Starting phenix.real_space_refine on Sat Jul 4 04:07:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ryr_24746/07_2026/7ryr_24746.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ryr_24746/07_2026/7ryr_24746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ryr_24746/07_2026/7ryr_24746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ryr_24746/07_2026/7ryr_24746.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ryr_24746/07_2026/7ryr_24746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ryr_24746/07_2026/7ryr_24746.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ryr_24746/07_2026/7ryr_24746.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ryr_24746/07_2026/7ryr_24746.cif" } resolution = 3.6 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= 0.004 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 6124 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 28 5.16 5 C 8636 2.51 5 N 2080 2.21 5 O 2272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 13024 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3094 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 23, 'TRANS': 365} Chain breaks: 2 Chain: "C" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3094 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 23, 'TRANS': 365} Chain breaks: 2 Chain: "D" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3094 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 23, 'TRANS': 365} Chain breaks: 2 Chain: "B" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3094 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 23, 'TRANS': 365} Chain breaks: 2 Chain: "A" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 171 Unusual residues: {'PGW': 8} Classifications: {'RNA': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 259 Unresolved non-hydrogen angles: 302 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PGW:plan-1': 5, 'PGW:plan-2': 5, 'PGW:plan-3': 6} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 171 Unusual residues: {'PGW': 8} Classifications: {'RNA': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 259 Unresolved non-hydrogen angles: 302 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PGW:plan-1': 5, 'PGW:plan-2': 5, 'PGW:plan-3': 6} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 153 Unusual residues: {'PGW': 6} Classifications: {'RNA': 1, 'undetermined': 6} Modifications used: {'rna3p': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PGW:plan-1': 3, 'PGW:plan-2': 3, 'PGW:plan-3': 4} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 153 Unusual residues: {'PGW': 6} Classifications: {'RNA': 1, 'undetermined': 6} Modifications used: {'rna3p': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PGW:plan-1': 3, 'PGW:plan-2': 3, 'PGW:plan-3': 4} Unresolved non-hydrogen planarities: 36 Time building chain proxies: 2.28, per 1000 atoms: 0.18 Number of scatterers: 13024 At special positions: 0 Unit cell: (108.009, 108.009, 113.464, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 8 15.00 O 2272 8.00 N 2080 7.00 C 8636 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 486.5 milliseconds 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2952 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 8 sheets defined 64.5% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 11 through 36 removed outlier: 3.895A pdb=" N VAL A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 43 through 55 removed outlier: 3.690A pdb=" N ALA A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 89 removed outlier: 4.028A pdb=" N LEU A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 107 through 113 removed outlier: 4.022A pdb=" N VAL A 110 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 119 Processing helix chain 'A' and resid 131 through 159 removed outlier: 3.637A pdb=" N LEU A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN A 159 " --> pdb=" O TRP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 182 Processing helix chain 'A' and resid 193 through 208 removed outlier: 3.687A pdb=" N ALA A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 224 Processing helix chain 'A' and resid 226 through 246 removed outlier: 3.569A pdb=" N GLU A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A 242 " --> pdb=" O ARG A 238 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS A 246 " --> pdb=" O PHE A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 268 removed outlier: 3.951A pdb=" N ARG A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE A 257 " --> pdb=" O GLN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 removed outlier: 4.192A pdb=" N GLU A 278 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 292 Processing helix chain 'A' and resid 307 through 314 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.569A pdb=" N ILE A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 404 Processing helix chain 'A' and resid 404 through 418 Processing helix chain 'C' and resid 11 through 36 removed outlier: 3.895A pdb=" N VAL C 17 " --> pdb=" O LEU C 13 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 20 " --> pdb=" O LYS C 16 " (cutoff:3.500A) Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 43 through 55 removed outlier: 3.690A pdb=" N ALA C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 89 removed outlier: 4.028A pdb=" N LEU C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 107 through 113 removed outlier: 4.022A pdb=" N VAL C 110 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 119 Processing helix chain 'C' and resid 131 through 159 removed outlier: 3.637A pdb=" N LEU C 140 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN C 159 " --> pdb=" O TRP C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 182 Processing helix chain 'C' and resid 193 through 208 removed outlier: 3.687A pdb=" N ALA C 208 " --> pdb=" O GLU C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 224 Processing helix chain 'C' and resid 226 through 246 removed outlier: 3.569A pdb=" N GLU C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE C 242 " --> pdb=" O ARG C 238 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS C 246 " --> pdb=" O PHE C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 268 removed outlier: 3.951A pdb=" N ARG C 255 " --> pdb=" O GLU C 251 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE C 257 " --> pdb=" O GLN C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 278 removed outlier: 4.191A pdb=" N GLU C 278 " --> pdb=" O VAL C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 292 Processing helix chain 'C' and resid 307 through 314 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.570A pdb=" N ILE C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 404 Processing helix chain 'C' and resid 404 through 418 Processing helix chain 'D' and resid 11 through 36 removed outlier: 3.895A pdb=" N VAL D 17 " --> pdb=" O LEU D 13 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU D 20 " --> pdb=" O LYS D 16 " (cutoff:3.500A) Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 43 through 55 removed outlier: 3.690A pdb=" N ALA D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 89 removed outlier: 4.028A pdb=" N LEU D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 99 Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 107 through 113 removed outlier: 4.022A pdb=" N VAL D 110 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 131 through 159 removed outlier: 3.638A pdb=" N LEU D 140 " --> pdb=" O ARG D 136 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU D 158 " --> pdb=" O GLY D 154 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN D 159 " --> pdb=" O TRP D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 182 Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.687A pdb=" N ALA D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 224 Processing helix chain 'D' and resid 226 through 246 removed outlier: 3.569A pdb=" N GLU D 234 " --> pdb=" O LEU D 230 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR D 245 " --> pdb=" O ALA D 241 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS D 246 " --> pdb=" O PHE D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 268 removed outlier: 3.951A pdb=" N ARG D 255 " --> pdb=" O GLU D 251 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE D 257 " --> pdb=" O GLN D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 278 removed outlier: 4.192A pdb=" N GLU D 278 " --> pdb=" O VAL D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 292 Processing helix chain 'D' and resid 307 through 314 Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.570A pdb=" N ILE D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 404 through 418 Processing helix chain 'B' and resid 11 through 36 removed outlier: 3.896A pdb=" N VAL B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 20 " --> pdb=" O LYS B 16 " (cutoff:3.500A) Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 43 through 55 removed outlier: 3.689A pdb=" N ALA B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 89 removed outlier: 4.028A pdb=" N LEU B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 107 through 113 removed outlier: 4.022A pdb=" N VAL B 110 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG B 111 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 119 Processing helix chain 'B' and resid 131 through 159 removed outlier: 3.637A pdb=" N LEU B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 158 " --> pdb=" O GLY B 154 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN B 159 " --> pdb=" O TRP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 182 Processing helix chain 'B' and resid 193 through 208 removed outlier: 3.688A pdb=" N ALA B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 224 Processing helix chain 'B' and resid 226 through 246 removed outlier: 3.569A pdb=" N GLU B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE B 242 " --> pdb=" O ARG B 238 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 268 removed outlier: 3.951A pdb=" N ARG B 255 " --> pdb=" O GLU B 251 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE B 257 " --> pdb=" O GLN B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 278 removed outlier: 4.192A pdb=" N GLU B 278 " --> pdb=" O VAL B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 292 Processing helix chain 'B' and resid 307 through 314 Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.569A pdb=" N ILE B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 404 Processing helix chain 'B' and resid 404 through 418 Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 322 removed outlier: 6.860A pdb=" N ASP A 388 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 330 removed outlier: 6.491A pdb=" N VAL A 381 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 318 through 322 removed outlier: 6.860A pdb=" N ASP C 388 " --> pdb=" O ASN C 342 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 327 through 330 removed outlier: 6.491A pdb=" N VAL C 381 " --> pdb=" O ILE C 328 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 318 through 322 removed outlier: 6.860A pdb=" N ASP D 388 " --> pdb=" O ASN D 342 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 327 through 330 removed outlier: 6.492A pdb=" N VAL D 381 " --> pdb=" O ILE D 328 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 318 through 322 removed outlier: 6.860A pdb=" N ASP B 388 " --> pdb=" O ASN B 342 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 327 through 330 removed outlier: 6.492A pdb=" N VAL B 381 " --> pdb=" O ILE B 328 " (cutoff:3.500A) 672 hydrogen bonds defined for protein. 1944 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: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2014 1.32 - 1.44: 3298 1.44 - 1.56: 7900 1.56 - 1.68: 20 1.68 - 1.81: 48 Bond restraints: 13280 Sorted by residual: bond pdb=" C10 PGW B 503 " pdb=" C9 PGW B 503 " ideal model delta sigma weight residual 1.333 1.509 -0.176 2.00e-02 2.50e+03 7.74e+01 bond pdb=" C10 PGW C 503 " pdb=" C9 PGW C 503 " ideal model delta sigma weight residual 1.333 1.509 -0.176 2.00e-02 2.50e+03 7.73e+01 bond pdb=" C10 PGW A 503 " pdb=" C9 PGW A 503 " ideal model delta sigma weight residual 1.333 1.509 -0.176 2.00e-02 2.50e+03 7.71e+01 bond pdb=" C10 PGW D 503 " pdb=" C9 PGW D 503 " ideal model delta sigma weight residual 1.333 1.509 -0.176 2.00e-02 2.50e+03 7.71e+01 bond pdb=" CA SER C 157 " pdb=" CB SER C 157 " ideal model delta sigma weight residual 1.529 1.470 0.059 1.64e-02 3.72e+03 1.29e+01 ... (remaining 13275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 17187 2.61 - 5.21: 628 5.21 - 7.82: 98 7.82 - 10.42: 15 10.42 - 13.03: 8 Bond angle restraints: 17936 Sorted by residual: angle pdb=" N LEU D 91 " pdb=" CA LEU D 91 " pdb=" C LEU D 91 " ideal model delta sigma weight residual 111.82 104.65 7.17 1.16e+00 7.43e-01 3.83e+01 angle pdb=" N LEU B 91 " pdb=" CA LEU B 91 " pdb=" C LEU B 91 " ideal model delta sigma weight residual 111.82 104.65 7.17 1.16e+00 7.43e-01 3.82e+01 angle pdb=" N LEU A 91 " pdb=" CA LEU A 91 " pdb=" C LEU A 91 " ideal model delta sigma weight residual 111.82 104.67 7.15 1.16e+00 7.43e-01 3.80e+01 angle pdb=" N LEU C 91 " pdb=" CA LEU C 91 " pdb=" C LEU C 91 " ideal model delta sigma weight residual 111.82 104.70 7.12 1.16e+00 7.43e-01 3.77e+01 angle pdb=" CA ASP C 92 " pdb=" C ASP C 92 " pdb=" O ASP C 92 " ideal model delta sigma weight residual 121.56 115.40 6.16 1.09e+00 8.42e-01 3.19e+01 ... (remaining 17931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.02: 7840 35.02 - 70.04: 172 70.04 - 105.06: 20 105.06 - 140.08: 8 140.08 - 175.10: 4 Dihedral angle restraints: 8044 sinusoidal: 3476 harmonic: 4568 Sorted by residual: dihedral pdb=" C01 PGW C 502 " pdb=" C19 PGW C 502 " pdb=" O03 PGW C 502 " pdb=" O04 PGW C 502 " ideal model delta sinusoidal sigma weight residual 9.00 -166.10 175.10 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C01 PGW A 502 " pdb=" C19 PGW A 502 " pdb=" O03 PGW A 502 " pdb=" O04 PGW A 502 " ideal model delta sinusoidal sigma weight residual 9.00 -166.08 175.08 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C01 PGW D 502 " pdb=" C19 PGW D 502 " pdb=" O03 PGW D 502 " pdb=" O04 PGW D 502 " ideal model delta sinusoidal sigma weight residual 9.00 -166.06 175.06 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 8041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1857 0.087 - 0.175: 195 0.175 - 0.262: 32 0.262 - 0.350: 4 0.350 - 0.437: 4 Chirality restraints: 2092 Sorted by residual: chirality pdb=" CA LYS D 246 " pdb=" N LYS D 246 " pdb=" C LYS D 246 " pdb=" CB LYS D 246 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" CA LYS A 246 " pdb=" N LYS A 246 " pdb=" C LYS A 246 " pdb=" CB LYS A 246 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.77e+00 chirality pdb=" CA LYS B 246 " pdb=" N LYS B 246 " pdb=" C LYS B 246 " pdb=" CB LYS B 246 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.76e+00 ... (remaining 2089 not shown) Planarity restraints: 2168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW B 503 " 0.091 2.00e-02 2.50e+03 9.04e-02 8.17e+01 pdb=" C10 PGW B 503 " -0.091 2.00e-02 2.50e+03 pdb=" C8 PGW B 503 " 0.090 2.00e-02 2.50e+03 pdb=" C9 PGW B 503 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW D 503 " -0.090 2.00e-02 2.50e+03 9.03e-02 8.16e+01 pdb=" C10 PGW D 503 " 0.091 2.00e-02 2.50e+03 pdb=" C8 PGW D 503 " -0.090 2.00e-02 2.50e+03 pdb=" C9 PGW D 503 " 0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW A 503 " -0.090 2.00e-02 2.50e+03 9.03e-02 8.16e+01 pdb=" C10 PGW A 503 " 0.091 2.00e-02 2.50e+03 pdb=" C8 PGW A 503 " -0.090 2.00e-02 2.50e+03 pdb=" C9 PGW A 503 " 0.090 2.00e-02 2.50e+03 ... (remaining 2165 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 847 2.74 - 3.28: 12793 3.28 - 3.82: 19621 3.82 - 4.36: 23486 4.36 - 4.90: 40988 Nonbonded interactions: 97735 Sorted by model distance: nonbonded pdb=" OE1 GLU D 308 " pdb=" OH TYR D 404 " model vdw 2.197 3.040 nonbonded pdb=" OE1 GLU A 308 " pdb=" OH TYR A 404 " model vdw 2.197 3.040 nonbonded pdb=" OE1 GLU C 308 " pdb=" OH TYR C 404 " model vdw 2.198 3.040 nonbonded pdb=" OE1 GLU B 308 " pdb=" OH TYR B 404 " model vdw 2.198 3.040 nonbonded pdb=" O GLN D 119 " pdb=" OG1 THR D 123 " model vdw 2.245 3.040 ... (remaining 97730 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.040 Find NCS groups from input model: 0.070 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 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 : 0.007 0.176 13280 Z= 0.438 Angle : 1.128 13.029 17936 Z= 0.651 Chirality : 0.059 0.437 2092 Planarity : 0.008 0.090 2168 Dihedral : 16.171 175.101 5092 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.60 % Allowed : 1.50 % Favored : 97.90 % Cbeta Deviations : 0.27 % 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: -1.65 (0.22), residues: 1532 helix: -0.52 (0.17), residues: 988 sheet: -1.63 (0.47), residues: 132 loop : -1.98 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 273 TYR 0.023 0.001 TYR A 26 PHE 0.019 0.002 PHE C 365 TRP 0.007 0.001 TRP B 264 HIS 0.002 0.001 HIS B 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00732 / 0.44 (13280) covalent geometry : angle 1.12829 / 0.65 (17936) hydrogen bonds : bond 0.20473 / 13.70 ( 672) hydrogen bonds : angle 7.21285 / 5.19 ( 1944) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 235 time to evaluate : 0.419 Fit side-chains REVERT: A 334 MET cc_start: 0.5592 (tmm) cc_final: 0.5244 (tmm) REVERT: C 110 VAL cc_start: 0.8653 (m) cc_final: 0.8427 (p) REVERT: C 289 MET cc_start: 0.8364 (mmm) cc_final: 0.8142 (mmm) REVERT: D 110 VAL cc_start: 0.8688 (m) cc_final: 0.8441 (p) REVERT: D 289 MET cc_start: 0.8328 (mmm) cc_final: 0.8117 (mmm) outliers start: 8 outliers final: 4 residues processed: 243 average time/residue: 0.0811 time to fit residues: 31.2209 Evaluate side-chains 191 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 187 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain B residue 92 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 GLN C 196 GLN B 410 GLN B 412 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.159925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.123615 restraints weight = 17433.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113584 restraints weight = 23994.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.113228 restraints weight = 22134.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.112500 restraints weight = 21585.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.112872 restraints weight = 18814.321| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13280 Z= 0.154 Angle : 0.694 12.325 17936 Z= 0.336 Chirality : 0.042 0.150 2092 Planarity : 0.006 0.061 2168 Dihedral : 12.509 138.981 2152 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.15 % Allowed : 7.81 % Favored : 89.04 % 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: -1.01 (0.22), residues: 1532 helix: 0.01 (0.17), residues: 984 sheet: -1.66 (0.46), residues: 124 loop : -1.71 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 273 TYR 0.016 0.001 TYR A 25 PHE 0.029 0.001 PHE B 40 TRP 0.006 0.001 TRP D 155 HIS 0.002 0.001 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (13280) covalent geometry : angle 0.69397 / 0.34 (17936) hydrogen bonds : bond 0.04229 / 2.79 ( 672) hydrogen bonds : angle 4.40023 / 3.15 ( 1944) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 205 time to evaluate : 0.388 Fit side-chains REVERT: A 221 LEU cc_start: 0.7975 (mp) cc_final: 0.7718 (mp) REVERT: A 290 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6551 (mp0) outliers start: 42 outliers final: 25 residues processed: 229 average time/residue: 0.0745 time to fit residues: 27.4672 Evaluate side-chains 197 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 393 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 127 optimal weight: 0.0000 chunk 121 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 chunk 149 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.159368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.123620 restraints weight = 17650.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.112347 restraints weight = 22164.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.111217 restraints weight = 23557.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.111319 restraints weight = 21078.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.111512 restraints weight = 20094.070| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13280 Z= 0.129 Angle : 0.657 11.843 17936 Z= 0.313 Chirality : 0.041 0.148 2092 Planarity : 0.005 0.065 2168 Dihedral : 11.447 134.059 2146 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.38 % Allowed : 12.09 % Favored : 84.53 % 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: -0.48 (0.22), residues: 1532 helix: 0.42 (0.18), residues: 984 sheet: -1.79 (0.45), residues: 124 loop : -1.39 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 417 TYR 0.011 0.001 TYR D 25 PHE 0.027 0.001 PHE B 40 TRP 0.004 0.001 TRP B 155 HIS 0.003 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (13280) covalent geometry : angle 0.65685 / 0.31 (17936) hydrogen bonds : bond 0.03561 / 2.33 ( 672) hydrogen bonds : angle 3.92145 / 2.78 ( 1944) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 194 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 290 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6663 (mp0) REVERT: A 389 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8350 (pp) REVERT: C 290 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: C 389 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8475 (pp) REVERT: D 290 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: D 389 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8438 (pp) REVERT: B 290 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6767 (mp0) REVERT: B 389 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8319 (pp) outliers start: 45 outliers final: 26 residues processed: 226 average time/residue: 0.0764 time to fit residues: 27.7347 Evaluate side-chains 214 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 393 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 126 optimal weight: 0.5980 chunk 125 optimal weight: 0.5980 chunk 30 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 44 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 21 optimal weight: 0.5980 chunk 134 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 159 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.158903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.121250 restraints weight = 17427.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.112141 restraints weight = 22327.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.112018 restraints weight = 20306.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.112003 restraints weight = 19963.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.112079 restraints weight = 17245.097| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13280 Z= 0.127 Angle : 0.645 11.525 17936 Z= 0.303 Chirality : 0.041 0.141 2092 Planarity : 0.005 0.059 2168 Dihedral : 11.031 134.307 2146 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.90 % Allowed : 14.56 % Favored : 81.53 % 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: -0.41 (0.23), residues: 1532 helix: 0.48 (0.18), residues: 1020 sheet: -1.78 (0.44), residues: 124 loop : -1.55 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 417 TYR 0.009 0.001 TYR A 175 PHE 0.021 0.001 PHE D 40 TRP 0.004 0.001 TRP D 264 HIS 0.002 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (13280) covalent geometry : angle 0.64501 / 0.30 (17936) hydrogen bonds : bond 0.03348 / 2.19 ( 672) hydrogen bonds : angle 3.76850 / 2.68 ( 1944) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 191 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 290 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6778 (mp0) REVERT: A 389 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8387 (pp) REVERT: C 290 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: C 389 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8495 (pp) REVERT: D 206 LEU cc_start: 0.8344 (pp) cc_final: 0.8103 (mt) REVERT: D 289 MET cc_start: 0.8428 (mmm) cc_final: 0.8223 (mmm) REVERT: D 290 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6966 (mp0) REVERT: D 389 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8431 (pp) REVERT: B 119 GLN cc_start: 0.6736 (OUTLIER) cc_final: 0.5710 (pm20) REVERT: B 290 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6863 (mp0) REVERT: B 389 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8343 (pp) outliers start: 52 outliers final: 27 residues processed: 228 average time/residue: 0.0774 time to fit residues: 28.0785 Evaluate side-chains 208 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 393 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 110 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 130 optimal weight: 0.4980 chunk 14 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 7 optimal weight: 0.0370 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 410 GLN B 412 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.160102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.122712 restraints weight = 17465.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113687 restraints weight = 21385.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.112783 restraints weight = 20139.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.112937 restraints weight = 17921.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.113065 restraints weight = 16685.470| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13280 Z= 0.115 Angle : 0.639 11.149 17936 Z= 0.297 Chirality : 0.040 0.146 2092 Planarity : 0.005 0.058 2168 Dihedral : 10.711 133.938 2144 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.43 % Allowed : 16.07 % Favored : 79.50 % 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: -0.15 (0.23), residues: 1532 helix: 0.68 (0.18), residues: 1024 sheet: -1.66 (0.45), residues: 124 loop : -1.46 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 417 TYR 0.007 0.001 TYR D 25 PHE 0.020 0.001 PHE A 40 TRP 0.004 0.001 TRP A 176 HIS 0.001 0.000 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (13280) covalent geometry : angle 0.63891 / 0.30 (17936) hydrogen bonds : bond 0.02964 / 1.94 ( 672) hydrogen bonds : angle 3.65277 / 2.60 ( 1944) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 176 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 119 GLN cc_start: 0.6718 (OUTLIER) cc_final: 0.5888 (pm20) REVERT: A 164 ASN cc_start: 0.8935 (OUTLIER) cc_final: 0.8716 (t0) REVERT: A 290 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6699 (mp0) REVERT: A 389 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8375 (pp) REVERT: C 119 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.5714 (pm20) REVERT: C 206 LEU cc_start: 0.8329 (pp) cc_final: 0.8117 (mt) REVERT: C 290 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: C 389 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8485 (pp) REVERT: D 119 GLN cc_start: 0.7114 (OUTLIER) cc_final: 0.5815 (pm20) REVERT: D 290 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7034 (mp0) REVERT: D 389 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8462 (pp) REVERT: D 391 ARG cc_start: 0.8662 (ttp80) cc_final: 0.8456 (ttp80) REVERT: B 290 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: B 389 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8347 (pp) outliers start: 59 outliers final: 33 residues processed: 219 average time/residue: 0.0702 time to fit residues: 24.5698 Evaluate side-chains 214 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 169 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 393 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 90 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 98 optimal weight: 0.3980 chunk 84 optimal weight: 0.0270 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 26 optimal weight: 0.4980 chunk 77 optimal weight: 0.8980 chunk 148 optimal weight: 0.4980 chunk 121 optimal weight: 0.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.160574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.123123 restraints weight = 17342.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.112956 restraints weight = 21532.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.112006 restraints weight = 20695.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.112587 restraints weight = 17626.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.112867 restraints weight = 15789.965| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13280 Z= 0.113 Angle : 0.632 11.069 17936 Z= 0.292 Chirality : 0.040 0.133 2092 Planarity : 0.005 0.058 2168 Dihedral : 10.551 133.951 2144 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.80 % Allowed : 15.84 % Favored : 79.35 % 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: 0.11 (0.23), residues: 1532 helix: 0.87 (0.18), residues: 1028 sheet: -1.57 (0.44), residues: 128 loop : -1.35 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 417 TYR 0.008 0.001 TYR A 390 PHE 0.024 0.001 PHE B 40 TRP 0.004 0.001 TRP D 264 HIS 0.002 0.000 HIS D 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (13280) covalent geometry : angle 0.63214 / 0.29 (17936) hydrogen bonds : bond 0.02868 / 1.88 ( 672) hydrogen bonds : angle 3.57327 / 2.54 ( 1944) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 176 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 119 GLN cc_start: 0.6798 (OUTLIER) cc_final: 0.6043 (pm20) REVERT: A 290 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6833 (mp0) REVERT: A 389 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8336 (pp) REVERT: C 119 GLN cc_start: 0.7131 (OUTLIER) cc_final: 0.5640 (pm20) REVERT: C 290 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: C 389 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8444 (pp) REVERT: D 119 GLN cc_start: 0.7097 (OUTLIER) cc_final: 0.5675 (pm20) REVERT: D 290 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: D 389 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8381 (pp) REVERT: B 119 GLN cc_start: 0.6798 (OUTLIER) cc_final: 0.5971 (pm20) REVERT: B 290 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: B 389 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8384 (pp) outliers start: 64 outliers final: 35 residues processed: 224 average time/residue: 0.0721 time to fit residues: 25.6186 Evaluate side-chains 211 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 164 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 389 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 89 optimal weight: 0.0070 chunk 143 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 0.0770 chunk 95 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 412 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.160328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.123407 restraints weight = 17320.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.113459 restraints weight = 21580.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.113027 restraints weight = 19814.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.113153 restraints weight = 17259.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.113113 restraints weight = 16529.112| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13280 Z= 0.114 Angle : 0.643 11.081 17936 Z= 0.293 Chirality : 0.040 0.132 2092 Planarity : 0.005 0.060 2168 Dihedral : 10.529 133.972 2144 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.20 % Allowed : 17.34 % Favored : 78.45 % 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: 0.31 (0.24), residues: 1532 helix: 1.09 (0.18), residues: 1008 sheet: -1.53 (0.45), residues: 128 loop : -1.38 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 417 TYR 0.010 0.001 TYR A 404 PHE 0.018 0.001 PHE A 40 TRP 0.003 0.001 TRP D 264 HIS 0.001 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (13280) covalent geometry : angle 0.64342 / 0.29 (17936) hydrogen bonds : bond 0.02863 / 1.87 ( 672) hydrogen bonds : angle 3.57017 / 2.55 ( 1944) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 167 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 119 GLN cc_start: 0.6707 (OUTLIER) cc_final: 0.5850 (pm20) REVERT: A 290 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6775 (mp0) REVERT: A 389 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8367 (pp) REVERT: C 119 GLN cc_start: 0.7112 (OUTLIER) cc_final: 0.5613 (pm20) REVERT: C 290 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: C 389 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8527 (pp) REVERT: D 119 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.5842 (pm20) REVERT: D 290 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6926 (mp0) REVERT: D 389 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8500 (pp) REVERT: B 119 GLN cc_start: 0.6822 (OUTLIER) cc_final: 0.5999 (pm20) REVERT: B 289 MET cc_start: 0.8516 (tpp) cc_final: 0.8302 (mmm) REVERT: B 290 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.7128 (mp0) REVERT: B 389 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8407 (pp) outliers start: 56 outliers final: 37 residues processed: 207 average time/residue: 0.0775 time to fit residues: 26.4647 Evaluate side-chains 210 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 161 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 389 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 65 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 97 optimal weight: 0.0980 chunk 103 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 140 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.159600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.122548 restraints weight = 17222.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.113315 restraints weight = 22480.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.112852 restraints weight = 20480.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.113017 restraints weight = 18321.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.113146 restraints weight = 16571.487| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13280 Z= 0.117 Angle : 0.647 11.443 17936 Z= 0.294 Chirality : 0.040 0.143 2092 Planarity : 0.005 0.062 2168 Dihedral : 10.577 133.981 2144 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.58 % Allowed : 17.42 % Favored : 78.00 % 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: 0.45 (0.24), residues: 1532 helix: 1.24 (0.18), residues: 984 sheet: -1.28 (0.46), residues: 124 loop : -1.35 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 417 TYR 0.008 0.001 TYR A 175 PHE 0.018 0.001 PHE A 40 TRP 0.004 0.001 TRP B 15 HIS 0.002 0.001 HIS B 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (13280) covalent geometry : angle 0.64688 / 0.29 (17936) hydrogen bonds : bond 0.02937 / 1.92 ( 672) hydrogen bonds : angle 3.56326 / 2.54 ( 1944) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 169 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 119 GLN cc_start: 0.6813 (OUTLIER) cc_final: 0.5875 (pm20) REVERT: A 290 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6750 (mp0) REVERT: A 389 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8391 (pp) REVERT: C 119 GLN cc_start: 0.7110 (OUTLIER) cc_final: 0.5721 (pm20) REVERT: C 164 ASN cc_start: 0.8913 (OUTLIER) cc_final: 0.8661 (t0) REVERT: C 290 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: C 389 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8485 (pp) REVERT: D 119 GLN cc_start: 0.7127 (OUTLIER) cc_final: 0.5791 (pm20) REVERT: D 164 ASN cc_start: 0.8925 (OUTLIER) cc_final: 0.8687 (t0) REVERT: D 290 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6915 (mp0) REVERT: D 389 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8423 (pp) REVERT: D 417 ARG cc_start: 0.8367 (ttp80) cc_final: 0.7995 (ttp80) REVERT: B 119 GLN cc_start: 0.6871 (OUTLIER) cc_final: 0.5998 (pm20) REVERT: B 290 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: B 389 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8438 (pp) outliers start: 61 outliers final: 42 residues processed: 210 average time/residue: 0.0736 time to fit residues: 25.1284 Evaluate side-chains 216 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 160 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 389 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 42 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 119 optimal weight: 0.0050 chunk 29 optimal weight: 0.6980 chunk 110 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 4 optimal weight: 0.0870 chunk 90 optimal weight: 0.8980 overall best weight: 0.4772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.160096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.124666 restraints weight = 17485.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 75)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.113709 restraints weight = 22619.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.113038 restraints weight = 22687.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.113194 restraints weight = 20482.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.113412 restraints weight = 18677.938| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13280 Z= 0.113 Angle : 0.659 11.394 17936 Z= 0.297 Chirality : 0.040 0.130 2092 Planarity : 0.005 0.063 2168 Dihedral : 10.542 133.848 2144 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.43 % Allowed : 17.57 % Favored : 78.00 % 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: 0.54 (0.24), residues: 1532 helix: 1.32 (0.18), residues: 984 sheet: -1.26 (0.46), residues: 124 loop : -1.36 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 417 TYR 0.009 0.001 TYR A 404 PHE 0.021 0.001 PHE B 365 TRP 0.004 0.001 TRP A 15 HIS 0.002 0.000 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (13280) covalent geometry : angle 0.65858 / 0.30 (17936) hydrogen bonds : bond 0.02793 / 1.83 ( 672) hydrogen bonds : angle 3.55762 / 2.54 ( 1944) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 164 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 119 GLN cc_start: 0.6790 (OUTLIER) cc_final: 0.5775 (pm20) REVERT: A 290 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6793 (mp0) REVERT: A 389 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8385 (pp) REVERT: C 119 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.5717 (pm20) REVERT: C 164 ASN cc_start: 0.8926 (OUTLIER) cc_final: 0.8677 (t0) REVERT: C 290 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: C 389 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8473 (pp) REVERT: D 119 GLN cc_start: 0.7009 (OUTLIER) cc_final: 0.5708 (pm20) REVERT: D 164 ASN cc_start: 0.8923 (OUTLIER) cc_final: 0.8694 (t0) REVERT: D 290 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6908 (mp0) REVERT: D 389 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8438 (pp) REVERT: D 417 ARG cc_start: 0.8455 (ttp80) cc_final: 0.8094 (ttp80) REVERT: B 119 GLN cc_start: 0.6811 (OUTLIER) cc_final: 0.5963 (pm20) REVERT: B 290 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: B 389 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8450 (pp) outliers start: 59 outliers final: 42 residues processed: 203 average time/residue: 0.0768 time to fit residues: 25.4040 Evaluate side-chains 216 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 160 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 389 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 106 optimal weight: 5.9990 chunk 91 optimal weight: 0.0980 chunk 50 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 chunk 31 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.158327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.122680 restraints weight = 17498.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.111924 restraints weight = 22530.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.110843 restraints weight = 23016.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.111230 restraints weight = 19690.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.111452 restraints weight = 16684.062| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13280 Z= 0.130 Angle : 0.675 12.168 17936 Z= 0.306 Chirality : 0.041 0.137 2092 Planarity : 0.005 0.063 2168 Dihedral : 10.763 134.048 2144 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.13 % Allowed : 17.64 % Favored : 78.23 % 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: 0.51 (0.23), residues: 1532 helix: 1.31 (0.18), residues: 984 sheet: -1.26 (0.46), residues: 124 loop : -1.40 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 417 TYR 0.009 0.001 TYR C 175 PHE 0.023 0.001 PHE C 365 TRP 0.005 0.001 TRP C 155 HIS 0.002 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (13280) covalent geometry : angle 0.67500 / 0.31 (17936) hydrogen bonds : bond 0.03186 / 2.08 ( 672) hydrogen bonds : angle 3.62611 / 2.58 ( 1944) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 167 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 119 GLN cc_start: 0.6834 (OUTLIER) cc_final: 0.5709 (pm20) REVERT: A 290 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6786 (mp0) REVERT: A 389 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8466 (pp) REVERT: C 119 GLN cc_start: 0.7111 (OUTLIER) cc_final: 0.5772 (pm20) REVERT: C 290 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7263 (mp0) REVERT: C 389 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8464 (pp) REVERT: D 119 GLN cc_start: 0.7137 (OUTLIER) cc_final: 0.5802 (pm20) REVERT: D 290 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6917 (mp0) REVERT: D 389 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8461 (pp) REVERT: D 417 ARG cc_start: 0.8507 (ttp80) cc_final: 0.8097 (ttp80) REVERT: B 119 GLN cc_start: 0.6820 (OUTLIER) cc_final: 0.5937 (pm20) REVERT: B 290 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: B 389 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8505 (pp) outliers start: 55 outliers final: 41 residues processed: 203 average time/residue: 0.0780 time to fit residues: 25.5707 Evaluate side-chains 215 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 162 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 389 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 28 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 121 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 196 GLN B 196 GLN B 410 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.158665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.123251 restraints weight = 17424.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.111889 restraints weight = 21969.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.111358 restraints weight = 21428.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.111415 restraints weight = 19278.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.111802 restraints weight = 16390.823| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13280 Z= 0.124 Angle : 0.673 12.238 17936 Z= 0.305 Chirality : 0.041 0.137 2092 Planarity : 0.005 0.063 2168 Dihedral : 10.748 133.810 2144 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.13 % Allowed : 17.72 % Favored : 78.15 % 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: 0.54 (0.23), residues: 1532 helix: 1.34 (0.18), residues: 984 sheet: -1.23 (0.47), residues: 124 loop : -1.41 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 417 TYR 0.011 0.001 TYR A 404 PHE 0.015 0.001 PHE A 40 TRP 0.004 0.001 TRP A 15 HIS 0.002 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (13280) covalent geometry : angle 0.67307 / 0.31 (17936) hydrogen bonds : bond 0.03042 / 1.99 ( 672) hydrogen bonds : angle 3.62078 / 2.58 ( 1944) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1929.49 seconds wall clock time: 33 minutes 57.12 seconds (2037.12 seconds total)