 (mtm180) cc_final: 0.6756 (mtp180) REVERT: A 777 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7675 (mm) REVERT: A 794 LYS cc_start: 0.6349 (ttmt) cc_final: 0.6114 (ptpt) REVERT: A 831 ASP cc_start: 0.7013 (t0) cc_final: 0.6806 (t0) REVERT: A 832 LEU cc_start: 0.8283 (mt) cc_final: 0.7974 (mp) REVERT: A 973 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7881 (mt-10) REVERT: A 1033 MET cc_start: 0.9447 (ptm) cc_final: 0.9236 (ptp) REVERT: B 55 LEU cc_start: 0.8802 (tp) cc_final: 0.8491 (mt) REVERT: B 181 LYS cc_start: 0.6167 (tptm) cc_final: 0.5683 (ttpp) REVERT: B 201 TYR cc_start: 0.8074 (t80) cc_final: 0.7759 (t80) REVERT: B 307 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.6862 (mtp180) REVERT: B 467 PRO cc_start: 0.7418 (Cg_exo) cc_final: 0.7144 (Cg_endo) REVERT: B 476 TYR cc_start: 0.8598 (OUTLIER) cc_final: 0.8073 (m-80) REVERT: B 702 SER cc_start: 0.9260 (OUTLIER) cc_final: 0.8923 (p) REVERT: B 737 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8099 (tt) REVERT: B 777 LEU cc_start: 0.8170 (pp) cc_final: 0.7765 (mm) REVERT: B 831 ASP cc_start: 0.7372 (t0) cc_final: 0.7086 (t0) REVERT: B 926 THR cc_start: 0.8002 (OUTLIER) cc_final: 0.7747 (t) REVERT: B 940 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8443 (tt0) REVERT: B 966 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7580 (ttp80) REVERT: C 135 ASP cc_start: 0.6915 (m-30) cc_final: 0.6149 (m-30) REVERT: C 163 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7680 (mp0) REVERT: C 201 TYR cc_start: 0.8068 (t80) cc_final: 0.7712 (t80) REVERT: C 307 ARG cc_start: 0.7772 (mtm180) cc_final: 0.6901 (mtp-110) REVERT: C 633 GLN cc_start: 0.8324 (mm-40) cc_final: 0.8077 (mm-40) REVERT: C 663 THR cc_start: 0.7674 (OUTLIER) cc_final: 0.7401 (p) REVERT: C 731 GLU cc_start: 0.8094 (mp0) cc_final: 0.7856 (mt-10) REVERT: C 777 LEU cc_start: 0.8161 (pp) cc_final: 0.7926 (pt) REVERT: C 794 LYS cc_start: 0.6381 (ttpp) cc_final: 0.6103 (ptpt) REVERT: C 807 ASN cc_start: 0.8181 (m-40) cc_final: 0.7939 (m-40) REVERT: C 831 ASP cc_start: 0.6953 (t0) cc_final: 0.6551 (t0) REVERT: C 940 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8320 (tt0) REVERT: C 1002 ARG cc_start: 0.8690 (tpt170) cc_final: 0.7931 (ttm110) outliers start: 92 outliers final: 74 residues processed: 282 average time/residue: 1.2115 time to fit residues: 408.0998 Evaluate side-chains 292 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 206 time to evaluate : 2.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1110 ASP Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 476 TYR Chi-restraints excluded: chain B residue 519 ASP Chi-restraints excluded: chain B residue 558 ASP Chi-restraints excluded: chain B residue 589 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 810 THR Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 940 GLN Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 966 ARG Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1105 VAL Chi-restraints excluded: chain B residue 1106 SER Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 358 ASN Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 702 SER Chi-restraints excluded: chain C residue 723 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain C residue 885 MET Chi-restraints excluded: chain C residue 940 GLN Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 968 ASP Chi-restraints excluded: chain C residue 1026 CYS Chi-restraints excluded: chain C residue 1105 VAL Chi-restraints excluded: chain C residue 1106 SER Chi-restraints excluded: chain C residue 1119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 276 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 305 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 198 optimal weight: 4.9990 chunk 70 optimal weight: 0.3980 chunk 32 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 chunk 303 optimal weight: 4.9990 chunk 254 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 938 ASN B 916 GLN C 97 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.130816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.099463 restraints weight = 32280.448| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.08 r_work: 0.2829 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.215 27501 Z= 0.217 Angle : 0.743 59.165 37614 Z= 0.408 Chirality : 0.046 0.275 4457 Planarity : 0.005 0.050 4731 Dihedral : 6.138 59.914 5487 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.08 % Favored : 96.83 % Rotamer: Outliers : 3.24 % Allowed : 15.47 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 3252 helix: 1.48 (0.19), residues: 732 sheet: 0.45 (0.18), residues: 759 loop : -0.79 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 424 HIS 0.004 0.001 HIS B1047 PHE 0.014 0.002 PHE A 630 TYR 0.023 0.001 TYR B1050 ARG 0.004 0.000 ARG B1022 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 54) link_NAG-ASN : angle 2.22338 ( 162) link_BETA1-4 : bond 0.00425 ( 40) link_BETA1-4 : angle 1.44190 ( 120) hydrogen bonds : bond 0.05463 ( 1028) hydrogen bonds : angle 5.58553 ( 2997) SS BOND : bond 0.00438 ( 45) SS BOND : angle 2.07036 ( 90) covalent geometry : bond 0.00465 (27362) covalent geometry : angle 0.72071 (37242) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18412.45 seconds wall clock time: 319 minutes 47.89 seconds (19187.89 seconds total)