Starting phenix.real_space_refine on Sat Sep 12 20:30:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ryr_24746/09_2026/7ryr_24746.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ryr_24746/09_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_24746/09_2026/7ryr_24746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ryr_24746/09_2026/7ryr_24746.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ryr_24746/09_2026/7ryr_24746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ryr_24746/09_2026/7ryr_24746.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ryr_24746/09_2026/7ryr_24746.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ryr_24746/09_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-2.2.1-6174/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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: 2.61, per 1000 atoms: 0.20 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: 1.18 Conformation dependent library (CDL) restraints added in 532.7 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: 0.27 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: 1.89 Time building geometry restraints manager: 1.56 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: 17171 2.61 - 5.21: 628 5.21 - 7.82: 102 7.82 - 10.42: 27 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: 7844 35.02 - 70.04: 172 70.04 - 105.06: 20 105.06 - 140.08: 4 140.08 - 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: 1849 0.087 - 0.175: 199 0.175 - 0.262: 32 0.262 - 0.350: 8 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: 0.03 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.310 Find NCS groups from input model: 0.110 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.990 ------------------------------------------------------------------------------- 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 : 1.157 13.029 17936 Z= 0.653 Chirality : 0.060 0.437 2092 Planarity : 0.008 0.090 2168 Dihedral : 15.770 175.101 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 0.00734 / 0.44 (13280) covalent geometry : angle 1.15747 / 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 : 0.496 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: 0.0833 time to fit residues: 32.3631 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 : 0.358 ------------------------------------------------------------------------------- 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 = 0.3824 r_free = 0.3824 target = 0.159653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.123338 restraints weight = 17444.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.113274 restraints weight = 24052.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.112700 restraints weight = 22764.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.112634 restraints weight = 21531.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.112604 restraints weight = 20301.627| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1694 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= 0.144 Angle : 0.729 12.342 17936 Z= 0.339 Chirality : 0.042 0.149 2092 Planarity : 0.006 0.063 2168 Dihedral : 11.048 140.294 2152 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.08 % Allowed : 7.88 % 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: -1.05 (0.22), residues: 1532 helix: -0.02 (0.17), residues: 984 sheet: -1.72 (0.46), residues: 124 loop : -1.71 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 136 TYR 0.016 0.001 TYR A 25 PHE 0.029 0.001 PHE B 40 TRP 0.005 0.001 TRP D 155 HIS 0.003 0.001 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (13280) covalent geometry : angle 0.72862 / 0.34 (17936) hydrogen bonds : bond 0.04319 / 2.85 ( 672) hydrogen bonds : angle 4.39284 / 3.14 ( 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 245 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 204 time to evaluate : 0.459 Fit side-chains REVERT: A 221 LEU cc_start: 0.7973 (mp) cc_final: 0.7717 (mp) REVERT: A 290 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6565 (mp0) outliers start: 41 outliers final: 24 residues processed: 227 average time/residue: 0.0822 time to fit residues: 29.6981 Evaluate side-chains 198 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 5 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 129 optimal weight: 0.6980 chunk 149 optimal weight: 4.9990 chunk 148 optimal weight: 20.0000 chunk 117 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 159 GLN B 196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.158849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.122875 restraints weight = 17619.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.112868 restraints weight = 22091.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.111593 restraints weight = 21758.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.111839 restraints weight = 20243.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.111827 restraints weight = 19096.298| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2160 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 : 0.691 12.029 17936 Z= 0.315 Chirality : 0.042 0.154 2092 Planarity : 0.005 0.066 2168 Dihedral : 9.926 105.951 2146 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.38 % Allowed : 12.39 % Favored : 84.23 % 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: -0.53 (0.22), residues: 1532 helix: 0.39 (0.18), residues: 984 sheet: -1.85 (0.45), residues: 124 loop : -1.42 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 417 TYR 0.010 0.001 TYR D 25 PHE 0.027 0.001 PHE B 40 TRP 0.004 0.001 TRP A 155 HIS 0.003 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (13280) covalent geometry : angle 0.69144 / 0.32 (17936) hydrogen bonds : bond 0.03677 / 2.41 ( 672) hydrogen bonds : angle 3.96359 / 2.81 ( 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 238 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 193 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 290 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6714 (mp0) REVERT: A 389 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8365 (pp) REVERT: C 290 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6946 (mp0) REVERT: C 389 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8497 (pp) REVERT: D 290 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6929 (mp0) REVERT: D 389 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8437 (pp) REVERT: B 290 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6776 (mp0) REVERT: B 389 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8349 (pp) outliers start: 45 outliers final: 28 residues processed: 225 average time/residue: 0.0793 time to fit residues: 28.7937 Evaluate side-chains 215 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 179 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 C residue 393 ASP 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 373 LEU 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: 0.9980 chunk 125 optimal weight: 0.6980 chunk 30 optimal weight: 0.0870 chunk 49 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 60 optimal weight: 0.2980 chunk 120 optimal weight: 8.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.159535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.121254 restraints weight = 17367.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.112782 restraints weight = 21660.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.112513 restraints weight = 21414.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.112826 restraints weight = 18298.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.112773 restraints weight = 16826.442| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13280 Z= 0.118 Angle : 0.670 11.560 17936 Z= 0.302 Chirality : 0.041 0.146 2092 Planarity : 0.005 0.059 2168 Dihedral : 9.292 81.027 2146 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.83 % Allowed : 14.64 % 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: 0.50 (0.18), residues: 1016 sheet: -1.75 (0.45), residues: 124 loop : -1.59 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 417 TYR 0.009 0.001 TYR D 25 PHE 0.020 0.001 PHE D 40 TRP 0.004 0.001 TRP A 264 HIS 0.003 0.001 HIS B 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (13280) covalent geometry : angle 0.67046 / 0.30 (17936) hydrogen bonds : bond 0.03257 / 2.13 ( 672) hydrogen bonds : angle 3.75065 / 2.66 ( 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 239 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 188 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 290 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6639 (mp0) REVERT: A 389 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8367 (pp) REVERT: C 290 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6988 (mp0) REVERT: C 389 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8464 (pp) REVERT: D 206 LEU cc_start: 0.8310 (pp) cc_final: 0.8083 (mt) REVERT: D 289 MET cc_start: 0.8439 (mmm) cc_final: 0.8210 (mmm) REVERT: D 290 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: D 389 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8427 (pp) REVERT: B 290 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: B 389 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8364 (pp) outliers start: 51 outliers final: 28 residues processed: 222 average time/residue: 0.0807 time to fit residues: 28.8843 Evaluate side-chains 203 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 318 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 373 LEU 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 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: 6.9990 chunk 0 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 chunk 111 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.158851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.121935 restraints weight = 17509.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.112340 restraints weight = 21527.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.111567 restraints weight = 21084.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.111646 restraints weight = 18539.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.111994 restraints weight = 16591.460| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13280 Z= 0.122 Angle : 0.675 11.431 17936 Z= 0.302 Chirality : 0.041 0.147 2092 Planarity : 0.005 0.058 2168 Dihedral : 9.128 69.456 2144 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.43 % Allowed : 16.59 % Favored : 78.98 % 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: -0.19 (0.23), residues: 1532 helix: 0.64 (0.18), residues: 1024 sheet: -1.63 (0.46), residues: 124 loop : -1.47 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 417 TYR 0.009 0.001 TYR A 175 PHE 0.019 0.001 PHE A 40 TRP 0.004 0.001 TRP D 264 HIS 0.003 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (13280) covalent geometry : angle 0.67493 / 0.30 (17936) hydrogen bonds : bond 0.03265 / 2.13 ( 672) hydrogen bonds : angle 3.70318 / 2.63 ( 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 : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 GLN cc_start: 0.6710 (OUTLIER) cc_final: 0.5951 (pm20) REVERT: A 164 ASN cc_start: 0.8985 (OUTLIER) cc_final: 0.8776 (t0) REVERT: A 290 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6832 (mp0) REVERT: A 389 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8415 (pp) REVERT: C 119 GLN cc_start: 0.7112 (OUTLIER) cc_final: 0.5701 (pm20) REVERT: C 290 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7175 (mp0) REVERT: C 389 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8527 (pp) REVERT: D 119 GLN cc_start: 0.7172 (OUTLIER) cc_final: 0.5882 (pm20) REVERT: D 290 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: D 389 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8525 (pp) REVERT: B 119 GLN cc_start: 0.6764 (OUTLIER) cc_final: 0.5712 (pm20) REVERT: B 290 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: B 389 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8406 (pp) outliers start: 59 outliers final: 35 residues processed: 219 average time/residue: 0.0794 time to fit residues: 27.6822 Evaluate side-chains 216 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 164 ASN 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 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 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 373 LEU 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 95 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 90 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 148 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.155326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.118611 restraints weight = 17451.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.105529 restraints weight = 22174.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.104957 restraints weight = 20966.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.105313 restraints weight = 19067.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.105363 restraints weight = 17716.744| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13280 Z= 0.173 Angle : 0.712 12.148 17936 Z= 0.319 Chirality : 0.043 0.143 2092 Planarity : 0.005 0.057 2168 Dihedral : 9.721 65.248 2144 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.80 % Allowed : 15.92 % Favored : 79.28 % 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: -0.16 (0.23), residues: 1532 helix: 0.75 (0.18), residues: 980 sheet: -1.63 (0.44), residues: 128 loop : -1.49 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 417 TYR 0.012 0.001 TYR A 175 PHE 0.025 0.001 PHE B 40 TRP 0.009 0.001 TRP A 155 HIS 0.003 0.001 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (13280) covalent geometry : angle 0.71199 / 0.32 (17936) hydrogen bonds : bond 0.04057 / 2.65 ( 672) hydrogen bonds : angle 3.85988 / 2.74 ( 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 241 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 177 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 GLN cc_start: 0.6796 (OUTLIER) cc_final: 0.5926 (pm20) REVERT: A 290 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6938 (mp0) REVERT: A 389 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8509 (pp) REVERT: C 119 GLN cc_start: 0.7108 (OUTLIER) cc_final: 0.5601 (pm20) REVERT: C 290 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: C 389 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8546 (pp) REVERT: D 119 GLN cc_start: 0.7090 (OUTLIER) cc_final: 0.5503 (pm20) REVERT: D 290 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: D 389 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8480 (pp) REVERT: B 119 GLN cc_start: 0.6817 (OUTLIER) cc_final: 0.5727 (pm20) REVERT: B 389 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8483 (pp) outliers start: 64 outliers final: 43 residues processed: 225 average time/residue: 0.0738 time to fit residues: 27.0561 Evaluate side-chains 222 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 168 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 85 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 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 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 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 373 LEU 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 26 TYR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 95 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 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 Chi-restraints excluded: chain B residue 393 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 89 optimal weight: 0.5980 chunk 143 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 13 optimal weight: 0.0170 chunk 44 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 104 optimal weight: 0.4980 chunk 151 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 = 0.158386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.121476 restraints weight = 17397.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.109406 restraints weight = 21569.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.109283 restraints weight = 21224.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.108881 restraints weight = 19937.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.109021 restraints weight = 18779.346| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2964 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= 0.114 Angle : 0.690 12.060 17936 Z= 0.301 Chirality : 0.041 0.147 2092 Planarity : 0.005 0.061 2168 Dihedral : 9.238 59.887 2144 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.50 % Allowed : 17.04 % 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: 0.14 (0.23), residues: 1532 helix: 1.00 (0.18), residues: 984 sheet: -1.51 (0.45), residues: 128 loop : -1.44 (0.33), residues: 420 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 0.021 0.001 PHE C 365 TRP 0.005 0.001 TRP A 176 HIS 0.002 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (13280) covalent geometry : angle 0.69049 / 0.30 (17936) hydrogen bonds : bond 0.03088 / 2.02 ( 672) hydrogen bonds : angle 3.67129 / 2.60 ( 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 236 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 176 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 GLN cc_start: 0.6759 (OUTLIER) cc_final: 0.5773 (pm20) REVERT: A 290 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6783 (mp0) REVERT: A 389 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8448 (pp) REVERT: C 119 GLN cc_start: 0.7054 (OUTLIER) cc_final: 0.5591 (pm20) REVERT: C 290 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7278 (mp0) REVERT: C 389 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8518 (pp) REVERT: D 119 GLN cc_start: 0.6994 (OUTLIER) cc_final: 0.5608 (pm20) REVERT: D 290 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: D 389 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8536 (pp) REVERT: B 119 GLN cc_start: 0.6852 (OUTLIER) cc_final: 0.5801 (pm20) REVERT: B 290 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: B 389 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8461 (pp) outliers start: 60 outliers final: 41 residues processed: 221 average time/residue: 0.0804 time to fit residues: 28.5155 Evaluate side-chains 218 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 165 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 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 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 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 373 LEU 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 26 TYR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 95 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 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 Chi-restraints excluded: chain B residue 393 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 65 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 97 optimal weight: 0.3980 chunk 103 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 106 optimal weight: 0.9980 chunk 89 optimal weight: 0.0980 chunk 83 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.158570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.121454 restraints weight = 17173.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.111223 restraints weight = 20895.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 99)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.109703 restraints weight = 19963.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.110102 restraints weight = 18589.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.110436 restraints weight = 14695.021| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3105 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= 0.115 Angle : 0.693 11.904 17936 Z= 0.300 Chirality : 0.041 0.145 2092 Planarity : 0.005 0.062 2168 Dihedral : 9.054 59.146 2144 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.20 % Allowed : 18.09 % Favored : 77.70 % 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 (0.23), residues: 1532 helix: 1.13 (0.18), residues: 984 sheet: -1.48 (0.45), residues: 128 loop : -1.37 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 417 TYR 0.008 0.001 TYR D 390 PHE 0.022 0.001 PHE C 365 TRP 0.004 0.001 TRP D 264 HIS 0.002 0.001 HIS B 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (13280) covalent geometry : angle 0.69297 / 0.30 (17936) hydrogen bonds : bond 0.03051 / 1.99 ( 672) hydrogen bonds : angle 3.63595 / 2.59 ( 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 229 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 173 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 GLN cc_start: 0.6855 (OUTLIER) cc_final: 0.5758 (pm20) REVERT: A 290 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6939 (mp0) REVERT: A 389 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8449 (pp) REVERT: C 119 GLN cc_start: 0.7061 (OUTLIER) cc_final: 0.5681 (pm20) REVERT: C 290 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: C 389 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8486 (pp) REVERT: C 417 ARG cc_start: 0.8545 (ttp80) cc_final: 0.8311 (ttp80) REVERT: D 119 GLN cc_start: 0.7090 (OUTLIER) cc_final: 0.5664 (pm20) REVERT: D 164 ASN cc_start: 0.8954 (OUTLIER) cc_final: 0.8712 (t0) REVERT: D 290 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: D 389 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8442 (pp) REVERT: D 417 ARG cc_start: 0.8412 (ttp80) cc_final: 0.8056 (ttp80) REVERT: B 119 GLN cc_start: 0.6898 (OUTLIER) cc_final: 0.5962 (pm20) REVERT: B 290 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7017 (mp0) REVERT: B 389 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8430 (pp) REVERT: B 410 GLN cc_start: 0.8477 (tp40) cc_final: 0.8191 (tp-100) outliers start: 56 outliers final: 37 residues processed: 214 average time/residue: 0.0742 time to fit residues: 25.8596 Evaluate side-chains 214 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 164 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 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 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 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 373 LEU 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 26 TYR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 95 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 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: 9.9990 chunk 35 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 119 optimal weight: 0.0010 chunk 29 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.1990 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.156179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.121768 restraints weight = 17530.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.112026 restraints weight = 23697.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.110633 restraints weight = 22250.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.110353 restraints weight = 21138.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.110264 restraints weight = 18182.006| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3200 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= 0.147 Angle : 0.716 12.185 17936 Z= 0.313 Chirality : 0.042 0.142 2092 Planarity : 0.005 0.062 2168 Dihedral : 9.455 58.876 2144 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.20 % Allowed : 18.02 % Favored : 77.78 % 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: 0.23 (0.23), residues: 1532 helix: 1.07 (0.18), residues: 984 sheet: -1.51 (0.45), residues: 128 loop : -1.41 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 417 TYR 0.011 0.001 TYR A 175 PHE 0.020 0.001 PHE C 365 TRP 0.007 0.001 TRP A 155 HIS 0.003 0.001 HIS D 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (13280) covalent geometry : angle 0.71578 / 0.31 (17936) hydrogen bonds : bond 0.03642 / 2.38 ( 672) hydrogen bonds : angle 3.76295 / 2.67 ( 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: 56 poor density : 167 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 GLN cc_start: 0.7212 (OUTLIER) cc_final: 0.5894 (pm20) REVERT: A 290 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6970 (mp0) REVERT: A 389 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8537 (pp) REVERT: C 119 GLN cc_start: 0.7254 (OUTLIER) cc_final: 0.5856 (pm20) REVERT: C 290 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7275 (mp0) REVERT: C 389 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8513 (pp) REVERT: C 417 ARG cc_start: 0.8498 (ttp80) cc_final: 0.8153 (ttp80) REVERT: D 119 GLN cc_start: 0.7170 (OUTLIER) cc_final: 0.5741 (pm20) REVERT: D 290 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7252 (mp0) REVERT: D 389 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8496 (pp) REVERT: D 417 ARG cc_start: 0.8405 (ttp80) cc_final: 0.8063 (ttp80) REVERT: B 119 GLN cc_start: 0.7022 (OUTLIER) cc_final: 0.6037 (pm20) REVERT: B 389 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8544 (pp) REVERT: B 410 GLN cc_start: 0.8428 (tp40) cc_final: 0.8153 (tp-100) outliers start: 56 outliers final: 40 residues processed: 205 average time/residue: 0.0802 time to fit residues: 26.8959 Evaluate side-chains 215 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 164 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 85 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 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 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 373 LEU 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 26 TYR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 95 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 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 Chi-restraints excluded: chain B residue 393 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 106 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 142 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 110 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 138 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.158474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.122898 restraints weight = 17550.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.111600 restraints weight = 21620.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.109738 restraints weight = 21838.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.109808 restraints weight = 19162.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.110108 restraints weight = 17304.390| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13280 Z= 0.114 Angle : 0.698 12.327 17936 Z= 0.303 Chirality : 0.041 0.146 2092 Planarity : 0.005 0.064 2168 Dihedral : 9.182 59.616 2144 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.98 % Allowed : 18.62 % Favored : 77.40 % 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: 0.38 (0.23), residues: 1532 helix: 1.20 (0.18), residues: 984 sheet: -1.54 (0.46), residues: 116 loop : -1.36 (0.33), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 417 TYR 0.007 0.001 TYR C 390 PHE 0.022 0.001 PHE B 365 TRP 0.004 0.001 TRP D 176 HIS 0.002 0.000 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (13280) covalent geometry : angle 0.69804 / 0.30 (17936) hydrogen bonds : bond 0.02989 / 1.95 ( 672) hydrogen bonds : angle 3.66117 / 2.60 ( 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 223 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 170 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 GLN cc_start: 0.7128 (OUTLIER) cc_final: 0.6027 (pm20) REVERT: A 290 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6862 (mp0) REVERT: A 389 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8469 (pp) REVERT: C 119 GLN cc_start: 0.7140 (OUTLIER) cc_final: 0.5882 (pm20) REVERT: C 290 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: C 389 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8509 (pp) REVERT: C 417 ARG cc_start: 0.8588 (ttp80) cc_final: 0.8256 (ttp80) REVERT: D 119 GLN cc_start: 0.7087 (OUTLIER) cc_final: 0.5760 (pm20) REVERT: D 290 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: D 389 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8452 (pp) REVERT: D 417 ARG cc_start: 0.8522 (ttp80) cc_final: 0.8153 (ttp80) REVERT: B 119 GLN cc_start: 0.6815 (OUTLIER) cc_final: 0.5826 (pm20) REVERT: B 290 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7113 (mp0) REVERT: B 389 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8496 (pp) REVERT: B 410 GLN cc_start: 0.8517 (tp40) cc_final: 0.8231 (tp-100) outliers start: 53 outliers final: 39 residues processed: 208 average time/residue: 0.0830 time to fit residues: 27.5452 Evaluate side-chains 217 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 166 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 85 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 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 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 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 373 LEU 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 26 TYR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 95 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 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: 0.4980 chunk 8 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 chunk 147 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.158147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.121552 restraints weight = 17448.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.109849 restraints weight = 22561.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.109708 restraints weight = 19717.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.109809 restraints weight = 20223.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.109935 restraints weight = 17135.688| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3309 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= 0.118 Angle : 0.702 12.200 17936 Z= 0.306 Chirality : 0.041 0.145 2092 Planarity : 0.005 0.063 2168 Dihedral : 9.130 59.714 2144 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.98 % Allowed : 18.84 % Favored : 77.18 % 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: 0.46 (0.24), residues: 1532 helix: 1.25 (0.18), residues: 984 sheet: -1.35 (0.47), residues: 124 loop : -1.33 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 417 TYR 0.008 0.001 TYR A 175 PHE 0.021 0.001 PHE C 365 TRP 0.004 0.001 TRP D 264 HIS 0.002 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (13280) covalent geometry : angle 0.70209 / 0.31 (17936) hydrogen bonds : bond 0.03069 / 2.01 ( 672) hydrogen bonds : angle 3.66705 / 2.60 ( 1944) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2079.47 seconds wall clock time: 36 minutes 38.00 seconds (2198.00 seconds total)