Starting phenix.real_space_refine on Mon Jul 6 14:52:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b36_44129/07_2026/9b36_44129.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b36_44129/07_2026/9b36_44129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b36_44129/07_2026/9b36_44129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b36_44129/07_2026/9b36_44129.map" model { file = "/net/cci-nas-00/data/ceres_data/9b36_44129/07_2026/9b36_44129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b36_44129/07_2026/9b36_44129.cif" } resolution = 4.29 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= -0.005 sd= 1.320 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: 8 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 14 5.49 5 S 172 5.16 5 C 23296 2.51 5 N 5768 2.21 5 O 7080 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 36342 Number of models: 1 Model: "" Number of chains: 44 Chain: "A" Number of atoms: 6684 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} Conformer: "B" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} bond proxies already assigned to first conformer: 6818 Chain: "B" Number of atoms: 6680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} Conformer: "B" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} bond proxies already assigned to first conformer: 6823 Chain: "C" Number of atoms: 6684 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} Conformer: "B" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} bond proxies already assigned to first conformer: 6818 Chain: "D" Number of atoms: 6680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} Conformer: "B" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} bond proxies already assigned to first conformer: 6823 Chain: "E" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1806 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 225} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 1809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1809 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 225} Chain: "G" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1806 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 225} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 1809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1809 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 225} Chain: "I" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 86 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "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: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 100 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "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: 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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" 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: "R" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 89 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 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: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 86 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 89 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 89 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "i" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 346 Unusual residues: {'2J9': 1, 'CLR': 4, 'POV': 4} Inner-chain residues flagged as termini: ['pdbres="GLU A1002 "'] Classifications: {'peptide': 1, 'undetermined': 9} Modifications used: {'COO': 1} Link IDs: {None: 9} Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 210 Unusual residues: {'2J9': 1, 'CLR': 1, 'POV': 3} Inner-chain residues flagged as termini: ['pdbres="GLU B1003 "'] Classifications: {'peptide': 1, 'undetermined': 5} Modifications used: {'COO': 1} Link IDs: {None: 5} Chain: "C" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 318 Unusual residues: {'2J9': 1, 'CLR': 3, 'POV': 4} Inner-chain residues flagged as termini: ['pdbres="GLU C1003 "'] Classifications: {'peptide': 1, 'undetermined': 8} Modifications used: {'COO': 1} Link IDs: {None: 8} Chain: "D" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 182 Unusual residues: {'2J9': 1, 'POV': 3} Inner-chain residues flagged as termini: ['pdbres="GLU D1003 "'] Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 12.06, per 1000 atoms: 0.33 Number of scatterers: 36342 At special positions: 0 Unit cell: (163.193, 160.495, 221.187, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 172 16.00 P 14 15.00 F 4 9.00 O 7080 8.00 N 5768 7.00 C 23296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.04 Simple disulfide: pdb=" SG CYS A 750 " - pdb=" SG CYS A 804 " distance=2.05 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.04 Simple disulfide: pdb=" SG CYS B 750 " - pdb=" SG CYS B 804 " distance=2.04 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.04 Simple disulfide: pdb=" SG CYS C 750 " - pdb=" SG CYS C 804 " distance=2.04 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.04 Simple disulfide: pdb=" SG CYS D 750 " - pdb=" SG CYS D 804 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA I 3 " - " MAN I 7 " " BMA K 3 " - " MAN K 7 " " BMA R 3 " - " MAN R 4 " " BMA W 3 " - " MAN W 7 " " BMA Y 3 " - " MAN Y 4 " " BMA f 3 " - " MAN f 4 " ALPHA1-6 " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " " BMA R 3 " - " MAN R 6 " " BMA U 3 " - " MAN U 4 " " BMA W 3 " - " MAN W 4 " " BMA Y 3 " - " MAN Y 6 " " BMA f 3 " - " MAN f 6 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 4 " BETA1-2 " MAN I 4 " - " NAG I 5 " " MAN K 4 " - " NAG K 5 " " MAN K 7 " - " NAG K 8 " " MAN R 4 " - " NAG R 5 " " MAN R 6 " - " NAG R 7 " " MAN W 4 " - " NAG W 5 " " MAN Y 4 " - " NAG Y 5 " " MAN Y 6 " - " NAG Y 7 " " MAN f 4 " - " NAG f 5 " " MAN f 6 " - " NAG f 7 " BETA1-3 " BMA P 3 " - " BMA P 4 " " BMA d 3 " - " BMA d 4 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG I 5 " - " GAL I 6 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG K 5 " - " GAL K 6 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG 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 W 5 " - " GAL W 6 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " 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 f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG I 1 " - " ASN A 546 " " NAG K 1 " - " ASN A 378 " " NAG L 1 " - " ASN A 67 " " NAG M 1 " - " ASN A 412 " " NAG N 1 " - " ASN A 275 " " NAG O 1 " - " ASN A 73 " " NAG P 1 " - " ASN B 546 " " NAG Q 1 " - " ASN B 751 " " NAG R 1 " - " ASN B 378 " " NAG S 1 " - " ASN B 67 " " NAG T 1 " - " ASN B 412 " " NAG U 1 " - " ASN B 275 " " NAG V 1 " - " ASN B 73 " " NAG W 1 " - " ASN C 546 " " NAG Y 1 " - " ASN C 378 " " NAG Z 1 " - " ASN C 67 " " NAG a 1 " - " ASN C 412 " " NAG b 1 " - " ASN C 275 " " NAG c 1 " - " ASN C 73 " " NAG d 1 " - " ASN D 546 " " NAG e 1 " - " ASN D 751 " " NAG f 1 " - " ASN D 378 " " NAG g 1 " - " ASN D 67 " " NAG h 1 " - " ASN D 412 " " NAG i 1 " - " ASN D 275 " " NAG j 1 " - " ASN D 73 " Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" NE2 HIS E 24 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" NE2 HIS F 24 " pdb=" ZN G1001 " pdb="ZN ZN G1001 " - pdb=" NE2 HIS G 24 " pdb=" ZN H1001 " pdb="ZN ZN H1001 " - pdb=" NE2 HIS H 24 " 8612 Ramachandran restraints generated. 4306 Oldfield, 0 Emsley, 4306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8076 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 58 sheets defined 35.7% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 51 through 65 removed outlier: 3.520A pdb=" N LEU A 55 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 102 removed outlier: 3.538A pdb=" N SER A 92 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 100 " --> pdb=" O CYS A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.760A pdb=" N ASN A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 167 removed outlier: 4.178A pdb=" N ARG A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 removed outlier: 3.579A pdb=" N ARG A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 removed outlier: 3.591A pdb=" N ILE A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 221 removed outlier: 3.582A pdb=" N GLU A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 246 removed outlier: 3.816A pdb=" N ALA A 236 " --> pdb=" O HIS A 232 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 238 " --> pdb=" O MET A 234 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 286 through 301 removed outlier: 3.858A pdb=" N ILE A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 337 removed outlier: 3.931A pdb=" N HIS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 333 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLN A 335 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 365 removed outlier: 3.550A pdb=" N ILE A 363 " --> pdb=" O PHE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 475 removed outlier: 3.614A pdb=" N THR A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.908A pdb=" N LYS A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 removed outlier: 3.913A pdb=" N LEU A 556 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 585 removed outlier: 3.958A pdb=" N SER A 575 " --> pdb=" O CYS A 571 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS A 576 " --> pdb=" O LEU A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.745A pdb=" N TRP A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 660 removed outlier: 3.700A pdb=" N ILE A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 648 " --> pdb=" O THR A 644 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 656 " --> pdb=" O THR A 652 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ALA A 657 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 658 " --> pdb=" O ASN A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 675 Processing helix chain 'A' and resid 688 through 697 Processing helix chain 'A' and resid 699 through 710 Processing helix chain 'A' and resid 712 through 717 removed outlier: 3.795A pdb=" N LEU A 717 " --> pdb=" O ARG A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 731 removed outlier: 3.915A pdb=" N VAL A 728 " --> pdb=" O GLY A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 746 removed outlier: 3.801A pdb=" N PHE A 744 " --> pdb=" O THR A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 788 removed outlier: 4.120A pdb=" N LYS A 777 " --> pdb=" O PRO A 773 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 778 " --> pdb=" O TYR A 774 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 783 " --> pdb=" O THR A 779 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 785 " --> pdb=" O ALA A 781 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU A 788 " --> pdb=" O GLN A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 800 removed outlier: 3.920A pdb=" N LYS A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 821 removed outlier: 3.717A pdb=" N ASN A 819 " --> pdb=" O GLY A 816 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 820 " --> pdb=" O VAL A 817 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLY A 821 " --> pdb=" O GLN A 818 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 816 through 821' Processing helix chain 'A' and resid 822 through 849 removed outlier: 3.803A pdb=" N PHE A 836 " --> pdb=" O VAL A 832 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 837 " --> pdb=" O LEU A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 852 No H-bonds generated for 'chain 'A' and resid 850 through 852' Processing helix chain 'A' and resid 857 through 868 removed outlier: 3.652A pdb=" N MET A 861 " --> pdb=" O PHE A 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 66 Processing helix chain 'B' and resid 89 through 102 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.614A pdb=" N ASN B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 167 removed outlier: 3.632A pdb=" N ARG B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 211 through 221 Processing helix chain 'B' and resid 231 through 244 removed outlier: 4.136A pdb=" N LEU B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 286 through 301 removed outlier: 3.896A pdb=" N ILE B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LEU B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 336 removed outlier: 3.566A pdb=" N LEU B 322 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 removed outlier: 3.659A pdb=" N MET B 360 " --> pdb=" O GLY B 356 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER B 361 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU B 362 " --> pdb=" O ARG B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 457 No H-bonds generated for 'chain 'B' and resid 455 through 457' Processing helix chain 'B' and resid 461 through 474 Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.803A pdb=" N GLU B 504 " --> pdb=" O GLY B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 560 through 583 removed outlier: 3.904A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N CYS B 576 " --> pdb=" O LEU B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.851A pdb=" N PHE B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TRP B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 659 removed outlier: 3.841A pdb=" N VAL B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 646 " --> pdb=" O PHE B 642 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN B 654 " --> pdb=" O SER B 650 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ALA B 656 " --> pdb=" O THR B 652 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ALA B 657 " --> pdb=" O ALA B 653 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 676 removed outlier: 3.923A pdb=" N LEU B 674 " --> pdb=" O SER B 670 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA B 675 " --> pdb=" O ALA B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 696 Processing helix chain 'B' and resid 699 through 712 removed outlier: 3.597A pdb=" N LYS B 704 " --> pdb=" O SER B 700 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER B 711 " --> pdb=" O ALA B 707 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG B 712 " --> pdb=" O PHE B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 717 removed outlier: 3.568A pdb=" N LEU B 717 " --> pdb=" O ARG B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 730 removed outlier: 3.801A pdb=" N THR B 730 " --> pdb=" O GLN B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 749 removed outlier: 3.894A pdb=" N GLN B 747 " --> pdb=" O GLU B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 789 removed outlier: 3.564A pdb=" N LEU B 783 " --> pdb=" O THR B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 799 removed outlier: 3.509A pdb=" N TRP B 798 " --> pdb=" O MET B 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 849 removed outlier: 3.760A pdb=" N ILE B 825 " --> pdb=" O GLY B 821 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL B 832 " --> pdb=" O ALA B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 870 removed outlier: 3.613A pdb=" N ARG B 866 " --> pdb=" O VAL B 862 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET B 867 " --> pdb=" O GLU B 863 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER B 868 " --> pdb=" O GLU B 864 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS B 870 " --> pdb=" O ARG B 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 65 removed outlier: 3.520A pdb=" N LEU C 55 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA C 60 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 102 removed outlier: 3.537A pdb=" N SER C 92 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER C 100 " --> pdb=" O CYS C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.760A pdb=" N ASN C 116 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 167 removed outlier: 4.177A pdb=" N ARG C 158 " --> pdb=" O SER C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 removed outlier: 3.579A pdb=" N ARG C 184 " --> pdb=" O THR C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 190 removed outlier: 3.591A pdb=" N ILE C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 221 removed outlier: 3.582A pdb=" N GLU C 217 " --> pdb=" O PRO C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 246 removed outlier: 3.816A pdb=" N ALA C 236 " --> pdb=" O HIS C 232 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE C 238 " --> pdb=" O MET C 234 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 270 Processing helix chain 'C' and resid 286 through 301 removed outlier: 3.859A pdb=" N ILE C 292 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 337 removed outlier: 3.930A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA C 333 " --> pdb=" O VAL C 329 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLN C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN C 336 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE C 337 " --> pdb=" O ALA C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 365 removed outlier: 3.549A pdb=" N ILE C 363 " --> pdb=" O PHE C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 475 removed outlier: 3.613A pdb=" N THR C 472 " --> pdb=" O ARG C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.908A pdb=" N LYS C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 removed outlier: 3.914A pdb=" N LEU C 556 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 585 removed outlier: 3.958A pdb=" N SER C 575 " --> pdb=" O CYS C 571 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS C 576 " --> pdb=" O LEU C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.746A pdb=" N TRP C 613 " --> pdb=" O LEU C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 660 removed outlier: 3.699A pdb=" N ILE C 635 " --> pdb=" O LEU C 631 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N VAL C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE C 648 " --> pdb=" O THR C 644 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA C 656 " --> pdb=" O THR C 652 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ALA C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE C 658 " --> pdb=" O ASN C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 675 Processing helix chain 'C' and resid 688 through 697 Processing helix chain 'C' and resid 699 through 710 Processing helix chain 'C' and resid 712 through 717 removed outlier: 3.795A pdb=" N LEU C 717 " --> pdb=" O ARG C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 731 removed outlier: 3.916A pdb=" N VAL C 728 " --> pdb=" O GLY C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 746 removed outlier: 3.802A pdb=" N PHE C 744 " --> pdb=" O THR C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 788 removed outlier: 4.121A pdb=" N LYS C 777 " --> pdb=" O PRO C 773 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE C 778 " --> pdb=" O TYR C 774 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU C 783 " --> pdb=" O THR C 779 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU C 785 " --> pdb=" O ALA C 781 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU C 788 " --> pdb=" O GLN C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 800 removed outlier: 3.921A pdb=" N LYS C 795 " --> pdb=" O LEU C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 821 removed outlier: 3.716A pdb=" N ASN C 819 " --> pdb=" O GLY C 816 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 820 " --> pdb=" O VAL C 817 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLY C 821 " --> pdb=" O GLN C 818 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 816 through 821' Processing helix chain 'C' and resid 822 through 849 removed outlier: 3.802A pdb=" N PHE C 836 " --> pdb=" O VAL C 832 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL C 837 " --> pdb=" O LEU C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 852 No H-bonds generated for 'chain 'C' and resid 850 through 852' Processing helix chain 'C' and resid 857 through 868 removed outlier: 3.652A pdb=" N MET C 861 " --> pdb=" O PHE C 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 66 Processing helix chain 'D' and resid 89 through 102 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.613A pdb=" N ASN D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 167 removed outlier: 3.630A pdb=" N ARG D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA D 159 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 211 through 221 Processing helix chain 'D' and resid 231 through 244 removed outlier: 4.137A pdb=" N LEU D 239 " --> pdb=" O ALA D 235 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 286 through 301 removed outlier: 3.896A pdb=" N ILE D 292 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE D 293 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET D 298 " --> pdb=" O GLU D 294 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU D 299 " --> pdb=" O LYS D 295 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LEU D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 336 removed outlier: 3.567A pdb=" N LEU D 322 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 365 removed outlier: 3.659A pdb=" N MET D 360 " --> pdb=" O GLY D 356 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N SER D 361 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU D 362 " --> pdb=" O ARG D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 457 No H-bonds generated for 'chain 'D' and resid 455 through 457' Processing helix chain 'D' and resid 461 through 474 Processing helix chain 'D' and resid 499 through 507 removed outlier: 3.802A pdb=" N GLU D 504 " --> pdb=" O GLY D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 560 through 583 removed outlier: 3.904A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N CYS D 576 " --> pdb=" O LEU D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.851A pdb=" N PHE D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TRP D 613 " --> pdb=" O LEU D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 659 removed outlier: 3.842A pdb=" N VAL D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE D 646 " --> pdb=" O PHE D 642 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN D 654 " --> pdb=" O SER D 650 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ALA D 656 " --> pdb=" O THR D 652 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ALA D 657 " --> pdb=" O ALA D 653 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 676 removed outlier: 3.923A pdb=" N LEU D 674 " --> pdb=" O SER D 670 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA D 675 " --> pdb=" O ALA D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 696 Processing helix chain 'D' and resid 699 through 712 removed outlier: 3.596A pdb=" N LYS D 704 " --> pdb=" O SER D 700 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER D 711 " --> pdb=" O ALA D 707 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG D 712 " --> pdb=" O PHE D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 717 removed outlier: 3.568A pdb=" N LEU D 717 " --> pdb=" O ARG D 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 730 removed outlier: 3.802A pdb=" N THR D 730 " --> pdb=" O GLN D 726 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 749 removed outlier: 3.893A pdb=" N GLN D 747 " --> pdb=" O GLU D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 789 removed outlier: 3.565A pdb=" N LEU D 783 " --> pdb=" O THR D 779 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 799 removed outlier: 3.508A pdb=" N TRP D 798 " --> pdb=" O MET D 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 849 removed outlier: 3.760A pdb=" N ILE D 825 " --> pdb=" O GLY D 821 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL D 832 " --> pdb=" O ALA D 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 856 through 870 removed outlier: 3.613A pdb=" N ARG D 866 " --> pdb=" O VAL D 862 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET D 867 " --> pdb=" O GLU D 863 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER D 868 " --> pdb=" O GLU D 864 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS D 870 " --> pdb=" O ARG D 866 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 18 removed outlier: 3.809A pdb=" N GLY E 18 " --> pdb=" O THR E 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 removed outlier: 3.809A pdb=" N GLY G 18 " --> pdb=" O THR G 15 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 43 removed outlier: 3.558A pdb=" N ASP A 79 " --> pdb=" O PHE A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 131 removed outlier: 3.940A pdb=" N GLY A 382 " --> pdb=" O TYR A 146 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG A 384 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TYR A 150 " --> pdb=" O ARG A 384 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 202 through 203 removed outlier: 8.060A pdb=" N ARG A 202 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N VAL A 174 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N THR A 173 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A 226 " --> pdb=" O ILE A 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 392 through 394 removed outlier: 3.619A pdb=" N SER A 393 " --> pdb=" O GLU A 400 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 400 " --> pdb=" O SER A 393 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 405 through 406 Processing sheet with id=AA6, first strand: chain 'A' and resid 435 through 437 removed outlier: 5.567A pdb=" N VAL A 435 " --> pdb=" O ARG A 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA8, first strand: chain 'A' and resid 532 through 535 removed outlier: 6.690A pdb=" N TYR A 764 " --> pdb=" O PHE A 533 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 681 through 683 removed outlier: 6.611A pdb=" N GLU A 681 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU A 736 " --> pdb=" O GLU A 681 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY A 683 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 9.310A pdb=" N GLU A 738 " --> pdb=" O GLY A 683 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N TYR A 733 " --> pdb=" O ARG A 543 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ARG A 543 " --> pdb=" O TYR A 733 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 540 " --> pdb=" O ILE A 755 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 37 through 43 removed outlier: 7.697A pdb=" N PHE B 38 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N GLN B 81 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLY B 40 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE B 83 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N PHE B 42 " --> pdb=" O ILE B 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 129 through 131 removed outlier: 3.898A pdb=" N GLY B 382 " --> pdb=" O TYR B 146 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TYR B 150 " --> pdb=" O ARG B 384 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 202 through 203 removed outlier: 7.692A pdb=" N ARG B 202 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL B 174 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR B 173 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ASP B 229 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL B 175 " --> pdb=" O ASP B 229 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 226 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE B 279 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N MET B 276 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 367 through 370 removed outlier: 3.566A pdb=" N TRP B 368 " --> pdb=" O ILE B 375 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 434 through 435 Processing sheet with id=AB6, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AB7, first strand: chain 'B' and resid 528 through 529 Processing sheet with id=AB8, first strand: chain 'B' and resid 534 through 536 removed outlier: 4.197A pdb=" N MET B 534 " --> pdb=" O TYR B 764 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 681 through 684 removed outlier: 6.627A pdb=" N GLU B 681 " --> pdb=" O ALA B 734 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU B 736 " --> pdb=" O GLU B 681 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY B 683 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N GLU B 738 " --> pdb=" O GLY B 683 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N TYR B 733 " --> pdb=" O ARG B 543 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ARG B 543 " --> pdb=" O TYR B 733 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 548 through 549 removed outlier: 4.200A pdb=" N GLU B 662 " --> pdb=" O ASN B 549 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 37 through 43 removed outlier: 3.559A pdb=" N ASP C 79 " --> pdb=" O PHE C 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 129 through 131 removed outlier: 3.940A pdb=" N GLY C 382 " --> pdb=" O TYR C 146 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG C 384 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TYR C 150 " --> pdb=" O ARG C 384 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 202 through 203 removed outlier: 8.061A pdb=" N ARG C 202 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N VAL C 174 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N THR C 173 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL C 226 " --> pdb=" O ILE C 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 392 through 394 removed outlier: 3.619A pdb=" N SER C 393 " --> pdb=" O GLU C 400 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU C 400 " --> pdb=" O SER C 393 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 405 through 406 Processing sheet with id=AC7, first strand: chain 'C' and resid 435 through 437 removed outlier: 5.568A pdb=" N VAL C 435 " --> pdb=" O ARG C 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AC9, first strand: chain 'C' and resid 532 through 535 removed outlier: 6.690A pdb=" N TYR C 764 " --> pdb=" O PHE C 533 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 681 through 683 removed outlier: 6.611A pdb=" N GLU C 681 " --> pdb=" O ALA C 734 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU C 736 " --> pdb=" O GLU C 681 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLY C 683 " --> pdb=" O LEU C 736 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N GLU C 738 " --> pdb=" O GLY C 683 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N TYR C 733 " --> pdb=" O ARG C 543 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ARG C 543 " --> pdb=" O TYR C 733 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE C 540 " --> pdb=" O ILE C 755 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 37 through 43 removed outlier: 7.697A pdb=" N PHE D 38 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N GLN D 81 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLY D 40 " --> pdb=" O GLN D 81 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE D 83 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N PHE D 42 " --> pdb=" O ILE D 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 129 through 131 removed outlier: 3.898A pdb=" N GLY D 382 " --> pdb=" O TYR D 146 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TYR D 150 " --> pdb=" O ARG D 384 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 202 through 203 removed outlier: 7.691A pdb=" N ARG D 202 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR D 173 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ASP D 229 " --> pdb=" O THR D 173 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL D 175 " --> pdb=" O ASP D 229 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL D 226 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE D 279 " --> pdb=" O PHE D 256 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N MET D 276 " --> pdb=" O LEU D 394 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 367 through 370 removed outlier: 3.566A pdb=" N TRP D 368 " --> pdb=" O ILE D 375 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 434 through 435 Processing sheet with id=AD7, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AD8, first strand: chain 'D' and resid 528 through 529 Processing sheet with id=AD9, first strand: chain 'D' and resid 534 through 536 removed outlier: 4.196A pdb=" N MET D 534 " --> pdb=" O TYR D 764 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 681 through 684 removed outlier: 6.627A pdb=" N GLU D 681 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU D 736 " --> pdb=" O GLU D 681 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY D 683 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N GLU D 738 " --> pdb=" O GLY D 683 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N TYR D 733 " --> pdb=" O ARG D 543 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ARG D 543 " --> pdb=" O TYR D 733 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 548 through 549 removed outlier: 4.200A pdb=" N GLU D 662 " --> pdb=" O ASN D 549 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.601A pdb=" N SER E 94 " --> pdb=" O ALA E 211 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY E 92 " --> pdb=" O PHE E 213 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER E 215 " --> pdb=" O ARG E 90 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG E 90 " --> pdb=" O SER E 215 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.601A pdb=" N SER E 94 " --> pdb=" O ALA E 211 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY E 92 " --> pdb=" O PHE E 213 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER E 215 " --> pdb=" O ARG E 90 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG E 90 " --> pdb=" O SER E 215 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL E 179 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 9 through 10 Processing sheet with id=AE6, first strand: chain 'E' and resid 49 through 54 Processing sheet with id=AE7, first strand: chain 'E' and resid 154 through 155 Processing sheet with id=AE8, first strand: chain 'E' and resid 128 through 130 removed outlier: 3.844A pdb=" N THR E 194 " --> pdb=" O SER E 110 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 36 through 39 removed outlier: 4.256A pdb=" N LYS F 36 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE F 212 " --> pdb=" O VAL F 7 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY F 92 " --> pdb=" O PHE F 213 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N VAL F 91 " --> pdb=" O PHE F 175 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU F 174 " --> pdb=" O ILE F 141 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 36 through 39 removed outlier: 4.256A pdb=" N LYS F 36 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE F 212 " --> pdb=" O VAL F 7 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY F 92 " --> pdb=" O PHE F 213 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL F 179 " --> pdb=" O VAL F 89 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 77 through 78 removed outlier: 3.511A pdb=" N TYR F 77 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA F 50 " --> pdb=" O PHE F 195 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE F 52 " --> pdb=" O ALA F 193 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR F 194 " --> pdb=" O SER F 110 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER F 108 " --> pdb=" O THR F 196 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU F 198 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE F 106 " --> pdb=" O LEU F 198 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 77 through 78 removed outlier: 3.511A pdb=" N TYR F 77 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA F 50 " --> pdb=" O PHE F 195 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE F 52 " --> pdb=" O ALA F 193 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR F 194 " --> pdb=" O SER F 110 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER F 108 " --> pdb=" O THR F 196 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU F 198 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE F 106 " --> pdb=" O LEU F 198 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 5 through 6 removed outlier: 3.602A pdb=" N SER G 94 " --> pdb=" O ALA G 211 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY G 92 " --> pdb=" O PHE G 213 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER G 215 " --> pdb=" O ARG G 90 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 5 through 6 removed outlier: 3.602A pdb=" N SER G 94 " --> pdb=" O ALA G 211 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY G 92 " --> pdb=" O PHE G 213 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER G 215 " --> pdb=" O ARG G 90 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL G 179 " --> pdb=" O VAL G 89 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 9 through 10 Processing sheet with id=AF7, first strand: chain 'G' and resid 49 through 54 Processing sheet with id=AF8, first strand: chain 'G' and resid 154 through 155 Processing sheet with id=AF9, first strand: chain 'G' and resid 128 through 130 removed outlier: 3.843A pdb=" N THR G 194 " --> pdb=" O SER G 110 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 36 through 39 removed outlier: 4.256A pdb=" N LYS H 36 " --> pdb=" O ILE H 27 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE H 212 " --> pdb=" O VAL H 7 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY H 92 " --> pdb=" O PHE H 213 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N VAL H 91 " --> pdb=" O PHE H 175 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU H 174 " --> pdb=" O ILE H 141 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 36 through 39 removed outlier: 4.256A pdb=" N LYS H 36 " --> pdb=" O ILE H 27 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE H 212 " --> pdb=" O VAL H 7 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY H 92 " --> pdb=" O PHE H 213 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL H 179 " --> pdb=" O VAL H 89 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 77 through 78 removed outlier: 3.511A pdb=" N TYR H 77 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA H 50 " --> pdb=" O PHE H 195 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE H 52 " --> pdb=" O ALA H 193 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR H 194 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER H 108 " --> pdb=" O THR H 196 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU H 198 " --> pdb=" O ILE H 106 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ILE H 106 " --> pdb=" O LEU H 198 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 77 through 78 removed outlier: 3.511A pdb=" N TYR H 77 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA H 50 " --> pdb=" O PHE H 195 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE H 52 " --> pdb=" O ALA H 193 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR H 194 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER H 108 " --> pdb=" O THR H 196 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU H 198 " --> pdb=" O ILE H 106 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ILE H 106 " --> pdb=" O LEU H 198 " (cutoff:3.500A) 1196 hydrogen bonds defined for protein. 3374 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: 8.26 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 5714 1.31 - 1.44: 10013 1.44 - 1.56: 21007 1.56 - 1.69: 96 1.69 - 1.81: 292 Bond restraints: 37122 Sorted by residual: bond pdb=" OAA 2J9 B1002 " pdb=" SAP 2J9 B1002 " ideal model delta sigma weight residual 1.452 1.658 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" OAA 2J9 D1002 " pdb=" SAP 2J9 D1002 " ideal model delta sigma weight residual 1.452 1.656 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" OAA 2J9 A1001 " pdb=" SAP 2J9 A1001 " ideal model delta sigma weight residual 1.452 1.655 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" OAA 2J9 C1002 " pdb=" SAP 2J9 C1002 " ideal model delta sigma weight residual 1.452 1.654 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" OAB 2J9 C1002 " pdb=" SAP 2J9 C1002 " ideal model delta sigma weight residual 1.452 1.652 -0.200 2.00e-02 2.50e+03 1.00e+02 ... (remaining 37117 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.67: 49921 6.67 - 13.35: 317 13.35 - 20.02: 4 20.02 - 26.70: 4 26.70 - 33.37: 8 Bond angle restraints: 50254 Sorted by residual: angle pdb=" CAH 2J9 B1002 " pdb=" CAN 2J9 B1002 " pdb=" NAO 2J9 B1002 " ideal model delta sigma weight residual 117.67 151.04 -33.37 3.00e+00 1.11e-01 1.24e+02 angle pdb=" CAH 2J9 D1002 " pdb=" CAN 2J9 D1002 " pdb=" NAO 2J9 D1002 " ideal model delta sigma weight residual 117.67 150.60 -32.93 3.00e+00 1.11e-01 1.20e+02 angle pdb=" CAH 2J9 A1001 " pdb=" CAN 2J9 A1001 " pdb=" NAO 2J9 A1001 " ideal model delta sigma weight residual 117.67 149.75 -32.08 3.00e+00 1.11e-01 1.14e+02 angle pdb=" CAG 2J9 C1002 " pdb=" CAN 2J9 C1002 " pdb=" NAO 2J9 C1002 " ideal model delta sigma weight residual 118.82 150.84 -32.02 3.00e+00 1.11e-01 1.14e+02 angle pdb=" CAH 2J9 C1002 " pdb=" CAN 2J9 C1002 " pdb=" NAO 2J9 C1002 " ideal model delta sigma weight residual 117.67 149.26 -31.59 3.00e+00 1.11e-01 1.11e+02 ... (remaining 50249 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.78: 22658 30.78 - 61.56: 874 61.56 - 92.34: 259 92.34 - 123.12: 204 123.12 - 153.90: 7 Dihedral angle restraints: 24002 sinusoidal: 11458 harmonic: 12544 Sorted by residual: dihedral pdb=" CA ALA E 207 " pdb=" C ALA E 207 " pdb=" N ASP E 208 " pdb=" CA ASP E 208 " ideal model delta harmonic sigma weight residual 180.00 109.71 70.29 0 5.00e+00 4.00e-02 1.98e+02 dihedral pdb=" CA ALA G 207 " pdb=" C ALA G 207 " pdb=" N ASP G 208 " pdb=" CA ASP G 208 " ideal model delta harmonic sigma weight residual 180.00 109.72 70.28 0 5.00e+00 4.00e-02 1.98e+02 dihedral pdb=" CA VAL F 47 " pdb=" C VAL F 47 " pdb=" N GLY F 48 " pdb=" CA GLY F 48 " ideal model delta harmonic sigma weight residual 180.00 117.97 62.03 0 5.00e+00 4.00e-02 1.54e+02 ... (remaining 23999 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.462: 5861 0.462 - 0.923: 7 0.923 - 1.385: 2 1.385 - 1.846: 0 1.846 - 2.308: 4 Chirality restraints: 5874 Sorted by residual: chirality pdb=" CAN 2J9 B1002 " pdb=" CAG 2J9 B1002 " pdb=" CAH 2J9 B1002 " pdb=" NAO 2J9 B1002 " both_signs ideal model delta sigma weight residual True 2.32 0.01 2.31 2.00e-01 2.50e+01 1.33e+02 chirality pdb=" CAN 2J9 D1002 " pdb=" CAG 2J9 D1002 " pdb=" CAH 2J9 D1002 " pdb=" NAO 2J9 D1002 " both_signs ideal model delta sigma weight residual True 2.32 0.02 2.30 2.00e-01 2.50e+01 1.32e+02 chirality pdb=" CAN 2J9 A1001 " pdb=" CAG 2J9 A1001 " pdb=" CAH 2J9 A1001 " pdb=" NAO 2J9 A1001 " both_signs ideal model delta sigma weight residual True 2.32 -0.03 2.29 2.00e-01 2.50e+01 1.31e+02 ... (remaining 5871 not shown) Planarity restraints: 6154 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 191 " -0.065 5.00e-02 4.00e+02 9.79e-02 1.53e+01 pdb=" N PRO C 192 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO C 192 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 192 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 191 " -0.064 5.00e-02 4.00e+02 9.76e-02 1.52e+01 pdb=" N PRO A 192 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 192 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 192 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 275 " 0.032 2.00e-02 2.50e+03 3.16e-02 1.25e+01 pdb=" CG ASN C 275 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN C 275 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN C 275 " -0.043 2.00e-02 2.50e+03 pdb=" C1 NAG b 1 " 0.036 2.00e-02 2.50e+03 ... (remaining 6151 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 829 2.66 - 3.22: 32632 3.22 - 3.78: 55235 3.78 - 4.34: 75846 4.34 - 4.90: 122602 Nonbonded interactions: 287144 Sorted by model distance: nonbonded pdb=" OD1 ASP H 19 " pdb="ZN ZN H1001 " model vdw 2.099 2.230 nonbonded pdb=" OD2 ASP E 10 " pdb="ZN ZN E1001 " model vdw 2.121 2.230 nonbonded pdb=" OD1 ASP E 19 " pdb="ZN ZN E1001 " model vdw 2.133 2.230 nonbonded pdb=" OD2 ASP F 10 " pdb="ZN ZN F1001 " model vdw 2.151 2.230 nonbonded pdb=" OD2 ASP G 10 " pdb="ZN ZN G1001 " model vdw 2.151 2.230 ... (remaining 287139 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 470 or resid 472 through 534 or resid 536 throu \ gh 874)) selection = (chain 'B' and (resid 33 through 470 or resid 472 through 534 or resid 536 throu \ gh 874)) selection = (chain 'C' and (resid 33 through 470 or resid 472 through 534 or resid 536 throu \ gh 874)) selection = (chain 'D' and (resid 33 through 470 or resid 472 through 534 or resid 536 throu \ gh 874)) } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 1 through 144 or (resid 145 through 146 and (name N or nam \ e CA or name C or name O or name CB )) or resid 147 through 1002)) selection = chain 'G' selection = (chain 'H' and (resid 1 through 144 or (resid 145 through 146 and (name N or nam \ e CA or name C or name O or name CB )) or resid 147 through 1002)) } ncs_group { reference = (chain 'I' and resid 1) selection = (chain 'K' and resid 2) selection = (chain 'R' and resid 1) selection = (chain 'W' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'f' and resid 1) } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'j' } ncs_group { reference = chain 'M' selection = chain 'S' selection = chain 'T' selection = chain 'a' selection = chain 'g' } ncs_group { reference = (chain 'P' and resid 1 through 3) selection = (chain 'U' and resid 1 through 3) selection = (chain 'd' and resid 1 through 3) selection = (chain 'h' and resid 1 through 3) selection = (chain 'i' and resid 1 through 3) } 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=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.050 Process input model: 42.540 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.130 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 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 : 0.009 0.206 37234 Z= 0.467 Angle : 1.508 33.369 50570 Z= 0.727 Chirality : 0.094 2.308 5874 Planarity : 0.008 0.098 6128 Dihedral : 20.530 153.895 15902 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.74 % Allowed : 14.05 % Favored : 85.21 % Rotamer: Outliers : 0.64 % Allowed : 4.74 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.92 % 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: -5.58 (0.09), residues: 4306 helix: -4.06 (0.06), residues: 1400 sheet: -3.77 (0.17), residues: 690 loop : -3.44 (0.11), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 133 TYR 0.032 0.003 TYR C 251 PHE 0.041 0.003 PHE D 735 TRP 0.038 0.004 TRP D 134 HIS 0.015 0.002 HIS A 593 Details of bonding type rmsd/Z covalent geometry : bond 0.00941 / 0.46 (37122) covalent geometry : angle 1.44907 / 0.71 (50254) SS BOND : bond 0.01177 / 0.62 ( 8) SS BOND : angle 1.20457 / 0.84 ( 16) hydrogen bonds : bond 0.29356 / 19.35 ( 1131) hydrogen bonds : angle 10.93563 / 7.46 ( 3374) metal coordination : bond 0.07021 / 2.73 ( 4) link_ALPHA1-3 : bond 0.01243 / 0.68 ( 6) link_ALPHA1-3 : angle 5.26551 / 3.65 ( 18) link_ALPHA1-6 : bond 0.01616 / 0.97 ( 9) link_ALPHA1-6 : angle 4.29284 / 3.07 ( 27) link_BETA1-2 : bond 0.01629 / 0.97 ( 10) link_BETA1-2 : angle 6.52186 / 3.68 ( 30) link_BETA1-3 : bond 0.00186 / 0.09 ( 2) link_BETA1-3 : angle 1.61849 / 1.01 ( 6) link_BETA1-4 : bond 0.01758 / 1.22 ( 47) link_BETA1-4 : angle 4.77252 / 2.98 ( 141) link_NAG-ASN : bond 0.01565 / 1.05 ( 26) link_NAG-ASN : angle 7.17796 / 4.94 ( 78) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8612 Ramachandran restraints generated. 4306 Oldfield, 0 Emsley, 4306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8612 Ramachandran restraints generated. 4306 Oldfield, 0 Emsley, 4306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 955 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 941 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.7019 (ttm110) cc_final: 0.6210 (mtm110) REVERT: A 114 SER cc_start: 0.8907 (m) cc_final: 0.8661 (t) REVERT: A 229 ASP cc_start: 0.8948 (t0) cc_final: 0.8572 (t0) REVERT: A 257 THR cc_start: 0.8099 (m) cc_final: 0.7889 (p) REVERT: A 286 ASN cc_start: 0.7650 (m-40) cc_final: 0.7246 (t0) REVERT: A 465 ASP cc_start: 0.7754 (t70) cc_final: 0.7363 (t0) REVERT: A 539 SER cc_start: 0.8740 (t) cc_final: 0.8527 (p) REVERT: A 565 MET cc_start: 0.7724 (mmm) cc_final: 0.7256 (mmt) REVERT: A 612 PHE cc_start: 0.8693 (m-80) cc_final: 0.8328 (m-10) REVERT: A 639 ILE cc_start: 0.8932 (mm) cc_final: 0.8594 (tp) REVERT: A 673 ASP cc_start: 0.8792 (m-30) cc_final: 0.8585 (t70) REVERT: A 698 LYS cc_start: 0.9363 (mttt) cc_final: 0.9097 (mmtt) REVERT: A 761 SER cc_start: 0.7896 (t) cc_final: 0.7425 (m) REVERT: A 861 MET cc_start: 0.8235 (mmp) cc_final: 0.7747 (mtm) REVERT: B 78 TYR cc_start: 0.7148 (p90) cc_final: 0.6925 (p90) REVERT: B 113 SER cc_start: 0.7909 (m) cc_final: 0.7591 (p) REVERT: B 130 ILE cc_start: 0.8703 (mm) cc_final: 0.8384 (mm) REVERT: B 248 MET cc_start: 0.7021 (mtp) cc_final: 0.6727 (mtp) REVERT: B 443 TYR cc_start: 0.7605 (m-80) cc_final: 0.7366 (m-80) REVERT: B 465 ASP cc_start: 0.8445 (m-30) cc_final: 0.8088 (m-30) REVERT: B 469 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8140 (mm-30) REVERT: B 563 ILE cc_start: 0.8733 (mm) cc_final: 0.8312 (mm) REVERT: B 572 LEU cc_start: 0.8886 (mm) cc_final: 0.8519 (mm) REVERT: B 576 CYS cc_start: 0.8625 (m) cc_final: 0.8038 (m) REVERT: B 584 PHE cc_start: 0.7819 (t80) cc_final: 0.7278 (m-80) REVERT: B 738 GLU cc_start: 0.7428 (mm-30) cc_final: 0.6951 (mm-30) REVERT: B 792 HIS cc_start: 0.8373 (t70) cc_final: 0.7716 (t-90) REVERT: B 841 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7868 (mt-10) REVERT: B 861 MET cc_start: 0.7030 (ttt) cc_final: 0.6720 (ttt) REVERT: B 867 MET cc_start: 0.7176 (ttt) cc_final: 0.6870 (ttt) REVERT: C 37 ARG cc_start: 0.7303 (ttm110) cc_final: 0.7103 (mtm110) REVERT: C 204 LEU cc_start: 0.8553 (mt) cc_final: 0.7967 (tp) REVERT: C 229 ASP cc_start: 0.8783 (t0) cc_final: 0.8346 (t0) REVERT: C 230 CYS cc_start: 0.7423 (m) cc_final: 0.7161 (m) REVERT: C 296 TRP cc_start: 0.7204 (t-100) cc_final: 0.6740 (t-100) REVERT: C 351 LYS cc_start: 0.8501 (tptp) cc_final: 0.8282 (tmtt) REVERT: C 465 ASP cc_start: 0.7668 (t70) cc_final: 0.7152 (t0) REVERT: C 501 MET cc_start: 0.7012 (mtm) cc_final: 0.6342 (mtm) REVERT: C 565 MET cc_start: 0.7720 (mmm) cc_final: 0.7365 (mmt) REVERT: C 566 TYR cc_start: 0.8484 (m-10) cc_final: 0.8264 (m-10) REVERT: C 612 PHE cc_start: 0.8579 (m-80) cc_final: 0.8065 (m-10) REVERT: C 639 ILE cc_start: 0.8962 (mm) cc_final: 0.8601 (tp) REVERT: C 698 LYS cc_start: 0.9374 (mttt) cc_final: 0.9159 (mmtt) REVERT: C 761 SER cc_start: 0.7643 (t) cc_final: 0.7283 (m) REVERT: C 793 MET cc_start: 0.7149 (mtt) cc_final: 0.6781 (tmm) REVERT: C 794 MET cc_start: 0.7570 (mtm) cc_final: 0.6739 (mtm) REVERT: C 861 MET cc_start: 0.8171 (mmp) cc_final: 0.7736 (mtm) REVERT: D 381 ASN cc_start: 0.8255 (p0) cc_final: 0.7895 (p0) REVERT: D 443 TYR cc_start: 0.7626 (m-80) cc_final: 0.7423 (m-80) REVERT: D 463 CYS cc_start: 0.9041 (m) cc_final: 0.8796 (m) REVERT: D 563 ILE cc_start: 0.8713 (mm) cc_final: 0.8260 (mm) REVERT: D 576 CYS cc_start: 0.8709 (m) cc_final: 0.8132 (m) REVERT: D 590 TYR cc_start: 0.6789 (p90) cc_final: 0.6259 (p90) REVERT: D 744 PHE cc_start: 0.7922 (t80) cc_final: 0.7600 (t80) REVERT: E 25 ILE cc_start: 0.9122 (tt) cc_final: 0.8875 (mt) REVERT: E 42 MET cc_start: 0.5829 (ttp) cc_final: 0.5591 (ttp) REVERT: E 53 ILE cc_start: 0.8056 (pp) cc_final: 0.7748 (mt) REVERT: E 55 ASN cc_start: 0.8701 (p0) cc_final: 0.8088 (p0) REVERT: E 126 LEU cc_start: 0.8557 (tp) cc_final: 0.8306 (tp) REVERT: F 46 LYS cc_start: 0.8295 (mttt) cc_final: 0.8045 (mmmm) REVERT: F 58 ASP cc_start: 0.7143 (m-30) cc_final: 0.6903 (m-30) REVERT: F 114 LYS cc_start: 0.7273 (mtpt) cc_final: 0.7021 (mmtt) REVERT: F 126 LEU cc_start: 0.8089 (tp) cc_final: 0.7811 (tp) REVERT: F 142 LEU cc_start: 0.8346 (pp) cc_final: 0.8145 (mp) REVERT: F 153 ASN cc_start: 0.7894 (m110) cc_final: 0.7188 (m-40) REVERT: F 192 GLU cc_start: 0.7582 (tt0) cc_final: 0.7285 (tm-30) REVERT: G 42 MET cc_start: 0.4012 (ttp) cc_final: 0.3730 (ttp) REVERT: G 93 LEU cc_start: 0.8212 (mt) cc_final: 0.7846 (mt) REVERT: G 179 VAL cc_start: 0.8301 (t) cc_final: 0.7865 (t) REVERT: G 213 PHE cc_start: 0.7982 (p90) cc_final: 0.7282 (p90) REVERT: H 12 TYR cc_start: 0.7820 (t80) cc_final: 0.7599 (t80) REVERT: H 36 LYS cc_start: 0.7922 (mmtt) cc_final: 0.7679 (mmtp) REVERT: H 55 ASN cc_start: 0.7412 (p0) cc_final: 0.7204 (p0) REVERT: H 77 TYR cc_start: 0.7359 (t80) cc_final: 0.6456 (t80) REVERT: H 114 LYS cc_start: 0.7860 (mtpt) cc_final: 0.7495 (tmtt) REVERT: H 191 PHE cc_start: 0.8352 (p90) cc_final: 0.8126 (p90) REVERT: H 192 GLU cc_start: 0.7907 (tt0) cc_final: 0.7528 (tm-30) REVERT: B 1003 GLU cc_start: 0.6530 (mm-30) cc_final: 0.6044 (mm-30) outliers start: 14 outliers final: 0 residues processed: 953 average time/residue: 0.2420 time to fit residues: 374.1578 Evaluate side-chains 533 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 533 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.1980 chunk 401 optimal weight: 4.9990 chunk 424 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS A 714 GLN A 786 GLN A 872 GLN B 65 ASN B 165 GLN B 604 ASN B 610 ASN B 721 ASN B 819 ASN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 HIS C 872 GLN D 111 HIS D 165 GLN D 604 ASN D 610 ASN D 621 GLN D 819 ASN E 14 ASN F 14 ASN ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.128386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.104387 restraints weight = 147986.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.105995 restraints weight = 162400.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.107985 restraints weight = 104718.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.109022 restraints weight = 70995.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.109611 restraints weight = 63150.618| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (6 function evaluations) r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 37234 Z= 0.169 Angle : 0.944 20.184 50570 Z= 0.442 Chirality : 0.053 0.656 5874 Planarity : 0.006 0.089 6128 Dihedral : 22.412 140.051 7876 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.40 % Allowed : 12.74 % Favored : 86.86 % Rotamer: Outliers : 0.27 % Allowed : 2.16 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.82 % 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: -4.25 (0.11), residues: 4306 helix: -2.09 (0.11), residues: 1428 sheet: -3.64 (0.17), residues: 712 loop : -3.03 (0.12), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 866 TYR 0.035 0.002 TYR B 566 PHE 0.024 0.002 PHE G 128 TRP 0.026 0.002 TRP C 589 HIS 0.011 0.001 HIS C 593 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 (37122) covalent geometry : angle 0.89312 / 0.43 (50254) SS BOND : bond 0.00580 / 0.35 ( 8) SS BOND : angle 1.00621 / 0.67 ( 16) hydrogen bonds : bond 0.05039 / 3.28 ( 1131) hydrogen bonds : angle 5.77762 / 3.94 ( 3374) metal coordination : bond 0.00382 / 0.16 ( 4) link_ALPHA1-3 : bond 0.01222 / 0.64 ( 6) link_ALPHA1-3 : angle 4.51094 / 2.96 ( 18) link_ALPHA1-6 : bond 0.01603 / 0.99 ( 9) link_ALPHA1-6 : angle 3.07861 / 2.19 ( 27) link_BETA1-2 : bond 0.01369 / 0.78 ( 10) link_BETA1-2 : angle 4.75028 / 2.60 ( 30) link_BETA1-3 : bond 0.00695 / 0.35 ( 2) link_BETA1-3 : angle 2.79044 / 1.63 ( 6) link_BETA1-4 : bond 0.01113 / 0.72 ( 47) link_BETA1-4 : angle 3.63033 / 2.32 ( 141) link_NAG-ASN : bond 0.01038 / 0.71 ( 26) link_NAG-ASN : angle 4.81073 / 3.47 ( 78) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8612 Ramachandran restraints generated. 4306 Oldfield, 0 Emsley, 4306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8612 Ramachandran restraints generated. 4306 Oldfield, 0 Emsley, 4306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 702 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.6961 (ttm110) cc_final: 0.6211 (mtp85) REVERT: A 50 MET cc_start: 0.8091 (ptt) cc_final: 0.7739 (ptt) REVERT: A 114 SER cc_start: 0.8616 (m) cc_final: 0.8340 (t) REVERT: A 199 LEU cc_start: 0.8910 (mm) cc_final: 0.8568 (mt) REVERT: A 229 ASP cc_start: 0.8622 (t0) cc_final: 0.8380 (t0) REVERT: A 565 MET cc_start: 0.7718 (mmm) cc_final: 0.7357 (mmm) REVERT: A 566 TYR cc_start: 0.8376 (m-10) cc_final: 0.8143 (m-10) REVERT: A 639 ILE cc_start: 0.9308 (mm) cc_final: 0.9076 (tp) REVERT: A 761 SER cc_start: 0.7430 (t) cc_final: 0.7161 (m) REVERT: A 861 MET cc_start: 0.8378 (mmp) cc_final: 0.7881 (mtm) REVERT: B 98 GLN cc_start: 0.8391 (mt0) cc_final: 0.8073 (mt0) REVERT: B 113 SER cc_start: 0.8206 (m) cc_final: 0.7752 (p) REVERT: B 130 ILE cc_start: 0.8637 (mm) cc_final: 0.8298 (mm) REVERT: B 248 MET cc_start: 0.7003 (mtp) cc_final: 0.6524 (mtp) REVERT: B 572 LEU cc_start: 0.8883 (mm) cc_final: 0.8301 (mm) REVERT: B 586 PRO cc_start: 0.8338 (Cg_endo) cc_final: 0.8070 (Cg_exo) REVERT: B 627 MET cc_start: 0.7222 (mmp) cc_final: 0.6970 (mmp) REVERT: B 738 GLU cc_start: 0.7669 (mm-30) cc_final: 0.6962 (mm-30) REVERT: C 37 ARG cc_start: 0.7309 (ttm110) cc_final: 0.7020 (mtm110) REVERT: C 199 LEU cc_start: 0.8950 (mm) cc_final: 0.8721 (mt) REVERT: C 323 MET cc_start: 0.7277 (tpp) cc_final: 0.7043 (tpp) REVERT: C 359 PHE cc_start: 0.7168 (t80) cc_final: 0.6910 (t80) REVERT: C 501 MET cc_start: 0.7511 (mtm) cc_final: 0.7050 (mtm) REVERT: C 565 MET cc_start: 0.7742 (mmm) cc_final: 0.7294 (mmt) REVERT: C 566 TYR cc_start: 0.8310 (m-10) cc_final: 0.7892 (m-10) REVERT: C 761 SER cc_start: 0.7235 (t) cc_final: 0.6923 (m) REVERT: C 841 GLU cc_start: 0.7492 (mt-10) cc_final: 0.6992 (mt-10) REVERT: C 861 MET cc_start: 0.8335 (mmp) cc_final: 0.7725 (mtm) REVERT: D 88 SER cc_start: 0.8369 (m) cc_final: 0.7868 (t) REVERT: D 166 PHE cc_start: 0.8386 (t80) cc_final: 0.7804 (t80) REVERT: D 247 MET cc_start: 0.8625 (ttp) cc_final: 0.8422 (ttp) REVERT: D 248 MET cc_start: 0.6826 (mtp) cc_final: 0.6607 (mtp) REVERT: D 340 MET cc_start: 0.6667 (ttp) cc_final: 0.6115 (ttm) REVERT: D 463 CYS cc_start: 0.8912 (m) cc_final: 0.8683 (m) REVERT: D 609 LEU cc_start: 0.8474 (tt) cc_final: 0.7866 (mt) REVERT: D 632 SER cc_start: 0.8824 (p) cc_final: 0.8294 (m) REVERT: E 129 MET cc_start: 0.6592 (ttm) cc_final: 0.6301 (ttt) REVERT: F 3 THR cc_start: 0.7319 (m) cc_final: 0.7114 (p) REVERT: F 46 LYS cc_start: 0.8116 (mttt) cc_final: 0.7743 (mmtt) REVERT: F 154 LEU cc_start: 0.8386 (tp) cc_final: 0.8171 (tp) REVERT: F 208 ASP cc_start: 0.5539 (t0) cc_final: 0.5253 (t0) REVERT: G 42 MET cc_start: 0.2793 (ttp) cc_final: 0.2570 (ttp) REVERT: G 175 PHE cc_start: 0.8660 (t80) cc_final: 0.8446 (t80) REVERT: G 179 VAL cc_start: 0.8038 (t) cc_final: 0.7761 (t) REVERT: H 8 GLU cc_start: 0.7242 (pt0) cc_final: 0.6828 (pt0) REVERT: H 25 ILE cc_start: 0.9114 (tt) cc_final: 0.8913 (mm) REVERT: H 44 ASN cc_start: 0.6259 (t0) cc_final: 0.5864 (t0) REVERT: H 141 ILE cc_start: 0.7868 (mt) cc_final: 0.7657 (mp) REVERT: H 156 LEU cc_start: 0.6267 (mt) cc_final: 0.5963 (mt) REVERT: H 174 LEU cc_start: 0.7778 (mp) cc_final: 0.7404 (mp) REVERT: H 191 PHE cc_start: 0.8436 (p90) cc_final: 0.7996 (p90) REVERT: B 1003 GLU cc_start: 0.6118 (mm-30) cc_final: 0.5486 (mm-30) outliers start: 0 outliers final: 0 residues processed: 702 average time/residue: 0.2133 time to fit residues: 250.5690 Evaluate side-chains 486 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 486 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 285 optimal weight: 0.0670 chunk 11 optimal weight: 0.6980 chunk 370 optimal weight: 6.9990 chunk 242 optimal weight: 1.9990 chunk 187 optimal weight: 9.9990 chunk 166 optimal weight: 40.0000 chunk 270 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 290 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 417 optimal weight: 5.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 HIS A 508 HIS A 721 ASN B 111 HIS B 165 GLN B 328 HIS ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 593 HIS ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 GLN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 GLN D 328 HIS D 593 HIS D 654 ASN E 153 ASN F 51 HIS F 131 ASN ** H 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 143 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.126655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.103945 restraints weight = 114677.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.106498 restraints weight = 139936.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.107469 restraints weight = 92613.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.108038 restraints weight = 66444.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.109148 restraints weight = 58240.442| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3327 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3327 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 37234 Z= 0.172 Angle : 0.904 19.490 50570 Z= 0.420 Chirality : 0.052 0.595 5874 Planarity : 0.006 0.080 6128 Dihedral : 20.224 140.915 7876 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.42 % Allowed : 13.70 % Favored : 85.88 % Rotamer: Outliers : 0.27 % Allowed : 2.59 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.84 % 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: -3.49 (0.12), residues: 4306 helix: -1.04 (0.12), residues: 1460 sheet: -3.38 (0.18), residues: 728 loop : -2.87 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 873 TYR 0.043 0.002 TYR B 566 PHE 0.023 0.002 PHE F 128 TRP 0.020 0.002 TRP H 40 HIS 0.014 0.001 HIS C 593 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (37122) covalent geometry : angle 0.85512 / 0.41 (50254) SS BOND : bond 0.00219 / 0.13 ( 8) SS BOND : angle 0.58440 / 0.39 ( 16) hydrogen bonds : bond 0.04210 / 2.76 ( 1131) hydrogen bonds : angle 5.28845 / 3.60 ( 3374) metal coordination : bond 0.00193 / 0.09 ( 4) link_ALPHA1-3 : bond 0.01377 / 0.71 ( 6) link_ALPHA1-3 : angle 4.44255 / 2.84 ( 18) link_ALPHA1-6 : bond 0.01862 / 1.10 ( 9) link_ALPHA1-6 : angle 3.01408 / 2.23 ( 27) link_BETA1-2 : bond 0.01389 / 0.80 ( 10) link_BETA1-2 : angle 4.56986 / 2.50 ( 30) link_BETA1-3 : bond 0.00785 / 0.40 ( 2) link_BETA1-3 : angle 2.14261 / 1.24 ( 6) link_BETA1-4 : bond 0.01065 / 0.69 ( 47) link_BETA1-4 : angle 3.52518 / 2.27 ( 141) link_NAG-ASN : bond 0.00818 / 0.55 ( 26) link_NAG-ASN : angle 4.42227 / 3.27 ( 78) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8612 Ramachandran restraints generated. 4306 Oldfield, 0 Emsley, 4306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8612 Ramachandran restraints generated. 4306 Oldfield, 0 Emsley, 4306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 644 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.7025 (ttm110) cc_final: 0.6182 (mtp85) REVERT: A 50 MET cc_start: 0.7918 (ptt) cc_final: 0.7633 (ptt) REVERT: A 114 SER cc_start: 0.8584 (m) cc_final: 0.8211 (t) REVERT: A 199 LEU cc_start: 0.8931 (mm) cc_final: 0.8536 (mt) REVERT: A 230 CYS cc_start: 0.7753 (m) cc_final: 0.7472 (m) REVERT: A 565 MET cc_start: 0.7598 (mmm) cc_final: 0.7271 (mmt) REVERT: A 626 LEU cc_start: 0.8153 (mt) cc_final: 0.7619 (mt) REVERT: A 761 SER cc_start: 0.7256 (t) cc_final: 0.7029 (m) REVERT: A 794 MET cc_start: 0.7907 (mtm) cc_final: 0.7637 (mtt) REVERT: A 841 GLU cc_start: 0.7670 (mt-10) cc_final: 0.6950 (mt-10) REVERT: A 861 MET cc_start: 0.8456 (mmp) cc_final: 0.7831 (mtm) REVERT: B 98 GLN cc_start: 0.8393 (mt0) cc_final: 0.8131 (mt0) REVERT: B 113 SER cc_start: 0.8251 (m) cc_final: 0.7862 (p) REVERT: B 114 SER cc_start: 0.8392 (m) cc_final: 0.8150 (t) REVERT: B 130 ILE cc_start: 0.8672 (mm) cc_final: 0.8211 (mm) REVERT: B 234 MET cc_start: 0.8183 (ttm) cc_final: 0.7954 (ttm) REVERT: B 247 MET cc_start: 0.8464 (ttp) cc_final: 0.8158 (ttp) REVERT: B 248 MET cc_start: 0.7264 (mtp) cc_final: 0.6571 (mtp) REVERT: B 463 CYS cc_start: 0.8651 (m) cc_final: 0.8284 (m) REVERT: B 584 PHE cc_start: 0.7156 (t80) cc_final: 0.6890 (m-10) REVERT: B 658 PHE cc_start: 0.8882 (m-80) cc_final: 0.8536 (m-10) REVERT: C 114 SER cc_start: 0.8580 (m) cc_final: 0.8107 (t) REVERT: C 199 LEU cc_start: 0.8951 (mm) cc_final: 0.8673 (mt) REVERT: C 245 MET cc_start: 0.6543 (mmt) cc_final: 0.6313 (mmt) REVERT: C 312 LEU cc_start: 0.8097 (mt) cc_final: 0.7659 (mt) REVERT: C 347 CYS cc_start: 0.5928 (p) cc_final: 0.5575 (p) REVERT: C 359 PHE cc_start: 0.7120 (t80) cc_final: 0.6824 (t80) REVERT: C 565 MET cc_start: 0.7587 (mmm) cc_final: 0.7294 (mmt) REVERT: C 566 TYR cc_start: 0.8291 (m-10) cc_final: 0.7903 (m-10) REVERT: C 770 MET cc_start: 0.6854 (tpt) cc_final: 0.6513 (tpp) REVERT: C 810 LYS cc_start: 0.8260 (mmtt) cc_final: 0.7843 (mmpt) REVERT: C 841 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7194 (mt-10) REVERT: C 861 MET cc_start: 0.8343 (mmp) cc_final: 0.7746 (mtm) REVERT: D 88 SER cc_start: 0.8268 (m) cc_final: 0.7906 (t) REVERT: D 234 MET cc_start: 0.8235 (ttm) cc_final: 0.7934 (ttm) REVERT: D 463 CYS cc_start: 0.8803 (m) cc_final: 0.8408 (m) REVERT: D 770 MET cc_start: 0.7317 (tpp) cc_final: 0.6794 (tpt) REVERT: E 41 ASN cc_start: 0.7911 (t0) cc_final: 0.7607 (t0) REVERT: E 53 ILE cc_start: 0.8890 (pt) cc_final: 0.8469 (mt) REVERT: F 46 LYS cc_start: 0.8004 (mttt) cc_final: 0.7664 (mmtt) REVERT: F 176 TYR cc_start: 0.6912 (t80) cc_final: 0.6604 (t80) REVERT: F 208 ASP cc_start: 0.6173 (t0) cc_final: 0.5929 (t0) REVERT: G 93 LEU cc_start: 0.8169 (mt) cc_final: 0.7732 (mt) REVERT: H 8 GLU cc_start: 0.7348 (pt0) cc_final: 0.6911 (pt0) REVERT: H 44 ASN cc_start: 0.5817 (t0) cc_final: 0.5552 (t0) REVERT: H 141 ILE cc_start: 0.8015 (mt) cc_final: 0.7775 (mp) REVERT: H 156 LEU cc_start: 0.6539 (mt) cc_final: 0.6200 (mt) REVERT: H 174 LEU cc_start: 0.7670 (mp) cc_final: 0.7230 (mt) REVERT: H 191 PHE cc_start: 0.8417 (p90) cc_final: 0.8070 (p90) outliers start: 0 outliers final: 0 residues processed: 644 average time/residue: 0.2056 time to fit residues: 224.4128 Evaluate side-chains 467 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 467 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 89 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 129 optimal weight: 5.9990 chunk 345 optimal weight: 2.9990 chunk 234 optimal weight: 0.7980 chunk 386 optimal weight: 5.9990 chunk 256 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN A 186 GLN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN B 111 HIS ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 GLN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 HIS C 508 HIS D 654 ASN ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.124231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.102963 restraints weight = 136742.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.106586 restraints weight = 181839.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.107329 restraints weight = 71391.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.108691 restraints weight = 57852.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.108877 restraints weight = 45115.452| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3325 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 37234 Z= 0.208 Angle : 0.915 19.325 50570 Z= 0.424 Chirality : 0.053 0.569 5874 Planarity : 0.006 0.071 6128 Dihedral : 18.956 140.760 7876 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.40 % Allowed : 14.02 % Favored : 85.58 % Rotamer: Outliers : 0.27 % Allowed : 1.92 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.84 % 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: -3.15 (0.12), residues: 4306 helix: -0.59 (0.13), residues: 1456 sheet: -3.25 (0.18), residues: 672 loop : -2.81 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG G 158 TYR 0.026 0.002 TYR D 443 PHE 0.036 0.002 PHE B 359 TRP 0.023 0.002 TRP H 40 HIS 0.014 0.001 HIS C 593 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.21 (37122) covalent geometry : angle 0.86691 / 0.41 (50254) SS BOND : bond 0.00241 / 0.13 ( 8) SS BOND : angle 0.54557 / 0.32 ( 16) hydrogen bonds : bond 0.03907 / 2.51 ( 1131) hydrogen bonds : angle 5.19126 / 3.55 ( 3374) metal coordination : bond 0.00588 / 0.29 ( 4) link_ALPHA1-3 : bond 0.01247 / 0.63 ( 6) link_ALPHA1-3 : angle 4.54500 / 2.85 ( 18) link_ALPHA1-6 : bond 0.01993 / 1.14 ( 9) link_ALPHA1-6 : angle 3.35828 / 2.64 ( 27) link_BETA1-2 : bond 0.01434 / 0.84 ( 10) link_BETA1-2 : angle 4.43028 / 2.41 ( 30) link_BETA1-3 : bond 0.00668 / 0.34 ( 2) link_BETA1-3 : angle 2.04102 / 1.19 ( 6) link_BETA1-4 : bond 0.00995 / 0.65 ( 47) link_BETA1-4 : angle 3.53174 / 2.28 ( 141) link_NAG-ASN : bond 0.00877 / 0.61 ( 26) link_NAG-ASN : angle 4.35669 / 3.24 ( 78) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8612 Ramachandran restraints generated. 4306 Oldfield, 0 Emsley, 4306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8612 Ramachandran restraints generated. 4306 Oldfield, 0 Emsley, 4306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 586 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.6948 (ttm110) cc_final: 0.6371 (mtp-110) REVERT: A 50 MET cc_start: 0.7891 (ptt) cc_final: 0.7582 (ptt) REVERT: A 114 SER cc_start: 0.8518 (m) cc_final: 0.8004 (t) REVERT: A 199 LEU cc_start: 0.8959 (mm) cc_final: 0.8588 (mt) REVERT: A 565 MET cc_start: 0.7564 (mmm) cc_final: 0.7213 (mmt) REVERT: A 566 TYR cc_start: 0.8239 (m-10) cc_final: 0.7977 (m-10) REVERT: A 626 LEU cc_start: 0.8292 (mt) cc_final: 0.7777 (mt) REVERT: A 761 SER cc_start: 0.7282 (t) cc_final: 0.7066 (m) REVERT: A 794 MET cc_start: 0.7896 (mtm) cc_final: 0.7605 (mtt) REVERT: A 810 LYS cc_start: 0.8158 (mmtt) cc_final: 0.7798 (mmpt) REVERT: A 841 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7090 (mt-10) REVERT: A 861 MET cc_start: 0.8341 (mmp) cc_final: 0.7631 (mtm) REVERT: B 78 TYR cc_start: 0.6945 (p90) cc_final: 0.6643 (p90) REVERT: B 98 GLN cc_start: 0.8579 (mt0) cc_final: 0.8327 (mt0) REVERT: B 114 SER cc_start: 0.8703 (m) cc_final: 0.8221 (t) REVERT: B 130 ILE cc_start: 0.8683 (mm) cc_final: 0.8261 (mm) REVERT: B 247 MET cc_start: 0.8435 (ttp) cc_final: 0.8168 (ttp) REVERT: B 248 MET cc_start: 0.7675 (mtp) cc_final: 0.7206 (mtp) REVERT: B 463 CYS cc_start: 0.8615 (m) cc_final: 0.8232 (m) REVERT: B 572 LEU cc_start: 0.8772 (mm) cc_final: 0.8254 (mm) REVERT: B 584 PHE cc_start: 0.7190 (t80) cc_final: 0.6911 (m-10) REVERT: C 98 GLN cc_start: 0.7406 (mp-120) cc_final: 0.7095 (mm-40) REVERT: C 114 SER cc_start: 0.8535 (m) cc_final: 0.8149 (t) REVERT: C 199 LEU cc_start: 0.8986 (mm) cc_final: 0.8689 (mt) REVERT: C 347 CYS cc_start: 0.6048 (p) cc_final: 0.5834 (p) REVERT: C 565 MET cc_start: 0.7609 (mmm) cc_final: 0.7320 (mmt) REVERT: C 566 TYR cc_start: 0.8250 (m-10) cc_final: 0.7759 (m-10) REVERT: C 625 GLU cc_start: 0.6743 (pt0) cc_final: 0.6220 (pt0) REVERT: C 626 LEU cc_start: 0.8574 (mt) cc_final: 0.8118 (mt) REVERT: C 770 MET cc_start: 0.6796 (tpt) cc_final: 0.6529 (tpp) REVERT: C 836 PHE cc_start: 0.8060 (m-80) cc_final: 0.7809 (m-10) REVERT: C 841 GLU cc_start: 0.7478 (mt-10) cc_final: 0.6914 (mt-10) REVERT: C 861 MET cc_start: 0.8291 (mmp) cc_final: 0.7649 (mtm) REVERT: D 88 SER cc_start: 0.8295 (m) cc_final: 0.7906 (t) REVERT: D 130 ILE cc_start: 0.8771 (mm) cc_final: 0.8451 (mm) REVERT: D 234 MET cc_start: 0.8239 (ttm) cc_final: 0.7919 (ttm) REVERT: D 247 MET cc_start: 0.8481 (ttp) cc_final: 0.8175 (ttp) REVERT: D 248 MET cc_start: 0.7184 (mtp) cc_final: 0.6770 (mtp) REVERT: D 400 GLU cc_start: 0.7416 (mt-10) cc_final: 0.6861 (mt-10) REVERT: D 463 CYS cc_start: 0.8748 (m) cc_final: 0.8335 (m) REVERT: D 469 GLU cc_start: 0.7255 (tp30) cc_final: 0.6727 (tp30) REVERT: D 566 TYR cc_start: 0.7475 (m-80) cc_final: 0.7110 (m-80) REVERT: D 674 LEU cc_start: 0.9025 (mt) cc_final: 0.8809 (mp) REVERT: D 770 MET cc_start: 0.7284 (tpp) cc_final: 0.6938 (tpp) REVERT: D 786 GLN cc_start: 0.8363 (tm-30) cc_final: 0.8014 (tm-30) REVERT: E 41 ASN cc_start: 0.7856 (t0) cc_final: 0.7530 (t0) REVERT: E 53 ILE cc_start: 0.8990 (pt) cc_final: 0.8666 (mt) REVERT: F 176 TYR cc_start: 0.6883 (t80) cc_final: 0.6568 (t80) REVERT: F 208 ASP cc_start: 0.6170 (t0) cc_final: 0.5847 (t0) REVERT: H 8 GLU cc_start: 0.7612 (pt0) cc_final: 0.7297 (pt0) REVERT: H 44 ASN cc_start: 0.5953 (t0) cc_final: 0.5660 (t0) REVERT: H 155 GLU cc_start: 0.8093 (mp0) cc_final: 0.7695 (mp0) REVERT: H 156 LEU cc_start: 0.6756 (mt) cc_final: 0.6437 (mt) REVERT: H 158 ARG cc_start: 0.7175 (mmt180) cc_final: 0.6913 (mpt180) REVERT: H 174 LEU cc_start: 0.7600 (mp) cc_final: 0.7387 (mt) REVERT: H 191 PHE cc_start: 0.8474 (p90) cc_final: 0.8142 (p90) outliers start: 0 outliers final: 0 residues processed: 586 average time/residue: 0.1939 time to fit residues: 196.0811 Evaluate side-chains 455 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 17 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 83 optimal weight: 20.0000 chunk 321 optimal weight: 0.0470 chunk 120 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 298 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 255 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 overall best weight: 1.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 792 HIS ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 HIS ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 654 ASN ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN F 180 HIS G 166 GLN ** H 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.124253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.100448 restraints weight = 136159.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.103522 restraints weight = 165928.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.105030 restraints weight = 89054.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.105657 restraints weight = 66556.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.106615 restraints weight = 57031.187| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 37234 Z= 0.183 Angle : 0.884 18.650 50570 Z= 0.408 Chirality : 0.052 0.559 5874 Planarity : 0.005 0.070 6128 Dihedral : 18.245 140.944 7876 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.44 % Allowed : 13.60 % Favored : 85.95 % Rotamer: Outliers : 0.29 % Allowed : 2.00 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.77 % 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: -2.88 (0.12), residues: 4306 helix: -0.24 (0.13), residues: 1442 sheet: -3.03 (0.18), residues: 718 loop : -2.73 (0.13), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 663 TYR 0.017 0.002 TYR D 443 PHE 0.035 0.002 PHE B 166 TRP 0.022 0.002 TRP H 40 HIS 0.012 0.001 HIS H 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (37122) covalent geometry : angle 0.83243 / 0.40 (50254) SS BOND : bond 0.00261 / 0.16 ( 8) SS BOND : angle 0.55326 / 0.31 ( 16) hydrogen bonds : bond 0.03636 / 2.34 ( 1131) hydrogen bonds : angle 5.06155 / 3.46 ( 3374) metal coordination : bond 0.00437 / 0.21 ( 4) link_ALPHA1-3 : bond 0.01310 / 0.66 ( 6) link_ALPHA1-3 : angle 4.52027 / 2.84 ( 18) link_ALPHA1-6 : bond 0.02145 / 1.22 ( 9) link_ALPHA1-6 : angle 3.45410 / 2.67 ( 27) link_BETA1-2 : bond 0.01506 / 0.86 ( 10) link_BETA1-2 : angle 4.51227 / 2.49 ( 30) link_BETA1-3 : bond 0.00642 / 0.32 ( 2) link_BETA1-3 : angle 1.89142 / 1.09 ( 6) link_BETA1-4 : bond 0.01038 / 0.70 ( 47) link_BETA1-4 : angle 3.53994 / 2.26 ( 141) link_NAG-ASN : bond 0.00733 / 0.50 ( 26) link_NAG-ASN : angle 4.48888 / 3.24 ( 78) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8612 Ramachandran restraints generated. 4306 Oldfield, 0 Emsley, 4306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8612 Ramachandran restraints generated. 4306 Oldfield, 0 Emsley, 4306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 589 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.6839 (ttm110) cc_final: 0.6105 (mtp85) REVERT: A 50 MET cc_start: 0.7913 (ptt) cc_final: 0.7696 (ptt) REVERT: A 114 SER cc_start: 0.8555 (m) cc_final: 0.8080 (t) REVERT: A 199 LEU cc_start: 0.8993 (mm) cc_final: 0.8680 (mt) REVERT: A 218 MET cc_start: 0.7252 (tpp) cc_final: 0.6353 (tpp) REVERT: A 230 CYS cc_start: 0.7639 (m) cc_final: 0.7383 (m) REVERT: A 565 MET cc_start: 0.7679 (mmm) cc_final: 0.7408 (mmt) REVERT: A 626 LEU cc_start: 0.8358 (mt) cc_final: 0.7873 (mt) REVERT: A 705 MET cc_start: 0.8744 (mmm) cc_final: 0.8330 (mmm) REVERT: A 761 SER cc_start: 0.7194 (t) cc_final: 0.6945 (m) REVERT: A 794 MET cc_start: 0.7910 (mtm) cc_final: 0.7635 (mtt) REVERT: A 810 LYS cc_start: 0.8235 (mmtt) cc_final: 0.7813 (mmpt) REVERT: A 841 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7351 (mt-10) REVERT: A 861 MET cc_start: 0.8229 (mmp) cc_final: 0.7448 (mtm) REVERT: B 78 TYR cc_start: 0.6976 (p90) cc_final: 0.6613 (p90) REVERT: B 98 GLN cc_start: 0.8539 (mt0) cc_final: 0.8321 (mt0) REVERT: B 114 SER cc_start: 0.8530 (m) cc_final: 0.8285 (t) REVERT: B 130 ILE cc_start: 0.8733 (mm) cc_final: 0.8285 (mm) REVERT: B 248 MET cc_start: 0.7555 (mtp) cc_final: 0.6910 (mtp) REVERT: B 463 CYS cc_start: 0.8645 (m) cc_final: 0.8237 (m) REVERT: B 572 LEU cc_start: 0.8786 (mm) cc_final: 0.8254 (mm) REVERT: B 584 PHE cc_start: 0.7308 (t80) cc_final: 0.6909 (m-10) REVERT: B 792 HIS cc_start: 0.7922 (t-90) cc_final: 0.7644 (t-90) REVERT: C 98 GLN cc_start: 0.7539 (mp-120) cc_final: 0.7254 (mm-40) REVERT: C 114 SER cc_start: 0.8534 (m) cc_final: 0.8109 (t) REVERT: C 199 LEU cc_start: 0.8970 (mm) cc_final: 0.8746 (mt) REVERT: C 296 TRP cc_start: 0.7787 (t-100) cc_final: 0.7348 (t-100) REVERT: C 565 MET cc_start: 0.7690 (mmm) cc_final: 0.7335 (mmt) REVERT: C 566 TYR cc_start: 0.8242 (m-10) cc_final: 0.7814 (m-10) REVERT: C 575 SER cc_start: 0.8536 (p) cc_final: 0.8280 (m) REVERT: C 836 PHE cc_start: 0.8247 (m-80) cc_final: 0.7844 (m-10) REVERT: C 841 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7259 (mt-10) REVERT: C 861 MET cc_start: 0.8381 (mmp) cc_final: 0.7729 (mtm) REVERT: D 88 SER cc_start: 0.8330 (m) cc_final: 0.8017 (t) REVERT: D 130 ILE cc_start: 0.8789 (mm) cc_final: 0.8391 (mm) REVERT: D 247 MET cc_start: 0.8474 (ttp) cc_final: 0.8195 (ttp) REVERT: D 248 MET cc_start: 0.7304 (mtp) cc_final: 0.6998 (mtp) REVERT: D 400 GLU cc_start: 0.7493 (mt-10) cc_final: 0.6927 (mt-10) REVERT: D 463 CYS cc_start: 0.8711 (m) cc_final: 0.8295 (m) REVERT: D 469 GLU cc_start: 0.7309 (tp30) cc_final: 0.6953 (tp30) REVERT: D 609 LEU cc_start: 0.8584 (tt) cc_final: 0.7795 (mt) REVERT: D 612 PHE cc_start: 0.8029 (m-80) cc_final: 0.7713 (t80) REVERT: D 770 MET cc_start: 0.7308 (tpp) cc_final: 0.6993 (tpp) REVERT: D 815 LEU cc_start: 0.8747 (mt) cc_final: 0.8447 (mp) REVERT: E 41 ASN cc_start: 0.8080 (t0) cc_final: 0.7761 (t0) REVERT: E 53 ILE cc_start: 0.8975 (pt) cc_final: 0.8641 (mt) REVERT: F 94 SER cc_start: 0.7961 (t) cc_final: 0.7481 (p) REVERT: G 107 LEU cc_start: 0.8265 (pt) cc_final: 0.7895 (mt) REVERT: G 112 THR cc_start: 0.7795 (m) cc_final: 0.7538 (m) REVERT: G 141 ILE cc_start: 0.8918 (mt) cc_final: 0.8666 (mt) REVERT: G 166 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.7039 (pm20) REVERT: H 8 GLU cc_start: 0.7507 (pt0) cc_final: 0.7187 (pt0) REVERT: H 25 ILE cc_start: 0.9076 (tt) cc_final: 0.8778 (mm) REVERT: H 87 GLU cc_start: 0.6293 (tp30) cc_final: 0.5953 (tp30) REVERT: H 156 LEU cc_start: 0.6692 (mt) cc_final: 0.6297 (mt) REVERT: H 174 LEU cc_start: 0.7608 (mp) cc_final: 0.7355 (mp) REVERT: H 191 PHE cc_start: 0.8416 (p90) cc_final: 0.8084 (p90) outliers start: 1 outliers final: 0 residues processed: 590 average time/residue: 0.1934 time to fit residues: 195.3717 Evaluate side-chains 451 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 450 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 262 optimal weight: 0.7980 chunk 417 optimal weight: 8.9990 chunk 271 optimal weight: 0.8980 chunk 242 optimal weight: 0.5980 chunk 371 optimal weight: 0.9980 chunk 186 optimal weight: 6.9990 chunk 347 optimal weight: 6.9990 chunk 126 optimal weight: 0.0870 chunk 131 optimal weight: 0.9990 chunk 162 optimal weight: 0.3980 chunk 319 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 HIS B 165 GLN ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 ASN B 747 GLN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 HIS D 591 ASN ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN G 153 ASN ** H 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.126707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.103179 restraints weight = 138112.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.106765 restraints weight = 169611.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.108834 restraints weight = 78334.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.108950 restraints weight = 63031.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.110370 restraints weight = 51176.093| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 37234 Z= 0.139 Angle : 0.856 18.757 50570 Z= 0.394 Chirality : 0.050 0.553 5874 Planarity : 0.005 0.068 6128 Dihedral : 17.516 140.965 7876 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.44 % Allowed : 12.51 % Favored : 87.05 % Rotamer: Outliers : 0.35 % Allowed : 1.17 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.72 % 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: -2.56 (0.13), residues: 4306 helix: 0.09 (0.14), residues: 1438 sheet: -2.85 (0.19), residues: 704 loop : -2.60 (0.13), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 663 TYR 0.017 0.001 TYR E 12 PHE 0.024 0.002 PHE D 166 TRP 0.024 0.002 TRP H 40 HIS 0.010 0.001 HIS C 593 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (37122) covalent geometry : angle 0.80637 / 0.38 (50254) SS BOND : bond 0.00242 / 0.14 ( 8) SS BOND : angle 0.43180 / 0.25 ( 16) hydrogen bonds : bond 0.03426 / 2.21 ( 1131) hydrogen bonds : angle 4.93375 / 3.39 ( 3374) metal coordination : bond 0.00113 / 0.06 ( 4) link_ALPHA1-3 : bond 0.01420 / 0.72 ( 6) link_ALPHA1-3 : angle 4.38568 / 2.80 ( 18) link_ALPHA1-6 : bond 0.02064 / 1.20 ( 9) link_ALPHA1-6 : angle 3.52452 / 2.76 ( 27) link_BETA1-2 : bond 0.01488 / 0.85 ( 10) link_BETA1-2 : angle 4.55637 / 2.54 ( 30) link_BETA1-3 : bond 0.00578 / 0.29 ( 2) link_BETA1-3 : angle 1.93461 / 1.11 ( 6) link_BETA1-4 : bond 0.00966 / 0.62 ( 47) link_BETA1-4 : angle 3.33924 / 2.16 ( 141) link_NAG-ASN : bond 0.00750 / 0.52 ( 26) link_NAG-ASN : angle 4.32274 / 3.17 ( 78) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8612 Ramachandran restraints generated. 4306 Oldfield, 0 Emsley, 4306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8612 Ramachandran restraints generated. 4306 Oldfield, 0 Emsley, 4306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 592 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.6867 (ttm110) cc_final: 0.6013 (mtp85) REVERT: A 50 MET cc_start: 0.7957 (ptt) cc_final: 0.7644 (ptt) REVERT: A 114 SER cc_start: 0.8514 (m) cc_final: 0.8019 (t) REVERT: A 230 CYS cc_start: 0.7730 (m) cc_final: 0.7471 (m) REVERT: A 245 MET cc_start: 0.6391 (mmm) cc_final: 0.6100 (mmm) REVERT: A 565 MET cc_start: 0.7692 (mmm) cc_final: 0.7286 (mmt) REVERT: A 566 TYR cc_start: 0.8303 (m-10) cc_final: 0.8086 (m-10) REVERT: A 626 LEU cc_start: 0.8410 (mt) cc_final: 0.7921 (mt) REVERT: A 794 MET cc_start: 0.7789 (mtm) cc_final: 0.7504 (mtt) REVERT: A 810 LYS cc_start: 0.8144 (mmtt) cc_final: 0.7787 (mmpt) REVERT: A 841 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7397 (mt-10) REVERT: A 861 MET cc_start: 0.8214 (mmp) cc_final: 0.7387 (mtm) REVERT: B 78 TYR cc_start: 0.6982 (p90) cc_final: 0.6617 (p90) REVERT: B 114 SER cc_start: 0.8514 (m) cc_final: 0.8302 (t) REVERT: B 130 ILE cc_start: 0.8639 (mm) cc_final: 0.8317 (mm) REVERT: B 248 MET cc_start: 0.7648 (mtp) cc_final: 0.7153 (mtp) REVERT: B 316 MET cc_start: 0.7878 (ttm) cc_final: 0.7657 (tpp) REVERT: B 463 CYS cc_start: 0.8586 (m) cc_final: 0.8384 (m) REVERT: B 566 TYR cc_start: 0.8250 (m-80) cc_final: 0.7838 (m-80) REVERT: B 572 LEU cc_start: 0.8779 (mm) cc_final: 0.8255 (mm) REVERT: B 584 PHE cc_start: 0.7412 (t80) cc_final: 0.6922 (m-10) REVERT: B 770 MET cc_start: 0.7392 (tpp) cc_final: 0.7002 (tpp) REVERT: C 114 SER cc_start: 0.8484 (m) cc_final: 0.8063 (t) REVERT: C 296 TRP cc_start: 0.7672 (t-100) cc_final: 0.7325 (t-100) REVERT: C 565 MET cc_start: 0.7624 (mmm) cc_final: 0.7249 (mmt) REVERT: C 566 TYR cc_start: 0.8183 (m-10) cc_final: 0.7893 (m-10) REVERT: C 626 LEU cc_start: 0.8527 (mt) cc_final: 0.8055 (mt) REVERT: C 836 PHE cc_start: 0.8178 (m-80) cc_final: 0.7790 (m-10) REVERT: C 841 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7302 (mt-10) REVERT: C 861 MET cc_start: 0.8332 (mmp) cc_final: 0.7696 (mtm) REVERT: D 88 SER cc_start: 0.8361 (m) cc_final: 0.8084 (t) REVERT: D 130 ILE cc_start: 0.8783 (mm) cc_final: 0.8501 (mm) REVERT: D 143 ASP cc_start: 0.8129 (t0) cc_final: 0.7720 (t0) REVERT: D 247 MET cc_start: 0.8627 (ttp) cc_final: 0.8338 (ttp) REVERT: D 248 MET cc_start: 0.7195 (mtp) cc_final: 0.6864 (mtp) REVERT: D 292 ILE cc_start: 0.8929 (mm) cc_final: 0.8680 (mm) REVERT: D 316 MET cc_start: 0.8073 (ttm) cc_final: 0.7846 (tpp) REVERT: D 400 GLU cc_start: 0.7369 (mt-10) cc_final: 0.6865 (mt-10) REVERT: D 463 CYS cc_start: 0.8718 (m) cc_final: 0.8345 (m) REVERT: D 469 GLU cc_start: 0.7067 (tp30) cc_final: 0.6737 (tp30) REVERT: D 609 LEU cc_start: 0.8533 (tt) cc_final: 0.7594 (mt) REVERT: D 612 PHE cc_start: 0.8013 (m-80) cc_final: 0.7640 (t80) REVERT: D 815 LEU cc_start: 0.8756 (mt) cc_final: 0.8395 (mp) REVERT: E 41 ASN cc_start: 0.8073 (t0) cc_final: 0.7642 (t0) REVERT: E 53 ILE cc_start: 0.8966 (pt) cc_final: 0.8609 (mt) REVERT: F 61 LEU cc_start: 0.7624 (tp) cc_final: 0.7293 (tt) REVERT: F 94 SER cc_start: 0.8026 (t) cc_final: 0.7619 (p) REVERT: F 159 VAL cc_start: 0.5675 (p) cc_final: 0.4988 (m) REVERT: G 112 THR cc_start: 0.7698 (m) cc_final: 0.7405 (p) REVERT: G 141 ILE cc_start: 0.8985 (mt) cc_final: 0.8740 (mt) REVERT: G 153 ASN cc_start: 0.7285 (OUTLIER) cc_final: 0.7033 (p0) REVERT: G 192 GLU cc_start: 0.7206 (pt0) cc_final: 0.6931 (tt0) REVERT: H 8 GLU cc_start: 0.7290 (pt0) cc_final: 0.7028 (pt0) REVERT: H 25 ILE cc_start: 0.9023 (tt) cc_final: 0.8734 (mm) REVERT: H 141 ILE cc_start: 0.8167 (mt) cc_final: 0.7668 (tt) REVERT: H 156 LEU cc_start: 0.6649 (mt) cc_final: 0.6212 (mt) outliers start: 3 outliers final: 0 residues processed: 592 average time/residue: 0.2073 time to fit residues: 211.4698 Evaluate side-chains 453 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 452 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 38 optimal weight: 20.0000 chunk 379 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 413 optimal weight: 0.9990 chunk 191 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 71 optimal weight: 0.0170 chunk 357 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 chunk 306 optimal weight: 3.9990 chunk 350 optimal weight: 7.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 GLN A 328 HIS ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN B 165 GLN B 591 ASN B 792 HIS ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 HIS D 165 GLN D 591 ASN D 792 HIS E 83 ASN E 180 HIS G 121 HIS G 153 ASN ** G 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN ** H 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 ASN ** H 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.122052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.100715 restraints weight = 135223.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.103994 restraints weight = 187507.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.104892 restraints weight = 77840.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.105584 restraints weight = 60601.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.106116 restraints weight = 51535.404| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 37234 Z= 0.234 Angle : 0.910 17.725 50570 Z= 0.424 Chirality : 0.053 0.551 5874 Planarity : 0.005 0.065 6128 Dihedral : 17.092 140.550 7876 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.44 % Allowed : 14.28 % Favored : 85.28 % Rotamer: Outliers : 0.35 % Allowed : 1.28 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.75 % 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: -2.57 (0.13), residues: 4306 helix: 0.17 (0.13), residues: 1460 sheet: -2.96 (0.20), residues: 650 loop : -2.69 (0.13), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 133 TYR 0.025 0.002 TYR F 12 PHE 0.026 0.002 PHE B 166 TRP 0.030 0.002 TRP F 109 HIS 0.015 0.001 HIS H 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.23 (37122) covalent geometry : angle 0.86277 / 0.41 (50254) SS BOND : bond 0.00219 / 0.12 ( 8) SS BOND : angle 0.50405 / 0.26 ( 16) hydrogen bonds : bond 0.03740 / 2.41 ( 1131) hydrogen bonds : angle 5.04928 / 3.46 ( 3374) metal coordination : bond 0.00852 / 0.42 ( 4) link_ALPHA1-3 : bond 0.01136 / 0.57 ( 6) link_ALPHA1-3 : angle 4.69826 / 2.93 ( 18) link_ALPHA1-6 : bond 0.01756 / 1.08 ( 9) link_ALPHA1-6 : angle 3.09826 / 2.62 ( 27) link_BETA1-2 : bond 0.01457 / 0.82 ( 10) link_BETA1-2 : angle 4.58878 / 2.59 ( 30) link_BETA1-3 : bond 0.00613 / 0.31 ( 2) link_BETA1-3 : angle 1.95028 / 1.13 ( 6) link_BETA1-4 : bond 0.00972 / 0.64 ( 47) link_BETA1-4 : angle 3.36929 / 2.17 ( 141) link_NAG-ASN : bond 0.00747 / 0.51 ( 26) link_NAG-ASN : angle 4.45874 / 3.28 ( 78) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8612 Ramachandran restraints generated. 4306 Oldfield, 0 Emsley, 4306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8612 Ramachandran restraints generated. 4306 Oldfield, 0 Emsley, 4306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 546 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.6773 (ttm110) cc_final: 0.6300 (mtp-110) REVERT: A 50 MET cc_start: 0.7939 (ptt) cc_final: 0.7631 (ptt) REVERT: A 114 SER cc_start: 0.8450 (m) cc_final: 0.7972 (t) REVERT: A 199 LEU cc_start: 0.8987 (mm) cc_final: 0.8647 (mt) REVERT: A 230 CYS cc_start: 0.7894 (m) cc_final: 0.7596 (m) REVERT: A 248 MET cc_start: 0.8496 (mtp) cc_final: 0.7314 (mpp) REVERT: A 298 MET cc_start: 0.7924 (ppp) cc_final: 0.7722 (ppp) REVERT: A 340 MET cc_start: 0.4786 (ttp) cc_final: 0.4550 (ttt) REVERT: A 565 MET cc_start: 0.7665 (mmm) cc_final: 0.7382 (mmt) REVERT: A 575 SER cc_start: 0.8582 (p) cc_final: 0.8358 (m) REVERT: A 626 LEU cc_start: 0.8472 (mt) cc_final: 0.7946 (mt) REVERT: A 705 MET cc_start: 0.8265 (mmm) cc_final: 0.7699 (mmm) REVERT: A 794 MET cc_start: 0.8031 (mtm) cc_final: 0.7756 (mtt) REVERT: A 810 LYS cc_start: 0.8132 (mmtt) cc_final: 0.7743 (mmpt) REVERT: A 841 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7358 (mt-10) REVERT: A 861 MET cc_start: 0.8079 (mmp) cc_final: 0.7234 (mtm) REVERT: B 78 TYR cc_start: 0.6724 (p90) cc_final: 0.6454 (p90) REVERT: B 130 ILE cc_start: 0.8756 (mm) cc_final: 0.8415 (mm) REVERT: B 143 ASP cc_start: 0.8255 (t0) cc_final: 0.7820 (t70) REVERT: B 234 MET cc_start: 0.8423 (ttm) cc_final: 0.8112 (ttm) REVERT: B 248 MET cc_start: 0.7669 (mtp) cc_final: 0.7237 (mtp) REVERT: B 463 CYS cc_start: 0.8643 (m) cc_final: 0.8324 (m) REVERT: B 572 LEU cc_start: 0.8682 (mm) cc_final: 0.8085 (mm) REVERT: B 584 PHE cc_start: 0.7314 (t80) cc_final: 0.7025 (m-10) REVERT: B 770 MET cc_start: 0.7488 (tpp) cc_final: 0.7174 (tpp) REVERT: C 114 SER cc_start: 0.8488 (m) cc_final: 0.8033 (t) REVERT: C 199 LEU cc_start: 0.9030 (mm) cc_final: 0.8813 (mt) REVERT: C 296 TRP cc_start: 0.7782 (t-100) cc_final: 0.7384 (t-100) REVERT: C 340 MET cc_start: 0.4792 (ttp) cc_final: 0.4479 (ttt) REVERT: C 565 MET cc_start: 0.7613 (mmm) cc_final: 0.7242 (mmt) REVERT: C 566 TYR cc_start: 0.8206 (m-10) cc_final: 0.7952 (m-80) REVERT: C 626 LEU cc_start: 0.8406 (mt) cc_final: 0.7973 (mt) REVERT: C 836 PHE cc_start: 0.8077 (m-80) cc_final: 0.7680 (m-10) REVERT: C 841 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7366 (mt-10) REVERT: C 861 MET cc_start: 0.8317 (mmp) cc_final: 0.7656 (mtm) REVERT: D 88 SER cc_start: 0.8368 (m) cc_final: 0.8134 (t) REVERT: D 130 ILE cc_start: 0.8786 (mm) cc_final: 0.8473 (mm) REVERT: D 143 ASP cc_start: 0.8202 (t0) cc_final: 0.7889 (t0) REVERT: D 234 MET cc_start: 0.8420 (ttm) cc_final: 0.8155 (ttm) REVERT: D 247 MET cc_start: 0.8536 (ttp) cc_final: 0.8323 (ttp) REVERT: D 248 MET cc_start: 0.7561 (mtp) cc_final: 0.7076 (mtp) REVERT: D 400 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6739 (mt-10) REVERT: D 463 CYS cc_start: 0.8667 (m) cc_final: 0.8264 (m) REVERT: D 572 LEU cc_start: 0.8601 (mm) cc_final: 0.8203 (mm) REVERT: D 575 SER cc_start: 0.8334 (m) cc_final: 0.7661 (t) REVERT: D 612 PHE cc_start: 0.8106 (m-80) cc_final: 0.7802 (t80) REVERT: D 815 LEU cc_start: 0.8795 (mt) cc_final: 0.8495 (mp) REVERT: E 41 ASN cc_start: 0.8015 (t0) cc_final: 0.7807 (t0) REVERT: E 53 ILE cc_start: 0.9050 (pt) cc_final: 0.8642 (mt) REVERT: F 159 VAL cc_start: 0.6651 (p) cc_final: 0.5956 (m) REVERT: G 192 GLU cc_start: 0.7419 (pt0) cc_final: 0.7198 (pt0) REVERT: H 8 GLU cc_start: 0.7770 (pt0) cc_final: 0.7414 (pt0) REVERT: H 11 THR cc_start: 0.8516 (p) cc_final: 0.8267 (t) REVERT: H 54 TYR cc_start: 0.8471 (t80) cc_final: 0.8255 (t80) REVERT: H 141 ILE cc_start: 0.8214 (mt) cc_final: 0.7674 (tt) REVERT: H 174 LEU cc_start: 0.7739 (mp) cc_final: 0.7523 (mp) outliers start: 3 outliers final: 0 residues processed: 546 average time/residue: 0.2123 time to fit residues: 198.9762 Evaluate side-chains 433 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 433 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 71 optimal weight: 1.9990 chunk 148 optimal weight: 0.0670 chunk 188 optimal weight: 0.8980 chunk 147 optimal weight: 0.6980 chunk 407 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 102 optimal weight: 0.9980 chunk 410 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 GLN B 591 ASN B 604 ASN B 792 HIS ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 HIS D 165 GLN D 591 ASN ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 HIS H 124 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.126067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.100942 restraints weight = 138889.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.103284 restraints weight = 146841.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.104980 restraints weight = 91759.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.106055 restraints weight = 64177.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.106553 restraints weight = 58260.580| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37234 Z= 0.141 Angle : 0.856 17.658 50570 Z= 0.395 Chirality : 0.050 0.548 5874 Planarity : 0.005 0.067 6128 Dihedral : 16.611 140.975 7876 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.40 % Allowed : 12.33 % Favored : 87.28 % Rotamer: Outliers : 0.32 % Allowed : 0.51 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.72 % 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: -2.31 (0.13), residues: 4306 helix: 0.40 (0.14), residues: 1460 sheet: -2.69 (0.20), residues: 690 loop : -2.58 (0.13), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 60 TYR 0.042 0.001 TYR B 566 PHE 0.024 0.002 PHE H 195 TRP 0.028 0.002 TRP H 40 HIS 0.012 0.001 HIS H 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (37122) covalent geometry : angle 0.80819 / 0.38 (50254) SS BOND : bond 0.00249 / 0.15 ( 8) SS BOND : angle 0.47479 / 0.27 ( 16) hydrogen bonds : bond 0.03420 / 2.20 ( 1131) hydrogen bonds : angle 4.90257 / 3.37 ( 3374) metal coordination : bond 0.00201 / 0.10 ( 4) link_ALPHA1-3 : bond 0.01418 / 0.71 ( 6) link_ALPHA1-3 : angle 4.45099 / 2.83 ( 18) link_ALPHA1-6 : bond 0.01586 / 1.01 ( 9) link_ALPHA1-6 : angle 3.03617 / 2.55 ( 27) link_BETA1-2 : bond 0.01584 / 0.89 ( 10) link_BETA1-2 : angle 4.63811 / 2.65 ( 30) link_BETA1-3 : bond 0.00536 / 0.27 ( 2) link_BETA1-3 : angle 1.94595 / 1.11 ( 6) link_BETA1-4 : bond 0.00954 / 0.62 ( 47) link_BETA1-4 : angle 3.25906 / 2.10 ( 141) link_NAG-ASN : bond 0.00711 / 0.50 ( 26) link_NAG-ASN : angle 4.35827 / 3.22 ( 78) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8612 Ramachandran restraints generated. 4306 Oldfield, 0 Emsley, 4306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8612 Ramachandran restraints generated. 4306 Oldfield, 0 Emsley, 4306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 577 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.6833 (ttm110) cc_final: 0.6128 (mtp-110) REVERT: A 50 MET cc_start: 0.7981 (ptt) cc_final: 0.7673 (ptt) REVERT: A 114 SER cc_start: 0.8414 (m) cc_final: 0.7961 (t) REVERT: A 230 CYS cc_start: 0.8078 (m) cc_final: 0.7859 (m) REVERT: A 248 MET cc_start: 0.8528 (mtp) cc_final: 0.7775 (mpp) REVERT: A 323 MET cc_start: 0.7208 (tpt) cc_final: 0.6825 (tpp) REVERT: A 340 MET cc_start: 0.4858 (ttp) cc_final: 0.4537 (ttt) REVERT: A 565 MET cc_start: 0.7717 (mmm) cc_final: 0.7328 (mmt) REVERT: A 575 SER cc_start: 0.8352 (p) cc_final: 0.8130 (m) REVERT: A 626 LEU cc_start: 0.8435 (mt) cc_final: 0.7885 (mt) REVERT: A 705 MET cc_start: 0.8377 (mmm) cc_final: 0.7991 (mmm) REVERT: A 794 MET cc_start: 0.7789 (mtm) cc_final: 0.7519 (mtt) REVERT: A 810 LYS cc_start: 0.8196 (mmtt) cc_final: 0.7915 (mmpt) REVERT: A 841 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7336 (mt-10) REVERT: A 861 MET cc_start: 0.8242 (mmp) cc_final: 0.7312 (mtm) REVERT: B 78 TYR cc_start: 0.6886 (p90) cc_final: 0.6564 (p90) REVERT: B 130 ILE cc_start: 0.8704 (mm) cc_final: 0.8287 (mm) REVERT: B 143 ASP cc_start: 0.8267 (t0) cc_final: 0.7786 (t70) REVERT: B 234 MET cc_start: 0.8421 (ttm) cc_final: 0.8153 (ttm) REVERT: B 248 MET cc_start: 0.7541 (mtp) cc_final: 0.7226 (mtp) REVERT: B 572 LEU cc_start: 0.8737 (mm) cc_final: 0.8102 (mm) REVERT: B 584 PHE cc_start: 0.7421 (t80) cc_final: 0.6974 (m-10) REVERT: C 114 SER cc_start: 0.8372 (m) cc_final: 0.7992 (t) REVERT: C 296 TRP cc_start: 0.7683 (t-100) cc_final: 0.7395 (t-100) REVERT: C 565 MET cc_start: 0.7658 (mmm) cc_final: 0.7232 (mmt) REVERT: C 566 TYR cc_start: 0.8188 (m-10) cc_final: 0.7938 (m-80) REVERT: C 626 LEU cc_start: 0.8530 (mt) cc_final: 0.8135 (mt) REVERT: C 836 PHE cc_start: 0.8135 (m-80) cc_final: 0.7752 (m-10) REVERT: C 841 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7371 (mt-10) REVERT: C 861 MET cc_start: 0.8303 (mmp) cc_final: 0.7577 (mtm) REVERT: D 88 SER cc_start: 0.8311 (m) cc_final: 0.8082 (t) REVERT: D 130 ILE cc_start: 0.8699 (mm) cc_final: 0.8351 (mm) REVERT: D 234 MET cc_start: 0.8415 (ttm) cc_final: 0.8158 (ttm) REVERT: D 247 MET cc_start: 0.8536 (ttp) cc_final: 0.8264 (ttp) REVERT: D 248 MET cc_start: 0.7335 (mtp) cc_final: 0.6672 (mtp) REVERT: D 400 GLU cc_start: 0.7420 (mt-10) cc_final: 0.6821 (mt-10) REVERT: D 463 CYS cc_start: 0.8694 (m) cc_final: 0.8365 (m) REVERT: D 612 PHE cc_start: 0.8195 (m-80) cc_final: 0.7725 (t80) REVERT: D 778 ILE cc_start: 0.8703 (mt) cc_final: 0.8376 (mm) REVERT: D 790 LYS cc_start: 0.8486 (mmtm) cc_final: 0.8008 (tppt) REVERT: D 815 LEU cc_start: 0.8786 (mt) cc_final: 0.8420 (mp) REVERT: E 41 ASN cc_start: 0.8032 (t0) cc_final: 0.7656 (t0) REVERT: E 53 ILE cc_start: 0.9086 (pt) cc_final: 0.8686 (mt) REVERT: E 192 GLU cc_start: 0.6959 (tt0) cc_final: 0.6730 (tt0) REVERT: F 61 LEU cc_start: 0.7616 (tp) cc_final: 0.7341 (tt) REVERT: F 94 SER cc_start: 0.7995 (t) cc_final: 0.7559 (p) REVERT: F 159 VAL cc_start: 0.5748 (p) cc_final: 0.5159 (m) REVERT: G 141 ILE cc_start: 0.8975 (mt) cc_final: 0.8744 (mt) REVERT: G 166 GLN cc_start: 0.7913 (pm20) cc_final: 0.7466 (pm20) REVERT: G 192 GLU cc_start: 0.7317 (pt0) cc_final: 0.6982 (pt0) REVERT: H 8 GLU cc_start: 0.7753 (pt0) cc_final: 0.7351 (pt0) REVERT: H 101 LYS cc_start: 0.7882 (mtmm) cc_final: 0.7650 (mttt) REVERT: H 141 ILE cc_start: 0.8233 (mt) cc_final: 0.7743 (tt) REVERT: H 174 LEU cc_start: 0.7812 (mp) cc_final: 0.7556 (mt) outliers start: 2 outliers final: 0 residues processed: 577 average time/residue: 0.2084 time to fit residues: 207.4892 Evaluate side-chains 452 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 452 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 115 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 166 optimal weight: 40.0000 chunk 418 optimal weight: 0.9980 chunk 365 optimal weight: 2.9990 chunk 150 optimal weight: 0.0010 chunk 426 optimal weight: 2.9990 chunk 322 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 258 optimal weight: 0.9980 chunk 187 optimal weight: 4.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN B 123 ASN B 165 GLN B 591 ASN B 792 HIS ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 GLN D 591 ASN ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 HIS ** H 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 HIS H 143 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.124805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.103820 restraints weight = 120477.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.106236 restraints weight = 171744.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107597 restraints weight = 90714.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.108251 restraints weight = 63802.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.108825 restraints weight = 56319.876| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 37234 Z= 0.162 Angle : 0.856 17.650 50570 Z= 0.396 Chirality : 0.050 0.547 5874 Planarity : 0.005 0.073 6128 Dihedral : 16.228 140.745 7876 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.37 % Allowed : 13.21 % Favored : 86.42 % Rotamer: Outliers : 0.35 % Allowed : 0.45 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.65 % 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: -2.22 (0.13), residues: 4306 helix: 0.51 (0.14), residues: 1466 sheet: -2.63 (0.20), residues: 702 loop : -2.56 (0.13), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 158 TYR 0.040 0.002 TYR B 566 PHE 0.027 0.002 PHE G 191 TRP 0.029 0.002 TRP H 40 HIS 0.013 0.001 HIS H 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (37122) covalent geometry : angle 0.80961 / 0.39 (50254) SS BOND : bond 0.00214 / 0.13 ( 8) SS BOND : angle 0.40914 / 0.24 ( 16) hydrogen bonds : bond 0.03402 / 2.18 ( 1131) hydrogen bonds : angle 4.86978 / 3.34 ( 3374) metal coordination : bond 0.00257 / 0.12 ( 4) link_ALPHA1-3 : bond 0.01292 / 0.65 ( 6) link_ALPHA1-3 : angle 4.54534 / 2.90 ( 18) link_ALPHA1-6 : bond 0.01241 / 0.85 ( 9) link_ALPHA1-6 : angle 2.46322 / 1.87 ( 27) link_BETA1-2 : bond 0.01415 / 0.78 ( 10) link_BETA1-2 : angle 4.58102 / 2.60 ( 30) link_BETA1-3 : bond 0.00548 / 0.28 ( 2) link_BETA1-3 : angle 1.85830 / 1.06 ( 6) link_BETA1-4 : bond 0.00959 / 0.63 ( 47) link_BETA1-4 : angle 3.26798 / 2.11 ( 141) link_NAG-ASN : bond 0.00713 / 0.49 ( 26) link_NAG-ASN : angle 4.25758 / 3.16 ( 78) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8612 Ramachandran restraints generated. 4306 Oldfield, 0 Emsley, 4306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8612 Ramachandran restraints generated. 4306 Oldfield, 0 Emsley, 4306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 560 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.6876 (ttm110) cc_final: 0.6324 (mtp-110) REVERT: A 50 MET cc_start: 0.7875 (ptt) cc_final: 0.7599 (ptt) REVERT: A 114 SER cc_start: 0.8345 (m) cc_final: 0.7910 (t) REVERT: A 230 CYS cc_start: 0.8116 (m) cc_final: 0.7841 (m) REVERT: A 340 MET cc_start: 0.4758 (ttp) cc_final: 0.4518 (ttt) REVERT: A 565 MET cc_start: 0.7635 (mmm) cc_final: 0.7295 (mmt) REVERT: A 575 SER cc_start: 0.8407 (p) cc_final: 0.8193 (m) REVERT: A 626 LEU cc_start: 0.8283 (mt) cc_final: 0.8056 (mt) REVERT: A 705 MET cc_start: 0.8180 (mmm) cc_final: 0.7970 (mmm) REVERT: A 794 MET cc_start: 0.7871 (mtm) cc_final: 0.7583 (mtt) REVERT: A 810 LYS cc_start: 0.7999 (mmtt) cc_final: 0.7673 (mmpt) REVERT: A 841 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7249 (mt-10) REVERT: A 861 MET cc_start: 0.8100 (mmp) cc_final: 0.7168 (mtm) REVERT: B 78 TYR cc_start: 0.6818 (p90) cc_final: 0.6534 (p90) REVERT: B 130 ILE cc_start: 0.8750 (mm) cc_final: 0.8393 (mm) REVERT: B 143 ASP cc_start: 0.8397 (t0) cc_final: 0.7923 (t0) REVERT: B 234 MET cc_start: 0.8411 (ttm) cc_final: 0.8166 (ttm) REVERT: B 248 MET cc_start: 0.7588 (mtp) cc_final: 0.7263 (mtp) REVERT: B 316 MET cc_start: 0.7938 (ttm) cc_final: 0.7544 (tpp) REVERT: B 572 LEU cc_start: 0.8731 (mm) cc_final: 0.7996 (mm) REVERT: B 584 PHE cc_start: 0.7452 (t80) cc_final: 0.7060 (m-10) REVERT: C 114 SER cc_start: 0.8379 (m) cc_final: 0.7974 (t) REVERT: C 296 TRP cc_start: 0.7822 (t-100) cc_final: 0.7515 (t-100) REVERT: C 323 MET cc_start: 0.7594 (tpp) cc_final: 0.7063 (tpp) REVERT: C 565 MET cc_start: 0.7533 (mmm) cc_final: 0.7208 (mmt) REVERT: C 566 TYR cc_start: 0.8118 (m-10) cc_final: 0.7839 (m-10) REVERT: C 625 GLU cc_start: 0.6843 (pt0) cc_final: 0.6378 (pt0) REVERT: C 626 LEU cc_start: 0.8565 (mt) cc_final: 0.8193 (mt) REVERT: C 836 PHE cc_start: 0.7931 (m-80) cc_final: 0.7618 (m-10) REVERT: C 841 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7293 (mt-10) REVERT: C 861 MET cc_start: 0.8108 (mmp) cc_final: 0.7396 (mtm) REVERT: D 88 SER cc_start: 0.8359 (m) cc_final: 0.8126 (t) REVERT: D 130 ILE cc_start: 0.8757 (mm) cc_final: 0.8437 (mm) REVERT: D 143 ASP cc_start: 0.7985 (t0) cc_final: 0.7514 (t0) REVERT: D 234 MET cc_start: 0.8428 (ttm) cc_final: 0.8190 (ttm) REVERT: D 247 MET cc_start: 0.8581 (ttp) cc_final: 0.8348 (ttp) REVERT: D 248 MET cc_start: 0.7536 (mtp) cc_final: 0.6861 (mtp) REVERT: D 292 ILE cc_start: 0.8971 (mm) cc_final: 0.8679 (mm) REVERT: D 316 MET cc_start: 0.8125 (mmm) cc_final: 0.7915 (mmt) REVERT: D 324 TYR cc_start: 0.8619 (t80) cc_final: 0.8196 (t80) REVERT: D 400 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6668 (mt-10) REVERT: D 463 CYS cc_start: 0.8647 (m) cc_final: 0.8304 (m) REVERT: D 575 SER cc_start: 0.8293 (m) cc_final: 0.7603 (t) REVERT: D 612 PHE cc_start: 0.8085 (m-80) cc_final: 0.7724 (t80) REVERT: D 786 GLN cc_start: 0.8249 (tm-30) cc_final: 0.7813 (tp40) REVERT: D 815 LEU cc_start: 0.8759 (mt) cc_final: 0.8424 (mp) REVERT: E 41 ASN cc_start: 0.8081 (t0) cc_final: 0.7629 (t0) REVERT: E 53 ILE cc_start: 0.9043 (pt) cc_final: 0.8653 (mt) REVERT: F 159 VAL cc_start: 0.5941 (p) cc_final: 0.5308 (m) REVERT: G 192 GLU cc_start: 0.7508 (pt0) cc_final: 0.7301 (pt0) REVERT: H 8 GLU cc_start: 0.7892 (pt0) cc_final: 0.7569 (pt0) REVERT: H 11 THR cc_start: 0.8297 (p) cc_final: 0.7871 (t) REVERT: H 141 ILE cc_start: 0.8192 (mt) cc_final: 0.7666 (tt) REVERT: H 174 LEU cc_start: 0.7822 (mp) cc_final: 0.7549 (mt) outliers start: 3 outliers final: 0 residues processed: 560 average time/residue: 0.2031 time to fit residues: 196.4542 Evaluate side-chains 447 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 447 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 347 optimal weight: 6.9990 chunk 375 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 174 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 chunk 365 optimal weight: 2.9990 chunk 321 optimal weight: 0.0670 chunk 51 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 289 optimal weight: 0.9990 chunk 413 optimal weight: 4.9990 overall best weight: 0.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN B 591 ASN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 GLN D 591 ASN ** D 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN E 131 ASN ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 HIS H 121 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.126608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.101401 restraints weight = 137614.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.104021 restraints weight = 143478.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.105498 restraints weight = 87943.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.106063 restraints weight = 62154.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.108353 restraints weight = 55882.268| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3310 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 37234 Z= 0.142 Angle : 0.844 17.885 50570 Z= 0.389 Chirality : 0.050 0.538 5874 Planarity : 0.005 0.066 6128 Dihedral : 15.771 140.963 7876 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.40 % Allowed : 12.33 % Favored : 87.28 % Rotamer: Outliers : 0.35 % Allowed : 0.19 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.70 % 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: -2.14 (0.13), residues: 4306 helix: 0.54 (0.14), residues: 1478 sheet: -2.46 (0.20), residues: 694 loop : -2.55 (0.13), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 60 TYR 0.043 0.001 TYR B 566 PHE 0.024 0.001 PHE H 195 TRP 0.036 0.002 TRP H 40 HIS 0.012 0.001 HIS H 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (37122) covalent geometry : angle 0.79805 / 0.38 (50254) SS BOND : bond 0.00200 / 0.12 ( 8) SS BOND : angle 0.47615 / 0.29 ( 16) hydrogen bonds : bond 0.03313 / 2.13 ( 1131) hydrogen bonds : angle 4.84874 / 3.33 ( 3374) metal coordination : bond 0.00221 / 0.11 ( 4) link_ALPHA1-3 : bond 0.01337 / 0.66 ( 6) link_ALPHA1-3 : angle 4.45180 / 2.87 ( 18) link_ALPHA1-6 : bond 0.01220 / 0.87 ( 9) link_ALPHA1-6 : angle 1.99224 / 1.42 ( 27) link_BETA1-2 : bond 0.01285 / 0.71 ( 10) link_BETA1-2 : angle 4.58024 / 2.58 ( 30) link_BETA1-3 : bond 0.00498 / 0.25 ( 2) link_BETA1-3 : angle 1.83396 / 1.03 ( 6) link_BETA1-4 : bond 0.00958 / 0.61 ( 47) link_BETA1-4 : angle 3.25016 / 2.10 ( 141) link_NAG-ASN : bond 0.00709 / 0.49 ( 26) link_NAG-ASN : angle 4.24363 / 3.15 ( 78) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8612 Ramachandran restraints generated. 4306 Oldfield, 0 Emsley, 4306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8612 Ramachandran restraints generated. 4306 Oldfield, 0 Emsley, 4306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 572 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.6988 (ttm110) cc_final: 0.6148 (mtp-110) REVERT: A 50 MET cc_start: 0.7945 (ptt) cc_final: 0.7686 (ptt) REVERT: A 114 SER cc_start: 0.8423 (m) cc_final: 0.8003 (t) REVERT: A 292 ILE cc_start: 0.8059 (mm) cc_final: 0.7841 (mm) REVERT: A 323 MET cc_start: 0.7126 (tpt) cc_final: 0.6762 (tpp) REVERT: A 340 MET cc_start: 0.4995 (ttp) cc_final: 0.4775 (ttt) REVERT: A 565 MET cc_start: 0.7690 (mmm) cc_final: 0.7377 (mmt) REVERT: A 705 MET cc_start: 0.8249 (mmm) cc_final: 0.7764 (mmm) REVERT: A 794 MET cc_start: 0.7730 (mtm) cc_final: 0.7416 (mtt) REVERT: A 841 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7265 (mt-10) REVERT: A 861 MET cc_start: 0.8212 (mmp) cc_final: 0.7232 (mtm) REVERT: B 78 TYR cc_start: 0.6759 (p90) cc_final: 0.6445 (p90) REVERT: B 130 ILE cc_start: 0.8701 (mm) cc_final: 0.8305 (mm) REVERT: B 143 ASP cc_start: 0.8331 (t0) cc_final: 0.7333 (t0) REVERT: B 218 MET cc_start: 0.7981 (mtp) cc_final: 0.7771 (ttm) REVERT: B 234 MET cc_start: 0.8434 (ttm) cc_final: 0.8140 (ttm) REVERT: B 248 MET cc_start: 0.7516 (mtp) cc_final: 0.7141 (mtp) REVERT: B 566 TYR cc_start: 0.8351 (m-80) cc_final: 0.8103 (m-80) REVERT: B 572 LEU cc_start: 0.8750 (mm) cc_final: 0.8051 (mm) REVERT: B 584 PHE cc_start: 0.7593 (t80) cc_final: 0.7093 (m-10) REVERT: C 114 SER cc_start: 0.8511 (m) cc_final: 0.8213 (t) REVERT: C 287 THR cc_start: 0.8022 (p) cc_final: 0.7519 (t) REVERT: C 296 TRP cc_start: 0.7761 (t-100) cc_final: 0.7431 (t-100) REVERT: C 323 MET cc_start: 0.7621 (tpp) cc_final: 0.7066 (tpp) REVERT: C 565 MET cc_start: 0.7564 (mmm) cc_final: 0.7241 (mmt) REVERT: C 626 LEU cc_start: 0.8550 (mt) cc_final: 0.8196 (mt) REVERT: C 832 VAL cc_start: 0.8764 (t) cc_final: 0.8537 (t) REVERT: C 836 PHE cc_start: 0.8085 (m-80) cc_final: 0.7717 (m-10) REVERT: C 841 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7297 (mt-10) REVERT: C 861 MET cc_start: 0.8182 (mmp) cc_final: 0.7373 (mtm) REVERT: D 88 SER cc_start: 0.8346 (m) cc_final: 0.8119 (t) REVERT: D 130 ILE cc_start: 0.8718 (mm) cc_final: 0.8369 (mm) REVERT: D 143 ASP cc_start: 0.7988 (t0) cc_final: 0.7558 (t0) REVERT: D 234 MET cc_start: 0.8403 (ttm) cc_final: 0.8160 (ttm) REVERT: D 247 MET cc_start: 0.8647 (ttp) cc_final: 0.8395 (ttp) REVERT: D 248 MET cc_start: 0.7363 (mtp) cc_final: 0.6725 (mtp) REVERT: D 292 ILE cc_start: 0.9019 (mm) cc_final: 0.8681 (mm) REVERT: D 324 TYR cc_start: 0.8715 (t80) cc_final: 0.8260 (t80) REVERT: D 336 GLN cc_start: 0.7594 (mt0) cc_final: 0.7307 (tt0) REVERT: D 400 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6705 (mt-10) REVERT: D 463 CYS cc_start: 0.8637 (m) cc_final: 0.8300 (m) REVERT: D 612 PHE cc_start: 0.8109 (m-80) cc_final: 0.7674 (t80) REVERT: D 778 ILE cc_start: 0.8666 (mt) cc_final: 0.8347 (mm) REVERT: D 786 GLN cc_start: 0.8148 (tm-30) cc_final: 0.7936 (tm-30) REVERT: D 815 LEU cc_start: 0.8750 (mt) cc_final: 0.8402 (mp) REVERT: E 41 ASN cc_start: 0.7769 (t0) cc_final: 0.7340 (t0) REVERT: E 53 ILE cc_start: 0.9106 (pt) cc_final: 0.8785 (mt) REVERT: E 93 LEU cc_start: 0.8287 (mt) cc_final: 0.8075 (mt) REVERT: F 10 ASP cc_start: 0.6504 (t0) cc_final: 0.6215 (t0) REVERT: F 166 GLN cc_start: 0.7995 (mm-40) cc_final: 0.7729 (mm-40) REVERT: F 195 PHE cc_start: 0.6402 (t80) cc_final: 0.5899 (t80) REVERT: G 192 GLU cc_start: 0.7456 (pt0) cc_final: 0.7245 (pt0) REVERT: H 8 GLU cc_start: 0.8026 (pt0) cc_final: 0.7637 (pt0) REVERT: H 11 THR cc_start: 0.8425 (p) cc_final: 0.7992 (t) outliers start: 3 outliers final: 0 residues processed: 572 average time/residue: 0.2016 time to fit residues: 198.6781 Evaluate side-chains 458 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 458 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 284 optimal weight: 8.9990 chunk 377 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 400 optimal weight: 6.9990 chunk 47 optimal weight: 0.0980 chunk 109 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 277 optimal weight: 0.9990 chunk 409 optimal weight: 0.0050 chunk 396 optimal weight: 5.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 335 GLN B 165 GLN B 591 ASN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 HIS D 136 HIS D 165 GLN D 591 ASN ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 ASN H 121 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.127685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.102553 restraints weight = 141011.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.105134 restraints weight = 145060.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.106894 restraints weight = 86779.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107973 restraints weight = 61211.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.108493 restraints weight = 55241.853| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3315 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3315 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37234 Z= 0.133 Angle : 0.832 17.736 50570 Z= 0.384 Chirality : 0.049 0.534 5874 Planarity : 0.005 0.066 6128 Dihedral : 15.366 141.027 7876 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.33 % Allowed : 12.67 % Favored : 87.00 % Rotamer: Outliers : 0.35 % Allowed : 0.27 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.63 % 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: -2.01 (0.13), residues: 4306 helix: 0.68 (0.14), residues: 1464 sheet: -2.35 (0.21), residues: 680 loop : -2.50 (0.13), residues: 2162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 133 TYR 0.042 0.001 TYR B 566 PHE 0.027 0.001 PHE C 315 TRP 0.032 0.002 TRP H 40 HIS 0.012 0.001 HIS H 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (37122) covalent geometry : angle 0.78658 / 0.37 (50254) SS BOND : bond 0.00193 / 0.12 ( 8) SS BOND : angle 0.50548 / 0.31 ( 16) hydrogen bonds : bond 0.03239 / 2.11 ( 1131) hydrogen bonds : angle 4.78262 / 3.29 ( 3374) metal coordination : bond 0.00103 / 0.05 ( 4) link_ALPHA1-3 : bond 0.01462 / 0.71 ( 6) link_ALPHA1-3 : angle 4.40528 / 2.88 ( 18) link_ALPHA1-6 : bond 0.01202 / 0.85 ( 9) link_ALPHA1-6 : angle 1.83586 / 1.31 ( 27) link_BETA1-2 : bond 0.01264 / 0.71 ( 10) link_BETA1-2 : angle 4.50187 / 2.52 ( 30) link_BETA1-3 : bond 0.00502 / 0.25 ( 2) link_BETA1-3 : angle 1.74547 / 0.98 ( 6) link_BETA1-4 : bond 0.00972 / 0.62 ( 47) link_BETA1-4 : angle 3.24366 / 2.10 ( 141) link_NAG-ASN : bond 0.00718 / 0.49 ( 26) link_NAG-ASN : angle 4.21476 / 3.11 ( 78) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6301.78 seconds wall clock time: 110 minutes 17.10 seconds (6617.10 seconds total)