Starting phenix.real_space_refine on Sat Feb 7 06:28:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ofo_70440/02_2026/9ofo_70440_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ofo_70440/02_2026/9ofo_70440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ofo_70440/02_2026/9ofo_70440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ofo_70440/02_2026/9ofo_70440.map" model { file = "/net/cci-nas-00/data/ceres_data/9ofo_70440/02_2026/9ofo_70440_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ofo_70440/02_2026/9ofo_70440_neut.cif" } resolution = 2.82 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= 0.002 sd= 0.037 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 141 5.16 5 C 19083 2.51 5 N 4878 2.21 5 O 6168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30270 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 7768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 7768 Classifications: {'peptide': 1012} Link IDs: {'PTRANS': 36, 'TRANS': 975} Chain: "B" Number of atoms: 7768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 7768 Classifications: {'peptide': 1012} Link IDs: {'PTRANS': 36, 'TRANS': 975} Chain: "C" Number of atoms: 7768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 7768 Classifications: {'peptide': 1012} Link IDs: {'PTRANS': 36, 'TRANS': 975} Chain: "H" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 944 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "M" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 944 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "N" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "O" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 944 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "P" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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: "T" 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: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 7.43, per 1000 atoms: 0.25 Number of scatterers: 30270 At special positions: 0 Unit cell: (146.88, 143.64, 184.68, 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 141 16.00 O 6168 8.00 N 4878 7.00 C 19083 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 32 " - pdb=" SG CYS A 229 " distance=2.03 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS A 105 " distance=2.04 Simple disulfide: pdb=" SG CYS A 145 " - pdb=" SG CYS A 168 " distance=2.04 Simple disulfide: pdb=" SG CYS A 254 " - pdb=" SG CYS A 263 " distance=2.03 Simple disulfide: pdb=" SG CYS A 316 " - pdb=" SG CYS A 319 " distance=2.03 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 384 " distance=2.03 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 394 " distance=2.02 Simple disulfide: pdb=" SG CYS A 444 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 541 " - pdb=" SG CYS A 554 " distance=2.03 Simple disulfide: pdb=" SG CYS A 606 " - pdb=" SG CYS A 628 " distance=2.03 Simple disulfide: pdb=" SG CYS A 611 " - pdb=" SG CYS A 617 " distance=2.03 Simple disulfide: pdb=" SG CYS A 713 " - pdb=" SG CYS A 724 " distance=2.03 Simple disulfide: pdb=" SG CYS A 915 " - pdb=" SG CYS A 926 " distance=2.03 Simple disulfide: pdb=" SG CYS A 965 " - pdb=" SG CYS A1012 " distance=2.04 Simple disulfide: pdb=" SG CYS B 32 " - pdb=" SG CYS B 229 " distance=2.03 Simple disulfide: pdb=" SG CYS B 81 " - pdb=" SG CYS B 105 " distance=2.03 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 168 " distance=2.04 Simple disulfide: pdb=" SG CYS B 254 " - pdb=" SG CYS B 263 " distance=2.03 Simple disulfide: pdb=" SG CYS B 316 " - pdb=" SG CYS B 319 " distance=2.03 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 384 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 394 " distance=2.03 Simple disulfide: pdb=" SG CYS B 444 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 541 " - pdb=" SG CYS B 554 " distance=2.03 Simple disulfide: pdb=" SG CYS B 606 " - pdb=" SG CYS B 628 " distance=2.03 Simple disulfide: pdb=" SG CYS B 611 " - pdb=" SG CYS B 617 " distance=2.03 Simple disulfide: pdb=" SG CYS B 713 " - pdb=" SG CYS B 724 " distance=2.03 Simple disulfide: pdb=" SG CYS B 915 " - pdb=" SG CYS B 926 " distance=2.03 Simple disulfide: pdb=" SG CYS B 965 " - pdb=" SG CYS B1012 " distance=2.03 Simple disulfide: pdb=" SG CYS C 32 " - pdb=" SG CYS C 229 " distance=2.03 Simple disulfide: pdb=" SG CYS C 81 " - pdb=" SG CYS C 105 " distance=2.05 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 168 " distance=2.04 Simple disulfide: pdb=" SG CYS C 254 " - pdb=" SG CYS C 263 " distance=2.03 Simple disulfide: pdb=" SG CYS C 316 " - pdb=" SG CYS C 319 " distance=2.03 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 384 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 394 " distance=2.03 Simple disulfide: pdb=" SG CYS C 444 " - pdb=" SG CYS C 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 541 " - pdb=" SG CYS C 554 " distance=2.03 Simple disulfide: pdb=" SG CYS C 606 " - pdb=" SG CYS C 628 " distance=2.03 Simple disulfide: pdb=" SG CYS C 611 " - pdb=" SG CYS C 617 " distance=2.03 Simple disulfide: pdb=" SG CYS C 713 " - pdb=" SG CYS C 724 " distance=2.03 Simple disulfide: pdb=" SG CYS C 915 " - pdb=" SG CYS C 926 " distance=2.04 Simple disulfide: pdb=" SG CYS C 965 " - pdb=" SG CYS C1012 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.05 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.04 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.05 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 D 3 " - " MAN D 4 " " BMA T 3 " - " MAN T 4 " " BMA d 3 " - " MAN d 4 " ALPHA1-6 " BMA D 3 " - " MAN D 5 " " BMA T 3 " - " MAN T 5 " " BMA d 3 " - " MAN d 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " 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 X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG 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 k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " NAG-ASN " NAG A1201 " - " ASN A 111 " " NAG A1202 " - " ASN A 147 " " NAG A1203 " - " ASN A 176 " " NAG A1204 " - " ASN A 220 " " NAG A1205 " - " ASN A 332 " " NAG A1206 " - " ASN A 438 " " NAG A1207 " - " ASN A 462 " " NAG A1208 " - " ASN A 486 " " NAG A1209 " - " ASN A 516 " " NAG A1210 " - " ASN A 536 " " NAG A1211 " - " ASN A 540 " " NAG A1212 " - " ASN A 566 " " NAG A1213 " - " ASN A 585 " " NAG A1215 " - " ASN A1035 " " NAG B1201 " - " ASN B 111 " " NAG B1202 " - " ASN B 147 " " NAG B1203 " - " ASN B 176 " " NAG B1204 " - " ASN B 220 " " NAG B1205 " - " ASN B 332 " " NAG B1206 " - " ASN B 438 " " NAG B1207 " - " ASN B 462 " " NAG B1208 " - " ASN B 486 " " NAG B1209 " - " ASN B 516 " " NAG B1210 " - " ASN B 536 " " NAG B1211 " - " ASN B 540 " " NAG B1212 " - " ASN B 566 " " NAG B1213 " - " ASN B 585 " " NAG B1214 " - " ASN B 661 " " NAG B1215 " - " ASN B1035 " " NAG C1201 " - " ASN C 111 " " NAG C1202 " - " ASN C 147 " " NAG C1203 " - " ASN C 176 " " NAG C1204 " - " ASN C 220 " " NAG C1205 " - " ASN C 332 " " NAG C1206 " - " ASN C 438 " " NAG C1207 " - " ASN C 462 " " NAG C1208 " - " ASN C 486 " " NAG C1209 " - " ASN C 516 " " NAG C1210 " - " ASN C 536 " " NAG C1211 " - " ASN C 540 " " NAG C1212 " - " ASN C 566 " " NAG C1213 " - " ASN C 585 " " NAG C1214 " - " ASN C 661 " " NAG C1215 " - " ASN C1035 " " NAG D 1 " - " ASN A 62 " " NAG F 1 " - " ASN A 171 " " NAG G 1 " - " ASN A 242 " " NAG I 1 " - " ASN A 325 " " NAG J 1 " - " ASN A 579 " " NAG K 1 " - " ASN A 669 " " NAG Q 1 " - " ASN A 928 " " NAG R 1 " - " ASN A1013 " " NAG S 1 " - " ASN A1018 " " NAG T 1 " - " ASN B 62 " " NAG U 1 " - " ASN B 98 " " NAG V 1 " - " ASN B 171 " " NAG W 1 " - " ASN B 242 " " NAG X 1 " - " ASN B 325 " " NAG Y 1 " - " ASN B 579 " " NAG Z 1 " - " ASN B 669 " " NAG a 1 " - " ASN B 928 " " NAG b 1 " - " ASN B1013 " " NAG c 1 " - " ASN B1018 " " NAG d 1 " - " ASN C 62 " " NAG e 1 " - " ASN C 98 " " NAG f 1 " - " ASN C 171 " " NAG g 1 " - " ASN C 242 " " NAG h 1 " - " ASN C 325 " " NAG i 1 " - " ASN C 579 " " NAG j 1 " - " ASN C 669 " " NAG k 1 " - " ASN C 928 " " NAG l 1 " - " ASN C1013 " " NAG m 1 " - " ASN C1018 " Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.3 seconds 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6894 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 54 sheets defined 23.0% alpha, 37.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 126 through 129 removed outlier: 4.423A pdb=" N ARG A 129 " --> pdb=" O ASN A 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 126 through 129' Processing helix chain 'A' and resid 148 through 153 removed outlier: 4.128A pdb=" N SER A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY A 153 " --> pdb=" O THR A 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 148 through 153' Processing helix chain 'A' and resid 256 through 265 Processing helix chain 'A' and resid 371 through 376 removed outlier: 3.740A pdb=" N VAL A 374 " --> pdb=" O PHE A 371 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN A 375 " --> pdb=" O GLY A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 522 removed outlier: 4.030A pdb=" N GLY A 521 " --> pdb=" O THR A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 612 Processing helix chain 'A' and resid 614 through 622 removed outlier: 3.624A pdb=" N GLU A 619 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 620 " --> pdb=" O ARG A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 650 removed outlier: 4.125A pdb=" N CYS A 628 " --> pdb=" O TYR A 624 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS A 629 " --> pdb=" O THR A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 658 Processing helix chain 'A' and resid 692 through 697 Processing helix chain 'A' and resid 709 through 714 removed outlier: 3.766A pdb=" N THR A 714 " --> pdb=" O TYR A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 739 through 754 removed outlier: 3.891A pdb=" N ILE A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 763 removed outlier: 3.554A pdb=" N ALA A 763 " --> pdb=" O THR A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 779 removed outlier: 3.615A pdb=" N ALA A 770 " --> pdb=" O PRO A 766 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A 778 " --> pdb=" O ARG A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 809 Processing helix chain 'A' and resid 811 through 817 removed outlier: 5.356A pdb=" N GLN A 816 " --> pdb=" O ALA A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 836 removed outlier: 3.661A pdb=" N VAL A 824 " --> pdb=" O ALA A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 848 removed outlier: 4.343A pdb=" N SER A 841 " --> pdb=" O GLN A 837 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU A 842 " --> pdb=" O GLN A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 851 No H-bonds generated for 'chain 'A' and resid 849 through 851' Processing helix chain 'A' and resid 859 through 865 Processing helix chain 'A' and resid 868 through 915 removed outlier: 4.216A pdb=" N GLN A 874 " --> pdb=" O PRO A 870 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG A 878 " --> pdb=" O GLN A 874 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 879 " --> pdb=" O GLN A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1004 No H-bonds generated for 'chain 'A' and resid 1002 through 1004' Processing helix chain 'A' and resid 1023 through 1027 Processing helix chain 'A' and resid 1033 through 1042 removed outlier: 3.691A pdb=" N GLN A1039 " --> pdb=" O ASN A1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 129 removed outlier: 4.428A pdb=" N ARG B 129 " --> pdb=" O ASN B 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 126 through 129' Processing helix chain 'B' and resid 148 through 153 removed outlier: 4.135A pdb=" N SER B 152 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY B 153 " --> pdb=" O THR B 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 148 through 153' Processing helix chain 'B' and resid 256 through 266 Processing helix chain 'B' and resid 332 through 336 Processing helix chain 'B' and resid 372 through 376 removed outlier: 4.004A pdb=" N ASN B 375 " --> pdb=" O GLY B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 522 removed outlier: 3.978A pdb=" N GLY B 521 " --> pdb=" O THR B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 612 Processing helix chain 'B' and resid 614 through 622 removed outlier: 3.550A pdb=" N GLU B 619 " --> pdb=" O VAL B 615 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 620 " --> pdb=" O ARG B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 650 removed outlier: 4.319A pdb=" N LYS B 629 " --> pdb=" O THR B 625 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 631 " --> pdb=" O ALA B 627 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 646 " --> pdb=" O GLU B 642 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B 647 " --> pdb=" O SER B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 658 Processing helix chain 'B' and resid 690 through 697 Processing helix chain 'B' and resid 709 through 716 removed outlier: 3.558A pdb=" N THR B 714 " --> pdb=" O TYR B 710 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS B 715 " --> pdb=" O LYS B 711 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY B 716 " --> pdb=" O LYS B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 728 Processing helix chain 'B' and resid 739 through 754 removed outlier: 3.813A pdb=" N ILE B 754 " --> pdb=" O LEU B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 763 removed outlier: 3.507A pdb=" N ALA B 763 " --> pdb=" O THR B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 779 removed outlier: 3.587A pdb=" N ALA B 770 " --> pdb=" O PRO B 766 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL B 778 " --> pdb=" O ARG B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 809 Processing helix chain 'B' and resid 811 through 817 removed outlier: 5.344A pdb=" N GLN B 816 " --> pdb=" O ALA B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 848 removed outlier: 3.700A pdb=" N VAL B 824 " --> pdb=" O ALA B 820 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN B 838 " --> pdb=" O VAL B 834 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N GLY B 839 " --> pdb=" O VAL B 835 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ASN B 840 " --> pdb=" O ASN B 836 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER B 841 " --> pdb=" O GLN B 837 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU B 842 " --> pdb=" O GLN B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 851 No H-bonds generated for 'chain 'B' and resid 849 through 851' Processing helix chain 'B' and resid 859 through 867 Processing helix chain 'B' and resid 868 through 915 removed outlier: 4.250A pdb=" N GLN B 874 " --> pdb=" O PRO B 870 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG B 878 " --> pdb=" O GLN B 874 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 879 " --> pdb=" O GLN B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 1002 through 1004 No H-bonds generated for 'chain 'B' and resid 1002 through 1004' Processing helix chain 'B' and resid 1023 through 1027 Processing helix chain 'B' and resid 1037 through 1042 Processing helix chain 'C' and resid 148 through 153 removed outlier: 3.840A pdb=" N SER C 152 " --> pdb=" O ASN C 148 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY C 153 " --> pdb=" O THR C 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 148 through 153' Processing helix chain 'C' and resid 256 through 266 Processing helix chain 'C' and resid 518 through 522 removed outlier: 4.076A pdb=" N GLY C 521 " --> pdb=" O THR C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 612 Processing helix chain 'C' and resid 614 through 622 removed outlier: 3.593A pdb=" N GLU C 619 " --> pdb=" O VAL C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 650 removed outlier: 4.111A pdb=" N CYS C 628 " --> pdb=" O TYR C 624 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LYS C 629 " --> pdb=" O THR C 625 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER C 647 " --> pdb=" O SER C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 658 Processing helix chain 'C' and resid 692 through 697 Processing helix chain 'C' and resid 709 through 716 removed outlier: 3.764A pdb=" N THR C 714 " --> pdb=" O TYR C 710 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS C 715 " --> pdb=" O LYS C 711 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY C 716 " --> pdb=" O LYS C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 728 Processing helix chain 'C' and resid 739 through 754 removed outlier: 3.979A pdb=" N ILE C 754 " --> pdb=" O LEU C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 763 removed outlier: 3.903A pdb=" N ALA C 763 " --> pdb=" O THR C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 766 through 777 removed outlier: 3.543A pdb=" N ALA C 770 " --> pdb=" O PRO C 766 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 809 Processing helix chain 'C' and resid 811 through 817 removed outlier: 5.345A pdb=" N GLN C 816 " --> pdb=" O ALA C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 836 removed outlier: 3.628A pdb=" N VAL C 824 " --> pdb=" O ALA C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 837 through 848 removed outlier: 4.460A pdb=" N SER C 841 " --> pdb=" O GLN C 837 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU C 842 " --> pdb=" O GLN C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 851 No H-bonds generated for 'chain 'C' and resid 849 through 851' Processing helix chain 'C' and resid 859 through 865 Processing helix chain 'C' and resid 868 through 915 removed outlier: 4.271A pdb=" N GLN C 874 " --> pdb=" O PRO C 870 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN C 875 " --> pdb=" O GLN C 871 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG C 878 " --> pdb=" O GLN C 874 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU C 879 " --> pdb=" O GLN C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 1002 through 1004 No H-bonds generated for 'chain 'C' and resid 1002 through 1004' Processing helix chain 'C' and resid 1020 through 1027 removed outlier: 4.724A pdb=" N GLN C1025 " --> pdb=" O SER C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1042 removed outlier: 3.941A pdb=" N GLN C1039 " --> pdb=" O ASN C1035 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER C1042 " --> pdb=" O LEU C1038 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.504A pdb=" N ASP H 86 " --> pdb=" O ARG H 83 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 87' Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.237A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.570A pdb=" N THR M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 4.137A pdb=" N ILE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.565A pdb=" N TYR O 32 " --> pdb=" O PHE O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 84 removed outlier: 5.478A pdb=" N VAL A 70 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N VAL A 243 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ARG A 72 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL A 241 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N PHE A 74 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL A 239 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA A 237 " --> pdb=" O PRO A 76 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU A 233 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N LEU A 82 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL A 231 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N SER A 84 " --> pdb=" O CYS A 229 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N CYS A 229 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 230 " --> pdb=" O ASN A 120 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N HIS A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N PHE A 201 " --> pdb=" O TYR A 208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 84 removed outlier: 5.478A pdb=" N VAL A 70 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N VAL A 243 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ARG A 72 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL A 241 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N PHE A 74 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL A 239 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA A 237 " --> pdb=" O PRO A 76 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU A 233 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N LEU A 82 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL A 231 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N SER A 84 " --> pdb=" O CYS A 229 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N CYS A 229 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ASP A 238 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N TYR A 253 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU A 240 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE A 251 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ASN A 242 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 95 through 96 removed outlier: 3.751A pdb=" N ALA A 140 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N CYS A 168 " --> pdb=" O VAL A 183 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 273 through 277 removed outlier: 6.532A pdb=" N GLN A 500 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALA A 511 " --> pdb=" O GLN A 500 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL A 502 " --> pdb=" O VAL A 509 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 437 through 438 removed outlier: 4.773A pdb=" N ILE A 489 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LEU A 479 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TYR A 471 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 323 through 327 removed outlier: 5.879A pdb=" N SER A 407 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU A 402 " --> pdb=" O SER A 407 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ASN A 409 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA A 400 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY A 411 " --> pdb=" O ILE A 398 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 338 through 339 removed outlier: 5.271A pdb=" N LYS A 379 " --> pdb=" O GLY A 420 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLY A 420 " --> pdb=" O LYS A 379 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N SER A 418 " --> pdb=" O GLY A 381 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL A 383 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N SER A 416 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE A 385 " --> pdb=" O TYR A 414 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR A 414 " --> pdb=" O PHE A 385 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 546 through 548 Processing sheet with id=AA9, first strand: chain 'A' and resid 565 through 566 removed outlier: 5.961A pdb=" N ARG A 565 " --> pdb=" O PHE B 652 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 578 through 596 removed outlier: 6.783A pdb=" N ASN A 579 " --> pdb=" O GLU A 959 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU A 959 " --> pdb=" O ASN A 579 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N SER A 581 " --> pdb=" O ASP A 957 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASP A 957 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TYR A 955 " --> pdb=" O PRO A 583 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASN A 585 " --> pdb=" O THR A 953 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 933 " --> pdb=" O THR A 948 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU A 950 " --> pdb=" O HIS A 931 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N HIS A 931 " --> pdb=" O LEU A 950 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 578 through 596 removed outlier: 6.783A pdb=" N ASN A 579 " --> pdb=" O GLU A 959 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU A 959 " --> pdb=" O ASN A 579 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N SER A 581 " --> pdb=" O ASP A 957 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASP A 957 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TYR A 955 " --> pdb=" O PRO A 583 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASN A 585 " --> pdb=" O THR A 953 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLU A 959 " --> pdb=" O LYS A 983 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU A 981 " --> pdb=" O TRP A 961 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 602 through 604 Processing sheet with id=AB4, first strand: chain 'A' and resid 651 through 652 Processing sheet with id=AB5, first strand: chain 'A' and resid 1006 through 1009 removed outlier: 3.749A pdb=" N GLY A 971 " --> pdb=" O ILE A1009 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 69 through 84 removed outlier: 5.336A pdb=" N VAL B 70 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL B 243 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ARG B 72 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL B 241 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N PHE B 74 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL B 239 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA B 237 " --> pdb=" O PRO B 76 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B 233 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU B 82 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL B 231 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR B 230 " --> pdb=" O ASN B 120 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N HIS B 200 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N PHE B 201 " --> pdb=" O TYR B 208 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 69 through 84 removed outlier: 5.336A pdb=" N VAL B 70 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL B 243 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ARG B 72 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL B 241 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N PHE B 74 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL B 239 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA B 237 " --> pdb=" O PRO B 76 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B 233 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU B 82 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL B 231 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ASP B 238 " --> pdb=" O TYR B 253 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N TYR B 253 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU B 240 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE B 251 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASN B 242 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 94 through 96 removed outlier: 3.516A pdb=" N ALA B 140 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N CYS B 168 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.656A pdb=" N GLN B 500 " --> pdb=" O ALA B 511 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ALA B 511 " --> pdb=" O GLN B 500 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL B 502 " --> pdb=" O VAL B 509 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 437 through 438 removed outlier: 5.359A pdb=" N LEU B 479 " --> pdb=" O ILE B 492 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR B 471 " --> pdb=" O LEU B 479 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 323 through 327 removed outlier: 5.675A pdb=" N SER B 407 " --> pdb=" O LEU B 402 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LEU B 402 " --> pdb=" O SER B 407 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ASN B 409 " --> pdb=" O ALA B 400 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ALA B 400 " --> pdb=" O ASN B 409 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY B 411 " --> pdb=" O ILE B 398 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 338 through 340 removed outlier: 4.731A pdb=" N VAL B 383 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LYS B 379 " --> pdb=" O GLY B 420 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N GLY B 420 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER B 418 " --> pdb=" O GLY B 381 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL B 383 " --> pdb=" O SER B 416 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER B 416 " --> pdb=" O VAL B 383 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE B 385 " --> pdb=" O TYR B 414 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N TYR B 414 " --> pdb=" O PHE B 385 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 546 through 548 removed outlier: 3.546A pdb=" N LEU B 546 " --> pdb=" O VAL B 553 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.097A pdb=" N ARG B 565 " --> pdb=" O PHE C 652 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 579 through 596 removed outlier: 6.916A pdb=" N ASN B 579 " --> pdb=" O GLU B 959 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU B 959 " --> pdb=" O ASN B 579 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER B 581 " --> pdb=" O ASP B 957 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASP B 957 " --> pdb=" O SER B 581 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR B 955 " --> pdb=" O PRO B 583 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASN B 585 " --> pdb=" O THR B 953 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE B 933 " --> pdb=" O THR B 948 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU B 950 " --> pdb=" O HIS B 931 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N HIS B 931 " --> pdb=" O LEU B 950 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 579 through 596 removed outlier: 6.916A pdb=" N ASN B 579 " --> pdb=" O GLU B 959 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU B 959 " --> pdb=" O ASN B 579 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER B 581 " --> pdb=" O ASP B 957 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASP B 957 " --> pdb=" O SER B 581 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR B 955 " --> pdb=" O PRO B 583 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASN B 585 " --> pdb=" O THR B 953 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU B 959 " --> pdb=" O LYS B 983 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU B 981 " --> pdb=" O TRP B 961 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 602 through 604 Processing sheet with id=AC9, first strand: chain 'B' and resid 1006 through 1009 removed outlier: 3.829A pdb=" N GLY B 971 " --> pdb=" O ILE B1009 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N CYS B 965 " --> pdb=" O ILE B1019 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 69 through 84 removed outlier: 6.201A pdb=" N SER C 235 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU C 79 " --> pdb=" O LEU C 233 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU C 233 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N CYS C 81 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL C 231 " --> pdb=" O CYS C 81 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N TRP C 83 " --> pdb=" O CYS C 229 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N CYS C 229 " --> pdb=" O TRP C 83 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR C 230 " --> pdb=" O ASN C 120 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N HIS C 200 " --> pdb=" O SER C 196 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N PHE C 201 " --> pdb=" O TYR C 208 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 69 through 84 removed outlier: 6.201A pdb=" N SER C 235 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU C 79 " --> pdb=" O LEU C 233 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU C 233 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N CYS C 81 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL C 231 " --> pdb=" O CYS C 81 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N TRP C 83 " --> pdb=" O CYS C 229 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N CYS C 229 " --> pdb=" O TRP C 83 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ASP C 238 " --> pdb=" O TYR C 253 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N TYR C 253 " --> pdb=" O ASP C 238 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU C 240 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE C 251 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASN C 242 " --> pdb=" O ALA C 249 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 95 through 96 removed outlier: 3.713A pdb=" N ALA C 140 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N CYS C 168 " --> pdb=" O VAL C 183 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 273 through 277 removed outlier: 3.674A pdb=" N GLY C 510 " --> pdb=" O VAL C 502 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TYR C 504 " --> pdb=" O VAL C 508 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N VAL C 508 " --> pdb=" O TYR C 504 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 437 through 438 removed outlier: 5.497A pdb=" N LEU C 479 " --> pdb=" O ILE C 492 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYR C 471 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 323 through 327 removed outlier: 5.912A pdb=" N SER C 407 " --> pdb=" O LEU C 402 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU C 402 " --> pdb=" O SER C 407 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ASN C 409 " --> pdb=" O ALA C 400 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ALA C 400 " --> pdb=" O ASN C 409 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY C 411 " --> pdb=" O ILE C 398 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 338 through 340 removed outlier: 4.591A pdb=" N VAL C 383 " --> pdb=" O VAL C 340 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LYS C 379 " --> pdb=" O GLY C 420 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N GLY C 420 " --> pdb=" O LYS C 379 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER C 418 " --> pdb=" O GLY C 381 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL C 383 " --> pdb=" O SER C 416 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N SER C 416 " --> pdb=" O VAL C 383 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE C 385 " --> pdb=" O TYR C 414 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR C 414 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 546 through 548 removed outlier: 3.549A pdb=" N LEU C 546 " --> pdb=" O VAL C 553 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 579 through 596 removed outlier: 6.461A pdb=" N ASN C 579 " --> pdb=" O GLU C 959 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLU C 959 " --> pdb=" O ASN C 579 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N SER C 581 " --> pdb=" O ASP C 957 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASP C 957 " --> pdb=" O SER C 581 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N TYR C 955 " --> pdb=" O PRO C 583 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASN C 585 " --> pdb=" O THR C 953 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE C 933 " --> pdb=" O THR C 948 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU C 950 " --> pdb=" O HIS C 931 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N HIS C 931 " --> pdb=" O LEU C 950 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 579 through 596 removed outlier: 6.461A pdb=" N ASN C 579 " --> pdb=" O GLU C 959 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLU C 959 " --> pdb=" O ASN C 579 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N SER C 581 " --> pdb=" O ASP C 957 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASP C 957 " --> pdb=" O SER C 581 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N TYR C 955 " --> pdb=" O PRO C 583 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASN C 585 " --> pdb=" O THR C 953 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLU C 959 " --> pdb=" O LYS C 983 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU C 981 " --> pdb=" O TRP C 961 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 602 through 604 Processing sheet with id=AE3, first strand: chain 'C' and resid 1006 through 1009 removed outlier: 3.751A pdb=" N GLY C 971 " --> pdb=" O ILE C1009 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N CYS C 965 " --> pdb=" O ILE C1019 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.528A pdb=" N ALA H 50 " --> pdb=" O TYR H 58 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR H 102 " --> pdb=" O LYS H 94 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.528A pdb=" N ALA H 50 " --> pdb=" O TYR H 58 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.909A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.501A pdb=" N LEU L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AF1, first strand: chain 'M' and resid 57 through 59 removed outlier: 5.393A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N CYS M 92 " --> pdb=" O TRP M 103 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N TRP M 103 " --> pdb=" O CYS M 92 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYS M 94 " --> pdb=" O ASP M 101 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 57 through 59 removed outlier: 5.393A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.592A pdb=" N THR N 22 " --> pdb=" O SER N 7 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER N 67 " --> pdb=" O ASP N 70 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.725A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AF6, first strand: chain 'O' and resid 10 through 11 removed outlier: 5.986A pdb=" N GLY O 10 " --> pdb=" O SER O 110 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'O' and resid 10 through 11 removed outlier: 5.986A pdb=" N GLY O 10 " --> pdb=" O SER O 110 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N CYS O 92 " --> pdb=" O TRP O 103 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N TRP O 103 " --> pdb=" O CYS O 92 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS O 94 " --> pdb=" O ASP O 101 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'P' and resid 5 through 7 removed outlier: 3.515A pdb=" N THR P 22 " --> pdb=" O SER P 7 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP P 70 " --> pdb=" O SER P 67 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'P' and resid 10 through 12 removed outlier: 6.685A pdb=" N LEU P 11 " --> pdb=" O GLU P 105 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N TYR P 49 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) 1192 hydrogen bonds defined for protein. 3156 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.53 Time building geometry restraints manager: 3.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 4793 1.29 - 1.42: 8520 1.42 - 1.56: 17360 1.56 - 1.70: 14 1.70 - 1.83: 186 Bond restraints: 30873 Sorted by residual: bond pdb=" CA ASN C 536 " pdb=" C ASN C 536 " ideal model delta sigma weight residual 1.521 1.431 0.090 1.34e-02 5.57e+03 4.55e+01 bond pdb=" C ASN C 536 " pdb=" O ASN C 536 " ideal model delta sigma weight residual 1.236 1.150 0.086 1.28e-02 6.10e+03 4.54e+01 bond pdb=" C ASN B 98 " pdb=" N GLY B 99 " ideal model delta sigma weight residual 1.333 1.266 0.067 1.16e-02 7.43e+03 3.38e+01 bond pdb=" C1 NAG A1214 " pdb=" C2 NAG A1214 " ideal model delta sigma weight residual 1.532 1.628 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C1 NAG C1210 " pdb=" C2 NAG C1210 " ideal model delta sigma weight residual 1.532 1.623 -0.091 2.00e-02 2.50e+03 2.05e+01 ... (remaining 30868 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 41514 3.97 - 7.93: 476 7.93 - 11.90: 41 11.90 - 15.87: 9 15.87 - 19.84: 8 Bond angle restraints: 42048 Sorted by residual: angle pdb=" N ILE B 121 " pdb=" CA ILE B 121 " pdb=" C ILE B 121 " ideal model delta sigma weight residual 111.88 123.97 -12.09 1.06e+00 8.90e-01 1.30e+02 angle pdb=" N TYR B 624 " pdb=" CA TYR B 624 " pdb=" C TYR B 624 " ideal model delta sigma weight residual 109.76 93.91 15.85 1.59e+00 3.96e-01 9.93e+01 angle pdb=" N ASN C 122 " pdb=" CA ASN C 122 " pdb=" C ASN C 122 " ideal model delta sigma weight residual 110.28 123.67 -13.39 1.48e+00 4.57e-01 8.19e+01 angle pdb=" N ASN A 122 " pdb=" CA ASN A 122 " pdb=" C ASN A 122 " ideal model delta sigma weight residual 110.41 121.48 -11.07 1.23e+00 6.61e-01 8.09e+01 angle pdb=" N ASN C 120 " pdb=" CA ASN C 120 " pdb=" C ASN C 120 " ideal model delta sigma weight residual 109.62 120.52 -10.90 1.50e+00 4.44e-01 5.28e+01 ... (remaining 42043 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.29: 18086 20.29 - 40.59: 1337 40.59 - 60.88: 291 60.88 - 81.18: 118 81.18 - 101.47: 85 Dihedral angle restraints: 19917 sinusoidal: 9123 harmonic: 10794 Sorted by residual: dihedral pdb=" CB CYS B 32 " pdb=" SG CYS B 32 " pdb=" SG CYS B 229 " pdb=" CB CYS B 229 " ideal model delta sinusoidal sigma weight residual -86.00 -147.23 61.23 1 1.00e+01 1.00e-02 4.98e+01 dihedral pdb=" CB CYS A 316 " pdb=" SG CYS A 316 " pdb=" SG CYS A 319 " pdb=" CB CYS A 319 " ideal model delta sinusoidal sigma weight residual -86.00 -139.25 53.25 1 1.00e+01 1.00e-02 3.86e+01 dihedral pdb=" CB CYS C 316 " pdb=" SG CYS C 316 " pdb=" SG CYS C 319 " pdb=" CB CYS C 319 " ideal model delta sinusoidal sigma weight residual -86.00 -138.42 52.42 1 1.00e+01 1.00e-02 3.74e+01 ... (remaining 19914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.276: 5200 0.276 - 0.552: 21 0.552 - 0.828: 0 0.828 - 1.104: 1 1.104 - 1.381: 2 Chirality restraints: 5224 Sorted by residual: chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.42e+02 chirality pdb=" C1 BMA U 3 " pdb=" O4 NAG U 2 " pdb=" C2 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.20e+02 chirality pdb=" C1 NAG C1210 " pdb=" ND2 ASN C 536 " pdb=" C2 NAG C1210 " pdb=" O5 NAG C1210 " both_signs ideal model delta sigma weight residual False -2.40 -1.02 -1.38 2.00e-01 2.50e+01 4.76e+01 ... (remaining 5221 not shown) Planarity restraints: 5296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 2 " 0.325 2.00e-02 2.50e+03 2.73e-01 9.29e+02 pdb=" C7 NAG c 2 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG c 2 " 0.192 2.00e-02 2.50e+03 pdb=" N2 NAG c 2 " -0.469 2.00e-02 2.50e+03 pdb=" O7 NAG c 2 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1214 " 0.233 2.00e-02 2.50e+03 1.91e-01 4.56e+02 pdb=" C7 NAG A1214 " -0.064 2.00e-02 2.50e+03 pdb=" C8 NAG A1214 " 0.163 2.00e-02 2.50e+03 pdb=" N2 NAG A1214 " -0.312 2.00e-02 2.50e+03 pdb=" O7 NAG A1214 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1210 " 0.228 2.00e-02 2.50e+03 1.86e-01 4.31e+02 pdb=" C7 NAG C1210 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG C1210 " 0.165 2.00e-02 2.50e+03 pdb=" N2 NAG C1210 " -0.295 2.00e-02 2.50e+03 pdb=" O7 NAG C1210 " -0.023 2.00e-02 2.50e+03 ... (remaining 5293 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 77 2.59 - 3.16: 25993 3.16 - 3.74: 44863 3.74 - 4.32: 63390 4.32 - 4.90: 104112 Nonbonded interactions: 238435 Sorted by model distance: nonbonded pdb=" ND2 ASN A 98 " pdb=" C1 NAG E 1 " model vdw 2.007 3.550 nonbonded pdb=" ND2 ASN A 98 " pdb=" N2 NAG E 1 " model vdw 2.149 3.200 nonbonded pdb=" O4 NAG C1210 " pdb=" O6 NAG C1210 " model vdw 2.163 3.040 nonbonded pdb=" NE2 GLN B 786 " pdb=" NE2 GLN B 789 " model vdw 2.190 3.200 nonbonded pdb=" ND2 ASN A 661 " pdb=" C1 NAG A1214 " model vdw 2.229 3.550 ... (remaining 238430 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 'T' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'Q' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'a' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'k' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'R' selection = chain 'S' selection = chain 'V' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'f' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'm' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'P' } 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: 5.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 30.710 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.110 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:6.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.143 31045 Z= 0.275 Angle : 1.236 41.516 42516 Z= 0.596 Chirality : 0.071 1.381 5224 Planarity : 0.008 0.273 5223 Dihedral : 16.780 101.470 12879 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.48 % Favored : 96.39 % Rotamer: Outliers : 1.22 % Allowed : 20.02 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.13), residues: 3708 helix: -0.19 (0.18), residues: 678 sheet: 0.48 (0.16), residues: 981 loop : -0.55 (0.14), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 311 TYR 0.044 0.006 TYR B1043 PHE 0.038 0.002 PHE L 71 TRP 0.080 0.005 TRP M 47 HIS 0.005 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00542 (30873) covalent geometry : angle 1.10293 (42048) SS BOND : bond 0.00720 ( 48) SS BOND : angle 1.58271 ( 96) hydrogen bonds : bond 0.22334 ( 1116) hydrogen bonds : angle 8.36509 ( 3156) link_ALPHA1-3 : bond 0.00523 ( 3) link_ALPHA1-3 : angle 1.67514 ( 9) link_ALPHA1-6 : bond 0.01428 ( 3) link_ALPHA1-6 : angle 4.37259 ( 9) link_BETA1-4 : bond 0.01174 ( 45) link_BETA1-4 : angle 3.85179 ( 135) link_NAG-ASN : bond 0.02862 ( 73) link_NAG-ASN : angle 7.19968 ( 219) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 536 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASN cc_start: 0.8702 (t0) cc_final: 0.8359 (t0) REVERT: A 152 SER cc_start: 0.8908 (p) cc_final: 0.8533 (t) REVERT: A 315 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7807 (tptm) REVERT: A 335 LYS cc_start: 0.9031 (mttt) cc_final: 0.8733 (mttp) REVERT: A 406 LYS cc_start: 0.8399 (ptmt) cc_final: 0.8068 (ptmm) REVERT: A 512 MET cc_start: 0.9177 (OUTLIER) cc_final: 0.8535 (mtm) REVERT: A 515 GLU cc_start: 0.7817 (pm20) cc_final: 0.7448 (pm20) REVERT: A 524 ASN cc_start: 0.8111 (t0) cc_final: 0.7718 (t0) REVERT: A 629 LYS cc_start: 0.8941 (tttp) cc_final: 0.8700 (tmtt) REVERT: A 850 ARG cc_start: 0.9058 (mtp85) cc_final: 0.8790 (mtp85) REVERT: A 892 SER cc_start: 0.9132 (t) cc_final: 0.8883 (t) REVERT: A 1010 GLU cc_start: 0.8911 (tp30) cc_final: 0.8420 (tm-30) REVERT: B 119 TYR cc_start: 0.8996 (m-80) cc_final: 0.8678 (m-80) REVERT: B 131 THR cc_start: 0.8854 (p) cc_final: 0.8599 (t) REVERT: B 148 ASN cc_start: 0.8547 (m-40) cc_final: 0.8338 (t0) REVERT: B 515 GLU cc_start: 0.7929 (pm20) cc_final: 0.7644 (pm20) REVERT: B 832 GLN cc_start: 0.8665 (tt0) cc_final: 0.8258 (mm-40) REVERT: B 900 GLU cc_start: 0.8718 (tp30) cc_final: 0.8229 (tp30) REVERT: C 120 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.8445 (t0) REVERT: C 128 ARG cc_start: 0.8495 (ttm110) cc_final: 0.8137 (tpp80) REVERT: C 148 ASN cc_start: 0.8571 (m-40) cc_final: 0.8093 (t0) REVERT: C 295 TYR cc_start: 0.8700 (t80) cc_final: 0.8486 (t80) REVERT: C 546 LEU cc_start: 0.9006 (mt) cc_final: 0.8758 (mp) REVERT: C 586 TRP cc_start: 0.9180 (m100) cc_final: 0.8969 (m100) REVERT: C 616 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8485 (tpt-90) REVERT: C 637 ASN cc_start: 0.8909 (m-40) cc_final: 0.8704 (m-40) REVERT: C 655 LYS cc_start: 0.9012 (tptp) cc_final: 0.8701 (tttp) REVERT: C 832 GLN cc_start: 0.8774 (tp40) cc_final: 0.8196 (mm-40) REVERT: C 874 GLN cc_start: 0.8946 (mm-40) cc_final: 0.8617 (mm-40) REVERT: H 72 ASP cc_start: 0.8447 (t0) cc_final: 0.7852 (t0) REVERT: M 27 PHE cc_start: 0.7024 (p90) cc_final: 0.6588 (p90) REVERT: M 34 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.8234 (mmt) REVERT: M 66 ARG cc_start: 0.7599 (mtp85) cc_final: 0.7190 (mtp85) REVERT: M 79 TYR cc_start: 0.8464 (m-10) cc_final: 0.8198 (m-10) REVERT: M 100 SER cc_start: 0.9059 (p) cc_final: 0.8659 (p) REVERT: N 29 ILE cc_start: 0.8775 (mt) cc_final: 0.8555 (mp) REVERT: N 50 ASP cc_start: 0.8173 (t70) cc_final: 0.7887 (t0) REVERT: N 89 GLN cc_start: 0.7834 (tm-30) cc_final: 0.7216 (tm-30) REVERT: O 66 ARG cc_start: 0.7816 (mtp85) cc_final: 0.7272 (mtp-110) REVERT: O 72 ASP cc_start: 0.8580 (t0) cc_final: 0.7925 (t0) REVERT: O 78 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7886 (tt) REVERT: O 95 ASP cc_start: 0.8822 (t0) cc_final: 0.8527 (t70) REVERT: P 45 LYS cc_start: 0.8557 (mptp) cc_final: 0.8235 (mptp) REVERT: P 50 ASP cc_start: 0.8122 (t70) cc_final: 0.7793 (t0) REVERT: P 89 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.7188 (tm-30) outliers start: 39 outliers final: 17 residues processed: 558 average time/residue: 0.6373 time to fit residues: 421.6148 Evaluate side-chains 524 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 500 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 661 ASN Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 616 ARG Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 89 GLN Chi-restraints excluded: chain P residue 106 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.2980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 GLN A 854 GLN B 505 GLN B 854 GLN C 404 ASN C 848 GLN H 73 ASN ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN P 37 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.095091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.079477 restraints weight = 59721.876| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.73 r_work: 0.3053 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 31045 Z= 0.196 Angle : 0.774 13.694 42516 Z= 0.374 Chirality : 0.050 0.331 5224 Planarity : 0.004 0.042 5223 Dihedral : 10.555 67.342 6687 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.59 % Favored : 96.28 % Rotamer: Outliers : 4.04 % Allowed : 17.45 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.14), residues: 3708 helix: 1.01 (0.20), residues: 672 sheet: 0.54 (0.16), residues: 1005 loop : -0.56 (0.14), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 38 TYR 0.018 0.002 TYR A 167 PHE 0.025 0.002 PHE C 182 TRP 0.029 0.002 TRP H 47 HIS 0.006 0.001 HIS C 298 Details of bonding type rmsd covalent geometry : bond 0.00449 (30873) covalent geometry : angle 0.72195 (42048) SS BOND : bond 0.00547 ( 48) SS BOND : angle 1.17083 ( 96) hydrogen bonds : bond 0.05863 ( 1116) hydrogen bonds : angle 5.90115 ( 3156) link_ALPHA1-3 : bond 0.01093 ( 3) link_ALPHA1-3 : angle 2.00441 ( 9) link_ALPHA1-6 : bond 0.00972 ( 3) link_ALPHA1-6 : angle 2.35331 ( 9) link_BETA1-4 : bond 0.00600 ( 45) link_BETA1-4 : angle 2.58682 ( 135) link_NAG-ASN : bond 0.00738 ( 73) link_NAG-ASN : angle 3.31243 ( 219) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 523 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 SER cc_start: 0.8928 (p) cc_final: 0.8577 (t) REVERT: A 157 ILE cc_start: 0.7128 (OUTLIER) cc_final: 0.6798 (pt) REVERT: A 167 TYR cc_start: 0.8230 (m-80) cc_final: 0.7929 (m-80) REVERT: A 217 VAL cc_start: 0.9067 (m) cc_final: 0.8794 (p) REVERT: A 406 LYS cc_start: 0.8460 (ptmt) cc_final: 0.8157 (ptmm) REVERT: A 451 ASP cc_start: 0.8733 (m-30) cc_final: 0.8468 (m-30) REVERT: A 524 ASN cc_start: 0.7901 (t0) cc_final: 0.7556 (t0) REVERT: A 648 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8231 (tp30) REVERT: A 892 SER cc_start: 0.8979 (t) cc_final: 0.8659 (p) REVERT: A 1010 GLU cc_start: 0.8742 (tp30) cc_final: 0.8197 (tm-30) REVERT: B 317 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.7615 (t80) REVERT: B 328 LEU cc_start: 0.9320 (tp) cc_final: 0.9116 (tp) REVERT: B 423 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8620 (pt) REVERT: B 515 GLU cc_start: 0.8026 (pm20) cc_final: 0.7606 (pm20) REVERT: B 832 GLN cc_start: 0.8549 (tt0) cc_final: 0.8163 (mm-40) REVERT: C 38 ASN cc_start: 0.6207 (t0) cc_final: 0.6006 (t0) REVERT: C 120 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.8155 (t0) REVERT: C 128 ARG cc_start: 0.8515 (ttm110) cc_final: 0.8051 (tpp80) REVERT: C 148 ASN cc_start: 0.8506 (m-40) cc_final: 0.8047 (t0) REVERT: C 317 TYR cc_start: 0.8320 (OUTLIER) cc_final: 0.7397 (t80) REVERT: C 451 ASP cc_start: 0.8798 (m-30) cc_final: 0.8534 (m-30) REVERT: C 648 GLU cc_start: 0.8356 (tm-30) cc_final: 0.8116 (tm-30) REVERT: C 649 MET cc_start: 0.9032 (ttp) cc_final: 0.8797 (ttm) REVERT: C 655 LYS cc_start: 0.8912 (tptp) cc_final: 0.8678 (tttp) REVERT: C 832 GLN cc_start: 0.8799 (tp40) cc_final: 0.8272 (mm-40) REVERT: C 874 GLN cc_start: 0.8948 (mm-40) cc_final: 0.8640 (mm-40) REVERT: H 20 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8227 (mm) REVERT: H 27 PHE cc_start: 0.7409 (p90) cc_final: 0.7053 (p90) REVERT: H 66 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7830 (mtm-85) REVERT: H 72 ASP cc_start: 0.8429 (t0) cc_final: 0.7745 (t0) REVERT: M 27 PHE cc_start: 0.7316 (p90) cc_final: 0.7020 (p90) REVERT: M 66 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7374 (mtp-110) REVERT: N 29 ILE cc_start: 0.8969 (mt) cc_final: 0.8753 (mp) REVERT: N 50 ASP cc_start: 0.8324 (t70) cc_final: 0.8102 (t70) REVERT: N 61 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.6860 (ptt-90) REVERT: N 89 GLN cc_start: 0.7795 (tm-30) cc_final: 0.7173 (tm-30) REVERT: N 96 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7474 (pp) REVERT: O 79 TYR cc_start: 0.8387 (m-10) cc_final: 0.8175 (m-80) REVERT: P 50 ASP cc_start: 0.8108 (t70) cc_final: 0.7890 (t70) REVERT: P 89 GLN cc_start: 0.7394 (tm-30) cc_final: 0.7087 (tm-30) REVERT: P 94 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8216 (mm) outliers start: 129 outliers final: 60 residues processed: 593 average time/residue: 0.6300 time to fit residues: 444.6623 Evaluate side-chains 565 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 494 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 654 LYS Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 661 ASN Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 1020 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 703 LEU Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 61 ARG Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 96 LEU Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 85 THR Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain P residue 106 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 205 optimal weight: 2.9990 chunk 199 optimal weight: 0.3980 chunk 269 optimal weight: 3.9990 chunk 308 optimal weight: 0.0770 chunk 268 optimal weight: 0.6980 chunk 202 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 49 optimal weight: 0.2980 chunk 128 optimal weight: 1.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 ASN B 505 GLN B 854 GLN B1025 GLN ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 53 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.096688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.080949 restraints weight = 59311.754| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.74 r_work: 0.3079 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 31045 Z= 0.128 Angle : 0.695 12.186 42516 Z= 0.333 Chirality : 0.047 0.357 5224 Planarity : 0.004 0.041 5223 Dihedral : 8.171 59.593 6667 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.10 % Favored : 96.74 % Rotamer: Outliers : 3.41 % Allowed : 18.45 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.14), residues: 3708 helix: 1.45 (0.20), residues: 678 sheet: 0.59 (0.16), residues: 1011 loop : -0.48 (0.14), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG O 38 TYR 0.015 0.001 TYR O 100G PHE 0.025 0.001 PHE O 27 TRP 0.028 0.002 TRP M 36 HIS 0.004 0.001 HIS C 298 Details of bonding type rmsd covalent geometry : bond 0.00274 (30873) covalent geometry : angle 0.65092 (42048) SS BOND : bond 0.00447 ( 48) SS BOND : angle 1.02864 ( 96) hydrogen bonds : bond 0.04884 ( 1116) hydrogen bonds : angle 5.42888 ( 3156) link_ALPHA1-3 : bond 0.01149 ( 3) link_ALPHA1-3 : angle 1.80681 ( 9) link_ALPHA1-6 : bond 0.01276 ( 3) link_ALPHA1-6 : angle 2.00459 ( 9) link_BETA1-4 : bond 0.00620 ( 45) link_BETA1-4 : angle 2.33331 ( 135) link_NAG-ASN : bond 0.00606 ( 73) link_NAG-ASN : angle 2.87773 ( 219) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 536 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 SER cc_start: 0.8907 (p) cc_final: 0.8619 (t) REVERT: A 157 ILE cc_start: 0.6910 (OUTLIER) cc_final: 0.6548 (pt) REVERT: A 167 TYR cc_start: 0.8204 (m-80) cc_final: 0.7730 (m-80) REVERT: A 217 VAL cc_start: 0.9039 (m) cc_final: 0.8797 (p) REVERT: A 315 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7515 (tptm) REVERT: A 406 LYS cc_start: 0.8498 (ptmt) cc_final: 0.8173 (ptmm) REVERT: A 451 ASP cc_start: 0.8738 (m-30) cc_final: 0.8480 (m-30) REVERT: A 524 ASN cc_start: 0.7920 (t0) cc_final: 0.7564 (t0) REVERT: A 645 ASP cc_start: 0.8443 (p0) cc_final: 0.8201 (p0) REVERT: A 715 LYS cc_start: 0.8570 (tppt) cc_final: 0.8321 (ttmm) REVERT: A 832 GLN cc_start: 0.8775 (tt0) cc_final: 0.8503 (mt0) REVERT: A 892 SER cc_start: 0.8946 (t) cc_final: 0.8699 (p) REVERT: A 1025 GLN cc_start: 0.8549 (tm-30) cc_final: 0.8292 (tm130) REVERT: B 148 ASN cc_start: 0.8500 (OUTLIER) cc_final: 0.8282 (m-40) REVERT: B 317 TYR cc_start: 0.8281 (OUTLIER) cc_final: 0.7583 (t80) REVERT: B 328 LEU cc_start: 0.9318 (tp) cc_final: 0.9108 (tp) REVERT: B 423 ILE cc_start: 0.8849 (tp) cc_final: 0.8614 (pt) REVERT: B 515 GLU cc_start: 0.8059 (pm20) cc_final: 0.7578 (pm20) REVERT: B 832 GLN cc_start: 0.8541 (tt0) cc_final: 0.8240 (mm-40) REVERT: B 918 SER cc_start: 0.9084 (m) cc_final: 0.8871 (p) REVERT: B 995 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8105 (ttp) REVERT: C 128 ARG cc_start: 0.8513 (ttm110) cc_final: 0.8061 (tpp80) REVERT: C 148 ASN cc_start: 0.8466 (m-40) cc_final: 0.8032 (t0) REVERT: C 157 ILE cc_start: 0.7067 (OUTLIER) cc_final: 0.6689 (tt) REVERT: C 317 TYR cc_start: 0.8311 (OUTLIER) cc_final: 0.7411 (t80) REVERT: C 437 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8130 (tpt) REVERT: C 451 ASP cc_start: 0.8806 (m-30) cc_final: 0.8582 (m-30) REVERT: C 515 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7977 (pm20) REVERT: C 546 LEU cc_start: 0.8971 (mt) cc_final: 0.8718 (mp) REVERT: C 648 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8200 (tm-30) REVERT: C 832 GLN cc_start: 0.8757 (tp40) cc_final: 0.8215 (mm-40) REVERT: C 874 GLN cc_start: 0.8833 (mm-40) cc_final: 0.8565 (mm-40) REVERT: H 72 ASP cc_start: 0.8408 (t0) cc_final: 0.7613 (t0) REVERT: L 61 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7184 (ptt90) REVERT: M 34 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8175 (mmm) REVERT: M 66 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7454 (mtp-110) REVERT: M 100 SER cc_start: 0.8878 (p) cc_final: 0.8525 (p) REVERT: N 29 ILE cc_start: 0.8942 (mt) cc_final: 0.8720 (mp) REVERT: N 89 GLN cc_start: 0.7663 (tm-30) cc_final: 0.7041 (tm-30) REVERT: O 46 GLU cc_start: 0.8149 (pt0) cc_final: 0.7900 (pt0) REVERT: O 66 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8503 (ttp80) REVERT: O 75 LYS cc_start: 0.8845 (mtmm) cc_final: 0.8539 (mtmm) REVERT: P 45 LYS cc_start: 0.8628 (mptp) cc_final: 0.8311 (mptp) REVERT: P 50 ASP cc_start: 0.8071 (t70) cc_final: 0.7852 (t70) REVERT: P 89 GLN cc_start: 0.7358 (tm-30) cc_final: 0.6905 (tm-30) outliers start: 109 outliers final: 48 residues processed: 589 average time/residue: 0.6205 time to fit residues: 433.1123 Evaluate side-chains 567 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 506 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 654 LYS Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 661 ASN Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 995 MET Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 437 MET Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain C residue 703 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 66 ARG Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 85 THR Chi-restraints excluded: chain P residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 259 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 198 optimal weight: 0.2980 chunk 289 optimal weight: 0.9980 chunk 278 optimal weight: 0.6980 chunk 276 optimal weight: 2.9990 chunk 320 optimal weight: 4.9990 chunk 213 optimal weight: 1.9990 chunk 323 optimal weight: 0.8980 chunk 245 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 ASN B 854 GLN C 38 ASN C 837 GLN H 73 ASN ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.094554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.078907 restraints weight = 59358.488| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.74 r_work: 0.3042 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 31045 Z= 0.187 Angle : 0.702 12.684 42516 Z= 0.341 Chirality : 0.048 0.356 5224 Planarity : 0.004 0.046 5223 Dihedral : 7.685 58.971 6662 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.88 % Favored : 95.95 % Rotamer: Outliers : 4.17 % Allowed : 18.64 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.14), residues: 3708 helix: 1.48 (0.20), residues: 681 sheet: 0.56 (0.16), residues: 993 loop : -0.60 (0.14), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 99 TYR 0.022 0.002 TYR O 79 PHE 0.029 0.002 PHE A 166 TRP 0.026 0.002 TRP M 47 HIS 0.004 0.001 HIS C 844 Details of bonding type rmsd covalent geometry : bond 0.00435 (30873) covalent geometry : angle 0.66301 (42048) SS BOND : bond 0.00519 ( 48) SS BOND : angle 1.10820 ( 96) hydrogen bonds : bond 0.04981 ( 1116) hydrogen bonds : angle 5.34064 ( 3156) link_ALPHA1-3 : bond 0.01073 ( 3) link_ALPHA1-3 : angle 2.08297 ( 9) link_ALPHA1-6 : bond 0.01161 ( 3) link_ALPHA1-6 : angle 2.03926 ( 9) link_BETA1-4 : bond 0.00557 ( 45) link_BETA1-4 : angle 2.27319 ( 135) link_NAG-ASN : bond 0.00541 ( 73) link_NAG-ASN : angle 2.69472 ( 219) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 525 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 SER cc_start: 0.8922 (p) cc_final: 0.8628 (t) REVERT: A 157 ILE cc_start: 0.7141 (OUTLIER) cc_final: 0.6860 (pt) REVERT: A 167 TYR cc_start: 0.8282 (m-80) cc_final: 0.7895 (m-80) REVERT: A 217 VAL cc_start: 0.9049 (m) cc_final: 0.8812 (p) REVERT: A 315 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7548 (tptm) REVERT: A 406 LYS cc_start: 0.8537 (ptmt) cc_final: 0.8212 (ptmm) REVERT: A 451 ASP cc_start: 0.8780 (m-30) cc_final: 0.8523 (m-30) REVERT: A 524 ASN cc_start: 0.7934 (t0) cc_final: 0.7594 (t0) REVERT: A 527 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8010 (tm-30) REVERT: A 645 ASP cc_start: 0.8469 (p0) cc_final: 0.8225 (p0) REVERT: A 832 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8541 (mt0) REVERT: A 892 SER cc_start: 0.8964 (t) cc_final: 0.8668 (p) REVERT: B 148 ASN cc_start: 0.8537 (OUTLIER) cc_final: 0.8273 (m-40) REVERT: B 317 TYR cc_start: 0.8368 (OUTLIER) cc_final: 0.7562 (t80) REVERT: B 423 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8656 (pt) REVERT: B 515 GLU cc_start: 0.8103 (pm20) cc_final: 0.7643 (pm20) REVERT: B 711 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.9063 (ttpt) REVERT: B 832 GLN cc_start: 0.8564 (tt0) cc_final: 0.8198 (mm-40) REVERT: C 128 ARG cc_start: 0.8538 (ttm110) cc_final: 0.8068 (tpp80) REVERT: C 148 ASN cc_start: 0.8499 (m-40) cc_final: 0.8087 (t0) REVERT: C 157 ILE cc_start: 0.7183 (OUTLIER) cc_final: 0.6774 (tt) REVERT: C 317 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.7553 (t80) REVERT: C 451 ASP cc_start: 0.8845 (m-30) cc_final: 0.8588 (m-30) REVERT: C 515 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7956 (pm20) REVERT: C 648 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8243 (tm-30) REVERT: C 832 GLN cc_start: 0.8781 (tp40) cc_final: 0.8210 (mm-40) REVERT: C 874 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8581 (mm-40) REVERT: H 66 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7715 (ttp80) REVERT: H 72 ASP cc_start: 0.8472 (t0) cc_final: 0.7693 (t0) REVERT: H 83 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6916 (mpt-90) REVERT: L 61 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7093 (ptt90) REVERT: M 19 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7662 (mmm160) REVERT: M 27 PHE cc_start: 0.7351 (p90) cc_final: 0.6822 (p90) REVERT: M 66 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7791 (mtp-110) REVERT: N 18 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.6729 (ttp-170) REVERT: N 61 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.6897 (ptt-90) REVERT: N 89 GLN cc_start: 0.7781 (tm-30) cc_final: 0.7203 (tm-30) REVERT: N 94 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8307 (mm) REVERT: O 46 GLU cc_start: 0.8179 (pt0) cc_final: 0.7940 (pt0) REVERT: O 70 SER cc_start: 0.8736 (t) cc_final: 0.8400 (p) REVERT: O 75 LYS cc_start: 0.8857 (mtmm) cc_final: 0.8640 (mtmm) REVERT: P 45 LYS cc_start: 0.8645 (mptp) cc_final: 0.8356 (mptp) REVERT: P 50 ASP cc_start: 0.8150 (t70) cc_final: 0.7934 (t70) REVERT: P 89 GLN cc_start: 0.7481 (tm-30) cc_final: 0.6987 (tm-30) outliers start: 133 outliers final: 69 residues processed: 602 average time/residue: 0.6160 time to fit residues: 440.3228 Evaluate side-chains 593 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 506 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 654 LYS Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 832 GLN Chi-restraints excluded: chain A residue 837 GLN Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 661 ASN Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 711 LYS Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 1020 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 703 LEU Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain M residue 19 ARG Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain M residue 67 PHE Chi-restraints excluded: chain N residue 18 ARG Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 61 ARG Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 85 THR Chi-restraints excluded: chain P residue 93 ASN Chi-restraints excluded: chain P residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 141 optimal weight: 1.9990 chunk 165 optimal weight: 0.0470 chunk 166 optimal weight: 0.9990 chunk 350 optimal weight: 4.9990 chunk 356 optimal weight: 1.9990 chunk 271 optimal weight: 0.5980 chunk 154 optimal weight: 0.9990 chunk 354 optimal weight: 0.9980 chunk 222 optimal weight: 2.9990 chunk 308 optimal weight: 0.0980 chunk 228 optimal weight: 0.5980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 819 GLN B 837 GLN B 854 GLN B1025 GLN C 404 ASN H 73 ASN ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.096188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.080443 restraints weight = 59187.124| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.75 r_work: 0.3070 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 31045 Z= 0.127 Angle : 0.667 12.992 42516 Z= 0.324 Chirality : 0.046 0.303 5224 Planarity : 0.004 0.050 5223 Dihedral : 7.166 58.709 6657 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.40 % Favored : 96.44 % Rotamer: Outliers : 4.01 % Allowed : 19.67 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.14), residues: 3708 helix: 1.66 (0.20), residues: 678 sheet: 0.62 (0.16), residues: 1017 loop : -0.51 (0.14), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 99 TYR 0.023 0.001 TYR L 49 PHE 0.028 0.001 PHE A 166 TRP 0.024 0.002 TRP M 36 HIS 0.003 0.001 HIS C 298 Details of bonding type rmsd covalent geometry : bond 0.00282 (30873) covalent geometry : angle 0.63204 (42048) SS BOND : bond 0.00466 ( 48) SS BOND : angle 0.99519 ( 96) hydrogen bonds : bond 0.04414 ( 1116) hydrogen bonds : angle 5.14534 ( 3156) link_ALPHA1-3 : bond 0.01158 ( 3) link_ALPHA1-3 : angle 1.85260 ( 9) link_ALPHA1-6 : bond 0.01275 ( 3) link_ALPHA1-6 : angle 1.96483 ( 9) link_BETA1-4 : bond 0.00596 ( 45) link_BETA1-4 : angle 2.02031 ( 135) link_NAG-ASN : bond 0.00512 ( 73) link_NAG-ASN : angle 2.51080 ( 219) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 521 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 SER cc_start: 0.8871 (p) cc_final: 0.8609 (t) REVERT: A 157 ILE cc_start: 0.6857 (OUTLIER) cc_final: 0.6525 (pt) REVERT: A 167 TYR cc_start: 0.8077 (m-80) cc_final: 0.7582 (m-80) REVERT: A 217 VAL cc_start: 0.8902 (m) cc_final: 0.8675 (p) REVERT: A 315 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7485 (tptm) REVERT: A 406 LYS cc_start: 0.8349 (ptmt) cc_final: 0.8053 (ptmm) REVERT: A 451 ASP cc_start: 0.8437 (m-30) cc_final: 0.8180 (m-30) REVERT: A 524 ASN cc_start: 0.7754 (t0) cc_final: 0.7447 (t0) REVERT: A 527 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7615 (tm-30) REVERT: A 621 LEU cc_start: 0.8693 (tp) cc_final: 0.8442 (tm) REVERT: A 645 ASP cc_start: 0.8185 (p0) cc_final: 0.7982 (p0) REVERT: A 655 LYS cc_start: 0.8901 (tmmm) cc_final: 0.8690 (tttm) REVERT: A 832 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8358 (mt0) REVERT: A 892 SER cc_start: 0.8857 (t) cc_final: 0.8606 (p) REVERT: A 1025 GLN cc_start: 0.8376 (tm-30) cc_final: 0.8132 (tm130) REVERT: B 423 ILE cc_start: 0.8820 (tp) cc_final: 0.8612 (pt) REVERT: B 515 GLU cc_start: 0.7764 (pm20) cc_final: 0.7301 (pm20) REVERT: B 711 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8967 (ttpt) REVERT: B 732 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8793 (mtm) REVERT: B 832 GLN cc_start: 0.8336 (tt0) cc_final: 0.8001 (mm-40) REVERT: B 892 SER cc_start: 0.8865 (m) cc_final: 0.8545 (p) REVERT: B 995 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.7972 (ttp) REVERT: C 128 ARG cc_start: 0.8322 (ttm110) cc_final: 0.7910 (tpp80) REVERT: C 148 ASN cc_start: 0.8364 (m-40) cc_final: 0.8009 (t0) REVERT: C 157 ILE cc_start: 0.7012 (OUTLIER) cc_final: 0.6636 (tt) REVERT: C 317 TYR cc_start: 0.8268 (OUTLIER) cc_final: 0.7424 (t80) REVERT: C 451 ASP cc_start: 0.8529 (m-30) cc_final: 0.8265 (m-30) REVERT: C 515 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7631 (pm20) REVERT: C 648 GLU cc_start: 0.8262 (tm-30) cc_final: 0.8014 (tm-30) REVERT: C 674 ILE cc_start: 0.8787 (pp) cc_final: 0.8549 (mp) REVERT: C 814 ILE cc_start: 0.4424 (OUTLIER) cc_final: 0.4186 (pp) REVERT: C 832 GLN cc_start: 0.8637 (tp40) cc_final: 0.8086 (mm-40) REVERT: C 874 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8330 (mm-40) REVERT: H 66 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7997 (ttp80) REVERT: H 72 ASP cc_start: 0.8298 (t0) cc_final: 0.7471 (t0) REVERT: L 61 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7004 (ptt90) REVERT: M 19 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7801 (mmm160) REVERT: M 34 MET cc_start: 0.8221 (mtp) cc_final: 0.7919 (mtm) REVERT: M 66 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7752 (mtp-110) REVERT: M 100 SER cc_start: 0.8875 (p) cc_final: 0.8507 (p) REVERT: N 89 GLN cc_start: 0.7443 (tm-30) cc_final: 0.6895 (tm-30) REVERT: O 46 GLU cc_start: 0.8094 (pt0) cc_final: 0.7831 (pt0) REVERT: O 67 PHE cc_start: 0.6572 (OUTLIER) cc_final: 0.5682 (m-80) REVERT: O 70 SER cc_start: 0.8622 (t) cc_final: 0.8323 (p) REVERT: O 75 LYS cc_start: 0.8768 (mtmm) cc_final: 0.8540 (mtmm) REVERT: O 79 TYR cc_start: 0.8191 (m-10) cc_final: 0.7745 (m-80) REVERT: O 82 ASN cc_start: 0.7744 (OUTLIER) cc_final: 0.7035 (m-40) REVERT: P 45 LYS cc_start: 0.8509 (mptp) cc_final: 0.8167 (mptp) REVERT: P 89 GLN cc_start: 0.7191 (tm-30) cc_final: 0.6745 (tm-30) outliers start: 128 outliers final: 64 residues processed: 590 average time/residue: 0.6255 time to fit residues: 437.5930 Evaluate side-chains 585 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 505 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain A residue 654 LYS Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 832 GLN Chi-restraints excluded: chain A residue 926 CYS Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 661 ASN Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 711 LYS Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 995 MET Chi-restraints excluded: chain B residue 1020 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 703 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 814 ILE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 19 ARG Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain M residue 67 PHE Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 67 PHE Chi-restraints excluded: chain O residue 82 ASN Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 85 THR Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 190 optimal weight: 0.6980 chunk 301 optimal weight: 0.5980 chunk 247 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 342 optimal weight: 1.9990 chunk 343 optimal weight: 0.9980 chunk 291 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 637 ASN B 854 GLN C 837 GLN H 73 ASN ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.095229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.079627 restraints weight = 58926.051| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.73 r_work: 0.3046 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 31045 Z= 0.164 Angle : 0.683 13.386 42516 Z= 0.332 Chirality : 0.047 0.333 5224 Planarity : 0.004 0.052 5223 Dihedral : 7.101 59.574 6657 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.13 % Favored : 95.74 % Rotamer: Outliers : 4.35 % Allowed : 20.05 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.14), residues: 3708 helix: 1.69 (0.20), residues: 678 sheet: 0.59 (0.16), residues: 1041 loop : -0.55 (0.14), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 99 TYR 0.022 0.001 TYR N 49 PHE 0.032 0.002 PHE M 27 TRP 0.039 0.003 TRP O 47 HIS 0.003 0.001 HIS C 844 Details of bonding type rmsd covalent geometry : bond 0.00380 (30873) covalent geometry : angle 0.64932 (42048) SS BOND : bond 0.00545 ( 48) SS BOND : angle 1.04410 ( 96) hydrogen bonds : bond 0.04596 ( 1116) hydrogen bonds : angle 5.13543 ( 3156) link_ALPHA1-3 : bond 0.01118 ( 3) link_ALPHA1-3 : angle 1.94281 ( 9) link_ALPHA1-6 : bond 0.01259 ( 3) link_ALPHA1-6 : angle 1.98105 ( 9) link_BETA1-4 : bond 0.00549 ( 45) link_BETA1-4 : angle 2.01414 ( 135) link_NAG-ASN : bond 0.00491 ( 73) link_NAG-ASN : angle 2.50498 ( 219) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 515 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 SER cc_start: 0.8897 (p) cc_final: 0.8651 (t) REVERT: A 157 ILE cc_start: 0.7166 (OUTLIER) cc_final: 0.6862 (pt) REVERT: A 167 TYR cc_start: 0.8285 (m-80) cc_final: 0.7819 (m-80) REVERT: A 217 VAL cc_start: 0.9030 (m) cc_final: 0.8813 (p) REVERT: A 524 ASN cc_start: 0.7971 (t0) cc_final: 0.7621 (t0) REVERT: A 527 GLU cc_start: 0.8394 (tm-30) cc_final: 0.7911 (tm-30) REVERT: A 645 ASP cc_start: 0.8422 (p0) cc_final: 0.8209 (p0) REVERT: A 832 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8469 (mt0) REVERT: A 892 SER cc_start: 0.9017 (t) cc_final: 0.8773 (p) REVERT: A 1025 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8423 (tm130) REVERT: B 267 SER cc_start: 0.9233 (t) cc_final: 0.8890 (p) REVERT: B 423 ILE cc_start: 0.8907 (tp) cc_final: 0.8661 (pt) REVERT: B 515 GLU cc_start: 0.8103 (pm20) cc_final: 0.7589 (pm20) REVERT: B 711 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.9048 (ttpt) REVERT: B 732 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8927 (mtm) REVERT: B 832 GLN cc_start: 0.8537 (tt0) cc_final: 0.8145 (mm-40) REVERT: B 900 GLU cc_start: 0.8638 (tp30) cc_final: 0.8128 (tp30) REVERT: B 995 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8173 (ttp) REVERT: C 128 ARG cc_start: 0.8503 (ttm110) cc_final: 0.7914 (tpp80) REVERT: C 148 ASN cc_start: 0.8411 (m-40) cc_final: 0.8035 (t0) REVERT: C 157 ILE cc_start: 0.7182 (OUTLIER) cc_final: 0.6763 (tt) REVERT: C 317 TYR cc_start: 0.8395 (OUTLIER) cc_final: 0.7530 (t80) REVERT: C 451 ASP cc_start: 0.8834 (m-30) cc_final: 0.8570 (m-30) REVERT: C 515 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7930 (pm20) REVERT: C 648 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8314 (tm-30) REVERT: C 674 ILE cc_start: 0.8920 (pp) cc_final: 0.8710 (mp) REVERT: C 783 ASP cc_start: 0.8626 (t0) cc_final: 0.8194 (t0) REVERT: C 814 ILE cc_start: 0.4439 (OUTLIER) cc_final: 0.4217 (pp) REVERT: C 832 GLN cc_start: 0.8764 (tp40) cc_final: 0.8178 (mm-40) REVERT: C 874 GLN cc_start: 0.8832 (mm-40) cc_final: 0.8585 (mm-40) REVERT: H 66 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7758 (ttp80) REVERT: H 72 ASP cc_start: 0.8421 (t0) cc_final: 0.7615 (t0) REVERT: H 83 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.6857 (mpt-90) REVERT: L 61 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7050 (ptt90) REVERT: M 100 SER cc_start: 0.9016 (p) cc_final: 0.8670 (p) REVERT: N 18 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.6530 (ttp-170) REVERT: N 82 ASP cc_start: 0.7634 (m-30) cc_final: 0.7130 (m-30) REVERT: N 89 GLN cc_start: 0.7649 (tm-30) cc_final: 0.7106 (tm-30) REVERT: O 46 GLU cc_start: 0.8117 (pt0) cc_final: 0.7868 (pt0) REVERT: O 79 TYR cc_start: 0.8316 (m-10) cc_final: 0.7961 (m-80) REVERT: O 82 ASN cc_start: 0.7770 (OUTLIER) cc_final: 0.7428 (m-40) REVERT: P 89 GLN cc_start: 0.7396 (tm-30) cc_final: 0.7043 (tm-30) outliers start: 139 outliers final: 72 residues processed: 592 average time/residue: 0.6136 time to fit residues: 430.2178 Evaluate side-chains 586 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 500 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 654 LYS Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 832 GLN Chi-restraints excluded: chain A residue 837 GLN Chi-restraints excluded: chain A residue 926 CYS Chi-restraints excluded: chain A residue 1020 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 661 ASN Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 711 LYS Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 995 MET Chi-restraints excluded: chain B residue 999 ARG Chi-restraints excluded: chain B residue 1020 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 703 LEU Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 814 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 67 PHE Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 18 ARG Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 82 ASN Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 364 optimal weight: 2.9990 chunk 335 optimal weight: 0.0030 chunk 267 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 227 optimal weight: 2.9990 chunk 311 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 170 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 169 optimal weight: 0.6980 chunk 357 optimal weight: 0.4980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 854 GLN C 837 GLN H 73 ASN P 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.095515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.079817 restraints weight = 58963.973| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.75 r_work: 0.3058 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31045 Z= 0.141 Angle : 0.679 13.469 42516 Z= 0.330 Chirality : 0.046 0.320 5224 Planarity : 0.004 0.050 5223 Dihedral : 6.911 59.626 6657 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.64 % Favored : 96.22 % Rotamer: Outliers : 3.92 % Allowed : 20.55 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.14), residues: 3708 helix: 1.75 (0.20), residues: 678 sheet: 0.65 (0.16), residues: 1062 loop : -0.52 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 99 TYR 0.025 0.001 TYR L 49 PHE 0.039 0.001 PHE M 27 TRP 0.032 0.002 TRP M 47 HIS 0.003 0.001 HIS C 298 Details of bonding type rmsd covalent geometry : bond 0.00324 (30873) covalent geometry : angle 0.64710 (42048) SS BOND : bond 0.00458 ( 48) SS BOND : angle 1.01835 ( 96) hydrogen bonds : bond 0.04385 ( 1116) hydrogen bonds : angle 5.07148 ( 3156) link_ALPHA1-3 : bond 0.01088 ( 3) link_ALPHA1-3 : angle 1.76780 ( 9) link_ALPHA1-6 : bond 0.01262 ( 3) link_ALPHA1-6 : angle 1.93840 ( 9) link_BETA1-4 : bond 0.00562 ( 45) link_BETA1-4 : angle 1.93995 ( 135) link_NAG-ASN : bond 0.00478 ( 73) link_NAG-ASN : angle 2.43490 ( 219) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 525 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 SER cc_start: 0.8887 (p) cc_final: 0.8659 (t) REVERT: A 157 ILE cc_start: 0.7130 (OUTLIER) cc_final: 0.6819 (pt) REVERT: A 217 VAL cc_start: 0.9027 (m) cc_final: 0.8808 (p) REVERT: A 317 TYR cc_start: 0.8654 (OUTLIER) cc_final: 0.7929 (t80) REVERT: A 437 MET cc_start: 0.8945 (tpt) cc_final: 0.8423 (tpt) REVERT: A 524 ASN cc_start: 0.8001 (t0) cc_final: 0.7666 (t0) REVERT: A 527 GLU cc_start: 0.8417 (tm-30) cc_final: 0.7905 (tm-30) REVERT: A 621 LEU cc_start: 0.8645 (tp) cc_final: 0.8402 (tm) REVERT: A 645 ASP cc_start: 0.8387 (p0) cc_final: 0.8187 (p0) REVERT: A 832 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8491 (mt0) REVERT: A 892 SER cc_start: 0.8998 (t) cc_final: 0.8762 (p) REVERT: B 217 VAL cc_start: 0.9037 (p) cc_final: 0.8774 (t) REVERT: B 267 SER cc_start: 0.9235 (t) cc_final: 0.8892 (p) REVERT: B 423 ILE cc_start: 0.8906 (tp) cc_final: 0.8652 (pt) REVERT: B 515 GLU cc_start: 0.8098 (pm20) cc_final: 0.7650 (pm20) REVERT: B 711 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.9072 (ttpt) REVERT: B 832 GLN cc_start: 0.8536 (tt0) cc_final: 0.8132 (mm-40) REVERT: B 892 SER cc_start: 0.8987 (m) cc_final: 0.8712 (p) REVERT: B 900 GLU cc_start: 0.8495 (tp30) cc_final: 0.8052 (tp30) REVERT: B 995 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8126 (ttp) REVERT: C 148 ASN cc_start: 0.8428 (m-40) cc_final: 0.8083 (t0) REVERT: C 157 ILE cc_start: 0.7218 (OUTLIER) cc_final: 0.6803 (tt) REVERT: C 317 TYR cc_start: 0.8441 (OUTLIER) cc_final: 0.7612 (t80) REVERT: C 451 ASP cc_start: 0.8832 (m-30) cc_final: 0.8582 (m-30) REVERT: C 515 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7904 (pm20) REVERT: C 648 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8360 (tm-30) REVERT: C 814 ILE cc_start: 0.4301 (OUTLIER) cc_final: 0.3987 (mt) REVERT: C 832 GLN cc_start: 0.8763 (tp40) cc_final: 0.8175 (mm-40) REVERT: C 874 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8567 (mm-40) REVERT: C 1036 LYS cc_start: 0.8524 (tmmt) cc_final: 0.8278 (tmtp) REVERT: H 66 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7771 (ttp80) REVERT: H 72 ASP cc_start: 0.8411 (t0) cc_final: 0.7593 (t0) REVERT: H 83 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6866 (mpt-90) REVERT: L 61 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.6997 (ptt90) REVERT: M 46 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6347 (pm20) REVERT: M 66 ARG cc_start: 0.8259 (ttp80) cc_final: 0.8013 (ttp80) REVERT: M 100 SER cc_start: 0.8987 (p) cc_final: 0.8639 (p) REVERT: N 18 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.6451 (ttp-170) REVERT: N 82 ASP cc_start: 0.7669 (m-30) cc_final: 0.7282 (m-30) REVERT: N 89 GLN cc_start: 0.7573 (tm-30) cc_final: 0.7034 (tm-30) REVERT: O 46 GLU cc_start: 0.8166 (pt0) cc_final: 0.7915 (pt0) REVERT: O 66 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.7490 (ttp80) REVERT: O 79 TYR cc_start: 0.8281 (m-10) cc_final: 0.7953 (m-80) REVERT: O 82 ASN cc_start: 0.7712 (OUTLIER) cc_final: 0.7341 (m-40) REVERT: O 95 ASP cc_start: 0.8782 (t0) cc_final: 0.8558 (t0) REVERT: P 89 GLN cc_start: 0.7351 (tm-30) cc_final: 0.7003 (tm-30) REVERT: P 102 THR cc_start: 0.7743 (OUTLIER) cc_final: 0.7518 (p) outliers start: 125 outliers final: 77 residues processed: 593 average time/residue: 0.5989 time to fit residues: 421.2390 Evaluate side-chains 602 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 508 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 832 GLN Chi-restraints excluded: chain A residue 837 GLN Chi-restraints excluded: chain A residue 926 CYS Chi-restraints excluded: chain A residue 1020 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 661 ASN Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 711 LYS Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 995 MET Chi-restraints excluded: chain B residue 999 ARG Chi-restraints excluded: chain B residue 1020 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 703 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 814 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 67 PHE Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain N residue 18 ARG Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 66 ARG Chi-restraints excluded: chain O residue 82 ASN Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 85 THR Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain P residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 241 optimal weight: 0.1980 chunk 313 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 339 optimal weight: 1.9990 chunk 195 optimal weight: 0.6980 chunk 167 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 311 optimal weight: 0.8980 chunk 329 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN B 854 GLN B 875 GLN C 837 GLN H 73 ASN N 89 GLN P 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.094362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.078772 restraints weight = 58941.754| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.73 r_work: 0.3037 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 31045 Z= 0.186 Angle : 0.708 13.785 42516 Z= 0.345 Chirality : 0.047 0.362 5224 Planarity : 0.004 0.051 5223 Dihedral : 7.028 59.275 6657 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.23 % Favored : 95.63 % Rotamer: Outliers : 4.23 % Allowed : 21.08 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.14), residues: 3708 helix: 1.70 (0.20), residues: 678 sheet: 0.68 (0.16), residues: 1071 loop : -0.61 (0.14), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 99 TYR 0.017 0.002 TYR O 79 PHE 0.037 0.002 PHE A 166 TRP 0.044 0.003 TRP M 47 HIS 0.003 0.001 HIS C 844 Details of bonding type rmsd covalent geometry : bond 0.00438 (30873) covalent geometry : angle 0.67601 (42048) SS BOND : bond 0.00478 ( 48) SS BOND : angle 1.07164 ( 96) hydrogen bonds : bond 0.04678 ( 1116) hydrogen bonds : angle 5.13639 ( 3156) link_ALPHA1-3 : bond 0.01007 ( 3) link_ALPHA1-3 : angle 1.83290 ( 9) link_ALPHA1-6 : bond 0.01190 ( 3) link_ALPHA1-6 : angle 1.93478 ( 9) link_BETA1-4 : bond 0.00541 ( 45) link_BETA1-4 : angle 2.01567 ( 135) link_NAG-ASN : bond 0.00545 ( 73) link_NAG-ASN : angle 2.49134 ( 219) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 509 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 152 SER cc_start: 0.8877 (p) cc_final: 0.8658 (t) REVERT: A 167 TYR cc_start: 0.8215 (m-80) cc_final: 0.7920 (m-80) REVERT: A 217 VAL cc_start: 0.9043 (m) cc_final: 0.8828 (p) REVERT: A 317 TYR cc_start: 0.8667 (OUTLIER) cc_final: 0.7963 (t80) REVERT: A 437 MET cc_start: 0.8964 (tpt) cc_final: 0.8436 (tpt) REVERT: A 524 ASN cc_start: 0.8095 (t0) cc_final: 0.7776 (t0) REVERT: A 527 GLU cc_start: 0.8460 (tm-30) cc_final: 0.7971 (tm-30) REVERT: A 621 LEU cc_start: 0.8699 (tp) cc_final: 0.8430 (tm) REVERT: A 832 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8526 (mt0) REVERT: A 892 SER cc_start: 0.9009 (t) cc_final: 0.8724 (p) REVERT: B 148 ASN cc_start: 0.8502 (t0) cc_final: 0.8178 (m-40) REVERT: B 267 SER cc_start: 0.9228 (t) cc_final: 0.8896 (p) REVERT: B 423 ILE cc_start: 0.8934 (tp) cc_final: 0.8685 (pt) REVERT: B 515 GLU cc_start: 0.8123 (pm20) cc_final: 0.7661 (pm20) REVERT: B 680 SER cc_start: 0.7489 (OUTLIER) cc_final: 0.7020 (p) REVERT: B 711 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.9102 (ttpt) REVERT: B 832 GLN cc_start: 0.8569 (tt0) cc_final: 0.8183 (mm-40) REVERT: B 900 GLU cc_start: 0.8377 (tp30) cc_final: 0.8051 (tt0) REVERT: C 148 ASN cc_start: 0.8426 (m-40) cc_final: 0.8117 (t0) REVERT: C 157 ILE cc_start: 0.7205 (OUTLIER) cc_final: 0.6789 (tt) REVERT: C 317 TYR cc_start: 0.8412 (OUTLIER) cc_final: 0.7501 (t80) REVERT: C 515 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7891 (pm20) REVERT: C 648 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8343 (tm-30) REVERT: C 814 ILE cc_start: 0.4365 (OUTLIER) cc_final: 0.4075 (mt) REVERT: C 832 GLN cc_start: 0.8728 (tp40) cc_final: 0.8161 (mm-40) REVERT: C 874 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8527 (mm-40) REVERT: H 66 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7821 (ttp80) REVERT: H 72 ASP cc_start: 0.8433 (t0) cc_final: 0.7669 (t0) REVERT: H 83 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.6939 (mpt-90) REVERT: H 97 THR cc_start: 0.8697 (p) cc_final: 0.8471 (p) REVERT: L 61 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7019 (ptt90) REVERT: M 66 ARG cc_start: 0.8285 (ttp80) cc_final: 0.8065 (ttp80) REVERT: N 18 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.6497 (ttp-170) REVERT: N 82 ASP cc_start: 0.7647 (m-30) cc_final: 0.7224 (m-30) REVERT: N 89 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7147 (tm-30) REVERT: O 75 LYS cc_start: 0.8777 (mtmm) cc_final: 0.8345 (mppt) REVERT: O 79 TYR cc_start: 0.8370 (m-10) cc_final: 0.8030 (m-80) REVERT: O 82 ASN cc_start: 0.7809 (OUTLIER) cc_final: 0.7496 (m-40) REVERT: P 61 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7596 (ptt90) REVERT: P 89 GLN cc_start: 0.7424 (tm-30) cc_final: 0.7079 (tm-30) REVERT: P 102 THR cc_start: 0.7797 (OUTLIER) cc_final: 0.7528 (p) outliers start: 135 outliers final: 80 residues processed: 587 average time/residue: 0.6048 time to fit residues: 421.2134 Evaluate side-chains 588 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 492 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 832 GLN Chi-restraints excluded: chain A residue 837 GLN Chi-restraints excluded: chain A residue 1020 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 661 ASN Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 711 LYS Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 999 ARG Chi-restraints excluded: chain B residue 1020 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 703 LEU Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 814 ILE Chi-restraints excluded: chain C residue 999 ARG Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 67 PHE Chi-restraints excluded: chain N residue 18 ARG Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 82 ASN Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 61 ARG Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain P residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 246 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 218 optimal weight: 0.5980 chunk 181 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 200 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 165 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 ASN B 854 GLN C 296 HIS C 837 GLN H 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.094567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.079001 restraints weight = 58864.415| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.73 r_work: 0.3041 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 31045 Z= 0.172 Angle : 0.722 13.721 42516 Z= 0.351 Chirality : 0.047 0.361 5224 Planarity : 0.004 0.065 5223 Dihedral : 7.007 59.295 6657 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.05 % Favored : 95.79 % Rotamer: Outliers : 3.63 % Allowed : 21.93 % Favored : 74.44 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.14), residues: 3708 helix: 1.71 (0.20), residues: 678 sheet: 0.67 (0.16), residues: 1071 loop : -0.62 (0.14), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 99 TYR 0.023 0.002 TYR L 49 PHE 0.031 0.002 PHE A 166 TRP 0.045 0.003 TRP M 47 HIS 0.003 0.001 HIS C 844 Details of bonding type rmsd covalent geometry : bond 0.00404 (30873) covalent geometry : angle 0.69246 (42048) SS BOND : bond 0.00471 ( 48) SS BOND : angle 1.07081 ( 96) hydrogen bonds : bond 0.04593 ( 1116) hydrogen bonds : angle 5.11641 ( 3156) link_ALPHA1-3 : bond 0.01017 ( 3) link_ALPHA1-3 : angle 1.74737 ( 9) link_ALPHA1-6 : bond 0.01225 ( 3) link_ALPHA1-6 : angle 1.91045 ( 9) link_BETA1-4 : bond 0.00554 ( 45) link_BETA1-4 : angle 1.99482 ( 135) link_NAG-ASN : bond 0.00514 ( 73) link_NAG-ASN : angle 2.45624 ( 219) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 501 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: A 152 SER cc_start: 0.8868 (p) cc_final: 0.8647 (t) REVERT: A 217 VAL cc_start: 0.9042 (m) cc_final: 0.8826 (p) REVERT: A 317 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.7845 (t80) REVERT: A 437 MET cc_start: 0.8950 (tpt) cc_final: 0.8422 (tpt) REVERT: A 524 ASN cc_start: 0.8089 (t0) cc_final: 0.7775 (t0) REVERT: A 527 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8183 (tm-30) REVERT: A 621 LEU cc_start: 0.8694 (tp) cc_final: 0.8454 (tm) REVERT: A 832 GLN cc_start: 0.8788 (tt0) cc_final: 0.8486 (mt0) REVERT: A 892 SER cc_start: 0.8997 (t) cc_final: 0.8713 (p) REVERT: A 900 GLU cc_start: 0.8504 (tp30) cc_final: 0.8257 (tm-30) REVERT: B 148 ASN cc_start: 0.8504 (t0) cc_final: 0.8184 (m-40) REVERT: B 267 SER cc_start: 0.9230 (t) cc_final: 0.8901 (p) REVERT: B 423 ILE cc_start: 0.8937 (tp) cc_final: 0.8678 (pt) REVERT: B 515 GLU cc_start: 0.8117 (pm20) cc_final: 0.7645 (pm20) REVERT: B 832 GLN cc_start: 0.8564 (tt0) cc_final: 0.8144 (mm-40) REVERT: B 900 GLU cc_start: 0.8439 (tp30) cc_final: 0.7952 (tt0) REVERT: C 148 ASN cc_start: 0.8465 (m-40) cc_final: 0.8132 (t0) REVERT: C 157 ILE cc_start: 0.7183 (OUTLIER) cc_final: 0.6779 (tt) REVERT: C 317 TYR cc_start: 0.8454 (OUTLIER) cc_final: 0.7593 (t80) REVERT: C 451 ASP cc_start: 0.8839 (m-30) cc_final: 0.8519 (m-30) REVERT: C 515 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7887 (pm20) REVERT: C 648 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8389 (tm-30) REVERT: C 814 ILE cc_start: 0.4343 (OUTLIER) cc_final: 0.4072 (mt) REVERT: C 832 GLN cc_start: 0.8722 (tp40) cc_final: 0.8159 (mm-40) REVERT: C 874 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8540 (mm-40) REVERT: C 902 ARG cc_start: 0.8830 (ttp-110) cc_final: 0.7920 (ttp-110) REVERT: C 1036 LYS cc_start: 0.8507 (tmmt) cc_final: 0.8220 (tmtp) REVERT: H 66 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7842 (ttp80) REVERT: H 72 ASP cc_start: 0.8420 (t0) cc_final: 0.7631 (t0) REVERT: H 83 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6891 (mpt-90) REVERT: H 97 THR cc_start: 0.8681 (p) cc_final: 0.8453 (p) REVERT: L 61 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7018 (ptt90) REVERT: M 66 ARG cc_start: 0.8321 (ttp80) cc_final: 0.8111 (ttp80) REVERT: M 81 GLN cc_start: 0.7804 (tp40) cc_final: 0.7545 (tp40) REVERT: N 18 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.6491 (ttp-170) REVERT: N 82 ASP cc_start: 0.7681 (m-30) cc_final: 0.7314 (m-30) REVERT: N 89 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7394 (tm-30) REVERT: O 66 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.7424 (ttp80) REVERT: O 75 LYS cc_start: 0.8795 (mtmm) cc_final: 0.8343 (mppt) REVERT: O 79 TYR cc_start: 0.8359 (m-10) cc_final: 0.8012 (m-80) REVERT: O 82 ASN cc_start: 0.7694 (OUTLIER) cc_final: 0.7325 (m-40) REVERT: P 61 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7583 (ptt90) REVERT: P 89 GLN cc_start: 0.7422 (tm-30) cc_final: 0.7084 (tm-30) REVERT: P 102 THR cc_start: 0.7858 (OUTLIER) cc_final: 0.7630 (p) outliers start: 116 outliers final: 78 residues processed: 570 average time/residue: 0.6110 time to fit residues: 412.0005 Evaluate side-chains 584 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 492 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 837 GLN Chi-restraints excluded: chain A residue 1020 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 661 ASN Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 999 ARG Chi-restraints excluded: chain B residue 1020 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 703 LEU Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 814 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 67 PHE Chi-restraints excluded: chain N residue 18 ARG Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 66 ARG Chi-restraints excluded: chain O residue 82 ASN Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 61 ARG Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain P residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 234 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 368 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 70 optimal weight: 0.1980 chunk 260 optimal weight: 0.8980 chunk 274 optimal weight: 0.8980 chunk 282 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 130 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 854 GLN C 404 ASN H 73 ASN P 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.095438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.079875 restraints weight = 58558.769| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.72 r_work: 0.3060 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31045 Z= 0.140 Angle : 0.703 13.443 42516 Z= 0.342 Chirality : 0.046 0.341 5224 Planarity : 0.004 0.049 5223 Dihedral : 6.863 59.012 6657 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.86 % Favored : 95.98 % Rotamer: Outliers : 2.91 % Allowed : 22.71 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.14), residues: 3708 helix: 1.79 (0.20), residues: 678 sheet: 0.71 (0.16), residues: 1068 loop : -0.58 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 38 TYR 0.025 0.001 TYR L 49 PHE 0.029 0.001 PHE A 166 TRP 0.049 0.003 TRP M 47 HIS 0.002 0.001 HIS C 298 Details of bonding type rmsd covalent geometry : bond 0.00320 (30873) covalent geometry : angle 0.67375 (42048) SS BOND : bond 0.00448 ( 48) SS BOND : angle 0.98210 ( 96) hydrogen bonds : bond 0.04303 ( 1116) hydrogen bonds : angle 5.04545 ( 3156) link_ALPHA1-3 : bond 0.01034 ( 3) link_ALPHA1-3 : angle 1.63812 ( 9) link_ALPHA1-6 : bond 0.01322 ( 3) link_ALPHA1-6 : angle 1.83110 ( 9) link_BETA1-4 : bond 0.00551 ( 45) link_BETA1-4 : angle 1.89646 ( 135) link_NAG-ASN : bond 0.00518 ( 73) link_NAG-ASN : angle 2.41186 ( 219) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7416 Ramachandran restraints generated. 3708 Oldfield, 0 Emsley, 3708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 515 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 SER cc_start: 0.8863 (p) cc_final: 0.8654 (t) REVERT: A 167 TYR cc_start: 0.8199 (m-80) cc_final: 0.7931 (m-80) REVERT: A 217 VAL cc_start: 0.9020 (m) cc_final: 0.8808 (p) REVERT: A 317 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.7869 (t80) REVERT: A 437 MET cc_start: 0.8931 (tpt) cc_final: 0.8400 (tpt) REVERT: A 524 ASN cc_start: 0.8020 (t0) cc_final: 0.7702 (t0) REVERT: A 527 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8199 (tm-30) REVERT: A 621 LEU cc_start: 0.8637 (tp) cc_final: 0.8422 (tm) REVERT: A 648 GLU cc_start: 0.8534 (tp30) cc_final: 0.8330 (tp30) REVERT: A 832 GLN cc_start: 0.8777 (tt0) cc_final: 0.8507 (mt0) REVERT: A 892 SER cc_start: 0.9009 (t) cc_final: 0.8776 (p) REVERT: B 148 ASN cc_start: 0.8535 (t0) cc_final: 0.8196 (m-40) REVERT: B 217 VAL cc_start: 0.9053 (p) cc_final: 0.8801 (t) REVERT: B 267 SER cc_start: 0.9227 (t) cc_final: 0.8900 (p) REVERT: B 515 GLU cc_start: 0.8092 (pm20) cc_final: 0.7639 (pm20) REVERT: B 785 LEU cc_start: 0.8590 (pp) cc_final: 0.8046 (mt) REVERT: B 832 GLN cc_start: 0.8538 (tt0) cc_final: 0.8107 (mm-40) REVERT: B 892 SER cc_start: 0.8995 (m) cc_final: 0.8747 (p) REVERT: B 900 GLU cc_start: 0.8442 (tp30) cc_final: 0.8071 (tp30) REVERT: C 148 ASN cc_start: 0.8481 (m-40) cc_final: 0.8180 (t0) REVERT: C 157 ILE cc_start: 0.7193 (OUTLIER) cc_final: 0.6721 (tt) REVERT: C 317 TYR cc_start: 0.8458 (OUTLIER) cc_final: 0.7555 (t80) REVERT: C 451 ASP cc_start: 0.8831 (m-30) cc_final: 0.8490 (m-30) REVERT: C 515 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7875 (pm20) REVERT: C 648 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8337 (tm-30) REVERT: C 814 ILE cc_start: 0.4172 (OUTLIER) cc_final: 0.3937 (mt) REVERT: C 832 GLN cc_start: 0.8717 (tp40) cc_final: 0.8162 (mm-40) REVERT: C 874 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8530 (mm-40) REVERT: C 902 ARG cc_start: 0.8805 (ttp-110) cc_final: 0.8411 (ttp-110) REVERT: C 1036 LYS cc_start: 0.8506 (tmmt) cc_final: 0.8243 (tmtp) REVERT: H 72 ASP cc_start: 0.8398 (t0) cc_final: 0.7516 (t0) REVERT: H 97 THR cc_start: 0.8694 (p) cc_final: 0.8458 (p) REVERT: M 66 ARG cc_start: 0.8306 (ttp80) cc_final: 0.8102 (ttp80) REVERT: M 100 SER cc_start: 0.9038 (p) cc_final: 0.8682 (p) REVERT: N 18 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.6488 (ttp-170) REVERT: N 50 ASP cc_start: 0.8271 (t0) cc_final: 0.8022 (t0) REVERT: N 82 ASP cc_start: 0.7622 (m-30) cc_final: 0.7259 (m-30) REVERT: O 66 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.7350 (ttp80) REVERT: O 75 LYS cc_start: 0.8783 (mtmm) cc_final: 0.8367 (mppt) REVERT: O 79 TYR cc_start: 0.8279 (m-10) cc_final: 0.8001 (m-80) REVERT: O 82 ASN cc_start: 0.7674 (OUTLIER) cc_final: 0.7296 (m-40) REVERT: P 61 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7348 (ptp90) REVERT: P 89 GLN cc_start: 0.7427 (tm-30) cc_final: 0.7066 (tm-30) outliers start: 93 outliers final: 71 residues processed: 572 average time/residue: 0.6097 time to fit residues: 413.2830 Evaluate side-chains 576 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 496 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 837 GLN Chi-restraints excluded: chain A residue 926 CYS Chi-restraints excluded: chain A residue 1020 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 661 ASN Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 999 ARG Chi-restraints excluded: chain B residue 1020 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 515 GLU Chi-restraints excluded: chain C residue 703 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 814 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 67 PHE Chi-restraints excluded: chain N residue 18 ARG Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 66 ARG Chi-restraints excluded: chain O residue 82 ASN Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 61 ARG Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 93 optimal weight: 0.0170 chunk 332 optimal weight: 0.9980 chunk 231 optimal weight: 0.5980 chunk 102 optimal weight: 0.3980 chunk 137 optimal weight: 0.8980 chunk 264 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 240 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 73 ASN O 39 GLN P 37 GLN P 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.095707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.080122 restraints weight = 59160.497| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.74 r_work: 0.3060 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 31045 Z= 0.144 Angle : 0.716 15.328 42516 Z= 0.349 Chirality : 0.047 0.346 5224 Planarity : 0.004 0.056 5223 Dihedral : 6.813 59.292 6657 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.80 % Favored : 96.06 % Rotamer: Outliers : 3.07 % Allowed : 22.90 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.14), residues: 3708 helix: 1.81 (0.20), residues: 678 sheet: 0.72 (0.16), residues: 1065 loop : -0.58 (0.14), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 38 TYR 0.024 0.001 TYR N 49 PHE 0.045 0.001 PHE A 166 TRP 0.055 0.003 TRP C 358 HIS 0.003 0.001 HIS C 298 Details of bonding type rmsd covalent geometry : bond 0.00334 (30873) covalent geometry : angle 0.68675 (42048) SS BOND : bond 0.00521 ( 48) SS BOND : angle 1.27061 ( 96) hydrogen bonds : bond 0.04273 ( 1116) hydrogen bonds : angle 5.02496 ( 3156) link_ALPHA1-3 : bond 0.01021 ( 3) link_ALPHA1-3 : angle 1.64625 ( 9) link_ALPHA1-6 : bond 0.01306 ( 3) link_ALPHA1-6 : angle 1.82833 ( 9) link_BETA1-4 : bond 0.00548 ( 45) link_BETA1-4 : angle 1.87604 ( 135) link_NAG-ASN : bond 0.00521 ( 73) link_NAG-ASN : angle 2.40537 ( 219) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10713.43 seconds wall clock time: 183 minutes 16.47 seconds (10996.47 seconds total)