Starting phenix.real_space_refine on Sat Sep 28 04:47:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryr_24746/09_2024/7ryr_24746.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryr_24746/09_2024/7ryr_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryr_24746/09_2024/7ryr_24746.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryr_24746/09_2024/7ryr_24746.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryr_24746/09_2024/7ryr_24746.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryr_24746/09_2024/7ryr_24746.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13024 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3094 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 23, 'TRANS': 365} Chain breaks: 2 Chain: "C" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3094 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 23, 'TRANS': 365} Chain breaks: 2 Chain: "D" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3094 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 23, 'TRANS': 365} Chain breaks: 2 Chain: "B" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3094 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 23, 'TRANS': 365} Chain breaks: 2 Chain: "A" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 171 Unusual residues: {'PGW': 8} Classifications: {'RNA': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 259 Unresolved non-hydrogen angles: 302 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PGW:plan-1': 5, 'PGW:plan-2': 5, 'PGW:plan-3': 6} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 171 Unusual residues: {'PGW': 8} Classifications: {'RNA': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 259 Unresolved non-hydrogen angles: 302 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PGW:plan-1': 5, 'PGW:plan-2': 5, 'PGW:plan-3': 6} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 153 Unusual residues: {'PGW': 6} Classifications: {'RNA': 1, 'undetermined': 6} Modifications used: {'rna3p': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PGW:plan-1': 3, 'PGW:plan-2': 3, 'PGW:plan-3': 4} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 153 Unusual residues: {'PGW': 6} Classifications: {'RNA': 1, 'undetermined': 6} Modifications used: {'rna3p': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 179 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: 7.96, per 1000 atoms: 0.61 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: 3.40 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.47 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: 3.63 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2014 1.32 - 1.44: 3298 1.44 - 1.56: 7900 1.56 - 1.68: 20 1.68 - 1.81: 48 Bond restraints: 13280 Sorted by residual: bond pdb=" C10 PGW B 503 " pdb=" C9 PGW B 503 " ideal model delta sigma weight residual 1.333 1.509 -0.176 2.00e-02 2.50e+03 7.74e+01 bond pdb=" C10 PGW C 503 " pdb=" C9 PGW C 503 " ideal model delta sigma weight residual 1.333 1.509 -0.176 2.00e-02 2.50e+03 7.73e+01 bond pdb=" C10 PGW A 503 " pdb=" C9 PGW A 503 " ideal model delta sigma weight residual 1.333 1.509 -0.176 2.00e-02 2.50e+03 7.71e+01 bond pdb=" C10 PGW D 503 " pdb=" C9 PGW D 503 " ideal model delta sigma weight residual 1.333 1.509 -0.176 2.00e-02 2.50e+03 7.71e+01 bond pdb=" CA SER C 157 " pdb=" CB SER C 157 " ideal model delta sigma weight residual 1.529 1.470 0.059 1.64e-02 3.72e+03 1.29e+01 ... (remaining 13275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 17187 2.61 - 5.21: 628 5.21 - 7.82: 98 7.82 - 10.42: 15 10.42 - 13.03: 8 Bond angle restraints: 17936 Sorted by residual: angle pdb=" N LEU D 91 " pdb=" CA LEU D 91 " pdb=" C LEU D 91 " ideal model delta sigma weight residual 111.82 104.65 7.17 1.16e+00 7.43e-01 3.83e+01 angle pdb=" N LEU B 91 " pdb=" CA LEU B 91 " pdb=" C LEU B 91 " ideal model delta sigma weight residual 111.82 104.65 7.17 1.16e+00 7.43e-01 3.82e+01 angle pdb=" N LEU A 91 " pdb=" CA LEU A 91 " pdb=" C LEU A 91 " ideal model delta sigma weight residual 111.82 104.67 7.15 1.16e+00 7.43e-01 3.80e+01 angle pdb=" N LEU C 91 " pdb=" CA LEU C 91 " pdb=" C LEU C 91 " ideal model delta sigma weight residual 111.82 104.70 7.12 1.16e+00 7.43e-01 3.77e+01 angle pdb=" CA ASP C 92 " pdb=" C ASP C 92 " pdb=" O ASP C 92 " ideal model delta sigma weight residual 121.56 115.40 6.16 1.09e+00 8.42e-01 3.19e+01 ... (remaining 17931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.02: 7872 35.02 - 70.04: 192 70.04 - 105.06: 20 105.06 - 140.08: 32 140.08 - 175.10: 12 Dihedral angle restraints: 8128 sinusoidal: 3560 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 8125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1857 0.087 - 0.175: 195 0.175 - 0.262: 32 0.262 - 0.350: 4 0.350 - 0.437: 4 Chirality restraints: 2092 Sorted by residual: chirality pdb=" CA LYS D 246 " pdb=" N LYS D 246 " pdb=" C LYS D 246 " pdb=" CB LYS D 246 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" CA LYS A 246 " pdb=" N LYS A 246 " pdb=" C LYS A 246 " pdb=" CB LYS A 246 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.77e+00 chirality pdb=" CA LYS B 246 " pdb=" N LYS B 246 " pdb=" C LYS B 246 " pdb=" CB LYS B 246 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.76e+00 ... (remaining 2089 not shown) Planarity restraints: 2168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW B 503 " 0.091 2.00e-02 2.50e+03 9.04e-02 8.17e+01 pdb=" C10 PGW B 503 " -0.091 2.00e-02 2.50e+03 pdb=" C8 PGW B 503 " 0.090 2.00e-02 2.50e+03 pdb=" C9 PGW B 503 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW D 503 " -0.090 2.00e-02 2.50e+03 9.03e-02 8.16e+01 pdb=" C10 PGW D 503 " 0.091 2.00e-02 2.50e+03 pdb=" C8 PGW D 503 " -0.090 2.00e-02 2.50e+03 pdb=" C9 PGW D 503 " 0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW A 503 " -0.090 2.00e-02 2.50e+03 9.03e-02 8.16e+01 pdb=" C10 PGW A 503 " 0.091 2.00e-02 2.50e+03 pdb=" C8 PGW A 503 " -0.090 2.00e-02 2.50e+03 pdb=" C9 PGW A 503 " 0.090 2.00e-02 2.50e+03 ... (remaining 2165 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 847 2.74 - 3.28: 12793 3.28 - 3.82: 19621 3.82 - 4.36: 23486 4.36 - 4.90: 40988 Nonbonded interactions: 97735 Sorted by model distance: nonbonded pdb=" OE1 GLU D 308 " pdb=" OH TYR D 404 " model vdw 2.197 3.040 nonbonded pdb=" OE1 GLU A 308 " pdb=" OH TYR A 404 " model vdw 2.197 3.040 nonbonded pdb=" OE1 GLU C 308 " pdb=" OH TYR C 404 " model vdw 2.198 3.040 nonbonded pdb=" OE1 GLU B 308 " pdb=" OH TYR B 404 " model vdw 2.198 3.040 nonbonded pdb=" O GLN D 119 " pdb=" OG1 THR D 123 " model vdw 2.245 3.040 ... (remaining 97730 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 420 or resid 501 through 506 or (resid 507 and \ (name C15 or name C16 or name C17 or name C20 or name C21 or name C22 or name C2 \ 3 or name C24 or name C25 or name C26 or name C27)))) selection = (chain 'B' and (resid 10 through 420 or resid 501 through 505 or (resid 506 and \ (name C15 or name C16 or name C17 or name C22 or name C23 or name C24 or name C2 \ 5 or name C26 or name C27)) or (resid 507 and (name C15 or name C16 or name C17 \ or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name \ C26 or name C27)))) selection = (chain 'C' and (resid 10 through 420 or resid 501 through 506 or (resid 507 and \ (name C15 or name C16 or name C17 or name C20 or name C21 or name C22 or name C2 \ 3 or name C24 or name C25 or name C26 or name C27)))) selection = (chain 'D' and (resid 10 through 420 or resid 501 through 505 or (resid 506 and \ (name C15 or name C16 or name C17 or name C22 or name C23 or name C24 or name C2 \ 5 or name C26 or name C27)) or (resid 507 and (name C15 or name C16 or name C17 \ or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name \ C26 or name C27)))) } 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.150 Process input model: 30.590 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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= 0.481 Angle : 1.128 13.029 17936 Z= 0.651 Chirality : 0.059 0.437 2092 Planarity : 0.008 0.090 2168 Dihedral : 19.137 175.101 5176 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP B 264 HIS 0.002 0.001 HIS B 149 PHE 0.019 0.002 PHE C 365 TYR 0.023 0.001 TYR A 26 ARG 0.011 0.001 ARG B 273 *********************** 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 fitting. rotamer outliers: 8 poor density : 235 time to evaluate : 1.378 Fit side-chains REVERT: A 334 MET cc_start: 0.5592 (tmm) cc_final: 0.5245 (tmm) REVERT: C 110 VAL cc_start: 0.8653 (m) cc_final: 0.8428 (p) REVERT: C 289 MET cc_start: 0.8365 (mmm) cc_final: 0.8148 (mmm) REVERT: D 110 VAL cc_start: 0.8688 (m) cc_final: 0.8441 (p) outliers start: 8 outliers final: 4 residues processed: 243 average time/residue: 0.1979 time to fit residues: 74.7297 Evaluate side-chains 192 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 188 time to evaluate : 1.399 ------------------------------------------------------------------------------- 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 128 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 chunk 63 optimal weight: 0.2980 chunk 39 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 119 optimal weight: 0.0670 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 138 optimal weight: 0.0870 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 GLN C 196 GLN D 159 GLN D 196 GLN B 410 GLN B 412 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1519 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= 0.180 Angle : 0.703 11.712 17936 Z= 0.335 Chirality : 0.041 0.158 2092 Planarity : 0.006 0.062 2168 Dihedral : 18.023 141.293 2236 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.70 % Allowed : 7.81 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.22), residues: 1532 helix: 0.11 (0.18), residues: 960 sheet: -1.70 (0.46), residues: 124 loop : -1.61 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 176 HIS 0.003 0.001 HIS B 292 PHE 0.026 0.001 PHE B 40 TYR 0.015 0.001 TYR A 25 ARG 0.002 0.000 ARG A 255 *********************** 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 244 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 208 time to evaluate : 1.274 Fit side-chains REVERT: A 221 LEU cc_start: 0.7898 (mp) cc_final: 0.7674 (mp) REVERT: C 289 MET cc_start: 0.8256 (mmm) cc_final: 0.8024 (mmm) outliers start: 36 outliers final: 22 residues processed: 226 average time/residue: 0.1931 time to fit residues: 69.1788 Evaluate side-chains 200 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 178 time to evaluate : 1.715 ------------------------------------------------------------------------------- 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 400 ILE Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 164 ASN 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 372 ILE 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 76 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 138 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 47 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 159 GLN B 159 GLN B 196 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 13280 Z= 0.399 Angle : 0.779 13.233 17936 Z= 0.370 Chirality : 0.046 0.156 2092 Planarity : 0.006 0.068 2168 Dihedral : 17.028 135.441 2230 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.83 % Allowed : 12.31 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.22), residues: 1532 helix: 0.04 (0.17), residues: 992 sheet: -2.08 (0.42), residues: 128 loop : -1.66 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 155 HIS 0.005 0.002 HIS B 292 PHE 0.029 0.002 PHE B 40 TYR 0.017 0.002 TYR A 175 ARG 0.007 0.001 ARG C 417 *********************** 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 241 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 190 time to evaluate : 1.314 Fit side-chains REVERT: A 389 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8490 (pp) REVERT: C 221 LEU cc_start: 0.8229 (mp) cc_final: 0.8005 (mt) REVERT: C 290 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6874 (mp0) REVERT: C 389 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8536 (pp) REVERT: D 290 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6780 (mp0) REVERT: D 389 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8521 (pp) REVERT: B 389 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8434 (pp) outliers start: 51 outliers final: 30 residues processed: 231 average time/residue: 0.1975 time to fit residues: 72.5416 Evaluate side-chains 201 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 165 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 271 GLU 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 104 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 222 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 271 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 136 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 71 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 146 optimal weight: 0.0970 chunk 72 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2690 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= 0.179 Angle : 0.658 12.293 17936 Z= 0.310 Chirality : 0.041 0.144 2092 Planarity : 0.005 0.060 2168 Dihedral : 15.112 134.031 2228 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.28 % Allowed : 14.94 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.23), residues: 1532 helix: 0.47 (0.18), residues: 992 sheet: -1.89 (0.44), residues: 124 loop : -1.57 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 176 HIS 0.002 0.001 HIS A 281 PHE 0.019 0.001 PHE C 40 TYR 0.009 0.001 TYR B 404 ARG 0.007 0.000 ARG C 417 *********************** 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 244 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 187 time to evaluate : 1.473 Fit side-chains revert: symmetry clash REVERT: A 119 GLN cc_start: 0.6801 (OUTLIER) cc_final: 0.6060 (pm20) REVERT: A 221 LEU cc_start: 0.8126 (mp) cc_final: 0.7920 (mt) REVERT: A 389 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8396 (pp) REVERT: C 119 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.5879 (pm20) REVERT: C 289 MET cc_start: 0.8336 (mmm) cc_final: 0.8070 (mmm) REVERT: C 290 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.7088 (mp0) REVERT: C 389 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8486 (pp) REVERT: D 119 GLN cc_start: 0.7233 (OUTLIER) cc_final: 0.5697 (pm20) REVERT: D 290 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6945 (mp0) REVERT: D 389 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8466 (pp) REVERT: B 119 GLN cc_start: 0.6911 (OUTLIER) cc_final: 0.5875 (pm20) REVERT: B 290 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6837 (mp0) REVERT: B 389 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8414 (pp) outliers start: 57 outliers final: 30 residues processed: 224 average time/residue: 0.1994 time to fit residues: 70.5760 Evaluate side-chains 209 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 168 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 318 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 119 GLN 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 318 GLU Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 393 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 2.9990 chunk 83 optimal weight: 0.3980 chunk 2 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 60 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13280 Z= 0.230 Angle : 0.665 11.929 17936 Z= 0.313 Chirality : 0.042 0.143 2092 Planarity : 0.005 0.058 2168 Dihedral : 14.117 134.912 2228 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 5.71 % Allowed : 15.09 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.23), residues: 1532 helix: 0.59 (0.18), residues: 1000 sheet: -1.80 (0.44), residues: 124 loop : -1.49 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 155 HIS 0.003 0.001 HIS D 292 PHE 0.022 0.001 PHE D 40 TYR 0.011 0.001 TYR D 175 ARG 0.007 0.000 ARG C 417 *********************** 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 255 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 179 time to evaluate : 1.373 Fit side-chains REVERT: A 119 GLN cc_start: 0.6908 (OUTLIER) cc_final: 0.6017 (pm20) REVERT: A 285 LEU cc_start: 0.9030 (tp) cc_final: 0.8632 (tp) REVERT: A 289 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7500 (mpp) REVERT: A 389 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8450 (pp) REVERT: C 119 GLN cc_start: 0.7212 (OUTLIER) cc_final: 0.5691 (pm20) REVERT: C 290 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: C 389 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8505 (pp) REVERT: D 119 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.5648 (pm20) REVERT: D 164 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8750 (t0) REVERT: D 290 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: D 389 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8496 (pp) REVERT: B 119 GLN cc_start: 0.6938 (OUTLIER) cc_final: 0.5869 (pm20) REVERT: B 289 MET cc_start: 0.8287 (mmm) cc_final: 0.7875 (mmm) REVERT: B 290 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6904 (mp0) REVERT: B 389 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8425 (pp) outliers start: 76 outliers final: 48 residues processed: 233 average time/residue: 0.1983 time to fit residues: 71.8337 Evaluate side-chains 229 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 168 time to evaluate : 1.279 ------------------------------------------------------------------------------- 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 164 ASN Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain 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 164 ASN Chi-restraints excluded: chain C residue 179 THR 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 318 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 164 ASN Chi-restraints excluded: chain D residue 179 THR 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 318 GLU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 271 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13280 Z= 0.186 Angle : 0.657 11.617 17936 Z= 0.303 Chirality : 0.041 0.137 2092 Planarity : 0.005 0.058 2168 Dihedral : 13.306 134.391 2228 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 5.18 % Allowed : 16.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.23), residues: 1532 helix: 0.75 (0.18), residues: 1004 sheet: -1.65 (0.45), residues: 124 loop : -1.65 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 176 HIS 0.002 0.001 HIS B 99 PHE 0.021 0.001 PHE A 40 TYR 0.008 0.001 TYR D 175 ARG 0.005 0.000 ARG D 417 *********************** 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 246 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 177 time to evaluate : 1.598 Fit side-chains REVERT: A 119 GLN cc_start: 0.6948 (OUTLIER) cc_final: 0.5995 (pm20) REVERT: A 285 LEU cc_start: 0.8981 (tp) cc_final: 0.8538 (tp) REVERT: A 289 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7248 (mpp) REVERT: A 389 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8420 (pp) REVERT: A 391 ARG cc_start: 0.8598 (ttp80) cc_final: 0.8383 (ttp80) REVERT: C 119 GLN cc_start: 0.7116 (OUTLIER) cc_final: 0.5590 (pm20) REVERT: C 290 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: C 389 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8484 (pp) REVERT: D 119 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.5690 (pm20) REVERT: D 164 ASN cc_start: 0.9002 (OUTLIER) cc_final: 0.8735 (t0) REVERT: D 290 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: D 389 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8466 (pp) REVERT: B 119 GLN cc_start: 0.6871 (OUTLIER) cc_final: 0.5839 (pm20) REVERT: B 290 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: B 389 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8416 (pp) REVERT: B 410 GLN cc_start: 0.8397 (tp40) cc_final: 0.8108 (tp-100) outliers start: 69 outliers final: 44 residues processed: 223 average time/residue: 0.2041 time to fit residues: 72.2553 Evaluate side-chains 226 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 169 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE 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 271 GLU Chi-restraints excluded: chain A residue 289 MET 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 19 ILE 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 164 ASN Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 318 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 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 318 GLU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.0060 chunk 16 optimal weight: 0.5980 chunk 83 optimal weight: 8.9990 chunk 107 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 146 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13280 Z= 0.160 Angle : 0.659 11.300 17936 Z= 0.301 Chirality : 0.040 0.133 2092 Planarity : 0.005 0.061 2168 Dihedral : 12.776 134.066 2228 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.88 % Allowed : 17.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.23), residues: 1532 helix: 0.85 (0.18), residues: 1028 sheet: -1.53 (0.45), residues: 124 loop : -1.45 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 176 HIS 0.002 0.000 HIS B 99 PHE 0.021 0.001 PHE C 365 TYR 0.008 0.001 TYR B 404 ARG 0.007 0.000 ARG C 417 *********************** 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 242 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 177 time to evaluate : 1.386 Fit side-chains REVERT: A 119 GLN cc_start: 0.6878 (OUTLIER) cc_final: 0.5757 (pm20) REVERT: A 389 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8390 (pp) REVERT: A 391 ARG cc_start: 0.8571 (ttp80) cc_final: 0.8363 (ttp80) REVERT: C 119 GLN cc_start: 0.7094 (OUTLIER) cc_final: 0.5697 (pm20) REVERT: C 290 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7157 (mp0) REVERT: C 389 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8443 (pp) REVERT: D 119 GLN cc_start: 0.7185 (OUTLIER) cc_final: 0.5858 (pm20) REVERT: D 164 ASN cc_start: 0.8944 (OUTLIER) cc_final: 0.8714 (t0) REVERT: D 290 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.7046 (mp0) REVERT: D 389 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8461 (pp) REVERT: D 391 ARG cc_start: 0.8591 (ttp80) cc_final: 0.8388 (ttp80) REVERT: D 417 ARG cc_start: 0.8446 (ttp80) cc_final: 0.8082 (ttp80) REVERT: B 119 GLN cc_start: 0.6899 (OUTLIER) cc_final: 0.5967 (pm20) REVERT: B 290 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6893 (mp0) REVERT: B 389 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8389 (pp) REVERT: B 410 GLN cc_start: 0.8459 (tp40) cc_final: 0.8169 (tp-100) outliers start: 65 outliers final: 43 residues processed: 223 average time/residue: 0.2241 time to fit residues: 78.1672 Evaluate side-chains 222 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 167 time to evaluate : 1.374 ------------------------------------------------------------------------------- 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 179 THR Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 348 VAL 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 210 MET Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 318 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 19 ILE 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 222 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 389 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 44 optimal weight: 0.3980 chunk 28 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 13 optimal weight: 0.3980 chunk 115 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13280 Z= 0.169 Angle : 0.664 11.317 17936 Z= 0.302 Chirality : 0.040 0.131 2092 Planarity : 0.005 0.062 2168 Dihedral : 12.474 134.147 2228 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.80 % Allowed : 18.17 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.23), residues: 1532 helix: 1.09 (0.18), residues: 984 sheet: -1.58 (0.46), residues: 116 loop : -1.52 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 176 HIS 0.002 0.001 HIS B 292 PHE 0.022 0.001 PHE C 365 TYR 0.009 0.001 TYR A 404 ARG 0.006 0.000 ARG D 417 *********************** 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 237 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 173 time to evaluate : 1.495 Fit side-chains REVERT: A 119 GLN cc_start: 0.7160 (OUTLIER) cc_final: 0.6067 (pm20) REVERT: A 289 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.7709 (mpp) REVERT: A 389 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8447 (pp) REVERT: C 119 GLN cc_start: 0.7163 (OUTLIER) cc_final: 0.5857 (pm20) REVERT: C 290 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: C 389 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8436 (pp) REVERT: C 417 ARG cc_start: 0.8549 (ttp80) cc_final: 0.8318 (ttp80) REVERT: D 119 GLN cc_start: 0.7223 (OUTLIER) cc_final: 0.5964 (pm20) REVERT: D 164 ASN cc_start: 0.8966 (OUTLIER) cc_final: 0.8738 (t0) REVERT: D 290 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6906 (mp0) REVERT: D 389 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8456 (pp) REVERT: D 417 ARG cc_start: 0.8507 (ttp80) cc_final: 0.8103 (ttp80) REVERT: B 119 GLN cc_start: 0.6900 (OUTLIER) cc_final: 0.5910 (pm20) REVERT: B 290 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7016 (mp0) REVERT: B 389 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8397 (pp) REVERT: B 410 GLN cc_start: 0.8467 (tp40) cc_final: 0.8170 (tp-100) outliers start: 64 outliers final: 47 residues processed: 219 average time/residue: 0.2094 time to fit residues: 71.1606 Evaluate side-chains 226 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 166 time to evaluate : 1.361 ------------------------------------------------------------------------------- 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 179 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 348 VAL 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 179 THR 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 318 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 19 ILE 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 164 ASN Chi-restraints excluded: chain D residue 179 THR 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 318 GLU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 393 ASP Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 389 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 82 optimal weight: 0.2980 chunk 59 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 129 optimal weight: 0.2980 chunk 89 optimal weight: 0.4980 chunk 144 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13280 Z= 0.164 Angle : 0.666 11.355 17936 Z= 0.303 Chirality : 0.040 0.129 2092 Planarity : 0.005 0.062 2168 Dihedral : 12.222 134.009 2228 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.26 % Allowed : 18.02 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.23), residues: 1532 helix: 1.14 (0.18), residues: 984 sheet: -1.56 (0.46), residues: 116 loop : -1.48 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 176 HIS 0.002 0.000 HIS D 292 PHE 0.011 0.001 PHE A 40 TYR 0.009 0.001 TYR D 25 ARG 0.006 0.000 ARG D 417 *********************** 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 239 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 169 time to evaluate : 1.379 Fit side-chains REVERT: A 119 GLN cc_start: 0.7141 (OUTLIER) cc_final: 0.6107 (pm20) REVERT: A 289 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7872 (mpp) REVERT: A 389 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8390 (pp) REVERT: C 119 GLN cc_start: 0.7201 (OUTLIER) cc_final: 0.5867 (pm20) REVERT: C 164 ASN cc_start: 0.8943 (OUTLIER) cc_final: 0.8697 (t0) REVERT: C 290 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7142 (mp0) REVERT: C 389 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8384 (pp) REVERT: C 417 ARG cc_start: 0.8563 (ttp80) cc_final: 0.8221 (ttp80) REVERT: D 119 GLN cc_start: 0.7245 (OUTLIER) cc_final: 0.6078 (pm20) REVERT: D 164 ASN cc_start: 0.8965 (OUTLIER) cc_final: 0.8726 (t0) REVERT: D 290 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7070 (mp0) REVERT: D 389 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8440 (pp) REVERT: D 417 ARG cc_start: 0.8501 (ttp80) cc_final: 0.8117 (ttp80) REVERT: B 119 GLN cc_start: 0.6893 (OUTLIER) cc_final: 0.5982 (pm20) REVERT: B 290 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7061 (mp0) REVERT: B 389 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8416 (pp) REVERT: B 410 GLN cc_start: 0.8445 (tp40) cc_final: 0.8167 (tp-100) outliers start: 70 outliers final: 46 residues processed: 218 average time/residue: 0.1968 time to fit residues: 67.6515 Evaluate side-chains 226 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 166 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 40 PHE 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 179 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 289 MET 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 164 ASN Chi-restraints excluded: chain C residue 179 THR 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 318 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 19 ILE 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 164 ASN Chi-restraints excluded: chain D residue 179 THR 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 318 GLU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 179 THR 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 88 optimal weight: 0.7980 chunk 68 optimal weight: 0.0370 chunk 100 optimal weight: 5.9990 chunk 151 optimal weight: 0.4980 chunk 139 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 12 optimal weight: 0.1980 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13280 Z= 0.156 Angle : 0.666 11.440 17936 Z= 0.303 Chirality : 0.040 0.129 2092 Planarity : 0.005 0.064 2168 Dihedral : 11.892 133.910 2228 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.58 % Allowed : 18.47 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.24), residues: 1532 helix: 1.22 (0.18), residues: 984 sheet: -1.56 (0.46), residues: 116 loop : -1.45 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 176 HIS 0.001 0.000 HIS A 281 PHE 0.021 0.001 PHE C 365 TYR 0.011 0.001 TYR A 404 ARG 0.006 0.000 ARG D 417 ********************** 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 234 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 173 time to evaluate : 1.474 Fit side-chains REVERT: A 119 GLN cc_start: 0.7155 (OUTLIER) cc_final: 0.6218 (pm20) REVERT: A 389 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8352 (pp) REVERT: C 119 GLN cc_start: 0.7133 (OUTLIER) cc_final: 0.5990 (pm20) REVERT: C 164 ASN cc_start: 0.8921 (OUTLIER) cc_final: 0.8680 (t0) REVERT: C 290 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: C 389 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8359 (pp) REVERT: C 417 ARG cc_start: 0.8544 (ttp80) cc_final: 0.8202 (ttp80) REVERT: D 119 GLN cc_start: 0.7156 (OUTLIER) cc_final: 0.6065 (pm20) REVERT: D 164 ASN cc_start: 0.8941 (OUTLIER) cc_final: 0.8709 (t0) REVERT: D 290 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7077 (mp0) REVERT: D 389 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8324 (pp) REVERT: D 417 ARG cc_start: 0.8492 (ttp80) cc_final: 0.8113 (ttp80) REVERT: B 119 GLN cc_start: 0.6876 (OUTLIER) cc_final: 0.6018 (pm20) REVERT: B 290 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7112 (mp0) REVERT: B 389 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8392 (pp) REVERT: B 410 GLN cc_start: 0.8411 (tp40) cc_final: 0.8139 (tp-100) outliers start: 61 outliers final: 43 residues processed: 217 average time/residue: 0.1866 time to fit residues: 64.3101 Evaluate side-chains 224 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 168 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE 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 179 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 271 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 164 ASN Chi-restraints excluded: chain C residue 179 THR 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 318 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 19 ILE 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 164 ASN Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 387 CYS Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 182 THR 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 36 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.156406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.121782 restraints weight = 17397.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.109655 restraints weight = 22121.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.108179 restraints weight = 23717.896| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13280 Z= 0.218 Angle : 0.684 11.452 17936 Z= 0.314 Chirality : 0.041 0.131 2092 Planarity : 0.005 0.066 2168 Dihedral : 11.978 134.232 2228 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.50 % Allowed : 18.54 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.23), residues: 1532 helix: 1.12 (0.18), residues: 984 sheet: -1.61 (0.46), residues: 116 loop : -1.50 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 155 HIS 0.002 0.001 HIS A 281 PHE 0.022 0.001 PHE C 365 TYR 0.010 0.001 TYR B 175 ARG 0.005 0.000 ARG D 417 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2421.60 seconds wall clock time: 44 minutes 47.74 seconds (2687.74 seconds total)