Starting phenix.real_space_refine on Sun Jul 5 07:36:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bvj_44934/07_2026/9bvj_44934.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bvj_44934/07_2026/9bvj_44934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bvj_44934/07_2026/9bvj_44934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bvj_44934/07_2026/9bvj_44934.map" model { file = "/net/cci-nas-00/data/ceres_data/9bvj_44934/07_2026/9bvj_44934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bvj_44934/07_2026/9bvj_44934.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14610 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9595 2.51 5 N 2290 2.21 5 O 2635 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14620 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2787 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 16, 'TRANS': 325} Chain breaks: 1 Chain: "B" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2787 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 16, 'TRANS': 325} Chain breaks: 1 Chain: "C" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2787 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 16, 'TRANS': 325} Chain breaks: 1 Chain: "D" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2787 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 16, 'TRANS': 325} Chain breaks: 1 Chain: "E" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2787 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 16, 'TRANS': 325} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 107 Unusual residues: {'PIO': 5, 'PX4': 4} Classifications: {'peptide': 1, 'undetermined': 9} Modifications used: {'COO': 1} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 444 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'PIO:plan-2': 5, 'PX4:plan-1': 1, 'PX4:plan-2': 3} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 102 Unusual residues: {'PIO': 5, 'PX4': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 444 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'PIO:plan-2': 5, 'PX4:plan-1': 1, 'PX4:plan-2': 3} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 102 Unusual residues: {'PIO': 5, 'PX4': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 444 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'PIO:plan-2': 5, 'PX4:plan-1': 1, 'PX4:plan-2': 3} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 102 Unusual residues: {'PIO': 5, 'PX4': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 444 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'PIO:plan-2': 5, 'PX4:plan-1': 1, 'PX4:plan-2': 3} Unresolved non-hydrogen planarities: 36 Chain: "E" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 102 Unusual residues: {'PIO': 5, 'PX4': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 444 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'PIO:plan-2': 5, 'PX4:plan-2': 3, 'PX4:plan-1': 1} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.32, per 1000 atoms: 0.16 Number of scatterers: 14620 At special positions: 0 Unit cell: (96.21, 98.348, 129.349, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2635 8.00 N 2290 7.00 C 9595 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 209 " distance=2.03 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 209 " distance=2.03 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 209 " distance=2.03 Simple disulfide: pdb=" SG CYS E 198 " - pdb=" SG CYS E 209 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG F 1 " - " ASN A 38 " " NAG G 1 " - " ASN B 38 " " NAG H 1 " - " ASN C 38 " " NAG I 1 " - " ASN D 38 " " NAG J 1 " - " ASN E 38 " Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 603.8 milliseconds 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3300 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 20 sheets defined 38.5% alpha, 40.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 9 through 18 removed outlier: 3.741A pdb=" N LEU A 14 " --> pdb=" O PRO A 10 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP A 15 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.595A pdb=" N MET A 89 " --> pdb=" O ASP A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 227 through 240 Processing helix chain 'A' and resid 241 through 244 Processing helix chain 'A' and resid 248 through 270 Processing helix chain 'A' and resid 281 through 309 removed outlier: 3.667A pdb=" N ARG A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 421 removed outlier: 3.822A pdb=" N ALA A 401 " --> pdb=" O THR A 397 " (cutoff:3.500A) Proline residue: A 404 - end of helix removed outlier: 3.537A pdb=" N LEU A 421 " --> pdb=" O ILE A 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 18 removed outlier: 3.741A pdb=" N LEU B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP B 15 " --> pdb=" O SER B 11 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.595A pdb=" N MET B 89 " --> pdb=" O ASP B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 227 through 240 Processing helix chain 'B' and resid 241 through 244 Processing helix chain 'B' and resid 248 through 270 Processing helix chain 'B' and resid 281 through 309 removed outlier: 3.667A pdb=" N ARG B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 421 removed outlier: 3.822A pdb=" N ALA B 401 " --> pdb=" O THR B 397 " (cutoff:3.500A) Proline residue: B 404 - end of helix removed outlier: 3.537A pdb=" N LEU B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 18 removed outlier: 3.741A pdb=" N LEU C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP C 15 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.596A pdb=" N MET C 89 " --> pdb=" O ASP C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 227 Processing helix chain 'C' and resid 227 through 240 Processing helix chain 'C' and resid 241 through 244 Processing helix chain 'C' and resid 248 through 270 Processing helix chain 'C' and resid 281 through 309 removed outlier: 3.666A pdb=" N ARG C 309 " --> pdb=" O ASN C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 421 removed outlier: 3.822A pdb=" N ALA C 401 " --> pdb=" O THR C 397 " (cutoff:3.500A) Proline residue: C 404 - end of helix removed outlier: 3.537A pdb=" N LEU C 421 " --> pdb=" O ILE C 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 18 removed outlier: 3.742A pdb=" N LEU D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP D 15 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET D 18 " --> pdb=" O LEU D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 74 Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.596A pdb=" N MET D 89 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 227 Processing helix chain 'D' and resid 227 through 240 Processing helix chain 'D' and resid 241 through 244 Processing helix chain 'D' and resid 248 through 270 Processing helix chain 'D' and resid 281 through 309 removed outlier: 3.667A pdb=" N ARG D 309 " --> pdb=" O ASN D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 421 removed outlier: 3.822A pdb=" N ALA D 401 " --> pdb=" O THR D 397 " (cutoff:3.500A) Proline residue: D 404 - end of helix removed outlier: 3.537A pdb=" N LEU D 421 " --> pdb=" O ILE D 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 18 removed outlier: 3.741A pdb=" N LEU E 14 " --> pdb=" O PRO E 10 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP E 15 " --> pdb=" O SER E 11 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 74 Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.595A pdb=" N MET E 89 " --> pdb=" O ASP E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 227 Processing helix chain 'E' and resid 227 through 240 Processing helix chain 'E' and resid 241 through 244 Processing helix chain 'E' and resid 248 through 270 Processing helix chain 'E' and resid 281 through 309 removed outlier: 3.667A pdb=" N ARG E 309 " --> pdb=" O ASN E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 421 removed outlier: 3.822A pdb=" N ALA E 401 " --> pdb=" O THR E 397 " (cutoff:3.500A) Proline residue: E 404 - end of helix removed outlier: 3.536A pdb=" N LEU E 421 " --> pdb=" O ILE E 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 84 removed outlier: 4.365A pdb=" N ASN A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASP A 57 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER A 50 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ARG A 59 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N PHE A 48 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN A 61 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN A 69 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASN A 38 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL A 37 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N GLU A 169 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL A 39 " --> pdb=" O GLU A 169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 107 removed outlier: 6.999A pdb=" N THR A 135 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA A 106 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR A 133 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASP A 57 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER A 50 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ARG A 59 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N PHE A 48 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN A 61 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN A 69 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASN A 38 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N GLN A 177 " --> pdb=" O CYS A 41 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE A 43 " --> pdb=" O GLN A 177 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100 removed outlier: 5.049A pdb=" N THR A 208 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N GLY A 160 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N LYS A 206 " --> pdb=" O GLY A 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 187 through 189 Processing sheet with id=AA5, first strand: chain 'B' and resid 82 through 84 removed outlier: 4.365A pdb=" N ASN B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASP B 57 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER B 50 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ARG B 59 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N PHE B 48 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN B 61 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASN B 38 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL B 37 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N GLU B 169 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL B 39 " --> pdb=" O GLU B 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 103 through 107 removed outlier: 7.000A pdb=" N THR B 135 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA B 106 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR B 133 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASP B 57 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER B 50 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ARG B 59 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N PHE B 48 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN B 61 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASN B 38 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N GLN B 177 " --> pdb=" O CYS B 41 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE B 43 " --> pdb=" O GLN B 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 100 removed outlier: 5.050A pdb=" N THR B 208 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N GLY B 160 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N LYS B 206 " --> pdb=" O GLY B 160 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 189 Processing sheet with id=AA9, first strand: chain 'C' and resid 82 through 84 removed outlier: 4.364A pdb=" N ASN C 125 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASP C 57 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER C 50 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ARG C 59 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N PHE C 48 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN C 61 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN C 69 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASN C 38 " --> pdb=" O ASN C 69 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL C 37 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N GLU C 169 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL C 39 " --> pdb=" O GLU C 169 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 103 through 107 removed outlier: 7.000A pdb=" N THR C 135 " --> pdb=" O LYS C 104 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA C 106 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR C 133 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASP C 57 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER C 50 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ARG C 59 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N PHE C 48 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN C 61 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN C 69 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASN C 38 " --> pdb=" O ASN C 69 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N GLN C 177 " --> pdb=" O CYS C 41 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE C 43 " --> pdb=" O GLN C 177 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 98 through 100 removed outlier: 5.049A pdb=" N THR C 208 " --> pdb=" O SER C 158 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N GLY C 160 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N LYS C 206 " --> pdb=" O GLY C 160 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 187 through 189 Processing sheet with id=AB4, first strand: chain 'D' and resid 82 through 84 removed outlier: 4.364A pdb=" N ASN D 125 " --> pdb=" O PHE D 121 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASP D 57 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER D 50 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ARG D 59 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N PHE D 48 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN D 61 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN D 69 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASN D 38 " --> pdb=" O ASN D 69 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL D 37 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N GLU D 169 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL D 39 " --> pdb=" O GLU D 169 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 103 through 107 removed outlier: 6.999A pdb=" N THR D 135 " --> pdb=" O LYS D 104 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA D 106 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR D 133 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASP D 57 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER D 50 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ARG D 59 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N PHE D 48 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN D 61 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN D 69 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASN D 38 " --> pdb=" O ASN D 69 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N GLN D 177 " --> pdb=" O CYS D 41 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE D 43 " --> pdb=" O GLN D 177 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 98 through 100 removed outlier: 5.049A pdb=" N THR D 208 " --> pdb=" O SER D 158 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N GLY D 160 " --> pdb=" O LYS D 206 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N LYS D 206 " --> pdb=" O GLY D 160 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 187 through 189 Processing sheet with id=AB8, first strand: chain 'E' and resid 82 through 84 removed outlier: 4.366A pdb=" N ASN E 125 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASP E 57 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER E 50 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ARG E 59 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N PHE E 48 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN E 61 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN E 69 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASN E 38 " --> pdb=" O ASN E 69 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL E 37 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N GLU E 169 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL E 39 " --> pdb=" O GLU E 169 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 103 through 107 removed outlier: 7.000A pdb=" N THR E 135 " --> pdb=" O LYS E 104 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA E 106 " --> pdb=" O THR E 133 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR E 133 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASP E 57 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER E 50 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ARG E 59 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N PHE E 48 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN E 61 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN E 69 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASN E 38 " --> pdb=" O ASN E 69 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N GLN E 177 " --> pdb=" O CYS E 41 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE E 43 " --> pdb=" O GLN E 177 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 98 through 100 removed outlier: 5.048A pdb=" N THR E 208 " --> pdb=" O SER E 158 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N GLY E 160 " --> pdb=" O LYS E 206 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N LYS E 206 " --> pdb=" O GLY E 160 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 187 through 189 770 hydrogen bonds defined for protein. 2250 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: 2.00 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2754 1.33 - 1.45: 3666 1.45 - 1.57: 8105 1.57 - 1.70: 230 1.70 - 1.82: 165 Bond restraints: 14920 Sorted by residual: bond pdb=" C9 PX4 A 510 " pdb=" O5 PX4 A 510 " ideal model delta sigma weight residual 1.327 1.468 -0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" C9 PX4 E 504 " pdb=" O5 PX4 E 504 " ideal model delta sigma weight residual 1.327 1.467 -0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" C9 PX4 D 510 " pdb=" O5 PX4 D 510 " ideal model delta sigma weight residual 1.327 1.467 -0.140 2.00e-02 2.50e+03 4.90e+01 bond pdb=" C9 PX4 B 510 " pdb=" O5 PX4 B 510 " ideal model delta sigma weight residual 1.327 1.467 -0.140 2.00e-02 2.50e+03 4.90e+01 bond pdb=" C9 PX4 B 508 " pdb=" O5 PX4 B 508 " ideal model delta sigma weight residual 1.327 1.467 -0.140 2.00e-02 2.50e+03 4.89e+01 ... (remaining 14915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 18868 1.94 - 3.87: 891 3.87 - 5.81: 241 5.81 - 7.75: 41 7.75 - 9.69: 29 Bond angle restraints: 20070 Sorted by residual: angle pdb=" C TYR C 228 " pdb=" N ILE C 229 " pdb=" CA ILE C 229 " ideal model delta sigma weight residual 120.24 122.94 -2.70 6.30e-01 2.52e+00 1.84e+01 angle pdb=" C TYR D 228 " pdb=" N ILE D 229 " pdb=" CA ILE D 229 " ideal model delta sigma weight residual 120.24 122.92 -2.68 6.30e-01 2.52e+00 1.81e+01 angle pdb=" C TYR A 228 " pdb=" N ILE A 229 " pdb=" CA ILE A 229 " ideal model delta sigma weight residual 120.24 122.91 -2.67 6.30e-01 2.52e+00 1.79e+01 angle pdb=" C TYR B 228 " pdb=" N ILE B 229 " pdb=" CA ILE B 229 " ideal model delta sigma weight residual 120.24 122.88 -2.64 6.30e-01 2.52e+00 1.75e+01 angle pdb=" C TYR E 228 " pdb=" N ILE E 229 " pdb=" CA ILE E 229 " ideal model delta sigma weight residual 120.24 122.86 -2.62 6.30e-01 2.52e+00 1.73e+01 ... (remaining 20065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 8170 17.66 - 35.32: 765 35.32 - 52.98: 95 52.98 - 70.64: 35 70.64 - 88.30: 10 Dihedral angle restraints: 9075 sinusoidal: 4000 harmonic: 5075 Sorted by residual: dihedral pdb=" CA GLU C 110 " pdb=" C GLU C 110 " pdb=" N VAL C 111 " pdb=" CA VAL C 111 " ideal model delta harmonic sigma weight residual -180.00 -157.44 -22.56 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA GLU B 110 " pdb=" C GLU B 110 " pdb=" N VAL B 111 " pdb=" CA VAL B 111 " ideal model delta harmonic sigma weight residual -180.00 -157.44 -22.56 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA GLU E 110 " pdb=" C GLU E 110 " pdb=" N VAL E 111 " pdb=" CA VAL E 111 " ideal model delta harmonic sigma weight residual -180.00 -157.45 -22.55 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 9072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1710 0.057 - 0.114: 406 0.114 - 0.171: 94 0.171 - 0.228: 0 0.228 - 0.286: 10 Chirality restraints: 2220 Sorted by residual: chirality pdb=" CG LEU C 421 " pdb=" CB LEU C 421 " pdb=" CD1 LEU C 421 " pdb=" CD2 LEU C 421 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CG LEU D 421 " pdb=" CB LEU D 421 " pdb=" CD1 LEU D 421 " pdb=" CD2 LEU D 421 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CG LEU A 421 " pdb=" CB LEU A 421 " pdb=" CD1 LEU A 421 " pdb=" CD2 LEU A 421 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 2217 not shown) Planarity restraints: 2490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 187 " 0.019 2.00e-02 2.50e+03 4.08e-02 1.67e+01 pdb=" C PHE A 187 " -0.071 2.00e-02 2.50e+03 pdb=" O PHE A 187 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU A 188 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 187 " 0.019 2.00e-02 2.50e+03 4.08e-02 1.67e+01 pdb=" C PHE E 187 " -0.071 2.00e-02 2.50e+03 pdb=" O PHE E 187 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU E 188 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 187 " 0.019 2.00e-02 2.50e+03 4.08e-02 1.66e+01 pdb=" C PHE B 187 " -0.070 2.00e-02 2.50e+03 pdb=" O PHE B 187 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU B 188 " 0.023 2.00e-02 2.50e+03 ... (remaining 2487 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 3951 2.82 - 3.34: 12570 3.34 - 3.86: 24094 3.86 - 4.38: 29357 4.38 - 4.90: 50391 Nonbonded interactions: 120363 Sorted by model distance: nonbonded pdb=" O LEU D 255 " pdb=" OG1 THR D 259 " model vdw 2.294 3.040 nonbonded pdb=" O LEU B 255 " pdb=" OG1 THR B 259 " model vdw 2.294 3.040 nonbonded pdb=" O LEU E 255 " pdb=" OG1 THR E 259 " model vdw 2.295 3.040 nonbonded pdb=" O LEU C 255 " pdb=" OG1 THR C 259 " model vdw 2.295 3.040 nonbonded pdb=" O LEU A 255 " pdb=" OG1 THR A 259 " model vdw 2.295 3.040 ... (remaining 120358 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 8 through 423 or resid 502 or resid 507 or resid 510)) selection = (chain 'B' and (resid 8 through 423 or resid 502 or resid 507 or resid 510)) selection = (chain 'C' and (resid 8 through 423 or resid 502 or resid 507 or resid 510)) selection = (chain 'D' and (resid 8 through 423 or resid 502 or resid 507 or resid 510)) selection = (chain 'E' and (resid 8 through 501 or (resid 506 and (name C1A or name C2A or n \ ame C3A or name C4A or name C5A or name C6A or name O1A or name O2C)) or resid 5 \ 09)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.010 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 : 0.012 0.141 14935 Z= 0.618 Angle : 1.028 9.685 20110 Z= 0.491 Chirality : 0.054 0.286 2220 Planarity : 0.006 0.058 2485 Dihedral : 13.520 88.296 5760 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.18), residues: 1690 helix: 0.06 (0.18), residues: 565 sheet: 0.52 (0.26), residues: 400 loop : -1.57 (0.18), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 29 TYR 0.029 0.002 TYR D 301 PHE 0.014 0.002 PHE A 99 TRP 0.006 0.001 TRP A 239 HIS 0.002 0.001 HIS E 109 Details of bonding type rmsd/Z covalent geometry : bond 0.01247 / 0.62 (14920) covalent geometry : angle 1.02384 / 0.49 (20070) SS BOND : bond 0.00080 / 0.04 ( 5) SS BOND : angle 4.14592 / 2.15 ( 10) hydrogen bonds : bond 0.13211 / 8.70 ( 675) hydrogen bonds : angle 5.62213 / 3.81 ( 2250) link_BETA1-4 : bond 0.00524 / 0.27 ( 5) link_BETA1-4 : angle 1.35701 / 0.77 ( 15) link_NAG-ASN : bond 0.00041 / 0.02 ( 5) link_NAG-ASN : angle 0.69413 / 0.42 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.745 Fit side-chains REVERT: A 12 ASP cc_start: 0.7985 (m-30) cc_final: 0.7587 (t0) REVERT: A 245 ASN cc_start: 0.8217 (p0) cc_final: 0.7973 (p0) REVERT: A 296 SER cc_start: 0.8903 (m) cc_final: 0.8615 (m) REVERT: B 12 ASP cc_start: 0.7966 (m-30) cc_final: 0.7562 (t0) REVERT: C 12 ASP cc_start: 0.8023 (m-30) cc_final: 0.7697 (t0) REVERT: C 59 ARG cc_start: 0.7902 (ttm110) cc_final: 0.7373 (ttt-90) REVERT: C 163 MET cc_start: 0.8762 (mmt) cc_final: 0.8479 (mmm) REVERT: C 296 SER cc_start: 0.8948 (m) cc_final: 0.8716 (m) REVERT: D 12 ASP cc_start: 0.8008 (m-30) cc_final: 0.7645 (t0) REVERT: E 12 ASP cc_start: 0.8049 (m-30) cc_final: 0.7703 (t0) REVERT: E 245 ASN cc_start: 0.8136 (p0) cc_final: 0.7925 (p0) REVERT: E 296 SER cc_start: 0.8917 (m) cc_final: 0.8644 (m) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.5630 time to fit residues: 118.2469 Evaluate side-chains 142 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.0980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN A 144 ASN A 171 GLN A 219 GLN ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN D 42 ASN D 144 ASN D 186 GLN E 171 GLN E 186 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.098723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.079180 restraints weight = 23845.528| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.95 r_work: 0.2866 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14935 Z= 0.121 Angle : 0.578 8.263 20110 Z= 0.288 Chirality : 0.042 0.160 2220 Planarity : 0.004 0.031 2485 Dihedral : 7.953 58.008 2405 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.35 % Allowed : 7.48 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.19), residues: 1690 helix: 1.42 (0.20), residues: 610 sheet: 0.74 (0.27), residues: 390 loop : -1.27 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 59 TYR 0.020 0.001 TYR C 301 PHE 0.010 0.001 PHE E 99 TRP 0.007 0.001 TRP C 68 HIS 0.002 0.001 HIS E 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (14920) covalent geometry : angle 0.57608 / 0.29 (20070) SS BOND : bond 0.00069 / 0.04 ( 5) SS BOND : angle 1.58259 / 0.82 ( 10) hydrogen bonds : bond 0.03845 / 2.52 ( 675) hydrogen bonds : angle 4.35526 / 2.95 ( 2250) link_BETA1-4 : bond 0.00325 / 0.17 ( 5) link_BETA1-4 : angle 1.19648 / 0.71 ( 15) link_NAG-ASN : bond 0.00047 / 0.02 ( 5) link_NAG-ASN : angle 0.71989 / 0.44 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.563 Fit side-chains REVERT: A 12 ASP cc_start: 0.8131 (m-30) cc_final: 0.7822 (t70) REVERT: A 296 SER cc_start: 0.9114 (m) cc_final: 0.8888 (m) REVERT: B 12 ASP cc_start: 0.8196 (m-30) cc_final: 0.7867 (t70) REVERT: B 18 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.7303 (ptt) REVERT: C 12 ASP cc_start: 0.8124 (m-30) cc_final: 0.7875 (t70) REVERT: C 18 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.7011 (ptt) REVERT: C 59 ARG cc_start: 0.8314 (ttm110) cc_final: 0.7602 (ttt-90) REVERT: C 163 MET cc_start: 0.8802 (mmt) cc_final: 0.8469 (mmm) REVERT: C 263 MET cc_start: 0.9200 (tpt) cc_final: 0.8797 (mmm) REVERT: C 398 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8280 (mp) REVERT: D 12 ASP cc_start: 0.8193 (m-30) cc_final: 0.7960 (t70) REVERT: E 8 MET cc_start: 0.7179 (ppp) cc_final: 0.6969 (ppp) REVERT: E 12 ASP cc_start: 0.8228 (m-30) cc_final: 0.7877 (t70) REVERT: E 56 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.7074 (mpt) REVERT: E 163 MET cc_start: 0.8822 (mmt) cc_final: 0.8539 (mmt) REVERT: E 245 ASN cc_start: 0.7885 (p0) cc_final: 0.7421 (p0) REVERT: E 296 SER cc_start: 0.9144 (m) cc_final: 0.8923 (m) outliers start: 21 outliers final: 5 residues processed: 156 average time/residue: 0.4557 time to fit residues: 79.9814 Evaluate side-chains 151 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 402 CYS Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 402 CYS Chi-restraints excluded: chain D residue 402 CYS Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 402 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 159 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 GLN A 186 GLN A 266 GLN B 42 ASN B 115 ASN B 266 GLN C 42 ASN E 42 ASN E 186 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.095360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.075888 restraints weight = 24273.395| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.95 r_work: 0.2804 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14935 Z= 0.166 Angle : 0.579 8.613 20110 Z= 0.290 Chirality : 0.043 0.196 2220 Planarity : 0.003 0.027 2485 Dihedral : 7.670 59.469 2405 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 2.45 % Allowed : 7.68 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.20), residues: 1690 helix: 1.98 (0.21), residues: 610 sheet: 0.71 (0.26), residues: 395 loop : -1.06 (0.20), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 59 TYR 0.022 0.002 TYR C 301 PHE 0.014 0.001 PHE D 48 TRP 0.007 0.001 TRP D 239 HIS 0.002 0.001 HIS E 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (14920) covalent geometry : angle 0.57735 / 0.29 (20070) SS BOND : bond 0.00197 / 0.10 ( 5) SS BOND : angle 1.55738 / 0.81 ( 10) hydrogen bonds : bond 0.03850 / 2.51 ( 675) hydrogen bonds : angle 4.14657 / 2.80 ( 2250) link_BETA1-4 : bond 0.00290 / 0.15 ( 5) link_BETA1-4 : angle 1.22602 / 0.74 ( 15) link_NAG-ASN : bond 0.00155 / 0.08 ( 5) link_NAG-ASN : angle 0.88581 / 0.54 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 0.559 Fit side-chains REVERT: A 12 ASP cc_start: 0.8240 (m-30) cc_final: 0.7918 (t70) REVERT: A 18 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.6651 (ptm) REVERT: A 110 GLU cc_start: 0.7622 (pm20) cc_final: 0.7392 (pm20) REVERT: B 8 MET cc_start: 0.7164 (ppp) cc_final: 0.6932 (ppp) REVERT: B 12 ASP cc_start: 0.8224 (m-30) cc_final: 0.7906 (t70) REVERT: B 18 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.6941 (ptp) REVERT: C 12 ASP cc_start: 0.8167 (m-30) cc_final: 0.7921 (t70) REVERT: C 59 ARG cc_start: 0.8288 (ttm110) cc_final: 0.7569 (ttt-90) REVERT: C 163 MET cc_start: 0.8807 (mmt) cc_final: 0.8535 (mmm) REVERT: C 263 MET cc_start: 0.9186 (tpt) cc_final: 0.8844 (mmm) REVERT: D 12 ASP cc_start: 0.8228 (m-30) cc_final: 0.8004 (t0) REVERT: E 12 ASP cc_start: 0.8214 (m-30) cc_final: 0.7941 (t70) REVERT: E 18 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.6337 (ptm) REVERT: E 245 ASN cc_start: 0.7993 (p0) cc_final: 0.7786 (p0) outliers start: 38 outliers final: 15 residues processed: 164 average time/residue: 0.4299 time to fit residues: 79.0892 Evaluate side-chains 158 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 402 CYS Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 402 CYS Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 402 CYS Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain D residue 402 CYS Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 402 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 84 optimal weight: 0.0870 chunk 112 optimal weight: 0.0270 chunk 103 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 166 optimal weight: 0.0040 chunk 82 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.6230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 107 ASN B 115 ASN B 266 GLN C 115 ASN E 115 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.095954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.075994 restraints weight = 24168.421| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.92 r_work: 0.2838 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14935 Z= 0.119 Angle : 0.565 9.307 20110 Z= 0.274 Chirality : 0.042 0.233 2220 Planarity : 0.003 0.027 2485 Dihedral : 7.391 58.650 2405 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.58 % Allowed : 9.68 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.20), residues: 1690 helix: 2.12 (0.21), residues: 615 sheet: 0.72 (0.26), residues: 395 loop : -0.92 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 59 TYR 0.022 0.001 TYR E 301 PHE 0.011 0.001 PHE E 99 TRP 0.005 0.001 TRP C 68 HIS 0.001 0.000 HIS E 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (14920) covalent geometry : angle 0.56361 / 0.27 (20070) SS BOND : bond 0.00202 / 0.10 ( 5) SS BOND : angle 1.25615 / 0.65 ( 10) hydrogen bonds : bond 0.03535 / 2.31 ( 675) hydrogen bonds : angle 4.01249 / 2.71 ( 2250) link_BETA1-4 : bond 0.00357 / 0.18 ( 5) link_BETA1-4 : angle 1.15177 / 0.70 ( 15) link_NAG-ASN : bond 0.00024 / 0.01 ( 5) link_NAG-ASN : angle 0.71794 / 0.44 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 148 time to evaluate : 0.524 Fit side-chains REVERT: A 8 MET cc_start: 0.7473 (ppp) cc_final: 0.7225 (ppp) REVERT: A 12 ASP cc_start: 0.8230 (m-30) cc_final: 0.7890 (t0) REVERT: A 18 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.6711 (ptm) REVERT: A 110 GLU cc_start: 0.7604 (pm20) cc_final: 0.7353 (pm20) REVERT: B 8 MET cc_start: 0.7159 (ppp) cc_final: 0.6956 (ppp) REVERT: B 12 ASP cc_start: 0.8281 (m-30) cc_final: 0.7953 (t70) REVERT: B 59 ARG cc_start: 0.8505 (ttm110) cc_final: 0.7747 (ttt-90) REVERT: B 91 ASP cc_start: 0.8411 (p0) cc_final: 0.8003 (t0) REVERT: C 8 MET cc_start: 0.7318 (ppp) cc_final: 0.7077 (ppp) REVERT: C 12 ASP cc_start: 0.8227 (m-30) cc_final: 0.7943 (t0) REVERT: C 59 ARG cc_start: 0.8316 (ttm110) cc_final: 0.7610 (ttt-90) REVERT: C 163 MET cc_start: 0.8865 (mmt) cc_final: 0.8573 (mmm) REVERT: C 263 MET cc_start: 0.9231 (tpt) cc_final: 0.8863 (mmm) REVERT: D 8 MET cc_start: 0.7380 (ppp) cc_final: 0.7079 (ppp) REVERT: D 12 ASP cc_start: 0.8255 (m-30) cc_final: 0.8003 (t0) REVERT: E 8 MET cc_start: 0.7335 (ppp) cc_final: 0.7055 (ppp) REVERT: E 12 ASP cc_start: 0.8248 (m-30) cc_final: 0.7968 (t70) REVERT: E 18 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.6381 (ptm) outliers start: 40 outliers final: 19 residues processed: 166 average time/residue: 0.4901 time to fit residues: 90.7012 Evaluate side-chains 164 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 402 CYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 402 CYS Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 402 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain D residue 402 CYS Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 402 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 86 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 154 optimal weight: 0.0970 chunk 28 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN A 177 GLN B 266 GLN C 115 ASN C 171 GLN E 115 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.095894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.076475 restraints weight = 24065.972| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.90 r_work: 0.2830 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14935 Z= 0.115 Angle : 0.560 9.441 20110 Z= 0.269 Chirality : 0.042 0.229 2220 Planarity : 0.003 0.028 2485 Dihedral : 7.186 58.704 2405 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.77 % Allowed : 10.84 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.20), residues: 1690 helix: 2.20 (0.21), residues: 615 sheet: 0.71 (0.26), residues: 395 loop : -0.86 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 59 TYR 0.022 0.001 TYR E 301 PHE 0.011 0.001 PHE E 99 TRP 0.005 0.001 TRP C 68 HIS 0.001 0.000 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (14920) covalent geometry : angle 0.55866 / 0.27 (20070) SS BOND : bond 0.00199 / 0.10 ( 5) SS BOND : angle 1.16391 / 0.61 ( 10) hydrogen bonds : bond 0.03439 / 2.25 ( 675) hydrogen bonds : angle 3.92676 / 2.65 ( 2250) link_BETA1-4 : bond 0.00355 / 0.18 ( 5) link_BETA1-4 : angle 1.16572 / 0.70 ( 15) link_NAG-ASN : bond 0.00015 / 0.01 ( 5) link_NAG-ASN : angle 0.71156 / 0.43 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 146 time to evaluate : 0.573 Fit side-chains REVERT: A 12 ASP cc_start: 0.8234 (m-30) cc_final: 0.7904 (t0) REVERT: A 18 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.6746 (ptm) REVERT: A 110 GLU cc_start: 0.7626 (pm20) cc_final: 0.7316 (pm20) REVERT: B 12 ASP cc_start: 0.8240 (m-30) cc_final: 0.7930 (t70) REVERT: B 59 ARG cc_start: 0.8535 (ttm110) cc_final: 0.7801 (ttt-90) REVERT: B 91 ASP cc_start: 0.8363 (p0) cc_final: 0.7994 (t0) REVERT: C 12 ASP cc_start: 0.8286 (m-30) cc_final: 0.8016 (t70) REVERT: C 59 ARG cc_start: 0.8354 (ttm110) cc_final: 0.7624 (ttt-90) REVERT: C 163 MET cc_start: 0.8895 (mmt) cc_final: 0.8574 (mmm) REVERT: C 263 MET cc_start: 0.9281 (tpt) cc_final: 0.8911 (mmm) REVERT: D 12 ASP cc_start: 0.8248 (m-30) cc_final: 0.8035 (t70) REVERT: E 8 MET cc_start: 0.7425 (ppp) cc_final: 0.7216 (ppp) REVERT: E 12 ASP cc_start: 0.8257 (m-30) cc_final: 0.7975 (t70) outliers start: 43 outliers final: 22 residues processed: 165 average time/residue: 0.5101 time to fit residues: 94.1589 Evaluate side-chains 163 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 402 CYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 402 CYS Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 402 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 402 CYS Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 402 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 149 optimal weight: 0.0770 chunk 141 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN A 177 GLN B 266 GLN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.094765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.075270 restraints weight = 23947.525| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.90 r_work: 0.2811 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14935 Z= 0.136 Angle : 0.570 9.924 20110 Z= 0.275 Chirality : 0.043 0.225 2220 Planarity : 0.003 0.029 2485 Dihedral : 7.110 57.899 2405 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.65 % Allowed : 11.94 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.20), residues: 1690 helix: 2.24 (0.21), residues: 615 sheet: 0.67 (0.26), residues: 400 loop : -0.88 (0.21), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 59 TYR 0.022 0.001 TYR E 301 PHE 0.012 0.001 PHE E 99 TRP 0.006 0.001 TRP E 68 HIS 0.001 0.000 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (14920) covalent geometry : angle 0.56886 / 0.27 (20070) SS BOND : bond 0.00236 / 0.12 ( 5) SS BOND : angle 1.18503 / 0.62 ( 10) hydrogen bonds : bond 0.03517 / 2.30 ( 675) hydrogen bonds : angle 3.94936 / 2.67 ( 2250) link_BETA1-4 : bond 0.00297 / 0.15 ( 5) link_BETA1-4 : angle 1.15863 / 0.70 ( 15) link_NAG-ASN : bond 0.00058 / 0.03 ( 5) link_NAG-ASN : angle 0.77576 / 0.47 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 0.578 Fit side-chains REVERT: A 12 ASP cc_start: 0.8308 (m-30) cc_final: 0.7942 (t70) REVERT: A 18 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.6710 (ptm) REVERT: A 110 GLU cc_start: 0.7654 (pm20) cc_final: 0.7369 (pm20) REVERT: A 245 ASN cc_start: 0.8493 (p0) cc_final: 0.8238 (p0) REVERT: B 8 MET cc_start: 0.7140 (ppp) cc_final: 0.6809 (ppp) REVERT: B 12 ASP cc_start: 0.8264 (m-30) cc_final: 0.7978 (t0) REVERT: B 59 ARG cc_start: 0.8552 (ttm110) cc_final: 0.7834 (ttt-90) REVERT: B 91 ASP cc_start: 0.8364 (p0) cc_final: 0.8043 (t0) REVERT: C 8 MET cc_start: 0.7311 (ppp) cc_final: 0.6962 (ppp) REVERT: C 12 ASP cc_start: 0.8239 (m-30) cc_final: 0.7957 (t0) REVERT: C 59 ARG cc_start: 0.8359 (ttm110) cc_final: 0.7615 (ttt-90) REVERT: C 163 MET cc_start: 0.8878 (mmt) cc_final: 0.8503 (mmm) REVERT: C 263 MET cc_start: 0.9230 (tpt) cc_final: 0.8884 (mmm) REVERT: D 8 MET cc_start: 0.7412 (ppp) cc_final: 0.7097 (ppp) REVERT: D 12 ASP cc_start: 0.8267 (m-30) cc_final: 0.8026 (t0) REVERT: E 12 ASP cc_start: 0.8266 (m-30) cc_final: 0.7994 (t70) outliers start: 41 outliers final: 23 residues processed: 164 average time/residue: 0.5391 time to fit residues: 98.6393 Evaluate side-chains 165 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 402 CYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 402 CYS Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 402 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 402 CYS Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 402 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 87 optimal weight: 0.4980 chunk 100 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 86 optimal weight: 0.0970 chunk 129 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 6 optimal weight: 0.0040 chunk 166 optimal weight: 0.7980 chunk 150 optimal weight: 5.9990 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 GLN B 266 GLN C 171 GLN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.095737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.076312 restraints weight = 23881.688| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.90 r_work: 0.2832 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14935 Z= 0.105 Angle : 0.563 10.203 20110 Z= 0.270 Chirality : 0.042 0.221 2220 Planarity : 0.003 0.032 2485 Dihedral : 6.935 57.147 2405 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.94 % Allowed : 13.35 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.20), residues: 1690 helix: 2.28 (0.21), residues: 615 sheet: 0.69 (0.26), residues: 395 loop : -0.83 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 59 TYR 0.023 0.001 TYR E 301 PHE 0.010 0.001 PHE E 99 TRP 0.005 0.001 TRP C 68 HIS 0.001 0.000 HIS E 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (14920) covalent geometry : angle 0.56164 / 0.27 (20070) SS BOND : bond 0.00191 / 0.10 ( 5) SS BOND : angle 1.04331 / 0.54 ( 10) hydrogen bonds : bond 0.03346 / 2.19 ( 675) hydrogen bonds : angle 3.87324 / 2.62 ( 2250) link_BETA1-4 : bond 0.00284 / 0.14 ( 5) link_BETA1-4 : angle 1.15243 / 0.70 ( 15) link_NAG-ASN : bond 0.00034 / 0.02 ( 5) link_NAG-ASN : angle 0.68171 / 0.41 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.576 Fit side-chains REVERT: A 12 ASP cc_start: 0.8308 (m-30) cc_final: 0.7948 (t70) REVERT: A 18 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.6694 (ptm) REVERT: A 110 GLU cc_start: 0.7590 (pm20) cc_final: 0.7326 (pm20) REVERT: A 245 ASN cc_start: 0.8471 (p0) cc_final: 0.8227 (p0) REVERT: B 8 MET cc_start: 0.7097 (ppp) cc_final: 0.6846 (ppp) REVERT: B 12 ASP cc_start: 0.8251 (m-30) cc_final: 0.7976 (t70) REVERT: B 59 ARG cc_start: 0.8534 (ttm110) cc_final: 0.7844 (ttt-90) REVERT: B 91 ASP cc_start: 0.8339 (p0) cc_final: 0.8078 (t0) REVERT: C 8 MET cc_start: 0.7276 (ppp) cc_final: 0.6953 (ppp) REVERT: C 12 ASP cc_start: 0.8278 (m-30) cc_final: 0.7991 (t0) REVERT: C 59 ARG cc_start: 0.8365 (ttm110) cc_final: 0.7623 (ttt-90) REVERT: C 163 MET cc_start: 0.8815 (mmt) cc_final: 0.8550 (mmm) REVERT: C 263 MET cc_start: 0.9269 (tpt) cc_final: 0.8911 (mmm) REVERT: D 8 MET cc_start: 0.7360 (ppp) cc_final: 0.7072 (ppp) REVERT: D 12 ASP cc_start: 0.8270 (m-30) cc_final: 0.8029 (t0) REVERT: E 8 MET cc_start: 0.7413 (ppp) cc_final: 0.7058 (ppp) REVERT: E 12 ASP cc_start: 0.8283 (m-30) cc_final: 0.7984 (t0) outliers start: 30 outliers final: 19 residues processed: 158 average time/residue: 0.5294 time to fit residues: 93.5060 Evaluate side-chains 161 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 402 CYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 402 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 398 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 GLN B 266 GLN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.094924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.075576 restraints weight = 24007.494| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.90 r_work: 0.2823 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14935 Z= 0.137 Angle : 0.575 10.371 20110 Z= 0.278 Chirality : 0.043 0.248 2220 Planarity : 0.003 0.029 2485 Dihedral : 6.901 56.220 2405 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.06 % Allowed : 13.55 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.20), residues: 1690 helix: 2.27 (0.21), residues: 615 sheet: 0.67 (0.26), residues: 400 loop : -0.89 (0.21), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 59 TYR 0.022 0.001 TYR E 301 PHE 0.012 0.001 PHE E 99 TRP 0.006 0.001 TRP D 68 HIS 0.001 0.000 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (14920) covalent geometry : angle 0.57358 / 0.28 (20070) SS BOND : bond 0.00234 / 0.12 ( 5) SS BOND : angle 1.12941 / 0.59 ( 10) hydrogen bonds : bond 0.03450 / 2.25 ( 675) hydrogen bonds : angle 3.89519 / 2.63 ( 2250) link_BETA1-4 : bond 0.00324 / 0.17 ( 5) link_BETA1-4 : angle 1.15269 / 0.70 ( 15) link_NAG-ASN : bond 0.00055 / 0.03 ( 5) link_NAG-ASN : angle 0.76746 / 0.47 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.617 Fit side-chains REVERT: A 12 ASP cc_start: 0.8335 (m-30) cc_final: 0.7950 (t0) REVERT: A 110 GLU cc_start: 0.7603 (pm20) cc_final: 0.7343 (pm20) REVERT: A 245 ASN cc_start: 0.8434 (p0) cc_final: 0.8159 (p0) REVERT: B 8 MET cc_start: 0.7102 (ppp) cc_final: 0.6871 (ppp) REVERT: B 12 ASP cc_start: 0.8256 (m-30) cc_final: 0.7987 (t70) REVERT: C 8 MET cc_start: 0.7309 (ppp) cc_final: 0.7034 (ppp) REVERT: C 12 ASP cc_start: 0.8240 (m-30) cc_final: 0.7970 (t0) REVERT: C 18 MET cc_start: 0.7008 (OUTLIER) cc_final: 0.6645 (ptt) REVERT: C 59 ARG cc_start: 0.8388 (ttm110) cc_final: 0.7621 (ttt-90) REVERT: C 163 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8559 (mmm) REVERT: C 263 MET cc_start: 0.9260 (tpt) cc_final: 0.8913 (mmm) REVERT: D 8 MET cc_start: 0.7322 (ppp) cc_final: 0.7057 (ppp) REVERT: D 12 ASP cc_start: 0.8273 (m-30) cc_final: 0.8037 (t0) REVERT: E 8 MET cc_start: 0.7361 (ppp) cc_final: 0.7138 (ppp) REVERT: E 12 ASP cc_start: 0.8293 (m-30) cc_final: 0.8000 (t0) REVERT: E 91 ASP cc_start: 0.8544 (p0) cc_final: 0.8106 (t0) outliers start: 32 outliers final: 20 residues processed: 156 average time/residue: 0.5338 time to fit residues: 93.1661 Evaluate side-chains 164 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 402 CYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 402 CYS Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 402 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 402 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 116 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 87 optimal weight: 0.0670 chunk 139 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 13 optimal weight: 0.0670 chunk 73 optimal weight: 1.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 GLN A 186 GLN B 266 GLN C 171 GLN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.096394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.076193 restraints weight = 24313.724| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 3.05 r_work: 0.2797 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14935 Z= 0.138 Angle : 0.584 10.577 20110 Z= 0.284 Chirality : 0.043 0.235 2220 Planarity : 0.003 0.045 2485 Dihedral : 6.855 55.080 2405 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.19 % Allowed : 13.55 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.20), residues: 1690 helix: 2.28 (0.21), residues: 615 sheet: 0.66 (0.26), residues: 400 loop : -0.90 (0.21), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 59 TYR 0.022 0.001 TYR E 301 PHE 0.013 0.001 PHE E 99 TRP 0.005 0.001 TRP C 68 HIS 0.001 0.000 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (14920) covalent geometry : angle 0.58321 / 0.28 (20070) SS BOND : bond 0.00235 / 0.12 ( 5) SS BOND : angle 1.12022 / 0.58 ( 10) hydrogen bonds : bond 0.03464 / 2.26 ( 675) hydrogen bonds : angle 3.89841 / 2.63 ( 2250) link_BETA1-4 : bond 0.00295 / 0.15 ( 5) link_BETA1-4 : angle 1.14431 / 0.69 ( 15) link_NAG-ASN : bond 0.00065 / 0.03 ( 5) link_NAG-ASN : angle 0.77817 / 0.47 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.604 Fit side-chains REVERT: A 12 ASP cc_start: 0.8341 (m-30) cc_final: 0.7952 (t0) REVERT: A 18 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.6826 (ptm) REVERT: A 245 ASN cc_start: 0.8341 (p0) cc_final: 0.8100 (p0) REVERT: B 12 ASP cc_start: 0.8219 (m-30) cc_final: 0.7930 (t0) REVERT: C 12 ASP cc_start: 0.8238 (m-30) cc_final: 0.7958 (t0) REVERT: C 59 ARG cc_start: 0.8340 (ttm110) cc_final: 0.7540 (ttt-90) REVERT: C 163 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8472 (mmm) REVERT: C 263 MET cc_start: 0.9156 (tpt) cc_final: 0.8822 (mmm) REVERT: D 8 MET cc_start: 0.7204 (ppp) cc_final: 0.6948 (ppp) REVERT: D 12 ASP cc_start: 0.8278 (m-30) cc_final: 0.8032 (t0) REVERT: E 8 MET cc_start: 0.7207 (ppp) cc_final: 0.6974 (ppp) REVERT: E 12 ASP cc_start: 0.8302 (m-30) cc_final: 0.8001 (t70) REVERT: E 91 ASP cc_start: 0.8531 (p0) cc_final: 0.8142 (t0) outliers start: 34 outliers final: 22 residues processed: 156 average time/residue: 0.5236 time to fit residues: 91.6203 Evaluate side-chains 164 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 402 CYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 402 CYS Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 402 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 402 CYS Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 402 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 60 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 139 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 GLN A 186 GLN B 115 ASN B 266 GLN D 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.094091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.074231 restraints weight = 24178.926| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.91 r_work: 0.2803 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14935 Z= 0.175 Angle : 0.611 10.838 20110 Z= 0.299 Chirality : 0.044 0.280 2220 Planarity : 0.003 0.046 2485 Dihedral : 6.933 53.839 2405 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.87 % Allowed : 14.32 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.20), residues: 1690 helix: 2.27 (0.21), residues: 615 sheet: 0.64 (0.25), residues: 400 loop : -0.90 (0.21), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 59 TYR 0.023 0.002 TYR C 301 PHE 0.014 0.001 PHE E 99 TRP 0.006 0.001 TRP C 68 HIS 0.002 0.001 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (14920) covalent geometry : angle 0.60945 / 0.30 (20070) SS BOND : bond 0.00275 / 0.14 ( 5) SS BOND : angle 1.20829 / 0.63 ( 10) hydrogen bonds : bond 0.03659 / 2.39 ( 675) hydrogen bonds : angle 3.98718 / 2.69 ( 2250) link_BETA1-4 : bond 0.00278 / 0.14 ( 5) link_BETA1-4 : angle 1.14746 / 0.70 ( 15) link_NAG-ASN : bond 0.00163 / 0.08 ( 5) link_NAG-ASN : angle 0.87826 / 0.53 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3380 Ramachandran restraints generated. 1690 Oldfield, 0 Emsley, 1690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.574 Fit side-chains REVERT: A 12 ASP cc_start: 0.8351 (m-30) cc_final: 0.7998 (t70) REVERT: A 245 ASN cc_start: 0.8451 (p0) cc_final: 0.8213 (p0) REVERT: B 12 ASP cc_start: 0.8298 (m-30) cc_final: 0.8015 (t0) REVERT: B 154 MET cc_start: 0.9056 (ttm) cc_final: 0.8841 (ttm) REVERT: C 8 MET cc_start: 0.7215 (ppp) cc_final: 0.6792 (ppp) REVERT: C 12 ASP cc_start: 0.8279 (m-30) cc_final: 0.8017 (t0) REVERT: C 59 ARG cc_start: 0.8429 (ttm110) cc_final: 0.7707 (ttt-90) REVERT: C 263 MET cc_start: 0.9269 (tpt) cc_final: 0.8924 (mmm) REVERT: D 8 MET cc_start: 0.7270 (ppp) cc_final: 0.7028 (ppp) REVERT: D 12 ASP cc_start: 0.8289 (m-30) cc_final: 0.8070 (t0) REVERT: E 8 MET cc_start: 0.7282 (ppp) cc_final: 0.7072 (ppp) REVERT: E 12 ASP cc_start: 0.8325 (m-30) cc_final: 0.8050 (t70) REVERT: E 91 ASP cc_start: 0.8510 (p0) cc_final: 0.8137 (t0) outliers start: 29 outliers final: 20 residues processed: 150 average time/residue: 0.5206 time to fit residues: 87.5568 Evaluate side-chains 158 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 402 CYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 402 CYS Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 402 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 402 CYS Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 402 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 24 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 GLN A 186 GLN B 115 ASN B 266 GLN C 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.093158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.073855 restraints weight = 24053.873| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.87 r_work: 0.2791 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 14935 Z= 0.171 Angle : 0.611 10.830 20110 Z= 0.298 Chirality : 0.044 0.241 2220 Planarity : 0.003 0.044 2485 Dihedral : 6.950 52.542 2405 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.87 % Allowed : 14.45 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.20), residues: 1690 helix: 2.43 (0.21), residues: 600 sheet: 0.63 (0.26), residues: 400 loop : -0.82 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 59 TYR 0.023 0.002 TYR C 301 PHE 0.014 0.001 PHE E 99 TRP 0.005 0.001 TRP C 68 HIS 0.002 0.001 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (14920) covalent geometry : angle 0.61027 / 0.30 (20070) SS BOND : bond 0.00252 / 0.13 ( 5) SS BOND : angle 1.16625 / 0.61 ( 10) hydrogen bonds : bond 0.03687 / 2.41 ( 675) hydrogen bonds : angle 4.00491 / 2.71 ( 2250) link_BETA1-4 : bond 0.00262 / 0.13 ( 5) link_BETA1-4 : angle 1.12633 / 0.68 ( 15) link_NAG-ASN : bond 0.00161 / 0.08 ( 5) link_NAG-ASN : angle 0.85457 / 0.52 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3418.07 seconds wall clock time: 59 minutes 31.20 seconds (3571.20 seconds total)