Starting phenix.real_space_refine on Tue Aug 26 11:27:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b36_44129/08_2025/9b36_44129.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b36_44129/08_2025/9b36_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_44129/08_2025/9b36_44129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b36_44129/08_2025/9b36_44129.map" model { file = "/net/cci-nas-00/data/ceres_data/9b36_44129/08_2025/9b36_44129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b36_44129/08_2025/9b36_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.11, 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: 3.16 Conformation dependent library (CDL) restraints added in 2.1 seconds Enol-peptide restraints added in 1.2 microseconds 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: 1.24 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: 7.12 Time building geometry restraints manager: 4.15 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 40.370 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 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 aren 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 covalent geometry : bond 0.00941 (37122) covalent geometry : angle 1.44907 (50254) SS BOND : bond 0.01177 ( 8) SS BOND : angle 1.20457 ( 16) hydrogen bonds : bond 0.29356 ( 1131) hydrogen bonds : angle 10.93563 ( 3374) metal coordination : bond 0.07021 ( 4) link_ALPHA1-3 : bond 0.01243 ( 6) link_ALPHA1-3 : angle 5.26551 ( 18) link_ALPHA1-6 : bond 0.01616 ( 9) link_ALPHA1-6 : angle 4.29284 ( 27) link_BETA1-2 : bond 0.01629 ( 10) link_BETA1-2 : angle 6.52186 ( 30) link_BETA1-3 : bond 0.00186 ( 2) link_BETA1-3 : angle 1.61849 ( 6) link_BETA1-4 : bond 0.01758 ( 47) link_BETA1-4 : angle 4.77252 ( 141) link_NAG-ASN : bond 0.01565 ( 26) link_NAG-ASN : angle 7.17796 ( 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 : 1.217 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: 0.7257 (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: 0.8582 (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: 0.6728 (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: 0.8304 (mm) REVERT: B 572 LEU cc_start: 0.8886 (mm) cc_final: 0.8516 (mm) REVERT: B 576 CYS cc_start: 0.8625 (m) cc_final: 0.8035 (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: 0.7867 (mt-10) REVERT: B 861 MET cc_start: 0.7030 (ttt) cc_final: 0.6721 (ttt) REVERT: B 867 MET cc_start: 0.7176 (ttt) cc_final: 0.6875 (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: 0.8347 (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: 0.6741 (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: 0.7367 (mmt) REVERT: C 566 TYR cc_start: 0.8484 (m-10) cc_final: 0.8266 (m-10) REVERT: C 612 PHE cc_start: 0.8579 (m-80) cc_final: 0.8064 (m-10) REVERT: C 639 ILE cc_start: 0.8962 (mm) cc_final: 0.8600 (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: 0.8131 (m) REVERT: D 590 TYR cc_start: 0.6789 (p90) cc_final: 0.6260 (p90) REVERT: D 744 PHE cc_start: 0.7922 (t80) cc_final: 0.7601 (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: 0.7810 (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: 0.7189 (m-40) REVERT: F 192 GLU cc_start: 0.7582 (tt0) cc_final: 0.7286 (tm-30) REVERT: G 42 MET cc_start: 0.4012 (ttp) cc_final: 0.3731 (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: 0.7819 (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: 0.6457 (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: 0.2135 time to fit residues: 328.6151 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 : 1.087 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 F 14 ASN ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.128259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.106265 restraints weight = 147857.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.110235 restraints weight = 183113.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111284 restraints weight = 70429.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.112169 restraints weight = 55920.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.112506 restraints weight = 45401.562| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3379 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 37234 Z= 0.170 Angle : 0.944 20.124 50570 Z= 0.441 Chirality : 0.054 0.649 5874 Planarity : 0.006 0.088 6128 Dihedral : 22.266 140.664 7876 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.37 % Allowed : 12.77 % Favored : 86.86 % Rotamer: Outliers : 0.27 % Allowed : 2.13 % Favored : 97.60 % 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 aren not related in a simple way. whole: -4.23 (0.11), residues: 4306 helix: -2.07 (0.11), residues: 1428 sheet: -3.64 (0.17), residues: 712 loop : -3.02 (0.12), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 866 TYR 0.035 0.002 TYR B 566 PHE 0.024 0.002 PHE G 128 TRP 0.025 0.002 TRP C 589 HIS 0.011 0.001 HIS C 593 Details of bonding type rmsd covalent geometry : bond 0.00358 (37122) covalent geometry : angle 0.89353 (50254) SS BOND : bond 0.01086 ( 8) SS BOND : angle 0.99250 ( 16) hydrogen bonds : bond 0.04849 ( 1131) hydrogen bonds : angle 5.73955 ( 3374) metal coordination : bond 0.00266 ( 4) link_ALPHA1-3 : bond 0.01319 ( 6) link_ALPHA1-3 : angle 4.50632 ( 18) link_ALPHA1-6 : bond 0.01582 ( 9) link_ALPHA1-6 : angle 3.06940 ( 27) link_BETA1-2 : bond 0.01398 ( 10) link_BETA1-2 : angle 4.68052 ( 30) link_BETA1-3 : bond 0.00685 ( 2) link_BETA1-3 : angle 2.76282 ( 6) link_BETA1-4 : bond 0.01157 ( 47) link_BETA1-4 : angle 3.62080 ( 141) link_NAG-ASN : bond 0.00833 ( 26) link_NAG-ASN : angle 4.79776 ( 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 701 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 701 time to evaluate : 0.918 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: A 37 ARG cc_start: 0.6934 (ttm110) cc_final: 0.6192 (mtp85) REVERT: A 50 MET cc_start: 0.8068 (ptt) cc_final: 0.7734 (ptt) REVERT: A 114 SER cc_start: 0.8636 (m) cc_final: 0.8363 (t) REVERT: A 199 LEU cc_start: 0.8905 (mm) cc_final: 0.8542 (mt) REVERT: A 229 ASP cc_start: 0.8637 (t0) cc_final: 0.8405 (t0) REVERT: A 565 MET cc_start: 0.7661 (mmm) cc_final: 0.7226 (mmt) REVERT: A 566 TYR cc_start: 0.8370 (m-10) cc_final: 0.8125 (m-10) REVERT: A 639 ILE cc_start: 0.9298 (mm) cc_final: 0.9084 (tp) REVERT: A 761 SER cc_start: 0.7372 (t) cc_final: 0.7125 (m) REVERT: A 861 MET cc_start: 0.8343 (mmp) cc_final: 0.7854 (mtm) REVERT: B 98 GLN cc_start: 0.8398 (mt0) cc_final: 0.8096 (mt0) REVERT: B 113 SER cc_start: 0.8188 (m) cc_final: 0.7753 (p) REVERT: B 130 ILE cc_start: 0.8646 (mm) cc_final: 0.8313 (mm) REVERT: B 248 MET cc_start: 0.6970 (mtp) cc_final: 0.6353 (mtp) REVERT: B 572 LEU cc_start: 0.8907 (mm) cc_final: 0.8378 (mm) REVERT: B 586 PRO cc_start: 0.8318 (Cg_endo) cc_final: 0.8059 (Cg_exo) REVERT: B 620 MET cc_start: 0.8941 (mmm) cc_final: 0.8682 (mmm) REVERT: B 627 MET cc_start: 0.7222 (mmp) cc_final: 0.6963 (mmp) REVERT: B 738 GLU cc_start: 0.7672 (mm-30) cc_final: 0.6962 (mm-30) REVERT: C 37 ARG cc_start: 0.7283 (ttm110) cc_final: 0.7009 (mtm110) REVERT: C 199 LEU cc_start: 0.8946 (mm) cc_final: 0.8698 (mt) REVERT: C 296 TRP cc_start: 0.7574 (t-100) cc_final: 0.6995 (t-100) REVERT: C 323 MET cc_start: 0.7202 (tpp) cc_final: 0.6983 (tpp) REVERT: C 359 PHE cc_start: 0.7159 (t80) cc_final: 0.6883 (t80) REVERT: C 501 MET cc_start: 0.7507 (mtm) cc_final: 0.7054 (mtm) REVERT: C 565 MET cc_start: 0.7670 (mmm) cc_final: 0.7237 (mmt) REVERT: C 566 TYR cc_start: 0.8299 (m-10) cc_final: 0.7884 (m-10) REVERT: C 761 SER cc_start: 0.7204 (t) cc_final: 0.6878 (m) REVERT: C 841 GLU cc_start: 0.7439 (mt-10) cc_final: 0.6945 (mt-10) REVERT: C 861 MET cc_start: 0.8304 (mmp) cc_final: 0.7702 (mtm) REVERT: D 88 SER cc_start: 0.8394 (m) cc_final: 0.7911 (t) REVERT: D 166 PHE cc_start: 0.8406 (t80) cc_final: 0.7840 (t80) REVERT: D 340 MET cc_start: 0.6561 (ttp) cc_final: 0.6006 (ttm) REVERT: D 463 CYS cc_start: 0.8932 (m) cc_final: 0.8698 (m) REVERT: D 609 LEU cc_start: 0.8469 (tt) cc_final: 0.7879 (mt) REVERT: D 632 SER cc_start: 0.8808 (p) cc_final: 0.8512 (p) REVERT: F 3 THR cc_start: 0.7286 (m) cc_final: 0.7071 (p) REVERT: F 46 LYS cc_start: 0.8114 (mttt) cc_final: 0.7747 (mmtt) REVERT: F 208 ASP cc_start: 0.5393 (t0) cc_final: 0.5024 (t0) REVERT: G 42 MET cc_start: 0.2781 (ttp) cc_final: 0.2556 (ttp) REVERT: G 175 PHE cc_start: 0.8663 (t80) cc_final: 0.8449 (t80) REVERT: G 179 VAL cc_start: 0.8020 (t) cc_final: 0.7740 (t) REVERT: H 25 ILE cc_start: 0.9101 (tt) cc_final: 0.8882 (mm) REVERT: H 44 ASN cc_start: 0.6172 (t0) cc_final: 0.5772 (t0) REVERT: H 141 ILE cc_start: 0.7882 (mt) cc_final: 0.7504 (tt) REVERT: H 156 LEU cc_start: 0.6277 (mt) cc_final: 0.5952 (mt) REVERT: H 174 LEU cc_start: 0.7759 (mp) cc_final: 0.7343 (mp) REVERT: H 191 PHE cc_start: 0.8451 (p90) cc_final: 0.8017 (p90) REVERT: B 1003 GLU cc_start: 0.6150 (mm-30) cc_final: 0.5521 (mm-30) outliers start: 0 outliers final: 0 residues processed: 701 average time/residue: 0.1898 time to fit residues: 222.1970 Evaluate side-chains 491 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 491 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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: 0.8980 chunk 11 optimal weight: 2.9990 chunk 370 optimal weight: 4.9990 chunk 242 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 chunk 166 optimal weight: 40.0000 chunk 270 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 290 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 417 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 B 654 ASN B 792 HIS ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 GLN ** C 335 GLN ** 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.124617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.101664 restraints weight = 114833.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.104028 restraints weight = 138895.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.104978 restraints weight = 95656.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.105636 restraints weight = 66713.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.106705 restraints weight = 59022.662| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 37234 Z= 0.203 Angle : 0.925 19.513 50570 Z= 0.431 Chirality : 0.053 0.597 5874 Planarity : 0.006 0.080 6128 Dihedral : 20.212 140.621 7876 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.42 % Allowed : 14.21 % Favored : 85.37 % Rotamer: Outliers : 0.27 % Allowed : 2.83 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.87 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.53 (0.12), residues: 4306 helix: -1.04 (0.12), residues: 1460 sheet: -3.56 (0.18), residues: 686 loop : -2.88 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 873 TYR 0.044 0.002 TYR B 566 PHE 0.024 0.002 PHE F 128 TRP 0.021 0.002 TRP H 40 HIS 0.014 0.001 HIS C 593 Details of bonding type rmsd covalent geometry : bond 0.00450 (37122) covalent geometry : angle 0.87702 (50254) SS BOND : bond 0.00284 ( 8) SS BOND : angle 0.59587 ( 16) hydrogen bonds : bond 0.04322 ( 1131) hydrogen bonds : angle 5.32605 ( 3374) metal coordination : bond 0.00390 ( 4) link_ALPHA1-3 : bond 0.01306 ( 6) link_ALPHA1-3 : angle 4.56438 ( 18) link_ALPHA1-6 : bond 0.01785 ( 9) link_ALPHA1-6 : angle 2.97052 ( 27) link_BETA1-2 : bond 0.01272 ( 10) link_BETA1-2 : angle 4.55489 ( 30) link_BETA1-3 : bond 0.00763 ( 2) link_BETA1-3 : angle 2.13713 ( 6) link_BETA1-4 : bond 0.01035 ( 47) link_BETA1-4 : angle 3.53693 ( 141) link_NAG-ASN : bond 0.00793 ( 26) link_NAG-ASN : angle 4.44423 ( 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 626 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 626 time to evaluate : 0.879 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: A 37 ARG cc_start: 0.7078 (ttm110) cc_final: 0.6217 (mtp85) REVERT: A 50 MET cc_start: 0.7935 (ptt) cc_final: 0.7651 (ptt) REVERT: A 114 SER cc_start: 0.8512 (m) cc_final: 0.8116 (t) REVERT: A 199 LEU cc_start: 0.8980 (mm) cc_final: 0.8601 (mt) REVERT: A 230 CYS cc_start: 0.7730 (m) cc_final: 0.7437 (m) REVERT: A 287 THR cc_start: 0.8051 (p) cc_final: 0.7559 (t) REVERT: A 563 ILE cc_start: 0.8727 (mm) cc_final: 0.8288 (mm) REVERT: A 565 MET cc_start: 0.7646 (mmm) cc_final: 0.7261 (mmt) REVERT: A 566 TYR cc_start: 0.8356 (m-10) cc_final: 0.8117 (m-10) REVERT: A 626 LEU cc_start: 0.8224 (mt) cc_final: 0.7690 (mt) REVERT: A 761 SER cc_start: 0.7250 (t) cc_final: 0.6985 (m) REVERT: A 794 MET cc_start: 0.7895 (mtm) cc_final: 0.7647 (mtt) REVERT: A 861 MET cc_start: 0.8404 (mmp) cc_final: 0.7739 (mtm) REVERT: B 98 GLN cc_start: 0.8474 (mt0) cc_final: 0.8235 (mt0) REVERT: B 113 SER cc_start: 0.8272 (m) cc_final: 0.7886 (p) REVERT: B 114 SER cc_start: 0.8453 (m) cc_final: 0.8184 (t) REVERT: B 130 ILE cc_start: 0.8714 (mm) cc_final: 0.8296 (mm) REVERT: B 234 MET cc_start: 0.8201 (ttm) cc_final: 0.7963 (ttm) REVERT: B 247 MET cc_start: 0.8413 (ttp) cc_final: 0.8149 (ttp) REVERT: B 248 MET cc_start: 0.7570 (mtp) cc_final: 0.6960 (mtp) REVERT: B 463 CYS cc_start: 0.8667 (m) cc_final: 0.8256 (m) REVERT: B 584 PHE cc_start: 0.7178 (t80) cc_final: 0.6893 (m-10) REVERT: B 627 MET cc_start: 0.8111 (mmp) cc_final: 0.7754 (mmp) REVERT: B 658 PHE cc_start: 0.8917 (m-80) cc_final: 0.8613 (m-10) REVERT: B 792 HIS cc_start: 0.7656 (t-90) cc_final: 0.7362 (t70) REVERT: C 37 ARG cc_start: 0.7355 (ttm110) cc_final: 0.6414 (mtm110) REVERT: C 152 ASP cc_start: 0.8333 (t0) cc_final: 0.8065 (t0) REVERT: C 199 LEU cc_start: 0.8976 (mm) cc_final: 0.8697 (mt) REVERT: C 296 TRP cc_start: 0.7548 (t-100) cc_final: 0.7327 (t-100) REVERT: C 347 CYS cc_start: 0.5949 (p) cc_final: 0.5609 (p) REVERT: C 565 MET cc_start: 0.7682 (mmm) cc_final: 0.7359 (mmt) REVERT: C 566 TYR cc_start: 0.8342 (m-10) cc_final: 0.7915 (m-10) REVERT: C 717 LEU cc_start: 0.8115 (mm) cc_final: 0.7904 (mt) REVERT: C 761 SER cc_start: 0.7056 (t) cc_final: 0.6803 (m) REVERT: C 770 MET cc_start: 0.6839 (tpt) cc_final: 0.6528 (tpp) REVERT: C 810 LYS cc_start: 0.8299 (mmtt) cc_final: 0.7868 (mmpt) REVERT: C 836 PHE cc_start: 0.7970 (m-80) cc_final: 0.7743 (m-10) REVERT: C 841 GLU cc_start: 0.7580 (mt-10) cc_final: 0.6976 (mt-10) REVERT: C 861 MET cc_start: 0.8376 (mmp) cc_final: 0.7754 (mtm) REVERT: D 88 SER cc_start: 0.8313 (m) cc_final: 0.7952 (t) REVERT: D 130 ILE cc_start: 0.8836 (mm) cc_final: 0.8500 (mm) REVERT: D 234 MET cc_start: 0.8259 (ttm) cc_final: 0.7972 (ttm) REVERT: D 247 MET cc_start: 0.8486 (ttp) cc_final: 0.8140 (ttp) REVERT: D 248 MET cc_start: 0.7311 (mtp) cc_final: 0.6697 (mtp) REVERT: D 463 CYS cc_start: 0.8800 (m) cc_final: 0.8405 (m) REVERT: D 563 ILE cc_start: 0.8900 (mm) cc_final: 0.8699 (mt) REVERT: D 770 MET cc_start: 0.7218 (tpp) cc_final: 0.6741 (tpt) REVERT: E 41 ASN cc_start: 0.8029 (t0) cc_final: 0.7717 (t0) REVERT: E 53 ILE cc_start: 0.8957 (pt) cc_final: 0.8588 (mt) REVERT: F 46 LYS cc_start: 0.8081 (mttt) cc_final: 0.7725 (mmtt) REVERT: F 208 ASP cc_start: 0.6400 (t0) cc_final: 0.5976 (t0) REVERT: G 25 ILE cc_start: 0.7431 (mt) cc_final: 0.7217 (mt) REVERT: G 93 LEU cc_start: 0.8195 (mt) cc_final: 0.7814 (mt) REVERT: H 8 GLU cc_start: 0.7700 (pt0) cc_final: 0.7347 (pt0) REVERT: H 44 ASN cc_start: 0.6220 (t0) cc_final: 0.5935 (t0) REVERT: H 141 ILE cc_start: 0.8067 (mt) cc_final: 0.7604 (tt) REVERT: H 156 LEU cc_start: 0.6353 (mt) cc_final: 0.5955 (mt) REVERT: H 174 LEU cc_start: 0.7680 (mp) cc_final: 0.7380 (mt) REVERT: H 191 PHE cc_start: 0.8484 (p90) cc_final: 0.8148 (p90) outliers start: 0 outliers final: 0 residues processed: 626 average time/residue: 0.1911 time to fit residues: 202.2497 Evaluate side-chains 464 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 464 time to evaluate : 1.217 ------------------------------------------------------------------------------- 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: 6.9990 chunk 76 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 345 optimal weight: 0.8980 chunk 234 optimal weight: 0.3980 chunk 386 optimal weight: 5.9990 chunk 256 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 192 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 GLN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 HIS ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 G 166 GLN ** H 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.126647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.101978 restraints weight = 136005.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.104010 restraints weight = 139190.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.105933 restraints weight = 90438.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.106775 restraints weight = 62027.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107491 restraints weight = 55965.346| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.3487 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= 0.154 Angle : 0.880 19.253 50570 Z= 0.405 Chirality : 0.051 0.572 5874 Planarity : 0.005 0.072 6128 Dihedral : 18.926 140.927 7876 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.40 % Allowed : 12.81 % Favored : 86.79 % Rotamer: Outliers : 0.27 % Allowed : 1.84 % Favored : 97.89 % 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 aren not related in a simple way. whole: -3.11 (0.12), residues: 4306 helix: -0.53 (0.13), residues: 1454 sheet: -3.18 (0.18), residues: 740 loop : -2.78 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 349 TYR 0.018 0.001 TYR A 251 PHE 0.032 0.002 PHE B 708 TRP 0.021 0.002 TRP H 40 HIS 0.014 0.001 HIS C 593 Details of bonding type rmsd covalent geometry : bond 0.00331 (37122) covalent geometry : angle 0.83080 (50254) SS BOND : bond 0.00270 ( 8) SS BOND : angle 0.49935 ( 16) hydrogen bonds : bond 0.03754 ( 1131) hydrogen bonds : angle 5.10572 ( 3374) metal coordination : bond 0.00136 ( 4) link_ALPHA1-3 : bond 0.01193 ( 6) link_ALPHA1-3 : angle 4.34177 ( 18) link_ALPHA1-6 : bond 0.02018 ( 9) link_ALPHA1-6 : angle 3.30537 ( 27) link_BETA1-2 : bond 0.01391 ( 10) link_BETA1-2 : angle 4.47876 ( 30) link_BETA1-3 : bond 0.00643 ( 2) link_BETA1-3 : angle 2.02570 ( 6) link_BETA1-4 : bond 0.00988 ( 47) link_BETA1-4 : angle 3.50948 ( 141) link_NAG-ASN : bond 0.01057 ( 26) link_NAG-ASN : angle 4.34233 ( 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 609 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 609 time to evaluate : 1.387 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: 0.6896 (ttm110) cc_final: 0.6119 (mtp85) REVERT: A 50 MET cc_start: 0.7937 (ptt) cc_final: 0.7670 (ptt) REVERT: A 114 SER cc_start: 0.8508 (m) cc_final: 0.8110 (t) REVERT: A 287 THR cc_start: 0.8138 (p) cc_final: 0.7642 (t) REVERT: A 565 MET cc_start: 0.7668 (mmm) cc_final: 0.7282 (mmt) REVERT: A 566 TYR cc_start: 0.8300 (m-10) cc_final: 0.8094 (m-10) REVERT: A 626 LEU cc_start: 0.8385 (mt) cc_final: 0.7943 (mt) REVERT: A 761 SER cc_start: 0.7239 (t) cc_final: 0.6997 (m) REVERT: A 794 MET cc_start: 0.7791 (mtm) cc_final: 0.7589 (mtt) REVERT: A 810 LYS cc_start: 0.8315 (mmtt) cc_final: 0.7861 (mmpt) REVERT: A 861 MET cc_start: 0.8403 (mmp) cc_final: 0.7705 (mtm) REVERT: B 98 GLN cc_start: 0.8395 (mt0) cc_final: 0.8160 (mt0) REVERT: B 114 SER cc_start: 0.8628 (m) cc_final: 0.8224 (t) REVERT: B 130 ILE cc_start: 0.8646 (mm) cc_final: 0.8273 (mm) REVERT: B 234 MET cc_start: 0.8161 (ttm) cc_final: 0.7955 (ttm) REVERT: B 247 MET cc_start: 0.8437 (ttp) cc_final: 0.8131 (ttp) REVERT: B 248 MET cc_start: 0.7552 (mtp) cc_final: 0.7094 (mtp) REVERT: B 566 TYR cc_start: 0.8571 (m-80) cc_final: 0.8265 (m-80) REVERT: B 584 PHE cc_start: 0.7374 (t80) cc_final: 0.6862 (m-10) REVERT: B 792 HIS cc_start: 0.7662 (t-90) cc_final: 0.7432 (t70) REVERT: C 37 ARG cc_start: 0.7351 (ttm110) cc_final: 0.6628 (mtm110) REVERT: C 114 SER cc_start: 0.8499 (m) cc_final: 0.8155 (t) REVERT: C 152 ASP cc_start: 0.8220 (t0) cc_final: 0.8010 (t0) REVERT: C 296 TRP cc_start: 0.7556 (t-100) cc_final: 0.7356 (t-100) REVERT: C 347 CYS cc_start: 0.6051 (p) cc_final: 0.5830 (p) REVERT: C 565 MET cc_start: 0.7677 (mmm) cc_final: 0.7361 (mmt) REVERT: C 566 TYR cc_start: 0.8254 (m-10) cc_final: 0.7936 (m-10) REVERT: C 625 GLU cc_start: 0.6877 (pt0) cc_final: 0.6635 (pt0) REVERT: C 841 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7341 (mt-10) REVERT: C 861 MET cc_start: 0.8374 (mmp) cc_final: 0.7726 (mtm) REVERT: D 88 SER cc_start: 0.8319 (m) cc_final: 0.7957 (t) REVERT: D 130 ILE cc_start: 0.8722 (mm) cc_final: 0.8383 (mm) REVERT: D 234 MET cc_start: 0.8238 (ttm) cc_final: 0.7991 (ttm) REVERT: D 247 MET cc_start: 0.8518 (ttp) cc_final: 0.8166 (ttp) REVERT: D 248 MET cc_start: 0.7316 (mtp) cc_final: 0.6886 (mtp) REVERT: D 400 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7152 (tt0) REVERT: D 463 CYS cc_start: 0.8758 (m) cc_final: 0.8360 (m) REVERT: D 469 GLU cc_start: 0.7271 (tp30) cc_final: 0.7025 (tp30) REVERT: D 563 ILE cc_start: 0.8846 (mm) cc_final: 0.8618 (mt) REVERT: D 590 TYR cc_start: 0.6917 (p90) cc_final: 0.6674 (p90) REVERT: D 674 LEU cc_start: 0.8926 (mt) cc_final: 0.8706 (mp) REVERT: D 770 MET cc_start: 0.7396 (tpp) cc_final: 0.6974 (tpp) REVERT: E 41 ASN cc_start: 0.7982 (t0) cc_final: 0.7616 (t0) REVERT: E 53 ILE cc_start: 0.8939 (pt) cc_final: 0.8572 (mt) REVERT: F 46 LYS cc_start: 0.7909 (mttt) cc_final: 0.7512 (mmtt) REVERT: F 208 ASP cc_start: 0.6332 (t0) cc_final: 0.5844 (t0) REVERT: G 16 ASP cc_start: 0.7539 (m-30) cc_final: 0.7304 (t70) REVERT: G 141 ILE cc_start: 0.8925 (mt) cc_final: 0.8691 (mt) REVERT: G 158 ARG cc_start: 0.6615 (mmm-85) cc_final: 0.6355 (mmm-85) REVERT: H 8 GLU cc_start: 0.7589 (pt0) cc_final: 0.7115 (pt0) REVERT: H 44 ASN cc_start: 0.5721 (t0) cc_final: 0.5492 (t0) REVERT: H 155 GLU cc_start: 0.8083 (mp0) cc_final: 0.7703 (mp0) REVERT: H 156 LEU cc_start: 0.6654 (mt) cc_final: 0.6309 (mt) REVERT: H 158 ARG cc_start: 0.7185 (mpt180) cc_final: 0.6902 (mpt180) REVERT: H 174 LEU cc_start: 0.8003 (mp) cc_final: 0.7744 (mt) REVERT: H 191 PHE cc_start: 0.8444 (p90) cc_final: 0.8109 (p90) outliers start: 0 outliers final: 0 residues processed: 609 average time/residue: 0.1734 time to fit residues: 181.4436 Evaluate side-chains 465 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 465 time to evaluate : 1.372 ------------------------------------------------------------------------------- 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: 5.9990 chunk 48 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 chunk 321 optimal weight: 0.9980 chunk 120 optimal weight: 0.0870 chunk 109 optimal weight: 6.9990 chunk 298 optimal weight: 8.9990 chunk 165 optimal weight: 0.9980 chunk 255 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 overall best weight: 2.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 HIS C 508 HIS ** D 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 654 ASN E 180 HIS ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 HIS ** G 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 ASN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.121974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.101113 restraints weight = 136782.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.104420 restraints weight = 185622.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.105167 restraints weight = 73000.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.105911 restraints weight = 58466.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.106648 restraints weight = 48407.890| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 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 = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 37234 Z= 0.253 Angle : 0.938 19.149 50570 Z= 0.437 Chirality : 0.054 0.562 5874 Planarity : 0.006 0.069 6128 Dihedral : 18.298 140.976 7876 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.42 % Allowed : 14.60 % Favored : 84.98 % Rotamer: Outliers : 0.27 % Allowed : 1.89 % Favored : 97.84 % 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 aren not related in a simple way. whole: -3.02 (0.12), residues: 4306 helix: -0.35 (0.13), residues: 1462 sheet: -2.99 (0.18), residues: 712 loop : -2.90 (0.13), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 663 TYR 0.025 0.002 TYR F 12 PHE 0.036 0.002 PHE B 166 TRP 0.025 0.002 TRP F 109 HIS 0.012 0.001 HIS C 593 Details of bonding type rmsd covalent geometry : bond 0.00573 (37122) covalent geometry : angle 0.88957 (50254) SS BOND : bond 0.00241 ( 8) SS BOND : angle 0.54847 ( 16) hydrogen bonds : bond 0.03887 ( 1131) hydrogen bonds : angle 5.19395 ( 3374) metal coordination : bond 0.00767 ( 4) link_ALPHA1-3 : bond 0.01252 ( 6) link_ALPHA1-3 : angle 4.73820 ( 18) link_ALPHA1-6 : bond 0.02019 ( 9) link_ALPHA1-6 : angle 3.48834 ( 27) link_BETA1-2 : bond 0.01527 ( 10) link_BETA1-2 : angle 4.54363 ( 30) link_BETA1-3 : bond 0.00669 ( 2) link_BETA1-3 : angle 1.90411 ( 6) link_BETA1-4 : bond 0.01061 ( 47) link_BETA1-4 : angle 3.54147 ( 141) link_NAG-ASN : bond 0.00826 ( 26) link_NAG-ASN : angle 4.44130 ( 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 568 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 568 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.6987 (ttm110) cc_final: 0.6184 (mtp85) REVERT: A 50 MET cc_start: 0.7936 (ptt) cc_final: 0.7613 (ptt) REVERT: A 114 SER cc_start: 0.8516 (m) cc_final: 0.8032 (t) REVERT: A 199 LEU cc_start: 0.9035 (mm) cc_final: 0.8702 (mt) REVERT: A 218 MET cc_start: 0.7007 (tpp) cc_final: 0.6214 (tpp) REVERT: A 230 CYS cc_start: 0.7692 (m) cc_final: 0.7414 (m) REVERT: A 287 THR cc_start: 0.8138 (p) cc_final: 0.7632 (t) REVERT: A 565 MET cc_start: 0.7579 (mmm) cc_final: 0.7220 (mmt) REVERT: A 566 TYR cc_start: 0.8282 (m-10) cc_final: 0.8072 (m-10) REVERT: A 626 LEU cc_start: 0.8444 (mt) cc_final: 0.8019 (mt) REVERT: A 761 SER cc_start: 0.7208 (t) cc_final: 0.6912 (m) REVERT: A 794 MET cc_start: 0.8043 (mtm) cc_final: 0.7816 (mtt) REVERT: A 810 LYS cc_start: 0.8159 (mmtt) cc_final: 0.7813 (mmpt) REVERT: A 841 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7088 (mt-10) REVERT: A 861 MET cc_start: 0.8021 (mmp) cc_final: 0.7375 (mtm) REVERT: B 78 TYR cc_start: 0.6930 (p90) cc_final: 0.6698 (p90) REVERT: B 130 ILE cc_start: 0.8801 (mm) cc_final: 0.8411 (mm) REVERT: B 248 MET cc_start: 0.7540 (mtp) cc_final: 0.6893 (mtp) REVERT: B 463 CYS cc_start: 0.8654 (m) cc_final: 0.8250 (m) REVERT: B 572 LEU cc_start: 0.8733 (mm) cc_final: 0.8215 (mm) REVERT: B 584 PHE cc_start: 0.7236 (t80) cc_final: 0.6983 (m-10) REVERT: C 37 ARG cc_start: 0.7410 (ttm110) cc_final: 0.6524 (mtp85) REVERT: C 98 GLN cc_start: 0.7487 (mp-120) cc_final: 0.7126 (mm-40) REVERT: C 114 SER cc_start: 0.8459 (m) cc_final: 0.7978 (t) REVERT: C 152 ASP cc_start: 0.8375 (t0) cc_final: 0.8172 (t0) REVERT: C 199 LEU cc_start: 0.9005 (mm) cc_final: 0.8775 (mt) REVERT: C 296 TRP cc_start: 0.7848 (t-100) cc_final: 0.7630 (t-100) REVERT: C 347 CYS cc_start: 0.6042 (p) cc_final: 0.5834 (p) REVERT: C 565 MET cc_start: 0.7630 (mmm) cc_final: 0.7252 (mmt) REVERT: C 566 TYR cc_start: 0.8250 (m-10) cc_final: 0.7776 (m-10) REVERT: C 575 SER cc_start: 0.8629 (p) cc_final: 0.8301 (m) REVERT: C 625 GLU cc_start: 0.6832 (pt0) cc_final: 0.6625 (pt0) REVERT: C 655 LEU cc_start: 0.9404 (tt) cc_final: 0.9169 (tt) REVERT: C 836 PHE cc_start: 0.7990 (m-80) cc_final: 0.7730 (m-10) REVERT: C 841 GLU cc_start: 0.7581 (mt-10) cc_final: 0.6974 (mt-10) REVERT: C 861 MET cc_start: 0.8305 (mmp) cc_final: 0.7670 (mtm) REVERT: D 88 SER cc_start: 0.8391 (m) cc_final: 0.8140 (t) REVERT: D 130 ILE cc_start: 0.8817 (mm) cc_final: 0.8464 (mm) REVERT: D 234 MET cc_start: 0.8330 (ttm) cc_final: 0.8126 (ttm) REVERT: D 247 MET cc_start: 0.8429 (ttp) cc_final: 0.8219 (ttp) REVERT: D 248 MET cc_start: 0.7502 (mtp) cc_final: 0.6936 (mtp) REVERT: D 400 GLU cc_start: 0.7490 (mt-10) cc_final: 0.6874 (mt-10) REVERT: D 463 CYS cc_start: 0.8729 (m) cc_final: 0.8327 (m) REVERT: D 469 GLU cc_start: 0.7303 (tp30) cc_final: 0.6950 (tp30) REVERT: D 590 TYR cc_start: 0.6840 (p90) cc_final: 0.6588 (p90) REVERT: D 770 MET cc_start: 0.7347 (tpp) cc_final: 0.7040 (tpp) REVERT: E 41 ASN cc_start: 0.8142 (t0) cc_final: 0.7881 (t0) REVERT: E 53 ILE cc_start: 0.8977 (pt) cc_final: 0.8746 (mt) REVERT: H 8 GLU cc_start: 0.7818 (pt0) cc_final: 0.7506 (pt0) REVERT: H 11 THR cc_start: 0.8505 (p) cc_final: 0.8295 (p) REVERT: H 156 LEU cc_start: 0.6444 (mt) cc_final: 0.5956 (mt) REVERT: H 174 LEU cc_start: 0.7972 (mp) cc_final: 0.7752 (mt) REVERT: H 191 PHE cc_start: 0.8406 (p90) cc_final: 0.8161 (p90) outliers start: 0 outliers final: 0 residues processed: 568 average time/residue: 0.1815 time to fit residues: 175.0528 Evaluate side-chains 437 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 437 time to evaluate : 1.351 ------------------------------------------------------------------------------- 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: 1.9990 chunk 417 optimal weight: 3.9990 chunk 271 optimal weight: 0.8980 chunk 242 optimal weight: 1.9990 chunk 371 optimal weight: 5.9990 chunk 186 optimal weight: 8.9990 chunk 347 optimal weight: 2.9990 chunk 126 optimal weight: 0.0370 chunk 131 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 319 optimal weight: 2.9990 overall best weight: 1.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 GLN ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 ASN B 792 HIS ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 HIS ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 GLN D 335 GLN D 591 ASN E 83 ASN G 124 ASN G 131 ASN ** H 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 HIS H 180 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.124118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.098786 restraints weight = 139060.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.101901 restraints weight = 146456.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.103630 restraints weight = 78626.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.105005 restraints weight = 55868.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.105565 restraints weight = 48446.532| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 37234 Z= 0.163 Angle : 0.875 18.602 50570 Z= 0.404 Chirality : 0.051 0.555 5874 Planarity : 0.005 0.073 6128 Dihedral : 17.701 141.026 7876 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.49 % Allowed : 13.02 % Favored : 86.49 % Rotamer: Outliers : 0.32 % Allowed : 1.36 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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 aren not related in a simple way. whole: -2.74 (0.13), residues: 4306 helix: -0.05 (0.13), residues: 1442 sheet: -2.97 (0.18), residues: 722 loop : -2.70 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 663 TYR 0.067 0.002 TYR D 566 PHE 0.028 0.002 PHE E 133 TRP 0.024 0.002 TRP H 40 HIS 0.010 0.001 HIS C 593 Details of bonding type rmsd covalent geometry : bond 0.00356 (37122) covalent geometry : angle 0.82557 (50254) SS BOND : bond 0.00225 ( 8) SS BOND : angle 0.50228 ( 16) hydrogen bonds : bond 0.03589 ( 1131) hydrogen bonds : angle 5.02627 ( 3374) metal coordination : bond 0.00287 ( 4) link_ALPHA1-3 : bond 0.01349 ( 6) link_ALPHA1-3 : angle 4.48836 ( 18) link_ALPHA1-6 : bond 0.02064 ( 9) link_ALPHA1-6 : angle 3.59000 ( 27) link_BETA1-2 : bond 0.01483 ( 10) link_BETA1-2 : angle 4.61261 ( 30) link_BETA1-3 : bond 0.00587 ( 2) link_BETA1-3 : angle 2.00114 ( 6) link_BETA1-4 : bond 0.00978 ( 47) link_BETA1-4 : angle 3.40630 ( 141) link_NAG-ASN : bond 0.00748 ( 26) link_NAG-ASN : angle 4.33117 ( 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 579 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 577 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.6800 (ttm110) cc_final: 0.6087 (mtp85) REVERT: A 50 MET cc_start: 0.7975 (ptt) cc_final: 0.7636 (ptt) REVERT: A 114 SER cc_start: 0.8485 (m) cc_final: 0.7998 (t) REVERT: A 245 MET cc_start: 0.6693 (mmm) cc_final: 0.6467 (mmm) REVERT: A 287 THR cc_start: 0.8198 (p) cc_final: 0.7691 (t) REVERT: A 565 MET cc_start: 0.7624 (mmm) cc_final: 0.7286 (mmt) REVERT: A 626 LEU cc_start: 0.8440 (mt) cc_final: 0.7960 (mt) REVERT: A 761 SER cc_start: 0.7080 (t) cc_final: 0.6834 (m) REVERT: A 794 MET cc_start: 0.7889 (mtm) cc_final: 0.7627 (mtt) REVERT: A 810 LYS cc_start: 0.8227 (mmtt) cc_final: 0.7795 (mmpt) REVERT: A 841 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7313 (mt-10) REVERT: A 861 MET cc_start: 0.8076 (mmp) cc_final: 0.7427 (mtm) REVERT: B 78 TYR cc_start: 0.6866 (p90) cc_final: 0.6507 (p90) REVERT: B 130 ILE cc_start: 0.8721 (mm) cc_final: 0.8329 (mm) REVERT: B 143 ASP cc_start: 0.8050 (t0) cc_final: 0.7444 (t0) REVERT: B 248 MET cc_start: 0.7698 (mtp) cc_final: 0.7185 (mtp) REVERT: B 463 CYS cc_start: 0.8610 (m) cc_final: 0.8183 (m) REVERT: B 572 LEU cc_start: 0.8749 (mm) cc_final: 0.8196 (mm) REVERT: B 584 PHE cc_start: 0.7399 (t80) cc_final: 0.7028 (m-10) REVERT: B 792 HIS cc_start: 0.7879 (t-90) cc_final: 0.7661 (t-90) REVERT: C 37 ARG cc_start: 0.7499 (ttm110) cc_final: 0.6933 (mtp-110) REVERT: C 114 SER cc_start: 0.8401 (m) cc_final: 0.7954 (t) REVERT: C 152 ASP cc_start: 0.8399 (t0) cc_final: 0.8189 (t0) REVERT: C 229 ASP cc_start: 0.8495 (t70) cc_final: 0.8293 (t0) REVERT: C 565 MET cc_start: 0.7702 (mmm) cc_final: 0.7286 (mmt) REVERT: C 566 TYR cc_start: 0.8186 (m-10) cc_final: 0.7797 (m-10) REVERT: C 836 PHE cc_start: 0.8192 (m-80) cc_final: 0.7811 (m-10) REVERT: C 841 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7152 (mt-10) REVERT: C 861 MET cc_start: 0.8390 (mmp) cc_final: 0.7683 (mtm) REVERT: D 88 SER cc_start: 0.8339 (m) cc_final: 0.8099 (t) REVERT: D 130 ILE cc_start: 0.8687 (mm) cc_final: 0.8348 (mm) REVERT: D 234 MET cc_start: 0.8414 (ttm) cc_final: 0.8125 (ttm) REVERT: D 238 ILE cc_start: 0.8985 (tp) cc_final: 0.8746 (tp) REVERT: D 247 MET cc_start: 0.8443 (ttp) cc_final: 0.8206 (ttp) REVERT: D 248 MET cc_start: 0.7468 (mtp) cc_final: 0.6961 (mtp) REVERT: D 292 ILE cc_start: 0.8944 (mm) cc_final: 0.8697 (mm) REVERT: D 400 GLU cc_start: 0.7537 (mt-10) cc_final: 0.6988 (mt-10) REVERT: D 463 CYS cc_start: 0.8767 (m) cc_final: 0.8386 (m) REVERT: D 469 GLU cc_start: 0.7222 (tp30) cc_final: 0.6882 (tp30) REVERT: D 590 TYR cc_start: 0.6761 (p90) cc_final: 0.6433 (p90) REVERT: D 609 LEU cc_start: 0.8580 (tt) cc_final: 0.7755 (mt) REVERT: D 612 PHE cc_start: 0.8034 (m-80) cc_final: 0.7706 (t80) REVERT: D 627 MET cc_start: 0.8884 (tpp) cc_final: 0.8378 (tpp) REVERT: D 770 MET cc_start: 0.7183 (tpp) cc_final: 0.6963 (tpp) REVERT: D 815 LEU cc_start: 0.8788 (mt) cc_final: 0.8432 (mp) REVERT: E 41 ASN cc_start: 0.8002 (t0) cc_final: 0.7676 (t0) REVERT: E 99 LEU cc_start: 0.8690 (tt) cc_final: 0.8322 (tp) REVERT: E 218 ASP cc_start: 0.7570 (p0) cc_final: 0.7015 (p0) REVERT: F 61 LEU cc_start: 0.7645 (tp) cc_final: 0.7316 (tt) REVERT: F 94 SER cc_start: 0.7983 (t) cc_final: 0.7502 (p) REVERT: F 159 VAL cc_start: 0.6240 (p) cc_final: 0.5635 (m) REVERT: F 218 ASP cc_start: 0.7632 (p0) cc_final: 0.7355 (p0) REVERT: G 112 THR cc_start: 0.7813 (m) cc_final: 0.7472 (p) REVERT: G 141 ILE cc_start: 0.8962 (mt) cc_final: 0.8731 (mt) REVERT: G 192 GLU cc_start: 0.7430 (pt0) cc_final: 0.6894 (tt0) REVERT: H 8 GLU cc_start: 0.7745 (pt0) cc_final: 0.7510 (pt0) REVERT: H 153 ASN cc_start: 0.8125 (m110) cc_final: 0.7880 (m-40) REVERT: H 156 LEU cc_start: 0.6744 (mt) cc_final: 0.6241 (mt) REVERT: H 174 LEU cc_start: 0.8007 (mp) cc_final: 0.7776 (mt) REVERT: H 191 PHE cc_start: 0.8379 (p90) cc_final: 0.8141 (p90) outliers start: 2 outliers final: 0 residues processed: 577 average time/residue: 0.1803 time to fit residues: 178.4245 Evaluate side-chains 448 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 448 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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: 30.0000 chunk 379 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 413 optimal weight: 2.9990 chunk 191 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 71 optimal weight: 0.0470 chunk 357 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 306 optimal weight: 3.9990 chunk 350 optimal weight: 8.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 HIS ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN B 165 GLN ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 ASN C 98 GLN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 HIS D 165 GLN D 591 ASN G 121 HIS ** G 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.119190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.096441 restraints weight = 136236.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.099307 restraints weight = 187607.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.100743 restraints weight = 92009.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.101565 restraints weight = 64270.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.102142 restraints weight = 55950.133| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 37234 Z= 0.296 Angle : 0.966 18.244 50570 Z= 0.455 Chirality : 0.054 0.559 5874 Planarity : 0.006 0.071 6128 Dihedral : 17.321 140.090 7876 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.51 % Allowed : 15.00 % Favored : 84.49 % Rotamer: Outliers : 0.32 % Allowed : 1.31 % 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 aren not related in a simple way. whole: -2.87 (0.12), residues: 4306 helix: -0.12 (0.13), residues: 1456 sheet: -2.95 (0.19), residues: 694 loop : -2.88 (0.13), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 133 TYR 0.030 0.002 TYR F 12 PHE 0.030 0.002 PHE A 153 TRP 0.032 0.003 TRP H 40 HIS 0.012 0.002 HIS H 180 Details of bonding type rmsd covalent geometry : bond 0.00671 (37122) covalent geometry : angle 0.92238 (50254) SS BOND : bond 0.00295 ( 8) SS BOND : angle 0.47532 ( 16) hydrogen bonds : bond 0.04021 ( 1131) hydrogen bonds : angle 5.27487 ( 3374) metal coordination : bond 0.00864 ( 4) link_ALPHA1-3 : bond 0.01089 ( 6) link_ALPHA1-3 : angle 4.86200 ( 18) link_ALPHA1-6 : bond 0.01555 ( 9) link_ALPHA1-6 : angle 3.08319 ( 27) link_BETA1-2 : bond 0.01286 ( 10) link_BETA1-2 : angle 4.63160 ( 30) link_BETA1-3 : bond 0.00573 ( 2) link_BETA1-3 : angle 1.95719 ( 6) link_BETA1-4 : bond 0.00993 ( 47) link_BETA1-4 : angle 3.39759 ( 141) link_NAG-ASN : bond 0.00750 ( 26) link_NAG-ASN : angle 4.36952 ( 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 539 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 537 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.7011 (ttm110) cc_final: 0.6504 (mtp-110) REVERT: A 50 MET cc_start: 0.8063 (ptt) cc_final: 0.7749 (ptt) REVERT: A 114 SER cc_start: 0.8400 (m) cc_final: 0.7970 (t) REVERT: A 199 LEU cc_start: 0.9081 (mm) cc_final: 0.8770 (mt) REVERT: A 287 THR cc_start: 0.8087 (p) cc_final: 0.7533 (t) REVERT: A 565 MET cc_start: 0.7666 (mmm) cc_final: 0.7304 (mmt) REVERT: A 566 TYR cc_start: 0.8368 (m-10) cc_final: 0.8162 (m-10) REVERT: A 575 SER cc_start: 0.8554 (p) cc_final: 0.8179 (m) REVERT: A 626 LEU cc_start: 0.8492 (mt) cc_final: 0.8045 (mt) REVERT: A 794 MET cc_start: 0.7987 (mtm) cc_final: 0.7764 (mtt) REVERT: A 810 LYS cc_start: 0.8210 (mmtt) cc_final: 0.7790 (mmpt) REVERT: A 861 MET cc_start: 0.8037 (mmp) cc_final: 0.7378 (mtm) REVERT: B 78 TYR cc_start: 0.6769 (p90) cc_final: 0.6557 (p90) REVERT: B 130 ILE cc_start: 0.8799 (mm) cc_final: 0.8446 (mm) REVERT: B 234 MET cc_start: 0.8488 (ttm) cc_final: 0.8170 (ttm) REVERT: B 248 MET cc_start: 0.7581 (mtp) cc_final: 0.7114 (mtp) REVERT: B 463 CYS cc_start: 0.8619 (m) cc_final: 0.8184 (m) REVERT: B 572 LEU cc_start: 0.8705 (mm) cc_final: 0.8063 (mm) REVERT: B 584 PHE cc_start: 0.7363 (t80) cc_final: 0.7024 (m-10) REVERT: B 770 MET cc_start: 0.7574 (tpp) cc_final: 0.7249 (tpp) REVERT: C 37 ARG cc_start: 0.7296 (ttm110) cc_final: 0.6895 (mtm110) REVERT: C 114 SER cc_start: 0.8394 (m) cc_final: 0.8067 (t) REVERT: C 199 LEU cc_start: 0.9038 (mm) cc_final: 0.8816 (mt) REVERT: C 287 THR cc_start: 0.8086 (p) cc_final: 0.7623 (t) REVERT: C 340 MET cc_start: 0.4629 (ttp) cc_final: 0.4359 (ttt) REVERT: C 565 MET cc_start: 0.7708 (mmm) cc_final: 0.7306 (mmt) REVERT: C 575 SER cc_start: 0.8698 (p) cc_final: 0.8299 (m) REVERT: C 836 PHE cc_start: 0.8210 (m-80) cc_final: 0.7801 (m-10) REVERT: C 861 MET cc_start: 0.8008 (mmp) cc_final: 0.7378 (mtm) REVERT: D 88 SER cc_start: 0.8407 (m) cc_final: 0.8099 (t) REVERT: D 130 ILE cc_start: 0.8815 (mm) cc_final: 0.8464 (mm) REVERT: D 248 MET cc_start: 0.7708 (mtp) cc_final: 0.7218 (mtp) REVERT: D 400 GLU cc_start: 0.7450 (mt-10) cc_final: 0.6842 (mt-10) REVERT: D 463 CYS cc_start: 0.8663 (m) cc_final: 0.8238 (m) REVERT: D 469 GLU cc_start: 0.7435 (tp30) cc_final: 0.7106 (tp30) REVERT: D 572 LEU cc_start: 0.8664 (mm) cc_final: 0.8199 (mm) REVERT: D 590 TYR cc_start: 0.6822 (p90) cc_final: 0.6606 (p90) REVERT: D 612 PHE cc_start: 0.8108 (m-80) cc_final: 0.7880 (t80) REVERT: E 99 LEU cc_start: 0.8731 (tt) cc_final: 0.8438 (tp) REVERT: F 81 LEU cc_start: 0.6920 (mp) cc_final: 0.6694 (mp) REVERT: F 141 ILE cc_start: 0.8365 (mt) cc_final: 0.8153 (mt) REVERT: F 159 VAL cc_start: 0.6988 (p) cc_final: 0.6428 (m) REVERT: F 195 PHE cc_start: 0.6511 (t80) cc_final: 0.5992 (t80) REVERT: F 218 ASP cc_start: 0.7881 (p0) cc_final: 0.7572 (p0) REVERT: G 28 ASP cc_start: 0.8540 (m-30) cc_final: 0.8302 (m-30) REVERT: G 49 THR cc_start: 0.8085 (m) cc_final: 0.7884 (m) REVERT: H 8 GLU cc_start: 0.8123 (pt0) cc_final: 0.7863 (pt0) REVERT: H 11 THR cc_start: 0.8500 (p) cc_final: 0.8086 (t) REVERT: H 54 TYR cc_start: 0.8461 (t80) cc_final: 0.8145 (t80) REVERT: H 141 ILE cc_start: 0.8327 (mt) cc_final: 0.7768 (tt) REVERT: H 174 LEU cc_start: 0.7942 (mp) cc_final: 0.7661 (mt) REVERT: H 191 PHE cc_start: 0.8445 (p90) cc_final: 0.8073 (p90) outliers start: 2 outliers final: 0 residues processed: 537 average time/residue: 0.1739 time to fit residues: 160.6455 Evaluate side-chains 421 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 421 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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: 6.9990 chunk 148 optimal weight: 7.9990 chunk 188 optimal weight: 0.6980 chunk 147 optimal weight: 0.2980 chunk 407 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 410 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 HIS ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 GLN ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 ASN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 HIS ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 GLN D 591 ASN E 131 ASN ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.124042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.100325 restraints weight = 139261.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.103689 restraints weight = 173708.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.105446 restraints weight = 81971.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.106322 restraints weight = 57309.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.107419 restraints weight = 49243.602| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 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 = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.4386 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= 0.149 Angle : 0.875 17.690 50570 Z= 0.406 Chirality : 0.051 0.557 5874 Planarity : 0.005 0.074 6128 Dihedral : 16.736 141.357 7876 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.35 % Favored : 87.23 % Rotamer: Outliers : 0.32 % Allowed : 0.56 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 1.70 % 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 aren not related in a simple way. whole: -2.56 (0.13), residues: 4306 helix: 0.13 (0.13), residues: 1478 sheet: -2.82 (0.19), residues: 716 loop : -2.69 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 60 TYR 0.066 0.002 TYR D 566 PHE 0.031 0.002 PHE D 584 TRP 0.086 0.002 TRP C 799 HIS 0.013 0.001 HIS H 121 Details of bonding type rmsd covalent geometry : bond 0.00321 (37122) covalent geometry : angle 0.82790 (50254) SS BOND : bond 0.00239 ( 8) SS BOND : angle 0.49281 ( 16) hydrogen bonds : bond 0.03556 ( 1131) hydrogen bonds : angle 5.00643 ( 3374) metal coordination : bond 0.00225 ( 4) link_ALPHA1-3 : bond 0.01444 ( 6) link_ALPHA1-3 : angle 4.47668 ( 18) link_ALPHA1-6 : bond 0.01611 ( 9) link_ALPHA1-6 : angle 3.11319 ( 27) link_BETA1-2 : bond 0.01507 ( 10) link_BETA1-2 : angle 4.65519 ( 30) link_BETA1-3 : bond 0.00557 ( 2) link_BETA1-3 : angle 1.97306 ( 6) link_BETA1-4 : bond 0.00971 ( 47) link_BETA1-4 : angle 3.31223 ( 141) link_NAG-ASN : bond 0.00752 ( 26) link_NAG-ASN : angle 4.27225 ( 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 582 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 580 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.7024 (ttm110) cc_final: 0.6542 (mtp-110) REVERT: A 50 MET cc_start: 0.7930 (ptt) cc_final: 0.7662 (ptt) REVERT: A 106 ILE cc_start: 0.9151 (mm) cc_final: 0.8904 (mt) REVERT: A 114 SER cc_start: 0.8334 (m) cc_final: 0.7910 (t) REVERT: A 230 CYS cc_start: 0.8012 (m) cc_final: 0.7698 (m) REVERT: A 248 MET cc_start: 0.8950 (mtp) cc_final: 0.7580 (mpp) REVERT: A 287 THR cc_start: 0.8206 (p) cc_final: 0.7696 (t) REVERT: A 565 MET cc_start: 0.7643 (mmm) cc_final: 0.7311 (mmt) REVERT: A 575 SER cc_start: 0.8365 (p) cc_final: 0.8116 (m) REVERT: A 626 LEU cc_start: 0.8487 (mt) cc_final: 0.8055 (mt) REVERT: A 794 MET cc_start: 0.7856 (mtm) cc_final: 0.7633 (mtt) REVERT: A 810 LYS cc_start: 0.8184 (mmtt) cc_final: 0.7779 (mmpt) REVERT: A 841 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7273 (mt-10) REVERT: A 861 MET cc_start: 0.8076 (mmp) cc_final: 0.7382 (mtm) REVERT: B 78 TYR cc_start: 0.6756 (p90) cc_final: 0.6508 (p90) REVERT: B 130 ILE cc_start: 0.8736 (mm) cc_final: 0.8396 (mm) REVERT: B 143 ASP cc_start: 0.8014 (t0) cc_final: 0.7043 (t0) REVERT: B 234 MET cc_start: 0.8350 (ttm) cc_final: 0.8071 (ttm) REVERT: B 248 MET cc_start: 0.7517 (mtp) cc_final: 0.7118 (mtp) REVERT: B 572 LEU cc_start: 0.8677 (mm) cc_final: 0.8097 (mm) REVERT: B 584 PHE cc_start: 0.7564 (t80) cc_final: 0.7123 (m-10) REVERT: B 792 HIS cc_start: 0.8058 (t70) cc_final: 0.7730 (t-90) REVERT: C 37 ARG cc_start: 0.7186 (ttm110) cc_final: 0.6939 (mtm110) REVERT: C 114 SER cc_start: 0.8444 (m) cc_final: 0.8060 (t) REVERT: C 287 THR cc_start: 0.8036 (p) cc_final: 0.7561 (t) REVERT: C 340 MET cc_start: 0.4752 (ttp) cc_final: 0.4423 (ttt) REVERT: C 565 MET cc_start: 0.7674 (mmm) cc_final: 0.7374 (mmt) REVERT: C 575 SER cc_start: 0.8543 (p) cc_final: 0.8267 (m) REVERT: C 836 PHE cc_start: 0.8186 (m-80) cc_final: 0.7777 (m-10) REVERT: C 841 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7298 (mt-10) REVERT: C 861 MET cc_start: 0.8048 (mmp) cc_final: 0.7393 (mtm) REVERT: D 130 ILE cc_start: 0.8749 (mm) cc_final: 0.8410 (mm) REVERT: D 248 MET cc_start: 0.7486 (mtp) cc_final: 0.7114 (mtp) REVERT: D 400 GLU cc_start: 0.7386 (mt-10) cc_final: 0.6748 (mt-10) REVERT: D 463 CYS cc_start: 0.8664 (m) cc_final: 0.8256 (m) REVERT: D 469 GLU cc_start: 0.7153 (tp30) cc_final: 0.6859 (tp30) REVERT: D 572 LEU cc_start: 0.8713 (mm) cc_final: 0.8201 (mm) REVERT: D 612 PHE cc_start: 0.8068 (m-80) cc_final: 0.7837 (t80) REVERT: D 786 GLN cc_start: 0.8399 (tm-30) cc_final: 0.7759 (tm-30) REVERT: D 815 LEU cc_start: 0.8720 (mt) cc_final: 0.8288 (mp) REVERT: E 41 ASN cc_start: 0.7918 (t0) cc_final: 0.7515 (t0) REVERT: F 61 LEU cc_start: 0.7727 (tp) cc_final: 0.7375 (tt) REVERT: F 195 PHE cc_start: 0.6485 (t80) cc_final: 0.5841 (t80) REVERT: F 210 ILE cc_start: 0.8608 (tt) cc_final: 0.8386 (tt) REVERT: H 8 GLU cc_start: 0.8150 (pt0) cc_final: 0.7931 (pt0) REVERT: H 191 PHE cc_start: 0.8364 (p90) cc_final: 0.8018 (p90) outliers start: 2 outliers final: 0 residues processed: 580 average time/residue: 0.1767 time to fit residues: 176.5992 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 : 0.990 ------------------------------------------------------------------------------- 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: 4.9990 chunk 166 optimal weight: 40.0000 chunk 418 optimal weight: 0.2980 chunk 365 optimal weight: 5.9990 chunk 150 optimal weight: 0.0050 chunk 426 optimal weight: 2.9990 chunk 322 optimal weight: 0.4980 chunk 55 optimal weight: 0.9990 chunk 258 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 GLN ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 ASN B 604 ASN B 792 HIS ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 HIS C 749 ASN D 165 GLN D 591 ASN ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 ASN G 153 ASN H 51 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.124143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.100934 restraints weight = 121451.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.104600 restraints weight = 153004.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.105407 restraints weight = 76637.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.105853 restraints weight = 61739.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.107298 restraints weight = 52503.632| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 37234 Z= 0.153 Angle : 0.868 17.845 50570 Z= 0.401 Chirality : 0.050 0.556 5874 Planarity : 0.005 0.071 6128 Dihedral : 16.326 140.811 7876 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.42 % Allowed : 13.16 % Favored : 86.42 % Rotamer: Outliers : 0.32 % Allowed : 0.64 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 1.70 % Twisted General : 0.68 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.39 (0.13), residues: 4306 helix: 0.36 (0.13), residues: 1480 sheet: -2.75 (0.19), residues: 718 loop : -2.66 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 133 TYR 0.026 0.002 TYR F 54 PHE 0.027 0.002 PHE E 191 TRP 0.038 0.002 TRP E 40 HIS 0.009 0.001 HIS C 593 Details of bonding type rmsd covalent geometry : bond 0.00339 (37122) covalent geometry : angle 0.82012 (50254) SS BOND : bond 0.00224 ( 8) SS BOND : angle 0.50720 ( 16) hydrogen bonds : bond 0.03459 ( 1131) hydrogen bonds : angle 4.91757 ( 3374) metal coordination : bond 0.00218 ( 4) link_ALPHA1-3 : bond 0.01339 ( 6) link_ALPHA1-3 : angle 4.48391 ( 18) link_ALPHA1-6 : bond 0.01258 ( 9) link_ALPHA1-6 : angle 2.67546 ( 27) link_BETA1-2 : bond 0.01490 ( 10) link_BETA1-2 : angle 4.62400 ( 30) link_BETA1-3 : bond 0.00512 ( 2) link_BETA1-3 : angle 1.81585 ( 6) link_BETA1-4 : bond 0.00965 ( 47) link_BETA1-4 : angle 3.29658 ( 141) link_NAG-ASN : bond 0.00792 ( 26) link_NAG-ASN : angle 4.40523 ( 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 577 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 575 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.6972 (ttm110) cc_final: 0.6584 (mtp-110) REVERT: A 50 MET cc_start: 0.7933 (ptt) cc_final: 0.7652 (ptt) REVERT: A 114 SER cc_start: 0.8333 (m) cc_final: 0.7977 (t) REVERT: A 230 CYS cc_start: 0.8074 (m) cc_final: 0.7813 (m) REVERT: A 248 MET cc_start: 0.8710 (mtp) cc_final: 0.7952 (mpp) REVERT: A 287 THR cc_start: 0.8125 (p) cc_final: 0.7584 (t) REVERT: A 565 MET cc_start: 0.7761 (mmm) cc_final: 0.7337 (mmt) REVERT: A 626 LEU cc_start: 0.8425 (mt) cc_final: 0.7973 (mt) REVERT: A 794 MET cc_start: 0.7854 (mtm) cc_final: 0.7590 (mtt) REVERT: A 810 LYS cc_start: 0.8180 (mmtt) cc_final: 0.7739 (mmpt) REVERT: A 841 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7404 (mt-10) REVERT: A 861 MET cc_start: 0.8058 (mmp) cc_final: 0.7369 (mtm) REVERT: B 78 TYR cc_start: 0.6806 (p90) cc_final: 0.6561 (p90) REVERT: B 130 ILE cc_start: 0.8747 (mm) cc_final: 0.8383 (mm) REVERT: B 143 ASP cc_start: 0.8027 (t0) cc_final: 0.7089 (t0) REVERT: B 234 MET cc_start: 0.8400 (ttm) cc_final: 0.8165 (ttm) REVERT: B 248 MET cc_start: 0.7597 (mtp) cc_final: 0.7297 (mtp) REVERT: B 463 CYS cc_start: 0.8633 (m) cc_final: 0.8234 (m) REVERT: B 572 LEU cc_start: 0.8673 (mm) cc_final: 0.8054 (mm) REVERT: B 584 PHE cc_start: 0.7561 (t80) cc_final: 0.7138 (m-10) REVERT: B 620 MET cc_start: 0.8903 (mmm) cc_final: 0.8602 (mmm) REVERT: C 37 ARG cc_start: 0.7243 (ttm110) cc_final: 0.6831 (mtm110) REVERT: C 114 SER cc_start: 0.8464 (m) cc_final: 0.8175 (t) REVERT: C 287 THR cc_start: 0.8055 (p) cc_final: 0.7575 (t) REVERT: C 565 MET cc_start: 0.7817 (mmm) cc_final: 0.7425 (mmt) REVERT: C 575 SER cc_start: 0.8428 (p) cc_final: 0.8198 (m) REVERT: C 626 LEU cc_start: 0.8484 (mt) cc_final: 0.8033 (mt) REVERT: C 836 PHE cc_start: 0.8305 (m-80) cc_final: 0.7779 (m-10) REVERT: C 841 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7296 (mt-10) REVERT: C 861 MET cc_start: 0.8010 (mmp) cc_final: 0.7309 (mtm) REVERT: D 130 ILE cc_start: 0.8725 (mm) cc_final: 0.8331 (mm) REVERT: D 234 MET cc_start: 0.8414 (ttm) cc_final: 0.8114 (ttm) REVERT: D 292 ILE cc_start: 0.8920 (mm) cc_final: 0.8700 (mm) REVERT: D 400 GLU cc_start: 0.7386 (mt-10) cc_final: 0.6750 (mt-10) REVERT: D 463 CYS cc_start: 0.8657 (m) cc_final: 0.8256 (m) REVERT: D 469 GLU cc_start: 0.7190 (tp30) cc_final: 0.6895 (tp30) REVERT: D 566 TYR cc_start: 0.7685 (m-80) cc_final: 0.7417 (m-80) REVERT: D 572 LEU cc_start: 0.8672 (mm) cc_final: 0.8154 (mm) REVERT: D 612 PHE cc_start: 0.8094 (m-80) cc_final: 0.7790 (t80) REVERT: E 41 ASN cc_start: 0.7761 (t0) cc_final: 0.7426 (t0) REVERT: F 159 VAL cc_start: 0.5938 (p) cc_final: 0.5316 (m) REVERT: F 166 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7491 (mm-40) REVERT: H 8 GLU cc_start: 0.8234 (pt0) cc_final: 0.7963 (pt0) REVERT: H 11 THR cc_start: 0.8337 (p) cc_final: 0.7885 (t) REVERT: H 141 ILE cc_start: 0.8322 (mt) cc_final: 0.7803 (tt) REVERT: H 158 ARG cc_start: 0.7369 (mpt180) cc_final: 0.7144 (mmt180) REVERT: H 191 PHE cc_start: 0.8370 (p90) cc_final: 0.8001 (p90) outliers start: 2 outliers final: 0 residues processed: 575 average time/residue: 0.1746 time to fit residues: 172.3707 Evaluate side-chains 449 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 449 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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: 5.9990 chunk 375 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 174 optimal weight: 5.9990 chunk 181 optimal weight: 0.7980 chunk 365 optimal weight: 3.9990 chunk 321 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 220 optimal weight: 0.9980 chunk 289 optimal weight: 1.9990 chunk 413 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 ASN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 HIS D 165 GLN D 591 ASN D 747 GLN E 153 ASN ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.122845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.101785 restraints weight = 137584.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.104944 restraints weight = 189243.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.105944 restraints weight = 77470.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.106673 restraints weight = 59399.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.107292 restraints weight = 49992.089| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 37234 Z= 0.188 Angle : 0.889 18.089 50570 Z= 0.413 Chirality : 0.051 0.550 5874 Planarity : 0.005 0.066 6128 Dihedral : 16.016 140.795 7876 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.40 % Allowed : 13.37 % Favored : 86.23 % Rotamer: Outliers : 0.32 % Allowed : 0.24 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.68 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.37 (0.13), residues: 4306 helix: 0.36 (0.13), residues: 1474 sheet: -2.80 (0.19), residues: 700 loop : -2.59 (0.13), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 800 TYR 0.044 0.002 TYR B 566 PHE 0.034 0.002 PHE G 191 TRP 0.037 0.002 TRP H 40 HIS 0.013 0.001 HIS H 121 Details of bonding type rmsd covalent geometry : bond 0.00426 (37122) covalent geometry : angle 0.84337 (50254) SS BOND : bond 0.00226 ( 8) SS BOND : angle 0.44404 ( 16) hydrogen bonds : bond 0.03525 ( 1131) hydrogen bonds : angle 4.97783 ( 3374) metal coordination : bond 0.00361 ( 4) link_ALPHA1-3 : bond 0.01268 ( 6) link_ALPHA1-3 : angle 4.56452 ( 18) link_ALPHA1-6 : bond 0.01177 ( 9) link_ALPHA1-6 : angle 2.17931 ( 27) link_BETA1-2 : bond 0.01364 ( 10) link_BETA1-2 : angle 4.62225 ( 30) link_BETA1-3 : bond 0.00516 ( 2) link_BETA1-3 : angle 1.83506 ( 6) link_BETA1-4 : bond 0.00951 ( 47) link_BETA1-4 : angle 3.29178 ( 141) link_NAG-ASN : bond 0.00699 ( 26) link_NAG-ASN : angle 4.38228 ( 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 557 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 555 time to evaluate : 1.153 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: 0.6928 (ttm110) cc_final: 0.6617 (mtp-110) REVERT: A 50 MET cc_start: 0.7923 (ptt) cc_final: 0.7617 (ptt) REVERT: A 114 SER cc_start: 0.8442 (m) cc_final: 0.8043 (t) REVERT: A 230 CYS cc_start: 0.8036 (m) cc_final: 0.7776 (m) REVERT: A 248 MET cc_start: 0.8531 (mtp) cc_final: 0.7400 (mpp) REVERT: A 287 THR cc_start: 0.8030 (p) cc_final: 0.7469 (t) REVERT: A 323 MET cc_start: 0.7175 (tpt) cc_final: 0.6816 (tpp) REVERT: A 565 MET cc_start: 0.7774 (mmm) cc_final: 0.7351 (mmt) REVERT: A 626 LEU cc_start: 0.8350 (mt) cc_final: 0.7923 (mt) REVERT: A 794 MET cc_start: 0.7885 (mtm) cc_final: 0.7623 (mtt) REVERT: A 810 LYS cc_start: 0.8056 (mmtt) cc_final: 0.7691 (mmpt) REVERT: A 841 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7373 (mt-10) REVERT: A 861 MET cc_start: 0.7992 (mmp) cc_final: 0.7329 (mtm) REVERT: B 78 TYR cc_start: 0.6774 (p90) cc_final: 0.6547 (p90) REVERT: B 130 ILE cc_start: 0.8768 (mm) cc_final: 0.8398 (mm) REVERT: B 143 ASP cc_start: 0.8113 (t0) cc_final: 0.7197 (t0) REVERT: B 234 MET cc_start: 0.8370 (ttm) cc_final: 0.8070 (ttm) REVERT: B 463 CYS cc_start: 0.8571 (m) cc_final: 0.8221 (m) REVERT: B 572 LEU cc_start: 0.8716 (mm) cc_final: 0.8003 (mm) REVERT: B 584 PHE cc_start: 0.7455 (t80) cc_final: 0.7094 (m-10) REVERT: B 620 MET cc_start: 0.8883 (mmm) cc_final: 0.8641 (mmm) REVERT: C 37 ARG cc_start: 0.7181 (ttm110) cc_final: 0.6846 (mtm110) REVERT: C 114 SER cc_start: 0.8397 (m) cc_final: 0.8092 (t) REVERT: C 287 THR cc_start: 0.7953 (p) cc_final: 0.7473 (t) REVERT: C 296 TRP cc_start: 0.7635 (t-100) cc_final: 0.7361 (t-100) REVERT: C 565 MET cc_start: 0.7783 (mmm) cc_final: 0.7393 (mmt) REVERT: C 575 SER cc_start: 0.8528 (p) cc_final: 0.8227 (m) REVERT: C 770 MET cc_start: 0.7147 (tpp) cc_final: 0.6441 (mmt) REVERT: C 836 PHE cc_start: 0.8230 (m-80) cc_final: 0.7743 (m-10) REVERT: C 841 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7269 (mt-10) REVERT: C 861 MET cc_start: 0.7954 (mmp) cc_final: 0.7274 (mtm) REVERT: D 130 ILE cc_start: 0.8761 (mm) cc_final: 0.8443 (mm) REVERT: D 234 MET cc_start: 0.8486 (ttm) cc_final: 0.8202 (ttm) REVERT: D 247 MET cc_start: 0.8634 (ttp) cc_final: 0.8432 (ttp) REVERT: D 463 CYS cc_start: 0.8581 (m) cc_final: 0.8202 (m) REVERT: D 469 GLU cc_start: 0.7118 (tp30) cc_final: 0.6871 (tp30) REVERT: D 566 TYR cc_start: 0.7422 (m-80) cc_final: 0.7119 (m-80) REVERT: D 572 LEU cc_start: 0.8613 (mm) cc_final: 0.8141 (mm) REVERT: D 612 PHE cc_start: 0.8030 (m-80) cc_final: 0.7805 (t80) REVERT: D 770 MET cc_start: 0.7427 (tpp) cc_final: 0.7059 (tpp) REVERT: D 778 ILE cc_start: 0.8682 (mt) cc_final: 0.8342 (mm) REVERT: D 815 LEU cc_start: 0.8892 (mt) cc_final: 0.8315 (mp) REVERT: E 192 GLU cc_start: 0.7358 (pt0) cc_final: 0.7112 (pt0) REVERT: F 159 VAL cc_start: 0.6141 (p) cc_final: 0.5522 (m) REVERT: F 195 PHE cc_start: 0.6580 (t80) cc_final: 0.6037 (t80) REVERT: F 210 ILE cc_start: 0.8763 (tt) cc_final: 0.8556 (tt) REVERT: G 192 GLU cc_start: 0.7734 (pt0) cc_final: 0.7526 (pt0) REVERT: H 8 GLU cc_start: 0.8213 (pt0) cc_final: 0.7986 (pt0) REVERT: H 11 THR cc_start: 0.8476 (p) cc_final: 0.8073 (t) REVERT: H 55 ASN cc_start: 0.7192 (p0) cc_final: 0.6858 (p0) REVERT: H 191 PHE cc_start: 0.8356 (p90) cc_final: 0.8025 (p90) outliers start: 2 outliers final: 0 residues processed: 555 average time/residue: 0.1728 time to fit residues: 166.2043 Evaluate side-chains 449 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 449 time to evaluate : 1.415 ------------------------------------------------------------------------------- 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: 0.9990 chunk 377 optimal weight: 5.9990 chunk 94 optimal weight: 0.3980 chunk 400 optimal weight: 0.0970 chunk 47 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 277 optimal weight: 0.9980 chunk 409 optimal weight: 0.7980 chunk 396 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 872 GLN ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 ASN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 HIS C 749 ASN D 129 HIS D 165 GLN D 591 ASN E 124 ASN ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 121 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 = 0.3607 r_free = 0.3607 target = 0.125453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.103720 restraints weight = 140636.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.106975 restraints weight = 189643.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.108583 restraints weight = 83711.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.108758 restraints weight = 69557.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.109855 restraints weight = 54723.580| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3334 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 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 = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3334 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 37234 Z= 0.139 Angle : 0.854 17.739 50570 Z= 0.394 Chirality : 0.050 0.545 5874 Planarity : 0.005 0.072 6128 Dihedral : 15.553 141.009 7876 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.40 % Allowed : 12.60 % Favored : 87.00 % Rotamer: Outliers : 0.32 % Allowed : 0.16 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.60 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.19 (0.13), residues: 4306 helix: 0.53 (0.14), residues: 1480 sheet: -2.60 (0.19), residues: 728 loop : -2.55 (0.13), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 748 TYR 0.044 0.002 TYR B 566 PHE 0.022 0.001 PHE D 584 TRP 0.033 0.002 TRP H 40 HIS 0.012 0.001 HIS H 121 Details of bonding type rmsd covalent geometry : bond 0.00302 (37122) covalent geometry : angle 0.80798 (50254) SS BOND : bond 0.00216 ( 8) SS BOND : angle 0.52339 ( 16) hydrogen bonds : bond 0.03396 ( 1131) hydrogen bonds : angle 4.85421 ( 3374) metal coordination : bond 0.00183 ( 4) link_ALPHA1-3 : bond 0.01375 ( 6) link_ALPHA1-3 : angle 4.53302 ( 18) link_ALPHA1-6 : bond 0.01218 ( 9) link_ALPHA1-6 : angle 1.90469 ( 27) link_BETA1-2 : bond 0.01275 ( 10) link_BETA1-2 : angle 4.55011 ( 30) link_BETA1-3 : bond 0.00495 ( 2) link_BETA1-3 : angle 1.77223 ( 6) link_BETA1-4 : bond 0.00967 ( 47) link_BETA1-4 : angle 3.25112 ( 141) link_NAG-ASN : bond 0.00713 ( 26) link_NAG-ASN : angle 4.33867 ( 78) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5356.37 seconds wall clock time: 93 minutes 59.93 seconds (5639.93 seconds total)