Starting phenix.real_space_refine on Mon Aug 25 04:53:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8epn_28531/08_2025/8epn_28531.cif Found real_map, /net/cci-nas-00/data/ceres_data/8epn_28531/08_2025/8epn_28531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8epn_28531/08_2025/8epn_28531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8epn_28531/08_2025/8epn_28531.map" model { file = "/net/cci-nas-00/data/ceres_data/8epn_28531/08_2025/8epn_28531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8epn_28531/08_2025/8epn_28531.cif" } resolution = 2.8 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= 0.002 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 99 5.16 5 C 15915 2.51 5 N 3993 2.21 5 O 5070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.03s 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: 25077 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 7816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 997, 7816 Classifications: {'peptide': 997} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 49, 'TRANS': 943} Chain breaks: 9 Chain: "B" Number of atoms: 7816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 997, 7816 Classifications: {'peptide': 997} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 49, 'TRANS': 943} Chain breaks: 9 Chain: "C" Number of atoms: 7816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 997, 7816 Classifications: {'peptide': 997} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 49, 'TRANS': 943} Chain breaks: 9 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 6.99, per 1000 atoms: 0.28 Number of scatterers: 25077 At special positions: 0 Unit cell: (145.39, 143.38, 175.54, 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 99 16.00 O 5070 8.00 N 3993 7.00 C 15915 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA L 3 " - " MAN L 4 " " BMA P 3 " - " MAN P 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 4 " " BMA W 3 " - " MAN W 4 " " BMA a 3 " - " MAN a 4 " " BMA b 3 " - " MAN b 4 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 4 " " BMA h 3 " - " MAN h 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA F 3 " - " MAN F 5 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " " BMA L 3 " - " MAN L 5 " " BMA P 3 " - " MAN P 5 " " BMA Q 3 " - " MAN Q 5 " " BMA R 3 " - " MAN R 5 " " BMA S 3 " - " MAN S 5 " " BMA W 3 " - " MAN W 5 " " BMA a 3 " - " MAN a 5 " " BMA b 3 " - " MAN b 5 " " BMA c 3 " - " MAN c 5 " " BMA d 3 " - " MAN d 5 " " BMA h 3 " - " MAN h 5 " 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 F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " 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 P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " 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 W 2 " - " BMA W 3 " " 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 b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A1201 " - " ASN A 709 " " NAG A1202 " - " ASN A 603 " " NAG A1203 " - " ASN A 165 " " NAG A1204 " - " ASN A 61 " " NAG A1205 " - " ASN A 234 " " NAG B1201 " - " ASN B 709 " " NAG B1202 " - " ASN B 603 " " NAG B1203 " - " ASN B 165 " " NAG B1204 " - " ASN B 61 " " NAG B1205 " - " ASN B 234 " " NAG C1201 " - " ASN C 709 " " NAG C1202 " - " ASN C 603 " " NAG C1203 " - " ASN C 165 " " NAG C1204 " - " ASN C 61 " " NAG C1205 " - " ASN C 234 " " NAG D 1 " - " ASN A 616 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 282 " " NAG G 1 " - " ASN A 343 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A 657 " " NAG J 1 " - " ASN A 122 " " NAG K 1 " - " ASN A1098 " " NAG L 1 " - " ASN A1134 " " NAG M 1 " - " ASN A1074 " " NAG N 1 " - " ASN A 331 " " NAG O 1 " - " ASN B 616 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 282 " " NAG R 1 " - " ASN B 343 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B 657 " " NAG U 1 " - " ASN B 122 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN B1074 " " NAG Y 1 " - " ASN B 331 " " NAG Z 1 " - " ASN C 616 " " NAG a 1 " - " ASN C 717 " " NAG b 1 " - " ASN C 282 " " NAG c 1 " - " ASN C 343 " " NAG d 1 " - " ASN C 801 " " NAG e 1 " - " ASN C 657 " " NAG f 1 " - " ASN C 122 " " NAG g 1 " - " ASN C1098 " " NAG h 1 " - " ASN C1134 " " NAG i 1 " - " ASN C1074 " " NAG j 1 " - " ASN C 331 " Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5622 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 43 sheets defined 26.5% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.108A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.967A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.518A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.635A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 853 through 856 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.518A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 891 removed outlier: 3.540A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.530A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 941 removed outlier: 4.290A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.076A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.295A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.113A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.525A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.641A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 853 through 856 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.511A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 891 removed outlier: 3.512A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.514A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.296A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.072A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.302A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.163A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.532A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.654A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 853 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 887 through 891 removed outlier: 3.517A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.542A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 941 removed outlier: 4.303A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.074A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.301A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 5.841A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.235A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.114A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE C 587 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.725A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.813A pdb=" N LEU A 244 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.938A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.072A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.120A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.029A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.579A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.827A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.270A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.968A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 5.926A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.257A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.730A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.753A pdb=" N LEU B 244 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.607A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.043A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.118A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B 587 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.048A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.581A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.786A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.249A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 5.907A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.707A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.691A pdb=" N LEU C 244 " --> pdb=" O LEU C 141 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.678A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.869A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.077A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.008A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.586A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.816A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.272A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE7, first strand: chain 'C' and resid 1081 through 1082 1007 hydrogen bonds defined for protein. 2757 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: 6.11 Time building geometry restraints manager: 2.83 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: 7757 1.34 - 1.46: 6330 1.46 - 1.58: 11395 1.58 - 1.70: 0 1.70 - 1.82: 123 Bond restraints: 25605 Sorted by residual: bond pdb=" C1 NAG A1201 " pdb=" O5 NAG A1201 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C1 NAG Y 1 " pdb=" O5 NAG Y 1 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" N THR C 393 " pdb=" CA THR C 393 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.20e-02 6.94e+03 7.16e+00 bond pdb=" C1 NAG j 1 " pdb=" O5 NAG j 1 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.89e+00 ... (remaining 25600 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 34064 2.33 - 4.67: 648 4.67 - 7.00: 108 7.00 - 9.33: 1 9.33 - 11.66: 3 Bond angle restraints: 34824 Sorted by residual: angle pdb=" C ASN A1135 " pdb=" N THR A1136 " pdb=" CA THR A1136 " ideal model delta sigma weight residual 121.70 133.36 -11.66 1.80e+00 3.09e-01 4.20e+01 angle pdb=" C ASN C1135 " pdb=" N THR C1136 " pdb=" CA THR C1136 " ideal model delta sigma weight residual 121.70 133.32 -11.62 1.80e+00 3.09e-01 4.17e+01 angle pdb=" C ASN B1135 " pdb=" N THR B1136 " pdb=" CA THR B1136 " ideal model delta sigma weight residual 121.70 133.30 -11.60 1.80e+00 3.09e-01 4.15e+01 angle pdb=" C ASN A 87 " pdb=" CA ASN A 87 " pdb=" CB ASN A 87 " ideal model delta sigma weight residual 117.23 111.18 6.05 1.36e+00 5.41e-01 1.98e+01 angle pdb=" C ASN C 87 " pdb=" CA ASN C 87 " pdb=" CB ASN C 87 " ideal model delta sigma weight residual 117.23 111.20 6.03 1.36e+00 5.41e-01 1.97e+01 ... (remaining 34819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.98: 15660 24.98 - 49.96: 826 49.96 - 74.94: 162 74.94 - 99.93: 134 99.93 - 124.91: 51 Dihedral angle restraints: 16833 sinusoidal: 8118 harmonic: 8715 Sorted by residual: dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual -86.00 -163.41 77.41 1 1.00e+01 1.00e-02 7.51e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual -86.00 -161.99 75.99 1 1.00e+01 1.00e-02 7.28e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual -86.00 -161.95 75.95 1 1.00e+01 1.00e-02 7.27e+01 ... (remaining 16830 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3685 0.072 - 0.144: 611 0.144 - 0.215: 12 0.215 - 0.287: 13 0.287 - 0.359: 14 Chirality restraints: 4335 Sorted by residual: chirality pdb=" C1 NAG d 1 " pdb=" ND2 ASN C 801 " pdb=" C2 NAG d 1 " pdb=" O5 NAG d 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN B 801 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 4332 not shown) Planarity restraints: 4362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B1132 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" C ILE B1132 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE B1132 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL B1133 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C1132 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.06e+00 pdb=" C ILE C1132 " 0.030 2.00e-02 2.50e+03 pdb=" O ILE C1132 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL C1133 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 138 " 0.029 5.00e-02 4.00e+02 4.33e-02 3.01e+00 pdb=" N PRO A 139 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 139 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 139 " 0.024 5.00e-02 4.00e+02 ... (remaining 4359 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2685 2.75 - 3.29: 23064 3.29 - 3.83: 39662 3.83 - 4.36: 45309 4.36 - 4.90: 79566 Nonbonded interactions: 190286 Sorted by model distance: nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.214 3.040 nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.219 3.040 nonbonded pdb=" OD1 ASP C 442 " pdb=" OH TYR C 451 " model vdw 2.235 3.040 nonbonded pdb=" OD1 ASP B 442 " pdb=" OH TYR B 451 " model vdw 2.243 3.040 nonbonded pdb=" NZ LYS C 825 " pdb=" O THR C 941 " model vdw 2.269 3.120 ... (remaining 190281 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'i' selection = chain 'j' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'L' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'W' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.640 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 26.080 Find NCS groups from input model: 0.700 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: 0.000 Load rotamer database and sin/cos tables:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 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 : 0.005 0.081 25758 Z= 0.238 Angle : 0.790 11.663 35256 Z= 0.363 Chirality : 0.053 0.359 4335 Planarity : 0.004 0.043 4314 Dihedral : 18.173 124.907 11130 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.84 % Allowed : 12.38 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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: -0.10 (0.15), residues: 2931 helix: 1.64 (0.21), residues: 669 sheet: 0.67 (0.21), residues: 543 loop : -1.06 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 457 TYR 0.021 0.001 TYR A 453 PHE 0.018 0.001 PHE A 140 TRP 0.012 0.002 TRP C 353 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00486 (25605) covalent geometry : angle 0.75109 (34824) SS BOND : bond 0.00275 ( 27) SS BOND : angle 1.05999 ( 54) hydrogen bonds : bond 0.21895 ( 1001) hydrogen bonds : angle 8.34392 ( 2757) link_ALPHA1-3 : bond 0.00427 ( 15) link_ALPHA1-3 : angle 1.75971 ( 45) link_ALPHA1-6 : bond 0.00614 ( 15) link_ALPHA1-6 : angle 1.58007 ( 45) link_BETA1-4 : bond 0.00545 ( 48) link_BETA1-4 : angle 2.03902 ( 144) link_NAG-ASN : bond 0.00438 ( 48) link_NAG-ASN : angle 3.14943 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 PHE cc_start: 0.7629 (m-80) cc_final: 0.7120 (m-80) REVERT: C 133 PHE cc_start: 0.7579 (m-80) cc_final: 0.7088 (m-80) outliers start: 22 outliers final: 19 residues processed: 116 average time/residue: 0.5201 time to fit residues: 73.3191 Evaluate side-chains 93 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 979 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.0770 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.118948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.073085 restraints weight = 60562.512| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 4.00 r_work: 0.2979 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25758 Z= 0.221 Angle : 0.700 9.142 35256 Z= 0.343 Chirality : 0.051 0.351 4335 Planarity : 0.005 0.049 4314 Dihedral : 14.342 115.004 5786 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.30 % Allowed : 11.34 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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: -0.20 (0.15), residues: 2931 helix: 1.66 (0.20), residues: 708 sheet: 0.68 (0.22), residues: 537 loop : -1.26 (0.13), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 646 TYR 0.021 0.002 TYR C1067 PHE 0.014 0.002 PHE B 135 TRP 0.013 0.002 TRP C 436 HIS 0.004 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00526 (25605) covalent geometry : angle 0.65652 (34824) SS BOND : bond 0.00487 ( 27) SS BOND : angle 0.85080 ( 54) hydrogen bonds : bond 0.08299 ( 1001) hydrogen bonds : angle 6.44975 ( 2757) link_ALPHA1-3 : bond 0.01087 ( 15) link_ALPHA1-3 : angle 2.23788 ( 45) link_ALPHA1-6 : bond 0.00931 ( 15) link_ALPHA1-6 : angle 2.04958 ( 45) link_BETA1-4 : bond 0.00406 ( 48) link_BETA1-4 : angle 1.95975 ( 144) link_NAG-ASN : bond 0.00471 ( 48) link_NAG-ASN : angle 2.95799 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 81 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: B 133 PHE cc_start: 0.7780 (m-80) cc_final: 0.7203 (m-80) REVERT: C 133 PHE cc_start: 0.7636 (m-80) cc_final: 0.7076 (m-80) outliers start: 60 outliers final: 20 residues processed: 134 average time/residue: 0.4369 time to fit residues: 73.3808 Evaluate side-chains 87 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 181 optimal weight: 4.9990 chunk 205 optimal weight: 9.9990 chunk 206 optimal weight: 5.9990 chunk 67 optimal weight: 0.0370 chunk 248 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 chunk 270 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 chunk 240 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.119064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.073005 restraints weight = 60580.756| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 4.07 r_work: 0.2966 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 25758 Z= 0.227 Angle : 0.696 9.777 35256 Z= 0.337 Chirality : 0.051 0.347 4335 Planarity : 0.005 0.048 4314 Dihedral : 12.540 116.269 5767 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.14 % Allowed : 11.30 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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 (0.15), residues: 2931 helix: 1.82 (0.21), residues: 687 sheet: 0.67 (0.21), residues: 564 loop : -1.25 (0.13), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 646 TYR 0.020 0.002 TYR C 380 PHE 0.017 0.002 PHE A 400 TRP 0.011 0.002 TRP A 436 HIS 0.004 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00542 (25605) covalent geometry : angle 0.65739 (34824) SS BOND : bond 0.00424 ( 27) SS BOND : angle 0.81346 ( 54) hydrogen bonds : bond 0.08363 ( 1001) hydrogen bonds : angle 6.06430 ( 2757) link_ALPHA1-3 : bond 0.01196 ( 15) link_ALPHA1-3 : angle 1.43371 ( 45) link_ALPHA1-6 : bond 0.01140 ( 15) link_ALPHA1-6 : angle 1.98828 ( 45) link_BETA1-4 : bond 0.00548 ( 48) link_BETA1-4 : angle 1.71796 ( 144) link_NAG-ASN : bond 0.00493 ( 48) link_NAG-ASN : angle 2.97815 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 87 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1144 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7535 (mm-30) REVERT: B 133 PHE cc_start: 0.7821 (m-80) cc_final: 0.7264 (m-80) REVERT: B 190 ARG cc_start: 0.7659 (ttp-170) cc_final: 0.7092 (ttm110) REVERT: B 227 VAL cc_start: 0.8861 (t) cc_final: 0.8571 (p) REVERT: B 314 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8197 (tm-30) REVERT: C 133 PHE cc_start: 0.7672 (m-80) cc_final: 0.7215 (m-80) REVERT: C 239 GLN cc_start: 0.7195 (tp-100) cc_final: 0.6854 (mm-40) REVERT: C 314 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8328 (tp40) REVERT: C 386 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7250 (mtpt) REVERT: C 740 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8357 (tpt) REVERT: C 1144 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7750 (mm-30) outliers start: 82 outliers final: 37 residues processed: 162 average time/residue: 0.4741 time to fit residues: 94.0673 Evaluate side-chains 112 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 71 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1018 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 105 optimal weight: 9.9990 chunk 278 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 9 optimal weight: 10.0000 chunk 241 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.119526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.072940 restraints weight = 60305.524| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 4.24 r_work: 0.2976 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 25758 Z= 0.199 Angle : 0.674 9.743 35256 Z= 0.321 Chirality : 0.050 0.339 4335 Planarity : 0.004 0.047 4314 Dihedral : 11.184 114.443 5765 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.64 % Allowed : 12.57 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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: -0.09 (0.15), residues: 2931 helix: 1.89 (0.21), residues: 687 sheet: 0.68 (0.21), residues: 570 loop : -1.23 (0.13), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1000 TYR 0.018 0.001 TYR A1067 PHE 0.020 0.002 PHE A 400 TRP 0.025 0.002 TRP A 353 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00472 (25605) covalent geometry : angle 0.63473 (34824) SS BOND : bond 0.00407 ( 27) SS BOND : angle 0.76474 ( 54) hydrogen bonds : bond 0.07744 ( 1001) hydrogen bonds : angle 5.89188 ( 2757) link_ALPHA1-3 : bond 0.01201 ( 15) link_ALPHA1-3 : angle 1.69707 ( 45) link_ALPHA1-6 : bond 0.01242 ( 15) link_ALPHA1-6 : angle 2.07002 ( 45) link_BETA1-4 : bond 0.00424 ( 48) link_BETA1-4 : angle 1.76126 ( 144) link_NAG-ASN : bond 0.00435 ( 48) link_NAG-ASN : angle 2.86924 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 78 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8178 (tm-30) REVERT: A 707 TYR cc_start: 0.8096 (m-80) cc_final: 0.7806 (m-10) REVERT: A 1144 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7803 (mm-30) REVERT: B 133 PHE cc_start: 0.7813 (m-80) cc_final: 0.7263 (m-80) REVERT: B 190 ARG cc_start: 0.7615 (ttp-170) cc_final: 0.7052 (ttm110) REVERT: B 227 VAL cc_start: 0.8853 (t) cc_final: 0.8560 (p) REVERT: B 314 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8212 (tm-30) REVERT: C 133 PHE cc_start: 0.7637 (m-80) cc_final: 0.7215 (m-80) REVERT: C 740 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8356 (tpt) outliers start: 69 outliers final: 29 residues processed: 142 average time/residue: 0.5041 time to fit residues: 87.6983 Evaluate side-chains 102 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 70 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 5 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 237 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 245 optimal weight: 10.0000 chunk 294 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.119821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.073851 restraints weight = 60729.599| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 4.13 r_work: 0.2996 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25758 Z= 0.160 Angle : 0.641 9.783 35256 Z= 0.303 Chirality : 0.049 0.335 4335 Planarity : 0.004 0.045 4314 Dihedral : 10.498 113.644 5761 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.61 % Allowed : 12.64 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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: 0.00 (0.15), residues: 2931 helix: 2.00 (0.21), residues: 687 sheet: 0.67 (0.21), residues: 576 loop : -1.17 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1000 TYR 0.017 0.001 TYR A1067 PHE 0.034 0.001 PHE B 541 TRP 0.028 0.002 TRP A 353 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00363 (25605) covalent geometry : angle 0.60161 (34824) SS BOND : bond 0.00409 ( 27) SS BOND : angle 0.99160 ( 54) hydrogen bonds : bond 0.07124 ( 1001) hydrogen bonds : angle 5.73271 ( 2757) link_ALPHA1-3 : bond 0.01249 ( 15) link_ALPHA1-3 : angle 1.44762 ( 45) link_ALPHA1-6 : bond 0.01277 ( 15) link_ALPHA1-6 : angle 2.07940 ( 45) link_BETA1-4 : bond 0.00456 ( 48) link_BETA1-4 : angle 1.70788 ( 144) link_NAG-ASN : bond 0.00432 ( 48) link_NAG-ASN : angle 2.81615 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 85 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 VAL cc_start: 0.8857 (t) cc_final: 0.8618 (p) REVERT: A 314 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8272 (tp40) REVERT: A 1144 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7825 (mm-30) REVERT: B 133 PHE cc_start: 0.7807 (m-80) cc_final: 0.7281 (m-80) REVERT: B 190 ARG cc_start: 0.7559 (ttp-170) cc_final: 0.6998 (ttm110) REVERT: B 227 VAL cc_start: 0.8861 (t) cc_final: 0.8575 (p) REVERT: B 314 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8199 (tm-30) REVERT: C 133 PHE cc_start: 0.7653 (m-80) cc_final: 0.7224 (m-80) REVERT: C 740 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8333 (tpt) outliers start: 68 outliers final: 42 residues processed: 148 average time/residue: 0.4778 time to fit residues: 87.0356 Evaluate side-chains 116 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 71 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 237 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 259 optimal weight: 0.5980 chunk 48 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 141 optimal weight: 20.0000 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.118998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.072821 restraints weight = 60617.101| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 4.15 r_work: 0.2971 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 25758 Z= 0.219 Angle : 0.678 9.852 35256 Z= 0.323 Chirality : 0.051 0.345 4335 Planarity : 0.005 0.073 4314 Dihedral : 10.190 114.852 5761 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.68 % Allowed : 13.03 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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: 0.00 (0.15), residues: 2931 helix: 2.07 (0.21), residues: 669 sheet: 0.71 (0.22), residues: 558 loop : -1.17 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 454 TYR 0.019 0.001 TYR C1067 PHE 0.019 0.002 PHE C 400 TRP 0.037 0.002 TRP A 353 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00525 (25605) covalent geometry : angle 0.63978 (34824) SS BOND : bond 0.00358 ( 27) SS BOND : angle 0.83561 ( 54) hydrogen bonds : bond 0.07904 ( 1001) hydrogen bonds : angle 5.80528 ( 2757) link_ALPHA1-3 : bond 0.01244 ( 15) link_ALPHA1-3 : angle 1.45270 ( 45) link_ALPHA1-6 : bond 0.01341 ( 15) link_ALPHA1-6 : angle 2.17247 ( 45) link_BETA1-4 : bond 0.00439 ( 48) link_BETA1-4 : angle 1.72196 ( 144) link_NAG-ASN : bond 0.00428 ( 48) link_NAG-ASN : angle 2.85777 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 79 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7847 (m-80) cc_final: 0.7217 (m-80) REVERT: A 314 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8295 (tp40) REVERT: B 133 PHE cc_start: 0.7827 (m-80) cc_final: 0.7305 (m-80) REVERT: B 190 ARG cc_start: 0.7587 (ttp-170) cc_final: 0.7014 (ttm110) REVERT: B 227 VAL cc_start: 0.8853 (t) cc_final: 0.8564 (p) REVERT: B 314 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8229 (tm-30) REVERT: B 794 ILE cc_start: 0.7596 (pt) cc_final: 0.7377 (mm) REVERT: C 133 PHE cc_start: 0.7688 (m-80) cc_final: 0.7279 (m-80) REVERT: C 239 GLN cc_start: 0.7220 (tp40) cc_final: 0.6672 (mm-40) REVERT: C 740 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8367 (tpt) outliers start: 70 outliers final: 41 residues processed: 144 average time/residue: 0.4396 time to fit residues: 79.3410 Evaluate side-chains 118 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 74 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 6.9990 chunk 224 optimal weight: 7.9990 chunk 259 optimal weight: 0.9980 chunk 174 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 226 optimal weight: 8.9990 chunk 287 optimal weight: 0.8980 chunk 115 optimal weight: 8.9990 chunk 162 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 179 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1036 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.121057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.075859 restraints weight = 60554.820| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 4.07 r_work: 0.3046 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25758 Z= 0.120 Angle : 0.601 9.861 35256 Z= 0.281 Chirality : 0.047 0.326 4335 Planarity : 0.004 0.056 4314 Dihedral : 9.153 111.314 5761 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.76 % Allowed : 13.87 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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: 0.21 (0.15), residues: 2931 helix: 2.36 (0.21), residues: 666 sheet: 0.82 (0.22), residues: 552 loop : -1.07 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 454 TYR 0.015 0.001 TYR A1067 PHE 0.020 0.001 PHE B 238 TRP 0.034 0.002 TRP A 353 HIS 0.002 0.000 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00242 (25605) covalent geometry : angle 0.56185 (34824) SS BOND : bond 0.00284 ( 27) SS BOND : angle 0.58700 ( 54) hydrogen bonds : bond 0.05879 ( 1001) hydrogen bonds : angle 5.43669 ( 2757) link_ALPHA1-3 : bond 0.01267 ( 15) link_ALPHA1-3 : angle 1.24696 ( 45) link_ALPHA1-6 : bond 0.01383 ( 15) link_ALPHA1-6 : angle 1.97480 ( 45) link_BETA1-4 : bond 0.00491 ( 48) link_BETA1-4 : angle 1.70897 ( 144) link_NAG-ASN : bond 0.00463 ( 48) link_NAG-ASN : angle 2.69402 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 97 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.7657 (p0) REVERT: A 227 VAL cc_start: 0.8825 (t) cc_final: 0.8571 (p) REVERT: A 314 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8284 (tp40) REVERT: A 786 LYS cc_start: 0.9189 (mmpt) cc_final: 0.8981 (mmtp) REVERT: A 1144 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7876 (mm-30) REVERT: B 133 PHE cc_start: 0.7754 (m-80) cc_final: 0.7205 (m-80) REVERT: B 190 ARG cc_start: 0.7541 (ttp-170) cc_final: 0.6978 (ttm110) REVERT: B 227 VAL cc_start: 0.8823 (t) cc_final: 0.8552 (p) REVERT: B 314 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8241 (tp40) REVERT: B 855 PHE cc_start: 0.7921 (p90) cc_final: 0.7644 (p90) REVERT: B 957 GLN cc_start: 0.8773 (tt0) cc_final: 0.8552 (tt0) REVERT: C 40 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.7817 (p0) REVERT: C 133 PHE cc_start: 0.7665 (m-80) cc_final: 0.7223 (m-80) REVERT: C 239 GLN cc_start: 0.7161 (tp40) cc_final: 0.6874 (mm110) REVERT: C 740 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8267 (tpt) outliers start: 46 outliers final: 29 residues processed: 137 average time/residue: 0.5023 time to fit residues: 83.9611 Evaluate side-chains 115 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 81 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 158 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 201 optimal weight: 0.7980 chunk 294 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 223 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 186 optimal weight: 2.9990 chunk 143 optimal weight: 0.3980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.121025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.075352 restraints weight = 60277.528| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 4.18 r_work: 0.3038 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25758 Z= 0.124 Angle : 0.602 9.846 35256 Z= 0.281 Chirality : 0.047 0.332 4335 Planarity : 0.004 0.055 4314 Dihedral : 8.731 111.941 5761 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.92 % Allowed : 14.21 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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: 0.26 (0.15), residues: 2931 helix: 2.29 (0.21), residues: 684 sheet: 0.80 (0.22), residues: 561 loop : -1.00 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 454 TYR 0.016 0.001 TYR A1067 PHE 0.020 0.001 PHE B 400 TRP 0.043 0.002 TRP B 353 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00264 (25605) covalent geometry : angle 0.56373 (34824) SS BOND : bond 0.00285 ( 27) SS BOND : angle 0.59020 ( 54) hydrogen bonds : bond 0.05978 ( 1001) hydrogen bonds : angle 5.36798 ( 2757) link_ALPHA1-3 : bond 0.01246 ( 15) link_ALPHA1-3 : angle 1.22920 ( 45) link_ALPHA1-6 : bond 0.01363 ( 15) link_ALPHA1-6 : angle 1.99681 ( 45) link_BETA1-4 : bond 0.00467 ( 48) link_BETA1-4 : angle 1.69963 ( 144) link_NAG-ASN : bond 0.00411 ( 48) link_NAG-ASN : angle 2.66472 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 92 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.7644 (p0) REVERT: A 227 VAL cc_start: 0.8823 (t) cc_final: 0.8574 (p) REVERT: A 314 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8278 (tp40) REVERT: A 386 LYS cc_start: 0.7466 (mttt) cc_final: 0.7081 (mttt) REVERT: A 786 LYS cc_start: 0.9204 (mmpt) cc_final: 0.8996 (mmtp) REVERT: A 1144 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7867 (mm-30) REVERT: B 40 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.7786 (p0) REVERT: B 133 PHE cc_start: 0.7763 (m-80) cc_final: 0.7187 (m-80) REVERT: B 190 ARG cc_start: 0.7537 (ttp-170) cc_final: 0.6975 (ttm110) REVERT: B 227 VAL cc_start: 0.8818 (t) cc_final: 0.8548 (p) REVERT: B 314 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8185 (tm-30) REVERT: B 855 PHE cc_start: 0.8014 (p90) cc_final: 0.7613 (p90) REVERT: B 957 GLN cc_start: 0.8802 (tt0) cc_final: 0.8579 (tt0) REVERT: C 40 ASP cc_start: 0.8504 (OUTLIER) cc_final: 0.7803 (p0) REVERT: C 133 PHE cc_start: 0.7665 (m-80) cc_final: 0.7234 (m-80) REVERT: C 227 VAL cc_start: 0.8812 (t) cc_final: 0.8570 (p) REVERT: C 239 GLN cc_start: 0.7186 (tp40) cc_final: 0.6794 (mm110) REVERT: C 380 TYR cc_start: 0.5904 (m-10) cc_final: 0.5578 (m-10) REVERT: C 386 LYS cc_start: 0.7464 (mttt) cc_final: 0.7232 (mttt) REVERT: C 740 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8266 (tpt) outliers start: 50 outliers final: 33 residues processed: 138 average time/residue: 0.4771 time to fit residues: 81.3443 Evaluate side-chains 119 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 80 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 81 optimal weight: 0.5980 chunk 267 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 155 optimal weight: 0.5980 chunk 181 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 259 optimal weight: 0.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.121490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.075499 restraints weight = 60003.159| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 4.27 r_work: 0.3021 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25758 Z= 0.134 Angle : 0.604 9.863 35256 Z= 0.283 Chirality : 0.047 0.333 4335 Planarity : 0.004 0.052 4314 Dihedral : 8.412 112.531 5759 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.88 % Allowed : 14.44 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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: 0.26 (0.15), residues: 2931 helix: 2.29 (0.21), residues: 684 sheet: 0.81 (0.22), residues: 555 loop : -1.00 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 454 TYR 0.020 0.001 TYR C 453 PHE 0.019 0.001 PHE C 400 TRP 0.041 0.002 TRP A 353 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00294 (25605) covalent geometry : angle 0.56602 (34824) SS BOND : bond 0.00291 ( 27) SS BOND : angle 0.58920 ( 54) hydrogen bonds : bond 0.06220 ( 1001) hydrogen bonds : angle 5.37935 ( 2757) link_ALPHA1-3 : bond 0.01220 ( 15) link_ALPHA1-3 : angle 1.21592 ( 45) link_ALPHA1-6 : bond 0.01352 ( 15) link_ALPHA1-6 : angle 2.00282 ( 45) link_BETA1-4 : bond 0.00473 ( 48) link_BETA1-4 : angle 1.70153 ( 144) link_NAG-ASN : bond 0.00396 ( 48) link_NAG-ASN : angle 2.63998 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 87 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.7637 (p0) REVERT: A 227 VAL cc_start: 0.8837 (t) cc_final: 0.8586 (p) REVERT: A 314 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8290 (tp40) REVERT: A 386 LYS cc_start: 0.7481 (mttt) cc_final: 0.7110 (mttt) REVERT: A 786 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8979 (mmtp) REVERT: A 1144 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7829 (mm-30) REVERT: B 40 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.7806 (p0) REVERT: B 133 PHE cc_start: 0.7767 (m-80) cc_final: 0.7244 (m-80) REVERT: B 190 ARG cc_start: 0.7570 (ttp-170) cc_final: 0.7013 (ttm110) REVERT: B 227 VAL cc_start: 0.8822 (t) cc_final: 0.8547 (p) REVERT: B 314 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8171 (tm-30) REVERT: B 957 GLN cc_start: 0.8805 (tt0) cc_final: 0.8579 (tt0) REVERT: C 40 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.7822 (p0) REVERT: C 133 PHE cc_start: 0.7664 (m-80) cc_final: 0.7245 (m-80) REVERT: C 227 VAL cc_start: 0.8814 (t) cc_final: 0.8570 (p) REVERT: C 239 GLN cc_start: 0.7244 (tp40) cc_final: 0.6875 (mm110) REVERT: C 380 TYR cc_start: 0.5963 (m-10) cc_final: 0.5630 (m-10) REVERT: C 541 PHE cc_start: 0.5411 (m-10) cc_final: 0.4805 (m-10) outliers start: 49 outliers final: 37 residues processed: 131 average time/residue: 0.4764 time to fit residues: 77.0911 Evaluate side-chains 128 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 85 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 157 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 206 optimal weight: 0.9980 chunk 257 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 212 optimal weight: 9.9990 chunk 259 optimal weight: 0.6980 chunk 119 optimal weight: 4.9990 chunk 269 optimal weight: 0.6980 chunk 236 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.121444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.075809 restraints weight = 60647.104| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 4.19 r_work: 0.3053 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25758 Z= 0.116 Angle : 0.591 9.845 35256 Z= 0.276 Chirality : 0.046 0.326 4335 Planarity : 0.004 0.050 4314 Dihedral : 8.119 111.587 5757 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.69 % Allowed : 14.75 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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: 0.31 (0.15), residues: 2931 helix: 2.34 (0.21), residues: 684 sheet: 0.88 (0.22), residues: 549 loop : -0.98 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 454 TYR 0.025 0.001 TYR B 453 PHE 0.021 0.001 PHE B 541 TRP 0.046 0.002 TRP B 353 HIS 0.002 0.000 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00239 (25605) covalent geometry : angle 0.55341 (34824) SS BOND : bond 0.00274 ( 27) SS BOND : angle 0.56053 ( 54) hydrogen bonds : bond 0.05673 ( 1001) hydrogen bonds : angle 5.32140 ( 2757) link_ALPHA1-3 : bond 0.01207 ( 15) link_ALPHA1-3 : angle 1.17756 ( 45) link_ALPHA1-6 : bond 0.01341 ( 15) link_ALPHA1-6 : angle 1.95833 ( 45) link_BETA1-4 : bond 0.00490 ( 48) link_BETA1-4 : angle 1.70303 ( 144) link_NAG-ASN : bond 0.00415 ( 48) link_NAG-ASN : angle 2.59065 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 93 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.7641 (p0) REVERT: A 227 VAL cc_start: 0.8817 (t) cc_final: 0.8575 (p) REVERT: A 314 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8283 (tp40) REVERT: A 386 LYS cc_start: 0.7472 (mttt) cc_final: 0.7159 (mttt) REVERT: A 786 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8983 (mmtp) REVERT: B 40 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.7805 (p0) REVERT: B 133 PHE cc_start: 0.7799 (m-80) cc_final: 0.7222 (m-80) REVERT: B 190 ARG cc_start: 0.7557 (ttp-170) cc_final: 0.7005 (ttm110) REVERT: B 227 VAL cc_start: 0.8807 (t) cc_final: 0.8545 (p) REVERT: B 314 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8151 (tm-30) REVERT: B 957 GLN cc_start: 0.8793 (tt0) cc_final: 0.8563 (tt0) REVERT: C 40 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.7820 (p0) REVERT: C 133 PHE cc_start: 0.7677 (m-80) cc_final: 0.7240 (m-80) REVERT: C 227 VAL cc_start: 0.8809 (t) cc_final: 0.8573 (p) REVERT: C 239 GLN cc_start: 0.7224 (tp40) cc_final: 0.6794 (mm110) REVERT: C 380 TYR cc_start: 0.6001 (m-10) cc_final: 0.5722 (m-10) REVERT: C 1144 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7873 (mm-30) outliers start: 44 outliers final: 35 residues processed: 134 average time/residue: 0.4812 time to fit residues: 78.5416 Evaluate side-chains 121 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 80 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 289 optimal weight: 0.9980 chunk 268 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 249 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 184 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.121216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.075677 restraints weight = 60589.177| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 4.17 r_work: 0.3046 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25758 Z= 0.122 Angle : 0.594 9.853 35256 Z= 0.278 Chirality : 0.046 0.329 4335 Planarity : 0.004 0.048 4314 Dihedral : 7.966 111.693 5757 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.80 % Allowed : 14.87 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % 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: 0.31 (0.15), residues: 2931 helix: 2.36 (0.21), residues: 684 sheet: 0.61 (0.21), residues: 597 loop : -0.93 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 454 TYR 0.020 0.001 TYR C 453 PHE 0.017 0.001 PHE B 238 TRP 0.040 0.002 TRP A 353 HIS 0.002 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00262 (25605) covalent geometry : angle 0.55767 (34824) SS BOND : bond 0.00279 ( 27) SS BOND : angle 0.56817 ( 54) hydrogen bonds : bond 0.05794 ( 1001) hydrogen bonds : angle 5.33725 ( 2757) link_ALPHA1-3 : bond 0.01187 ( 15) link_ALPHA1-3 : angle 1.19486 ( 45) link_ALPHA1-6 : bond 0.01324 ( 15) link_ALPHA1-6 : angle 1.95629 ( 45) link_BETA1-4 : bond 0.00485 ( 48) link_BETA1-4 : angle 1.69738 ( 144) link_NAG-ASN : bond 0.00395 ( 48) link_NAG-ASN : angle 2.57492 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9816.64 seconds wall clock time: 168 minutes 17.70 seconds (10097.70 seconds total)