Starting phenix.real_space_refine on Mon Aug 25 08:56:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wq0_37732/08_2025/8wq0_37732.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wq0_37732/08_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_37732/08_2025/8wq0_37732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wq0_37732/08_2025/8wq0_37732.map" model { file = "/net/cci-nas-00/data/ceres_data/8wq0_37732/08_2025/8wq0_37732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wq0_37732/08_2025/8wq0_37732.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 6.06, per 1000 atoms: 0.23 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: 2.58 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.28 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: 6.38 Time building geometry restraints manager: 3.32 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 1306) selection = (chain 'B' and resid 19 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: 1.500 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: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 25.900 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.090 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG B 545 TYR 0.031 0.001 TYR C1121 PHE 0.017 0.001 PHE A 104 TRP 0.033 0.002 TRP C 869 HIS 0.002 0.001 HIS A1031 Details of bonding type rmsd covalent geometry : bond 0.00425 (27362) covalent geometry : angle 0.66836 (37242) SS BOND : bond 0.00288 ( 45) SS BOND : angle 1.78361 ( 90) hydrogen bonds : bond 0.18054 ( 1028) hydrogen bonds : angle 7.86190 ( 2997) link_BETA1-4 : bond 0.00393 ( 40) link_BETA1-4 : angle 1.70569 ( 120) link_NAG-ASN : bond 0.00671 ( 54) link_NAG-ASN : angle 2.96359 ( 162) *********************** 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 : 0.838 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: 0.7550 (t80) REVERT: A 307 ARG cc_start: 0.7609 (mtm180) cc_final: 0.7355 (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: 0.7768 (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: 0.8664 (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: 0.7832 (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: 0.8004 (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: 0.8245 (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: 0.7157 (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: 0.8253 (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: 0.8171 (m-40) outliers start: 64 outliers final: 26 residues processed: 449 average time/residue: 0.5571 time to fit residues: 291.6707 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 : 0.901 ------------------------------------------------------------------------------- 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 197 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.0170 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 8.9990 overall best weight: 2.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 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 918 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 = 0.3492 r_free = 0.3492 target = 0.130662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.098858 restraints weight = 32546.484| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.06 r_work: 0.2810 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 27501 Z= 0.204 Angle : 0.696 9.886 37614 Z= 0.348 Chirality : 0.049 0.271 4457 Planarity : 0.005 0.058 4731 Dihedral : 8.727 66.251 5507 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.63 % Allowed : 13.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.14), residues: 3252 helix: 1.24 (0.19), residues: 729 sheet: 0.65 (0.19), residues: 696 loop : -0.73 (0.13), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1022 TYR 0.029 0.002 TYR B1050 PHE 0.018 0.002 PHE A 630 TRP 0.017 0.002 TRP C 869 HIS 0.007 0.002 HIS B1047 Details of bonding type rmsd covalent geometry : bond 0.00468 (27362) covalent geometry : angle 0.66516 (37242) SS BOND : bond 0.00518 ( 45) SS BOND : angle 1.94234 ( 90) hydrogen bonds : bond 0.06122 ( 1028) hydrogen bonds : angle 5.97022 ( 2997) link_BETA1-4 : bond 0.00481 ( 40) link_BETA1-4 : angle 1.80714 ( 120) link_NAG-ASN : bond 0.00508 ( 54) link_NAG-ASN : angle 2.46959 ( 162) *********************** 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 356 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 253 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.6293 (OUTLIER) cc_final: 0.5581 (p0) REVERT: A 108 MET cc_start: 0.8398 (mmm) cc_final: 0.7938 (mmm) REVERT: A 118 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7866 (ptt) REVERT: A 135 ASP cc_start: 0.7417 (m-30) cc_final: 0.6749 (m-30) REVERT: A 201 TYR cc_start: 0.8207 (t80) cc_final: 0.7684 (t80) REVERT: A 307 ARG cc_start: 0.7847 (mtm180) cc_final: 0.6621 (mtp180) REVERT: A 383 VAL cc_start: 0.9035 (OUTLIER) cc_final: 0.8766 (t) REVERT: A 440 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8649 (mttp) REVERT: A 467 PRO cc_start: 0.7615 (Cg_exo) cc_final: 0.7354 (Cg_endo) REVERT: A 648 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7967 (mm-30) REVERT: A 777 LEU cc_start: 0.7923 (pp) cc_final: 0.7606 (mm) REVERT: A 831 ASP cc_start: 0.6982 (t0) cc_final: 0.6641 (t0) REVERT: A 832 LEU cc_start: 0.8341 (mt) cc_final: 0.7969 (mp) REVERT: A 878 GLN cc_start: 0.8585 (pt0) cc_final: 0.8042 (tm-30) REVERT: A 884 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8571 (mt0) REVERT: A 916 GLN cc_start: 0.8557 (mt0) cc_final: 0.8345 (mt0) REVERT: A 940 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8437 (tt0) REVERT: A 973 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7918 (mt-10) REVERT: A 1091 ASN cc_start: 0.8596 (m-40) cc_final: 0.8336 (m-40) REVERT: B 46 ASP cc_start: 0.8302 (m-30) cc_final: 0.8023 (m-30) REVERT: B 108 MET cc_start: 0.8201 (mmm) cc_final: 0.7817 (mmm) REVERT: B 127 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7597 (ttt90) REVERT: B 135 ASP cc_start: 0.7168 (m-30) cc_final: 0.6386 (m-30) REVERT: B 181 LYS cc_start: 0.5967 (tptm) cc_final: 0.5665 (ttmt) REVERT: B 201 TYR cc_start: 0.8198 (t80) cc_final: 0.7811 (t80) REVERT: B 236 LEU cc_start: 0.6473 (OUTLIER) cc_final: 0.6248 (mt) REVERT: B 307 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.6751 (mtp180) REVERT: B 345 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8546 (ttt-90) REVERT: B 467 PRO cc_start: 0.7691 (Cg_exo) cc_final: 0.7368 (Cg_endo) REVERT: B 601 ASP cc_start: 0.7928 (m-30) cc_final: 0.7431 (m-30) REVERT: B 737 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8004 (tt) REVERT: B 777 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7624 (mm) REVERT: B 831 ASP cc_start: 0.7226 (t0) cc_final: 0.6843 (t0) REVERT: B 940 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8493 (tt0) REVERT: B 966 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7568 (ttp80) REVERT: B 1091 ASN cc_start: 0.8469 (m-40) cc_final: 0.8195 (m-40) REVERT: C 135 ASP cc_start: 0.7422 (m-30) cc_final: 0.6690 (m-30) REVERT: C 201 TYR cc_start: 0.8139 (t80) cc_final: 0.7807 (t80) REVERT: C 307 ARG cc_start: 0.7836 (mtm180) cc_final: 0.6941 (mtp180) REVERT: C 731 GLU cc_start: 0.8207 (mp0) cc_final: 0.7916 (mt-10) REVERT: C 737 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7892 (tt) REVERT: C 777 LEU cc_start: 0.7981 (pp) cc_final: 0.7639 (mm) REVERT: C 807 ASN cc_start: 0.8201 (m-40) cc_final: 0.7967 (m-40) REVERT: C 831 ASP cc_start: 0.7173 (t0) cc_final: 0.6899 (t0) REVERT: C 940 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8295 (tt0) REVERT: C 1091 ASN cc_start: 0.8641 (m-40) cc_final: 0.8411 (m-40) outliers start: 103 outliers final: 46 residues processed: 329 average time/residue: 0.6178 time to fit residues: 239.5642 Evaluate side-chains 288 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 225 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 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 884 GLN Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 940 GLN 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 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 306 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 304 optimal weight: 0.3980 chunk 196 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN B 506 ASN B 738 GLN B 916 GLN B1102 ASN C 97 ASN C 155 ASN C1102 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.132282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.100616 restraints weight = 32555.336| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.07 r_work: 0.2840 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 27501 Z= 0.138 Angle : 0.597 9.426 37614 Z= 0.300 Chirality : 0.045 0.248 4457 Planarity : 0.004 0.053 4731 Dihedral : 6.918 59.969 5491 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.46 % Favored : 97.45 % Rotamer: Outliers : 3.24 % Allowed : 14.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.14), residues: 3252 helix: 1.61 (0.19), residues: 708 sheet: 0.69 (0.18), residues: 780 loop : -0.65 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1022 TYR 0.023 0.001 TYR B1050 PHE 0.014 0.001 PHE A 630 TRP 0.012 0.001 TRP C 869 HIS 0.003 0.001 HIS B 196 Details of bonding type rmsd covalent geometry : bond 0.00311 (27362) covalent geometry : angle 0.56960 (37242) SS BOND : bond 0.00386 ( 45) SS BOND : angle 1.94319 ( 90) hydrogen bonds : bond 0.05187 ( 1028) hydrogen bonds : angle 5.63234 ( 2997) link_BETA1-4 : bond 0.00454 ( 40) link_BETA1-4 : angle 1.67071 ( 120) link_NAG-ASN : bond 0.00202 ( 54) link_NAG-ASN : angle 2.01278 ( 162) *********************** 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 336 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 244 time to evaluate : 0.816 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 108 MET cc_start: 0.8406 (mmm) cc_final: 0.7980 (mmm) REVERT: A 135 ASP cc_start: 0.7413 (m-30) cc_final: 0.6770 (m-30) REVERT: A 201 TYR cc_start: 0.8229 (t80) cc_final: 0.7707 (t80) REVERT: A 467 PRO cc_start: 0.7545 (Cg_exo) cc_final: 0.7345 (Cg_endo) REVERT: A 648 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7940 (mm-30) REVERT: A 777 LEU cc_start: 0.7896 (pp) cc_final: 0.7603 (mm) REVERT: A 831 ASP cc_start: 0.7059 (t0) cc_final: 0.6797 (t0) REVERT: A 832 LEU cc_start: 0.8344 (mt) cc_final: 0.7980 (mp) REVERT: A 866 THR cc_start: 0.8927 (m) cc_final: 0.8701 (p) REVERT: A 878 GLN cc_start: 0.8562 (pt0) cc_final: 0.8047 (tm-30) REVERT: A 890 ASN cc_start: 0.8664 (t0) cc_final: 0.8410 (m-40) REVERT: A 916 GLN cc_start: 0.8519 (mt0) cc_final: 0.8299 (mt0) REVERT: A 973 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7897 (mt-10) REVERT: A 1091 ASN cc_start: 0.8619 (m-40) cc_final: 0.8356 (m-40) REVERT: A 1119 THR cc_start: 0.8558 (OUTLIER) cc_final: 0.8357 (p) REVERT: B 46 ASP cc_start: 0.8350 (m-30) cc_final: 0.8070 (m-30) REVERT: B 55 LEU cc_start: 0.8782 (tp) cc_final: 0.8512 (mt) REVERT: B 135 ASP cc_start: 0.7107 (m-30) cc_final: 0.6363 (m-30) REVERT: B 181 LYS cc_start: 0.6000 (tptm) cc_final: 0.5729 (ttmt) REVERT: B 201 TYR cc_start: 0.8101 (t80) cc_final: 0.7719 (t80) REVERT: B 307 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.6770 (mtp180) REVERT: B 467 PRO cc_start: 0.7613 (Cg_exo) cc_final: 0.7300 (Cg_endo) REVERT: B 737 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8144 (tp) REVERT: B 777 LEU cc_start: 0.8036 (pp) cc_final: 0.7600 (mm) REVERT: B 831 ASP cc_start: 0.7207 (t0) cc_final: 0.6750 (t0) REVERT: B 832 LEU cc_start: 0.8595 (mt) cc_final: 0.8361 (mt) REVERT: B 940 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8510 (tt0) REVERT: B 1091 ASN cc_start: 0.8509 (m-40) cc_final: 0.8232 (m-40) REVERT: C 118 MET cc_start: 0.8190 (ptt) cc_final: 0.7917 (ptm) REVERT: C 135 ASP cc_start: 0.7410 (m-30) cc_final: 0.6696 (m-30) REVERT: C 156 ASN cc_start: 0.5670 (t0) cc_final: 0.5400 (t0) REVERT: C 201 TYR cc_start: 0.8071 (t80) cc_final: 0.7714 (t80) REVERT: C 307 ARG cc_start: 0.7813 (mtm180) cc_final: 0.6875 (mtp-110) REVERT: C 466 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7465 (mmtm) REVERT: C 633 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7872 (tp40) REVERT: C 731 GLU cc_start: 0.8158 (mp0) cc_final: 0.7935 (mt-10) REVERT: C 737 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7876 (tt) REVERT: C 777 LEU cc_start: 0.7968 (pp) cc_final: 0.7633 (mm) REVERT: C 794 LYS cc_start: 0.6100 (OUTLIER) cc_final: 0.5686 (ptmt) REVERT: C 807 ASN cc_start: 0.8140 (m-40) cc_final: 0.7892 (m-40) REVERT: C 831 ASP cc_start: 0.7014 (t0) cc_final: 0.6697 (t0) REVERT: C 878 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8352 (pt0) REVERT: C 940 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8295 (tt0) REVERT: C 1091 ASN cc_start: 0.8664 (m-40) cc_final: 0.8435 (m-40) outliers start: 92 outliers final: 49 residues processed: 312 average time/residue: 0.5534 time to fit residues: 203.9273 Evaluate side-chains 289 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 229 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 A residue 1119 THR 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 663 THR 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 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 1105 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 153 ILE 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 466 LYS Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 633 GLN 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 794 LYS Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain C residue 878 GLN 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 144 optimal weight: 0.9990 chunk 202 optimal weight: 5.9990 chunk 209 optimal weight: 0.9980 chunk 119 optimal weight: 7.9990 chunk 258 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 219 optimal weight: 3.9990 chunk 233 optimal weight: 4.9990 chunk 230 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 884 GLN A 938 ASN B 97 ASN B 506 ASN B 738 GLN B 916 GLN B1102 ASN C 97 ASN C 155 ASN C 433 GLN C 938 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.129683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.098061 restraints weight = 32235.045| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.09 r_work: 0.2798 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 27501 Z= 0.230 Angle : 0.702 15.341 37614 Z= 0.358 Chirality : 0.049 0.267 4457 Planarity : 0.005 0.054 4731 Dihedral : 6.678 59.634 5487 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.04 % Favored : 96.86 % Rotamer: Outliers : 4.47 % Allowed : 12.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.14), residues: 3252 helix: 1.25 (0.19), residues: 732 sheet: 0.50 (0.17), residues: 789 loop : -0.83 (0.13), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1022 TYR 0.025 0.002 TYR B1050 PHE 0.018 0.002 PHE C 77 TRP 0.012 0.003 TRP C 869 HIS 0.006 0.002 HIS B1047 Details of bonding type rmsd covalent geometry : bond 0.00542 (27362) covalent geometry : angle 0.66792 (37242) SS BOND : bond 0.00477 ( 45) SS BOND : angle 2.54904 ( 90) hydrogen bonds : bond 0.06306 ( 1028) hydrogen bonds : angle 5.85335 ( 2997) link_BETA1-4 : bond 0.00428 ( 40) link_BETA1-4 : angle 1.79730 ( 120) link_NAG-ASN : bond 0.00302 ( 54) link_NAG-ASN : angle 2.45318 ( 162) *********************** 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 350 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 223 time to evaluate : 0.984 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 119 ASN cc_start: 0.8669 (OUTLIER) cc_final: 0.8447 (t0) REVERT: A 127 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.6881 (ttp80) REVERT: A 201 TYR cc_start: 0.8167 (t80) cc_final: 0.7812 (t80) REVERT: A 440 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8576 (mttp) REVERT: A 648 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7941 (mm-30) REVERT: A 777 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7623 (mm) REVERT: A 794 LYS cc_start: 0.6318 (ttmt) cc_final: 0.6028 (ptmt) REVERT: A 831 ASP cc_start: 0.7050 (t0) cc_final: 0.6702 (t0) REVERT: A 832 LEU cc_start: 0.8279 (mt) cc_final: 0.7910 (mp) REVERT: A 916 GLN cc_start: 0.8562 (mt0) cc_final: 0.8325 (mt0) REVERT: A 971 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8068 (tm-30) REVERT: A 973 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7951 (mt-10) REVERT: A 1089 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8607 (pt0) REVERT: A 1091 ASN cc_start: 0.8678 (m-40) cc_final: 0.8307 (m-40) REVERT: B 25 ASP cc_start: 0.5762 (OUTLIER) cc_final: 0.5562 (p0) REVERT: B 46 ASP cc_start: 0.8350 (m-30) cc_final: 0.8024 (m-30) REVERT: B 135 ASP cc_start: 0.7114 (m-30) cc_final: 0.6311 (m-30) REVERT: B 181 LYS cc_start: 0.6083 (OUTLIER) cc_final: 0.5653 (ttpt) REVERT: B 201 TYR cc_start: 0.8085 (t80) cc_final: 0.7772 (t80) REVERT: B 307 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7267 (mtm-85) REVERT: B 467 PRO cc_start: 0.7630 (Cg_exo) cc_final: 0.7352 (Cg_endo) REVERT: B 737 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8119 (tt) REVERT: B 777 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7724 (mm) REVERT: B 831 ASP cc_start: 0.7320 (t0) cc_final: 0.6973 (t0) REVERT: B 926 THR cc_start: 0.7678 (OUTLIER) cc_final: 0.7301 (t) REVERT: B 940 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8486 (tt0) REVERT: C 25 ASP cc_start: 0.5751 (OUTLIER) cc_final: 0.5371 (p0) REVERT: C 201 TYR cc_start: 0.8190 (t80) cc_final: 0.7789 (t80) REVERT: C 307 ARG cc_start: 0.7732 (mtm180) cc_final: 0.6884 (mtp-110) REVERT: C 466 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7761 (mmtm) REVERT: C 702 SER cc_start: 0.9201 (OUTLIER) cc_final: 0.8966 (t) REVERT: C 731 GLU cc_start: 0.8182 (mp0) cc_final: 0.7872 (mt-10) REVERT: C 737 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.7979 (tt) REVERT: C 777 LEU cc_start: 0.8110 (pp) cc_final: 0.7856 (pt) REVERT: C 807 ASN cc_start: 0.8223 (m-40) cc_final: 0.7978 (m-40) REVERT: C 831 ASP cc_start: 0.6986 (t0) cc_final: 0.6594 (t0) REVERT: C 940 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8336 (tt0) REVERT: C 1033 MET cc_start: 0.9284 (ptm) cc_final: 0.9022 (ptm) outliers start: 127 outliers final: 66 residues processed: 324 average time/residue: 0.5101 time to fit residues: 195.8582 Evaluate side-chains 297 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 212 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 119 ASN Chi-restraints excluded: chain A residue 127 ARG 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 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 968 ASP Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1089 GLN 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 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 205 SER 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 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 694 THR Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 743 CYS 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 1105 VAL Chi-restraints excluded: chain B residue 1106 SER 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 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 466 LYS 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 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 926 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 71 optimal weight: 2.9990 chunk 262 optimal weight: 4.9990 chunk 241 optimal weight: 6.9990 chunk 216 optimal weight: 10.0000 chunk 218 optimal weight: 0.7980 chunk 283 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 234 optimal weight: 8.9990 chunk 145 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 425 ASN A 938 ASN B 506 ASN B 916 GLN C 97 ASN C 155 ASN C 938 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.130419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.098855 restraints weight = 32308.297| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.07 r_work: 0.2820 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 27501 Z= 0.181 Angle : 0.647 14.597 37614 Z= 0.328 Chirality : 0.046 0.261 4457 Planarity : 0.005 0.053 4731 Dihedral : 6.481 59.210 5487 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.55 % Favored : 97.36 % Rotamer: Outliers : 3.81 % Allowed : 13.88 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.14), residues: 3252 helix: 1.31 (0.19), residues: 732 sheet: 0.45 (0.17), residues: 771 loop : -0.83 (0.13), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 127 TYR 0.025 0.002 TYR B1050 PHE 0.014 0.002 PHE A 630 TRP 0.011 0.002 TRP B 424 HIS 0.005 0.001 HIS B1047 Details of bonding type rmsd covalent geometry : bond 0.00424 (27362) covalent geometry : angle 0.61092 (37242) SS BOND : bond 0.00440 ( 45) SS BOND : angle 2.34395 ( 90) hydrogen bonds : bond 0.05644 ( 1028) hydrogen bonds : angle 5.70803 ( 2997) link_BETA1-4 : bond 0.00444 ( 40) link_BETA1-4 : angle 1.60615 ( 120) link_NAG-ASN : bond 0.00280 ( 54) link_NAG-ASN : angle 2.51548 ( 162) *********************** 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 321 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 213 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ILE cc_start: 0.7369 (OUTLIER) cc_final: 0.7015 (mm) REVERT: A 201 TYR cc_start: 0.8123 (t80) cc_final: 0.7749 (t80) REVERT: A 440 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8580 (mttp) REVERT: A 648 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7846 (mm-30) REVERT: A 777 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7692 (mm) REVERT: A 794 LYS cc_start: 0.6262 (ttmt) cc_final: 0.5906 (ptmt) REVERT: A 831 ASP cc_start: 0.7040 (t0) cc_final: 0.6738 (t0) REVERT: A 832 LEU cc_start: 0.8314 (mt) cc_final: 0.7952 (mp) REVERT: A 916 GLN cc_start: 0.8561 (mt0) cc_final: 0.8326 (mt0) REVERT: A 971 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8027 (tm-30) REVERT: A 973 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7948 (mt-10) REVERT: A 1033 MET cc_start: 0.9485 (ptm) cc_final: 0.9243 (ptp) REVERT: A 1091 ASN cc_start: 0.8740 (m-40) cc_final: 0.8357 (m-40) REVERT: B 55 LEU cc_start: 0.8809 (tp) cc_final: 0.8493 (mt) REVERT: B 201 TYR cc_start: 0.8081 (t80) cc_final: 0.7790 (t80) REVERT: B 307 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7356 (mtm-85) REVERT: B 467 PRO cc_start: 0.7589 (Cg_exo) cc_final: 0.7309 (Cg_endo) REVERT: B 723 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8855 (ttp) REVERT: B 737 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8074 (tt) REVERT: B 777 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7730 (mm) REVERT: B 831 ASP cc_start: 0.7319 (t0) cc_final: 0.6901 (t0) REVERT: B 926 THR cc_start: 0.7823 (OUTLIER) cc_final: 0.7485 (t) REVERT: B 940 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8467 (tt0) REVERT: B 1084 SER cc_start: 0.7945 (OUTLIER) cc_final: 0.7705 (t) REVERT: C 201 TYR cc_start: 0.8150 (t80) cc_final: 0.7771 (t80) REVERT: C 307 ARG cc_start: 0.7683 (mtm180) cc_final: 0.6813 (mtp-110) REVERT: C 466 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7776 (mmtm) REVERT: C 731 GLU cc_start: 0.8131 (mp0) cc_final: 0.7892 (mt-10) REVERT: C 737 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7953 (tt) REVERT: C 777 LEU cc_start: 0.8148 (pp) cc_final: 0.7904 (pt) REVERT: C 794 LYS cc_start: 0.6274 (ttpp) cc_final: 0.5854 (ptmt) REVERT: C 807 ASN cc_start: 0.8193 (m-40) cc_final: 0.7949 (m-40) REVERT: C 831 ASP cc_start: 0.6931 (t0) cc_final: 0.6527 (t0) REVERT: C 940 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8338 (tt0) outliers start: 108 outliers final: 70 residues processed: 300 average time/residue: 0.5045 time to fit residues: 179.3147 Evaluate side-chains 295 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 210 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 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 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 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 926 THR Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 968 ASP Chi-restraints excluded: chain A residue 971 GLU 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 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 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 723 MET Chi-restraints excluded: chain B residue 730 THR Chi-restraints excluded: chain B residue 737 LEU Chi-restraints excluded: chain B residue 743 CYS 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 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 1084 SER 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 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 466 LYS Chi-restraints excluded: chain C residue 519 ASP 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 323 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 272 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 308 optimal weight: 3.9990 chunk 302 optimal weight: 0.7980 chunk 64 optimal weight: 0.0170 chunk 40 optimal weight: 0.7980 chunk 262 optimal weight: 1.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 819 GLN A 938 ASN B 113 GLN B 506 ASN B 916 GLN B 988 GLN B1102 ASN C 97 ASN C 938 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.131704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.100130 restraints weight = 32393.694| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.07 r_work: 0.2836 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 27501 Z= 0.134 Angle : 0.592 14.742 37614 Z= 0.300 Chirality : 0.044 0.258 4457 Planarity : 0.004 0.051 4731 Dihedral : 6.097 59.954 5487 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.89 % Favored : 97.02 % Rotamer: Outliers : 3.66 % Allowed : 14.27 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.14), residues: 3252 helix: 1.62 (0.19), residues: 714 sheet: 0.46 (0.17), residues: 762 loop : -0.72 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 127 TYR 0.023 0.001 TYR B1050 PHE 0.015 0.001 PHE C 630 TRP 0.010 0.001 TRP B 424 HIS 0.002 0.001 HIS C1031 Details of bonding type rmsd covalent geometry : bond 0.00305 (27362) covalent geometry : angle 0.55995 (37242) SS BOND : bond 0.00359 ( 45) SS BOND : angle 2.00233 ( 90) hydrogen bonds : bond 0.05012 ( 1028) hydrogen bonds : angle 5.52165 ( 2997) link_BETA1-4 : bond 0.00417 ( 40) link_BETA1-4 : angle 1.45561 ( 120) link_NAG-ASN : bond 0.00253 ( 54) link_NAG-ASN : angle 2.36880 ( 162) *********************** 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 327 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 223 time to evaluate : 1.009 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: 0.7331 (OUTLIER) cc_final: 0.6980 (mm) REVERT: A 201 TYR cc_start: 0.8121 (t80) cc_final: 0.7769 (t80) REVERT: A 777 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7685 (mm) REVERT: A 831 ASP cc_start: 0.7013 (t0) cc_final: 0.6732 (t0) REVERT: A 832 LEU cc_start: 0.8298 (mt) cc_final: 0.7946 (mp) REVERT: A 878 GLN cc_start: 0.8492 (pt0) cc_final: 0.7947 (tm-30) REVERT: A 916 GLN cc_start: 0.8546 (mt0) cc_final: 0.8295 (mt0) REVERT: A 971 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8016 (tm-30) REVERT: A 973 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7911 (mt-10) REVERT: A 1033 MET cc_start: 0.9467 (ptm) cc_final: 0.9211 (ptp) REVERT: A 1091 ASN cc_start: 0.8746 (m-40) cc_final: 0.8384 (m-40) REVERT: B 55 LEU cc_start: 0.8809 (tp) cc_final: 0.8491 (mt) REVERT: B 181 LYS cc_start: 0.6186 (ttmt) cc_final: 0.5833 (ttpt) REVERT: B 201 TYR cc_start: 0.8076 (t80) cc_final: 0.7796 (t80) REVERT: B 307 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.6892 (mtp180) REVERT: B 467 PRO cc_start: 0.7590 (Cg_exo) cc_final: 0.7318 (Cg_endo) REVERT: B 702 SER cc_start: 0.9262 (OUTLIER) cc_final: 0.8909 (p) REVERT: B 737 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8195 (tp) REVERT: B 777 LEU cc_start: 0.8178 (pp) cc_final: 0.7747 (mm) REVERT: B 831 ASP cc_start: 0.7251 (t0) cc_final: 0.6870 (t0) REVERT: B 926 THR cc_start: 0.7843 (OUTLIER) cc_final: 0.7548 (t) REVERT: B 940 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8510 (tt0) REVERT: C 201 TYR cc_start: 0.8130 (t80) cc_final: 0.7763 (t80) REVERT: C 307 ARG cc_start: 0.7686 (mtm180) cc_final: 0.6820 (mtp-110) REVERT: C 663 THR cc_start: 0.7749 (OUTLIER) cc_final: 0.7447 (p) REVERT: C 731 GLU cc_start: 0.8133 (mp0) cc_final: 0.7893 (mt-10) REVERT: C 737 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7919 (tt) REVERT: C 777 LEU cc_start: 0.8126 (pp) cc_final: 0.7881 (pt) REVERT: C 794 LYS cc_start: 0.6298 (ttpp) cc_final: 0.5898 (ptmt) REVERT: C 807 ASN cc_start: 0.8176 (m-40) cc_final: 0.7938 (m-40) REVERT: C 831 ASP cc_start: 0.6864 (t0) cc_final: 0.6476 (t0) REVERT: C 940 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8325 (tt0) REVERT: C 1033 MET cc_start: 0.9157 (ptm) cc_final: 0.8865 (ptm) outliers start: 104 outliers final: 68 residues processed: 303 average time/residue: 0.5422 time to fit residues: 194.9929 Evaluate side-chains 288 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 209 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 307 ARG 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 691 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 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 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 501 SER 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 723 MET 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 935 VAL Chi-restraints excluded: chain B residue 940 GLN 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 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 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 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.4645 > 50: distance: 6 - 10: 5.713 distance: 10 - 11: 6.768 distance: 11 - 12: 5.992 distance: 11 - 14: 8.522 distance: 12 - 13: 7.144 distance: 12 - 17: 8.806 distance: 14 - 15: 9.263 distance: 14 - 16: 13.838 distance: 18 - 19: 7.793 distance: 18 - 21: 25.043 distance: 19 - 20: 28.936 distance: 19 - 22: 3.926 distance: 22 - 23: 11.955 distance: 22 - 28: 19.142 distance: 23 - 24: 13.418 distance: 23 - 26: 9.632 distance: 24 - 25: 16.249 distance: 24 - 29: 13.752 distance: 26 - 27: 16.135 distance: 27 - 28: 9.766 distance: 29 - 30: 6.539 distance: 31 - 32: 6.727 distance: 31 - 35: 3.569 distance: 33 - 34: 11.002 distance: 35 - 36: 7.428 distance: 36 - 37: 4.085 distance: 36 - 39: 4.178 distance: 37 - 44: 4.447 distance: 38 - 163: 7.367 distance: 39 - 40: 7.733 distance: 40 - 41: 4.952 distance: 41 - 42: 5.999 distance: 42 - 43: 9.392 distance: 45 - 46: 8.470 distance: 45 - 48: 10.235 distance: 46 - 47: 4.290 distance: 46 - 53: 9.433 distance: 48 - 49: 13.964 distance: 49 - 50: 8.739 distance: 50 - 51: 10.906 distance: 50 - 52: 15.071 distance: 53 - 54: 9.103 distance: 53 - 166: 12.587 distance: 54 - 55: 5.194 distance: 54 - 57: 8.091 distance: 55 - 56: 15.709 distance: 55 - 60: 10.512 distance: 56 - 176: 18.135 distance: 57 - 58: 6.847 distance: 57 - 59: 11.195 distance: 60 - 61: 5.887 distance: 61 - 64: 6.736 distance: 62 - 63: 4.693 distance: 62 - 67: 3.250 distance: 64 - 65: 10.667 distance: 64 - 66: 7.525 distance: 67 - 68: 4.343 distance: 67 - 179: 6.718 distance: 68 - 69: 6.945 distance: 69 - 78: 6.275 distance: 71 - 72: 8.820 distance: 72 - 73: 3.367 distance: 74 - 75: 5.380 distance: 75 - 76: 6.794 distance: 75 - 77: 5.062 distance: 78 - 79: 7.915 distance: 80 - 81: 4.502 distance: 80 - 89: 6.839 distance: 82 - 83: 3.827 distance: 83 - 84: 3.308 distance: 83 - 85: 7.821 distance: 84 - 86: 5.535 distance: 85 - 87: 3.446 distance: 86 - 88: 5.121 distance: 87 - 88: 6.455