Starting phenix.real_space_refine on Thu Aug 6 20:28:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10mz_75297/08_2026/10mz_75297_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/10mz_75297/08_2026/10mz_75297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10mz_75297/08_2026/10mz_75297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10mz_75297/08_2026/10mz_75297.map" model { file = "/net/cci-nas-00/data/ceres_data/10mz_75297/08_2026/10mz_75297_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10mz_75297/08_2026/10mz_75297_neut.cif" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 10312 2.51 5 N 3026 2.21 5 O 3110 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16532 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2758 Classifications: {'peptide': 351} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 342} Chain: "B" Number of atoms: 2754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2754 Classifications: {'peptide': 350} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 341} Chain: "C" Number of atoms: 2754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2754 Classifications: {'peptide': 350} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 341} Chain: "D" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2758 Classifications: {'peptide': 351} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 342} Chain: "E" Number of atoms: 2754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2754 Classifications: {'peptide': 350} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 341} Chain: "F" Number of atoms: 2754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2754 Classifications: {'peptide': 350} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 341} Time building chain proxies: 3.86, per 1000 atoms: 0.23 Number of scatterers: 16532 At special positions: 0 Unit cell: (141.218, 117.502, 87.318, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 3110 8.00 N 3026 7.00 C 10312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 773.8 milliseconds 4180 Ramachandran restraints generated. 2090 Oldfield, 0 Emsley, 2090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3936 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 14 sheets defined 48.2% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 1 through 13 removed outlier: 3.634A pdb=" N LEU A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR A 12 " --> pdb=" O ASP A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 52 Processing helix chain 'A' and resid 55 through 66 Processing helix chain 'A' and resid 111 through 119 removed outlier: 3.991A pdb=" N ASN A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 149 Processing helix chain 'A' and resid 182 through 189 removed outlier: 3.712A pdb=" N ASN A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 193 removed outlier: 3.632A pdb=" N GLN A 193 " --> pdb=" O SER A 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 190 through 193' Processing helix chain 'A' and resid 207 through 219 Processing helix chain 'A' and resid 230 through 242 Processing helix chain 'A' and resid 243 through 256 removed outlier: 3.712A pdb=" N GLU A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN A 249 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 295 Processing helix chain 'A' and resid 297 through 307 removed outlier: 3.813A pdb=" N ALA A 305 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 326 Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 339 through 350 Processing helix chain 'B' and resid 2 through 13 removed outlier: 3.651A pdb=" N LEU B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B 12 " --> pdb=" O ASP B 8 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS B 13 " --> pdb=" O GLY B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 52 Processing helix chain 'B' and resid 55 through 66 Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 111 through 119 removed outlier: 3.787A pdb=" N ILE B 118 " --> pdb=" O GLN B 114 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 148 removed outlier: 3.613A pdb=" N MET B 138 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 193 removed outlier: 3.586A pdb=" N ALA B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 192 " --> pdb=" O LYS B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 219 Processing helix chain 'B' and resid 232 through 242 Processing helix chain 'B' and resid 243 through 257 removed outlier: 3.782A pdb=" N LEU B 252 " --> pdb=" O GLU B 248 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP B 253 " --> pdb=" O GLN B 249 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 292 Processing helix chain 'B' and resid 297 through 311 Processing helix chain 'B' and resid 314 through 324 removed outlier: 4.325A pdb=" N VAL B 324 " --> pdb=" O TYR B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 337 Processing helix chain 'B' and resid 340 through 350 Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 42 through 52 Processing helix chain 'C' and resid 55 through 66 Processing helix chain 'C' and resid 113 through 119 Processing helix chain 'C' and resid 135 through 149 removed outlier: 4.083A pdb=" N ALA C 139 " --> pdb=" O SER C 135 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA C 140 " --> pdb=" O THR C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 190 Processing helix chain 'C' and resid 205 through 218 removed outlier: 3.505A pdb=" N MET C 209 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 242 Processing helix chain 'C' and resid 243 through 257 removed outlier: 4.109A pdb=" N GLU C 248 " --> pdb=" O LYS C 244 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N GLN C 249 " --> pdb=" O GLU C 245 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN C 257 " --> pdb=" O ASP C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 295 Processing helix chain 'C' and resid 299 through 306 Processing helix chain 'C' and resid 307 through 311 Processing helix chain 'C' and resid 314 through 325 Processing helix chain 'C' and resid 329 through 337 Processing helix chain 'C' and resid 339 through 350 removed outlier: 4.094A pdb=" N LEU C 343 " --> pdb=" O SER C 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 1 through 13 removed outlier: 3.629A pdb=" N LEU D 11 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR D 12 " --> pdb=" O ASP D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 52 Processing helix chain 'D' and resid 55 through 66 Processing helix chain 'D' and resid 111 through 119 removed outlier: 3.990A pdb=" N ASN D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 149 Processing helix chain 'D' and resid 182 through 190 removed outlier: 3.623A pdb=" N ASN D 189 " --> pdb=" O VAL D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 193 No H-bonds generated for 'chain 'D' and resid 191 through 193' Processing helix chain 'D' and resid 207 through 219 Processing helix chain 'D' and resid 230 through 242 Processing helix chain 'D' and resid 243 through 256 removed outlier: 3.712A pdb=" N GLU D 248 " --> pdb=" O LYS D 244 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN D 249 " --> pdb=" O GLU D 245 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU D 256 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 295 Processing helix chain 'D' and resid 297 through 307 removed outlier: 3.806A pdb=" N ALA D 305 " --> pdb=" O LYS D 301 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 326 Processing helix chain 'D' and resid 329 through 337 Processing helix chain 'D' and resid 339 through 350 Processing helix chain 'E' and resid 2 through 13 removed outlier: 3.650A pdb=" N LEU E 11 " --> pdb=" O LEU E 7 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS E 13 " --> pdb=" O GLY E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 52 Processing helix chain 'E' and resid 55 through 66 Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 111 through 119 removed outlier: 3.736A pdb=" N ILE E 118 " --> pdb=" O GLN E 114 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA E 119 " --> pdb=" O ASN E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 148 removed outlier: 3.524A pdb=" N MET E 138 " --> pdb=" O LYS E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 193 removed outlier: 3.625A pdb=" N ALA E 186 " --> pdb=" O SER E 182 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU E 187 " --> pdb=" O TYR E 183 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG E 192 " --> pdb=" O LYS E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 219 Processing helix chain 'E' and resid 232 through 242 Processing helix chain 'E' and resid 243 through 257 removed outlier: 3.637A pdb=" N GLN E 249 " --> pdb=" O GLU E 245 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP E 253 " --> pdb=" O GLN E 249 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LEU E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 292 Processing helix chain 'E' and resid 297 through 311 Processing helix chain 'E' and resid 314 through 324 removed outlier: 4.238A pdb=" N VAL E 324 " --> pdb=" O TYR E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 337 removed outlier: 3.556A pdb=" N GLN E 331 " --> pdb=" O LYS E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 350 Processing helix chain 'F' and resid 2 through 13 Processing helix chain 'F' and resid 42 through 52 Processing helix chain 'F' and resid 55 through 66 Processing helix chain 'F' and resid 103 through 108 removed outlier: 3.755A pdb=" N LEU F 107 " --> pdb=" O THR F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 119 Processing helix chain 'F' and resid 135 through 149 removed outlier: 4.093A pdb=" N ALA F 139 " --> pdb=" O SER F 135 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA F 140 " --> pdb=" O THR F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 190 Processing helix chain 'F' and resid 205 through 218 Processing helix chain 'F' and resid 230 through 242 Processing helix chain 'F' and resid 243 through 257 removed outlier: 4.202A pdb=" N GLU F 248 " --> pdb=" O LYS F 244 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLN F 249 " --> pdb=" O GLU F 245 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU F 252 " --> pdb=" O GLU F 248 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN F 257 " --> pdb=" O ASP F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 295 Processing helix chain 'F' and resid 299 through 306 Processing helix chain 'F' and resid 307 through 311 Processing helix chain 'F' and resid 314 through 325 Processing helix chain 'F' and resid 329 through 337 Processing helix chain 'F' and resid 339 through 350 removed outlier: 4.148A pdb=" N LEU F 343 " --> pdb=" O SER F 339 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 36 removed outlier: 3.737A pdb=" N LEU A 27 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP A 17 " --> pdb=" O ARG A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 221 through 227 removed outlier: 3.901A pdb=" N CYS A 222 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 226 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY A 128 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU A 123 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL A 261 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU A 125 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ALA A 263 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL A 127 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLN A 265 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 174 removed outlier: 7.445A pdb=" N ILE A 153 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ARG A 174 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N THR A 155 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 33 through 36 removed outlier: 5.050A pdb=" N THR B 21 " --> pdb=" O PRO B 25 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 172 through 175 removed outlier: 6.983A pdb=" N ILE B 153 " --> pdb=" O THR B 172 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N ARG B 174 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N THR B 155 " --> pdb=" O ARG B 174 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA B 224 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU B 123 " --> pdb=" O GLY B 260 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE B 262 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LEU B 125 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N GLN B 264 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N HIS B 276 " --> pdb=" O LEU B 267 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 33 through 35 removed outlier: 3.661A pdb=" N ASP C 17 " --> pdb=" O ARG C 29 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE C 79 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 170 through 173 removed outlier: 6.369A pdb=" N ILE C 153 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR C 225 " --> pdb=" O ILE C 200 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA C 224 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU C 226 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU C 123 " --> pdb=" O GLY C 260 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ILE C 262 " --> pdb=" O LEU C 123 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU C 125 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N GLN C 264 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL C 127 " --> pdb=" O GLN C 264 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N LEU C 266 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 33 through 37 removed outlier: 4.035A pdb=" N ILE D 26 " --> pdb=" O GLN D 37 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU D 27 " --> pdb=" O TYR D 19 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP D 17 " --> pdb=" O ARG D 29 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 221 through 227 removed outlier: 3.934A pdb=" N CYS D 222 " --> pdb=" O GLY D 122 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU D 226 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY D 128 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU D 123 " --> pdb=" O LYS D 259 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL D 261 " --> pdb=" O LEU D 123 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU D 125 " --> pdb=" O VAL D 261 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ALA D 263 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL D 127 " --> pdb=" O ALA D 263 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLN D 265 " --> pdb=" O VAL D 127 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 171 through 174 removed outlier: 7.444A pdb=" N ILE D 153 " --> pdb=" O THR D 172 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ARG D 174 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N THR D 155 " --> pdb=" O ARG D 174 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 33 through 36 removed outlier: 5.046A pdb=" N THR E 21 " --> pdb=" O PRO E 25 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 172 through 175 removed outlier: 6.979A pdb=" N ILE E 153 " --> pdb=" O THR E 172 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ARG E 174 " --> pdb=" O ILE E 153 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR E 155 " --> pdb=" O ARG E 174 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA E 224 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU E 123 " --> pdb=" O GLY E 260 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ILE E 262 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU E 125 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLN E 264 " --> pdb=" O LEU E 125 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N HIS E 276 " --> pdb=" O LEU E 267 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 33 through 35 removed outlier: 3.682A pdb=" N ASP F 17 " --> pdb=" O ARG F 29 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE F 79 " --> pdb=" O VAL F 72 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 170 through 173 removed outlier: 6.310A pdb=" N ILE F 153 " --> pdb=" O THR F 172 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR F 225 " --> pdb=" O ILE F 200 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU F 226 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU F 123 " --> pdb=" O LEU F 258 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY F 260 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN F 264 " --> pdb=" O VAL F 127 " (cutoff:3.500A) 808 hydrogen bonds defined for protein. 2334 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.89 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5782 1.34 - 1.46: 2798 1.46 - 1.58: 8018 1.58 - 1.69: 0 1.69 - 1.81: 156 Bond restraints: 16754 Sorted by residual: bond pdb=" N PHE C 104 " pdb=" CA PHE C 104 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.30e-02 5.92e+03 6.05e+00 bond pdb=" CB PHE C 104 " pdb=" CG PHE C 104 " ideal model delta sigma weight residual 1.502 1.519 -0.017 2.30e-02 1.89e+03 5.73e-01 bond pdb=" C LEU E 266 " pdb=" O LEU E 266 " ideal model delta sigma weight residual 1.234 1.245 -0.010 1.41e-02 5.03e+03 5.16e-01 bond pdb=" C LEU B 266 " pdb=" O LEU B 266 " ideal model delta sigma weight residual 1.234 1.244 -0.010 1.41e-02 5.03e+03 4.99e-01 bond pdb=" N ASN C 271 " pdb=" CA ASN C 271 " ideal model delta sigma weight residual 1.460 1.471 -0.011 1.54e-02 4.22e+03 4.92e-01 ... (remaining 16749 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 22295 1.48 - 2.95: 244 2.95 - 4.43: 37 4.43 - 5.91: 4 5.91 - 7.39: 2 Bond angle restraints: 22582 Sorted by residual: angle pdb=" CA PHE C 104 " pdb=" C PHE C 104 " pdb=" O PHE C 104 " ideal model delta sigma weight residual 119.49 115.39 4.10 1.21e+00 6.83e-01 1.15e+01 angle pdb=" CA PHE C 104 " pdb=" C PHE C 104 " pdb=" N GLU C 105 " ideal model delta sigma weight residual 118.08 121.18 -3.10 1.30e+00 5.92e-01 5.69e+00 angle pdb=" CA PHE C 104 " pdb=" CB PHE C 104 " pdb=" CG PHE C 104 " ideal model delta sigma weight residual 113.80 116.13 -2.33 1.00e+00 1.00e+00 5.44e+00 angle pdb=" C LEU F 107 " pdb=" N LYS F 108 " pdb=" CA LYS F 108 " ideal model delta sigma weight residual 121.54 125.93 -4.39 1.91e+00 2.74e-01 5.28e+00 angle pdb=" C PHE C 104 " pdb=" CA PHE C 104 " pdb=" CB PHE C 104 " ideal model delta sigma weight residual 110.32 105.47 4.85 2.11e+00 2.25e-01 5.28e+00 ... (remaining 22577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.30: 9019 15.30 - 30.61: 940 30.61 - 45.91: 319 45.91 - 61.21: 28 61.21 - 76.52: 10 Dihedral angle restraints: 10316 sinusoidal: 4242 harmonic: 6074 Sorted by residual: dihedral pdb=" CG ARG E 35 " pdb=" CD ARG E 35 " pdb=" NE ARG E 35 " pdb=" CZ ARG E 35 " ideal model delta sinusoidal sigma weight residual 90.00 133.17 -43.17 2 1.50e+01 4.44e-03 9.99e+00 dihedral pdb=" CG ARG B 35 " pdb=" CD ARG B 35 " pdb=" NE ARG B 35 " pdb=" CZ ARG B 35 " ideal model delta sinusoidal sigma weight residual 90.00 133.17 -43.17 2 1.50e+01 4.44e-03 9.99e+00 dihedral pdb=" CB MET B 346 " pdb=" CG MET B 346 " pdb=" SD MET B 346 " pdb=" CE MET B 346 " ideal model delta sinusoidal sigma weight residual 60.00 113.03 -53.03 3 1.50e+01 4.44e-03 9.17e+00 ... (remaining 10313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1624 0.025 - 0.050: 613 0.050 - 0.075: 187 0.075 - 0.100: 89 0.100 - 0.124: 91 Chirality restraints: 2604 Sorted by residual: chirality pdb=" CA ILE A 328 " pdb=" N ILE A 328 " pdb=" C ILE A 328 " pdb=" CB ILE A 328 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA ILE D 328 " pdb=" N ILE D 328 " pdb=" C ILE D 328 " pdb=" CB ILE D 328 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA VAL E 242 " pdb=" N VAL E 242 " pdb=" C VAL E 242 " pdb=" CB VAL E 242 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 2601 not shown) Planarity restraints: 2960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 103 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.81e+00 pdb=" C THR C 103 " 0.023 2.00e-02 2.50e+03 pdb=" O THR C 103 " -0.009 2.00e-02 2.50e+03 pdb=" N PHE C 104 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 89 " 0.017 5.00e-02 4.00e+02 2.61e-02 1.09e+00 pdb=" N PRO B 90 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO B 90 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 90 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 89 " -0.017 5.00e-02 4.00e+02 2.50e-02 1.00e+00 pdb=" N PRO E 90 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO E 90 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 90 " -0.014 5.00e-02 4.00e+02 ... (remaining 2957 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2726 2.77 - 3.30: 15327 3.30 - 3.84: 26974 3.84 - 4.37: 29546 4.37 - 4.90: 52060 Nonbonded interactions: 126633 Sorted by model distance: nonbonded pdb=" OE2 GLU D 181 " pdb=" OG1 THR E 65 " model vdw 2.239 3.040 nonbonded pdb=" O GLY E 201 " pdb=" OG1 THR E 225 " model vdw 2.261 3.040 nonbonded pdb=" O GLY B 201 " pdb=" OG1 THR B 225 " model vdw 2.261 3.040 nonbonded pdb=" O GLY C 201 " pdb=" OG1 THR C 225 " model vdw 2.277 3.040 nonbonded pdb=" OE2 GLU A 181 " pdb=" OG1 THR B 65 " model vdw 2.278 3.040 ... (remaining 126628 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 350) selection = chain 'B' selection = chain 'C' selection = (chain 'D' and resid 1 through 350) selection = chain 'E' selection = chain 'F' } 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: 7.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.210 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 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 : 0.001 0.032 16754 Z= 0.078 Angle : 0.403 7.386 22582 Z= 0.220 Chirality : 0.037 0.124 2604 Planarity : 0.002 0.026 2960 Dihedral : 13.817 76.518 6380 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.19), residues: 2090 helix: 1.80 (0.18), residues: 928 sheet: 0.60 (0.27), residues: 462 loop : -1.54 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 275 TYR 0.005 0.001 TYR E 144 PHE 0.006 0.001 PHE F 279 HIS 0.006 0.000 HIS E 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00136 / 0.08 (16754) covalent geometry : angle 0.40346 / 0.22 (22582) hydrogen bonds : bond 0.17018 / 11.16 ( 808) hydrogen bonds : angle 5.81189 / 3.97 ( 2334) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4180 Ramachandran restraints generated. 2090 Oldfield, 0 Emsley, 2090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4180 Ramachandran restraints generated. 2090 Oldfield, 0 Emsley, 2090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ILE cc_start: 0.9267 (tt) cc_final: 0.9009 (pt) REVERT: A 213 MET cc_start: 0.9159 (mmm) cc_final: 0.8630 (mmm) REVERT: A 320 TYR cc_start: 0.9198 (t80) cc_final: 0.8936 (t80) REVERT: B 31 ASP cc_start: 0.7989 (m-30) cc_final: 0.7736 (t0) REVERT: B 109 LEU cc_start: 0.8736 (pt) cc_final: 0.8461 (tt) REVERT: B 233 GLN cc_start: 0.9257 (mp10) cc_final: 0.9048 (tm-30) REVERT: C 56 ASP cc_start: 0.9341 (m-30) cc_final: 0.9084 (p0) REVERT: C 109 LEU cc_start: 0.8752 (mm) cc_final: 0.8465 (mm) REVERT: C 157 GLU cc_start: 0.8283 (mt-10) cc_final: 0.8060 (mp0) REVERT: C 197 MET cc_start: 0.8271 (ttp) cc_final: 0.7927 (ttm) REVERT: C 213 MET cc_start: 0.9170 (tpp) cc_final: 0.8922 (tpt) REVERT: D 56 ASP cc_start: 0.9458 (m-30) cc_final: 0.9212 (p0) REVERT: D 178 LEU cc_start: 0.9267 (tp) cc_final: 0.8967 (tt) REVERT: D 198 ILE cc_start: 0.9283 (tt) cc_final: 0.9050 (pt) REVERT: D 213 MET cc_start: 0.9125 (mmm) cc_final: 0.8575 (mmm) REVERT: D 236 GLU cc_start: 0.9589 (tt0) cc_final: 0.8905 (tm-30) REVERT: D 240 HIS cc_start: 0.9334 (m90) cc_final: 0.8282 (m170) REVERT: E 31 ASP cc_start: 0.8064 (m-30) cc_final: 0.7804 (t0) REVERT: E 109 LEU cc_start: 0.8707 (pt) cc_final: 0.8467 (tt) REVERT: E 157 GLU cc_start: 0.8616 (pm20) cc_final: 0.8159 (pm20) REVERT: E 332 ASP cc_start: 0.9412 (t70) cc_final: 0.9111 (m-30) REVERT: F 56 ASP cc_start: 0.9328 (m-30) cc_final: 0.9026 (p0) REVERT: F 197 MET cc_start: 0.8169 (ttp) cc_final: 0.7817 (ttm) outliers start: 0 outliers final: 0 residues processed: 313 average time/residue: 0.1350 time to fit residues: 63.7645 Evaluate side-chains 176 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.0010 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.076079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.054423 restraints weight = 72742.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.056307 restraints weight = 39768.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.057523 restraints weight = 27479.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.058334 restraints weight = 21721.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.058876 restraints weight = 18689.606| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16754 Z= 0.152 Angle : 0.579 10.072 22582 Z= 0.294 Chirality : 0.041 0.175 2604 Planarity : 0.003 0.037 2960 Dihedral : 3.631 21.391 2306 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.25 % Allowed : 11.96 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.19), residues: 2090 helix: 1.86 (0.18), residues: 934 sheet: 0.32 (0.27), residues: 452 loop : -1.47 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 268 TYR 0.038 0.002 TYR E 320 PHE 0.022 0.001 PHE D 250 HIS 0.008 0.001 HIS B 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (16754) covalent geometry : angle 0.57892 / 0.29 (22582) hydrogen bonds : bond 0.03196 / 2.07 ( 808) hydrogen bonds : angle 4.68146 / 3.19 ( 2334) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4180 Ramachandran restraints generated. 2090 Oldfield, 0 Emsley, 2090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4180 Ramachandran restraints generated. 2090 Oldfield, 0 Emsley, 2090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 THR cc_start: 0.9554 (m) cc_final: 0.9166 (p) REVERT: A 178 LEU cc_start: 0.9122 (tt) cc_final: 0.8693 (tt) REVERT: A 209 MET cc_start: 0.9206 (mmm) cc_final: 0.8986 (mmp) REVERT: A 240 HIS cc_start: 0.9027 (m90) cc_final: 0.8623 (m-70) REVERT: A 312 MET cc_start: 0.7204 (ttm) cc_final: 0.6470 (ttp) REVERT: A 320 TYR cc_start: 0.9136 (t80) cc_final: 0.8929 (t80) REVERT: B 31 ASP cc_start: 0.8231 (m-30) cc_final: 0.7874 (t0) REVERT: B 109 LEU cc_start: 0.8841 (pt) cc_final: 0.8463 (tt) REVERT: B 138 MET cc_start: 0.8826 (mmm) cc_final: 0.8576 (mmm) REVERT: B 157 GLU cc_start: 0.8815 (pm20) cc_final: 0.8259 (pm20) REVERT: B 233 GLN cc_start: 0.9264 (mp10) cc_final: 0.9008 (tm-30) REVERT: B 244 LYS cc_start: 0.9636 (mmmt) cc_final: 0.9303 (mmmt) REVERT: C 10 MET cc_start: 0.7485 (tmm) cc_final: 0.7116 (ttp) REVERT: C 56 ASP cc_start: 0.9338 (m-30) cc_final: 0.9114 (p0) REVERT: C 109 LEU cc_start: 0.8645 (mm) cc_final: 0.8298 (mm) REVERT: C 113 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9251 (pt) REVERT: C 157 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8169 (mp0) REVERT: C 197 MET cc_start: 0.8120 (ttp) cc_final: 0.7859 (ttm) REVERT: C 312 MET cc_start: 0.7106 (mtp) cc_final: 0.4779 (mtp) REVERT: D 172 THR cc_start: 0.9554 (m) cc_final: 0.9152 (p) REVERT: D 178 LEU cc_start: 0.9272 (tp) cc_final: 0.9002 (tt) REVERT: D 198 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.8897 (mp) REVERT: D 200 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8969 (mm) REVERT: D 209 MET cc_start: 0.9191 (mmm) cc_final: 0.8986 (mmp) REVERT: D 240 HIS cc_start: 0.9182 (m90) cc_final: 0.8852 (m-70) REVERT: D 304 MET cc_start: 0.8903 (mtp) cc_final: 0.8596 (tpp) REVERT: D 312 MET cc_start: 0.7146 (ttm) cc_final: 0.6760 (ttm) REVERT: D 320 TYR cc_start: 0.9027 (t80) cc_final: 0.8663 (t80) REVERT: E 31 ASP cc_start: 0.8276 (m-30) cc_final: 0.7910 (t0) REVERT: E 109 LEU cc_start: 0.8853 (pt) cc_final: 0.8417 (tt) REVERT: E 157 GLU cc_start: 0.8810 (pm20) cc_final: 0.8201 (pm20) REVERT: E 223 MET cc_start: 0.7049 (mpp) cc_final: 0.6598 (mpp) REVERT: E 276 HIS cc_start: 0.6196 (m-70) cc_final: 0.5896 (m-70) REVERT: E 320 TYR cc_start: 0.9234 (m-80) cc_final: 0.8812 (m-80) REVERT: E 332 ASP cc_start: 0.9430 (t70) cc_final: 0.9166 (m-30) REVERT: F 197 MET cc_start: 0.8130 (ttp) cc_final: 0.7865 (ttm) outliers start: 22 outliers final: 11 residues processed: 209 average time/residue: 0.1412 time to fit residues: 44.6431 Evaluate side-chains 170 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 268 ARG Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 343 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 0.0270 chunk 72 optimal weight: 3.9990 chunk 181 optimal weight: 0.9980 chunk 184 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 99 optimal weight: 0.0370 chunk 141 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 134 optimal weight: 0.1980 overall best weight: 0.8518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 ASN D 69 ASN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 335 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.076030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.053871 restraints weight = 74063.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.055791 restraints weight = 39724.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.057014 restraints weight = 27360.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.057813 restraints weight = 21729.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.058342 restraints weight = 18776.269| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16754 Z= 0.136 Angle : 0.572 13.041 22582 Z= 0.284 Chirality : 0.041 0.200 2604 Planarity : 0.004 0.077 2960 Dihedral : 3.785 20.736 2306 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.76 % Allowed : 15.59 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.19), residues: 2090 helix: 1.70 (0.17), residues: 934 sheet: 0.36 (0.27), residues: 436 loop : -1.47 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 268 TYR 0.025 0.002 TYR E 320 PHE 0.017 0.001 PHE E 250 HIS 0.006 0.001 HIS B 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (16754) covalent geometry : angle 0.57153 / 0.28 (22582) hydrogen bonds : bond 0.02968 / 1.95 ( 808) hydrogen bonds : angle 4.57554 / 3.12 ( 2334) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4180 Ramachandran restraints generated. 2090 Oldfield, 0 Emsley, 2090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4180 Ramachandran restraints generated. 2090 Oldfield, 0 Emsley, 2090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 THR cc_start: 0.9545 (m) cc_final: 0.9144 (p) REVERT: A 178 LEU cc_start: 0.9099 (tt) cc_final: 0.8586 (tt) REVERT: A 240 HIS cc_start: 0.9008 (m90) cc_final: 0.8592 (m-70) REVERT: A 312 MET cc_start: 0.7173 (ttm) cc_final: 0.6698 (ttm) REVERT: A 320 TYR cc_start: 0.9133 (t80) cc_final: 0.8920 (t80) REVERT: B 31 ASP cc_start: 0.8262 (m-30) cc_final: 0.7968 (t0) REVERT: B 157 GLU cc_start: 0.8793 (pm20) cc_final: 0.8219 (pm20) REVERT: B 199 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8264 (mm) REVERT: B 244 LYS cc_start: 0.9675 (mmmt) cc_final: 0.9319 (mmmt) REVERT: B 275 ARG cc_start: 0.8296 (mpt90) cc_final: 0.7538 (ppt170) REVERT: B 321 GLN cc_start: 0.9277 (tm-30) cc_final: 0.9006 (tm-30) REVERT: B 332 ASP cc_start: 0.9378 (t0) cc_final: 0.9027 (m-30) REVERT: C 103 THR cc_start: 0.8641 (OUTLIER) cc_final: 0.8124 (t) REVERT: C 109 LEU cc_start: 0.8698 (mm) cc_final: 0.8205 (mm) REVERT: C 191 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8951 (mm) REVERT: C 197 MET cc_start: 0.8202 (ttp) cc_final: 0.7918 (ttm) REVERT: C 312 MET cc_start: 0.5847 (mtp) cc_final: 0.5402 (mtp) REVERT: D 178 LEU cc_start: 0.9297 (tp) cc_final: 0.9017 (tt) REVERT: D 223 MET cc_start: 0.8263 (mtp) cc_final: 0.8062 (ttm) REVERT: D 320 TYR cc_start: 0.9070 (t80) cc_final: 0.8740 (t80) REVERT: E 31 ASP cc_start: 0.8358 (m-30) cc_final: 0.8074 (t0) REVERT: E 109 LEU cc_start: 0.8712 (pt) cc_final: 0.8184 (tt) REVERT: E 157 GLU cc_start: 0.8798 (pm20) cc_final: 0.8185 (pm20) REVERT: E 223 MET cc_start: 0.7402 (mpp) cc_final: 0.6893 (mpp) REVERT: E 320 TYR cc_start: 0.9258 (m-80) cc_final: 0.8696 (m-80) REVERT: E 332 ASP cc_start: 0.9453 (t70) cc_final: 0.9166 (m-30) REVERT: F 54 MET cc_start: 0.8550 (mtp) cc_final: 0.8347 (mtm) REVERT: F 103 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8169 (t) REVERT: F 191 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8924 (mm) REVERT: F 197 MET cc_start: 0.8185 (ttp) cc_final: 0.7881 (ttm) outliers start: 31 outliers final: 11 residues processed: 189 average time/residue: 0.1301 time to fit residues: 38.2474 Evaluate side-chains 165 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 343 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 186 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN D 147 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 GLN ** F 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.073592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.051304 restraints weight = 75086.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.053155 restraints weight = 40921.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.054358 restraints weight = 28479.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.055128 restraints weight = 22773.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.055609 restraints weight = 19786.745| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16754 Z= 0.188 Angle : 0.595 10.216 22582 Z= 0.304 Chirality : 0.041 0.164 2604 Planarity : 0.004 0.068 2960 Dihedral : 4.056 25.760 2306 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.15 % Allowed : 16.67 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.19), residues: 2090 helix: 1.57 (0.17), residues: 924 sheet: 0.33 (0.27), residues: 448 loop : -1.60 (0.21), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 268 TYR 0.019 0.002 TYR E 320 PHE 0.013 0.001 PHE B 279 HIS 0.016 0.001 HIS D 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.19 (16754) covalent geometry : angle 0.59508 / 0.30 (22582) hydrogen bonds : bond 0.03153 / 2.10 ( 808) hydrogen bonds : angle 4.73389 / 3.26 ( 2334) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4180 Ramachandran restraints generated. 2090 Oldfield, 0 Emsley, 2090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4180 Ramachandran restraints generated. 2090 Oldfield, 0 Emsley, 2090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8770 (mtm) cc_final: 0.8514 (mtm) REVERT: A 240 HIS cc_start: 0.8984 (m90) cc_final: 0.8535 (m-70) REVERT: A 312 MET cc_start: 0.7222 (ttm) cc_final: 0.6744 (ttm) REVERT: A 320 TYR cc_start: 0.9130 (t80) cc_final: 0.8885 (t80) REVERT: B 31 ASP cc_start: 0.8521 (m-30) cc_final: 0.8269 (t0) REVERT: B 157 GLU cc_start: 0.8758 (pm20) cc_final: 0.8188 (pm20) REVERT: B 244 LYS cc_start: 0.9676 (mmmt) cc_final: 0.9331 (mmmt) REVERT: B 320 TYR cc_start: 0.9085 (m-80) cc_final: 0.8626 (m-80) REVERT: B 332 ASP cc_start: 0.9420 (t0) cc_final: 0.9071 (m-30) REVERT: C 10 MET cc_start: 0.7677 (tmm) cc_final: 0.7370 (ttp) REVERT: C 53 MET cc_start: 0.9041 (ptm) cc_final: 0.8611 (ppp) REVERT: C 103 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8015 (p) REVERT: C 197 MET cc_start: 0.8265 (ttp) cc_final: 0.7955 (ttm) REVERT: D 178 LEU cc_start: 0.9363 (tp) cc_final: 0.9070 (tt) REVERT: D 213 MET cc_start: 0.9118 (mmm) cc_final: 0.8755 (mmm) REVERT: D 312 MET cc_start: 0.7105 (ttm) cc_final: 0.6573 (ttm) REVERT: E 31 ASP cc_start: 0.8530 (m-30) cc_final: 0.8270 (t0) REVERT: E 157 GLU cc_start: 0.8757 (pm20) cc_final: 0.8247 (pm20) REVERT: E 199 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8167 (mm) REVERT: E 320 TYR cc_start: 0.9255 (m-80) cc_final: 0.8661 (m-80) REVERT: E 332 ASP cc_start: 0.9463 (t70) cc_final: 0.9182 (m-30) REVERT: F 10 MET cc_start: 0.7705 (tmm) cc_final: 0.7439 (ttp) REVERT: F 53 MET cc_start: 0.9006 (ptm) cc_final: 0.8758 (ppp) REVERT: F 103 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.7976 (p) REVERT: F 191 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9065 (mm) REVERT: F 197 MET cc_start: 0.8233 (ttp) cc_final: 0.7878 (ttm) outliers start: 38 outliers final: 19 residues processed: 186 average time/residue: 0.1271 time to fit residues: 36.8363 Evaluate side-chains 167 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 85 PHE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 298 HIS Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 298 HIS Chi-restraints excluded: chain F residue 308 GLN Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 343 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 208 optimal weight: 0.4980 chunk 132 optimal weight: 0.0770 chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 0.0570 chunk 175 optimal weight: 2.9990 chunk 87 optimal weight: 0.0060 chunk 22 optimal weight: 1.9990 chunk 106 optimal weight: 0.0370 chunk 203 optimal weight: 0.9980 chunk 18 optimal weight: 0.0870 overall best weight: 0.0528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 ASN A 69 ASN A 147 GLN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN D 147 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 240 HIS E 173 GLN ** F 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 335 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.076508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.054327 restraints weight = 72690.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.056245 restraints weight = 39204.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.057485 restraints weight = 27039.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.058284 restraints weight = 21396.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.058834 restraints weight = 18471.674| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16754 Z= 0.095 Angle : 0.578 11.975 22582 Z= 0.283 Chirality : 0.041 0.162 2604 Planarity : 0.003 0.054 2960 Dihedral : 3.784 17.737 2306 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.93 % Allowed : 18.31 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.19), residues: 2090 helix: 1.65 (0.18), residues: 918 sheet: 0.52 (0.27), residues: 448 loop : -1.58 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 237 TYR 0.016 0.001 TYR E 320 PHE 0.010 0.001 PHE E 250 HIS 0.011 0.001 HIS D 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 (16754) covalent geometry : angle 0.57768 / 0.28 (22582) hydrogen bonds : bond 0.02569 / 1.70 ( 808) hydrogen bonds : angle 4.41214 / 3.02 ( 2334) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4180 Ramachandran restraints generated. 2090 Oldfield, 0 Emsley, 2090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4180 Ramachandran restraints generated. 2090 Oldfield, 0 Emsley, 2090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 HIS cc_start: 0.8917 (m90) cc_final: 0.8606 (m-70) REVERT: A 312 MET cc_start: 0.7415 (ttm) cc_final: 0.7061 (ttm) REVERT: B 157 GLU cc_start: 0.8703 (pm20) cc_final: 0.8167 (pm20) REVERT: B 320 TYR cc_start: 0.8904 (m-80) cc_final: 0.8342 (m-80) REVERT: C 53 MET cc_start: 0.9005 (ptm) cc_final: 0.8520 (ppp) REVERT: C 103 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8008 (p) REVERT: C 109 LEU cc_start: 0.8777 (mm) cc_final: 0.8196 (mm) REVERT: C 197 MET cc_start: 0.8216 (ttp) cc_final: 0.7962 (ttm) REVERT: D 178 LEU cc_start: 0.9308 (tp) cc_final: 0.9032 (tt) REVERT: D 213 MET cc_start: 0.9018 (mmm) cc_final: 0.8687 (mmm) REVERT: E 31 ASP cc_start: 0.8409 (m-30) cc_final: 0.8181 (t0) REVERT: E 85 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8726 (m-10) REVERT: E 157 GLU cc_start: 0.8727 (pm20) cc_final: 0.8210 (pm20) REVERT: E 320 TYR cc_start: 0.9299 (m-80) cc_final: 0.8788 (m-80) REVERT: E 332 ASP cc_start: 0.9432 (t70) cc_final: 0.9154 (m-30) REVERT: F 103 THR cc_start: 0.8466 (OUTLIER) cc_final: 0.7967 (p) REVERT: F 197 MET cc_start: 0.8169 (ttp) cc_final: 0.7969 (ttm) REVERT: F 304 MET cc_start: 0.8725 (ppp) cc_final: 0.8465 (ppp) REVERT: F 320 TYR cc_start: 0.9243 (t80) cc_final: 0.9016 (t80) outliers start: 34 outliers final: 15 residues processed: 185 average time/residue: 0.1262 time to fit residues: 36.5034 Evaluate side-chains 163 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 308 GLN Chi-restraints excluded: chain F residue 319 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 20 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 112 optimal weight: 0.3980 chunk 22 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 149 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 162 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 335 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.075018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.052909 restraints weight = 74363.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.054758 restraints weight = 40174.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.055944 restraints weight = 27796.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.056735 restraints weight = 22132.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.057250 restraints weight = 19138.823| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16754 Z= 0.122 Angle : 0.572 10.417 22582 Z= 0.287 Chirality : 0.040 0.161 2604 Planarity : 0.003 0.034 2960 Dihedral : 3.845 17.777 2306 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.10 % Allowed : 18.88 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.19), residues: 2090 helix: 1.63 (0.18), residues: 918 sheet: 0.47 (0.27), residues: 448 loop : -1.56 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 268 TYR 0.013 0.001 TYR E 320 PHE 0.014 0.001 PHE A 250 HIS 0.006 0.001 HIS F 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (16754) covalent geometry : angle 0.57240 / 0.29 (22582) hydrogen bonds : bond 0.02695 / 1.82 ( 808) hydrogen bonds : angle 4.45303 / 3.05 ( 2334) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4180 Ramachandran restraints generated. 2090 Oldfield, 0 Emsley, 2090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4180 Ramachandran restraints generated. 2090 Oldfield, 0 Emsley, 2090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9109 (pt) REVERT: A 223 MET cc_start: 0.8669 (ttm) cc_final: 0.8130 (ttp) REVERT: A 240 HIS cc_start: 0.8962 (m90) cc_final: 0.8562 (m-70) REVERT: A 304 MET cc_start: 0.8152 (tpp) cc_final: 0.7891 (tpp) REVERT: A 312 MET cc_start: 0.7511 (ttm) cc_final: 0.7129 (ttm) REVERT: A 320 TYR cc_start: 0.9254 (t80) cc_final: 0.8941 (t80) REVERT: B 157 GLU cc_start: 0.8762 (pm20) cc_final: 0.8173 (pm20) REVERT: B 320 TYR cc_start: 0.9107 (m-80) cc_final: 0.8578 (m-80) REVERT: C 53 MET cc_start: 0.9046 (ptm) cc_final: 0.8585 (ppp) REVERT: C 103 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.7974 (p) REVERT: C 109 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8130 (mm) REVERT: C 197 MET cc_start: 0.8233 (ttp) cc_final: 0.7991 (ttm) REVERT: D 178 LEU cc_start: 0.9359 (tp) cc_final: 0.9086 (tt) REVERT: D 213 MET cc_start: 0.9014 (mmm) cc_final: 0.8656 (mmm) REVERT: D 312 MET cc_start: 0.7173 (ttm) cc_final: 0.6798 (ttm) REVERT: D 314 THR cc_start: 0.8273 (OUTLIER) cc_final: 0.7858 (p) REVERT: E 157 GLU cc_start: 0.8765 (pm20) cc_final: 0.8176 (pm20) REVERT: E 320 TYR cc_start: 0.9316 (m-80) cc_final: 0.8792 (m-80) REVERT: E 332 ASP cc_start: 0.9444 (t70) cc_final: 0.9178 (m-30) REVERT: F 103 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.7995 (p) REVERT: F 304 MET cc_start: 0.8675 (ppp) cc_final: 0.8324 (ppp) REVERT: F 320 TYR cc_start: 0.9243 (t80) cc_final: 0.8923 (t80) outliers start: 37 outliers final: 15 residues processed: 176 average time/residue: 0.1120 time to fit residues: 31.2497 Evaluate side-chains 160 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 308 GLN Chi-restraints excluded: chain F residue 319 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 208 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 185 optimal weight: 0.7980 chunk 209 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 335 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.074589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.053584 restraints weight = 74182.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.055381 restraints weight = 40770.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.056555 restraints weight = 28528.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.057281 restraints weight = 22918.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.057793 restraints weight = 20013.669| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16754 Z= 0.129 Angle : 0.599 10.745 22582 Z= 0.300 Chirality : 0.041 0.175 2604 Planarity : 0.003 0.075 2960 Dihedral : 3.938 20.202 2306 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.04 % Allowed : 19.44 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.19), residues: 2090 helix: 1.37 (0.18), residues: 948 sheet: 0.45 (0.27), residues: 448 loop : -1.61 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 268 TYR 0.012 0.001 TYR E 320 PHE 0.012 0.001 PHE D 250 HIS 0.006 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (16754) covalent geometry : angle 0.59947 / 0.30 (22582) hydrogen bonds : bond 0.02753 / 1.86 ( 808) hydrogen bonds : angle 4.50728 / 3.10 ( 2334) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4180 Ramachandran restraints generated. 2090 Oldfield, 0 Emsley, 2090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4180 Ramachandran restraints generated. 2090 Oldfield, 0 Emsley, 2090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.9282 (tt) cc_final: 0.8925 (tt) REVERT: A 240 HIS cc_start: 0.8937 (m90) cc_final: 0.8550 (m-70) REVERT: A 304 MET cc_start: 0.8239 (tpp) cc_final: 0.7964 (tpp) REVERT: A 312 MET cc_start: 0.7560 (ttm) cc_final: 0.7147 (ttm) REVERT: A 320 TYR cc_start: 0.9258 (t80) cc_final: 0.8979 (t80) REVERT: B 157 GLU cc_start: 0.8731 (pm20) cc_final: 0.8178 (pm20) REVERT: B 304 MET cc_start: 0.7568 (tmm) cc_final: 0.7038 (tpt) REVERT: B 320 TYR cc_start: 0.9164 (m-80) cc_final: 0.8629 (m-80) REVERT: C 53 MET cc_start: 0.8968 (ptm) cc_final: 0.8463 (ppp) REVERT: C 103 THR cc_start: 0.8566 (OUTLIER) cc_final: 0.8033 (p) REVERT: C 197 MET cc_start: 0.8205 (ttp) cc_final: 0.7975 (ttm) REVERT: C 320 TYR cc_start: 0.9152 (t80) cc_final: 0.8887 (t80) REVERT: D 178 LEU cc_start: 0.9381 (tp) cc_final: 0.9114 (tt) REVERT: D 213 MET cc_start: 0.9061 (mmm) cc_final: 0.8697 (mmm) REVERT: D 312 MET cc_start: 0.7290 (ttm) cc_final: 0.6870 (ttm) REVERT: D 314 THR cc_start: 0.8350 (OUTLIER) cc_final: 0.7901 (p) REVERT: E 157 GLU cc_start: 0.8723 (pm20) cc_final: 0.8393 (pm20) REVERT: E 320 TYR cc_start: 0.9299 (m-80) cc_final: 0.8751 (m-80) REVERT: E 332 ASP cc_start: 0.9442 (t70) cc_final: 0.9174 (m-30) REVERT: F 103 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8067 (p) REVERT: F 304 MET cc_start: 0.8702 (ppp) cc_final: 0.8348 (ppp) outliers start: 36 outliers final: 20 residues processed: 172 average time/residue: 0.1170 time to fit residues: 32.2344 Evaluate side-chains 158 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 85 PHE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 308 GLN Chi-restraints excluded: chain F residue 319 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 194 optimal weight: 2.9990 chunk 144 optimal weight: 0.0670 chunk 173 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 7 optimal weight: 0.0020 chunk 112 optimal weight: 0.0270 chunk 11 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 172 optimal weight: 0.9980 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 HIS ** F 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 335 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.076118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.053940 restraints weight = 76101.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.055803 restraints weight = 41188.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.057008 restraints weight = 28595.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.057797 restraints weight = 22853.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.058302 restraints weight = 19841.239| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16754 Z= 0.102 Angle : 0.592 11.463 22582 Z= 0.295 Chirality : 0.041 0.183 2604 Planarity : 0.003 0.059 2960 Dihedral : 3.893 18.947 2306 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.04 % Allowed : 19.84 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.19), residues: 2090 helix: 1.37 (0.18), residues: 942 sheet: 0.45 (0.27), residues: 448 loop : -1.55 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 268 TYR 0.012 0.001 TYR F 320 PHE 0.012 0.001 PHE F 104 HIS 0.007 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (16754) covalent geometry : angle 0.59182 / 0.30 (22582) hydrogen bonds : bond 0.02572 / 1.72 ( 808) hydrogen bonds : angle 4.43950 / 3.04 ( 2334) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4180 Ramachandran restraints generated. 2090 Oldfield, 0 Emsley, 2090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4180 Ramachandran restraints generated. 2090 Oldfield, 0 Emsley, 2090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.9282 (tt) cc_final: 0.8941 (tt) REVERT: A 198 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.8869 (pt) REVERT: A 240 HIS cc_start: 0.8943 (m90) cc_final: 0.8564 (m-70) REVERT: A 304 MET cc_start: 0.8223 (tpp) cc_final: 0.7983 (tpp) REVERT: A 312 MET cc_start: 0.7569 (ttm) cc_final: 0.7243 (ttm) REVERT: A 320 TYR cc_start: 0.9220 (t80) cc_final: 0.8934 (t80) REVERT: B 157 GLU cc_start: 0.8710 (pm20) cc_final: 0.8189 (pm20) REVERT: B 304 MET cc_start: 0.7557 (tmm) cc_final: 0.6965 (tpt) REVERT: B 320 TYR cc_start: 0.9194 (m-80) cc_final: 0.8641 (m-80) REVERT: C 10 MET cc_start: 0.7484 (tmm) cc_final: 0.7122 (ttp) REVERT: C 53 MET cc_start: 0.8948 (ptm) cc_final: 0.8424 (ppp) REVERT: C 103 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.7973 (p) REVERT: C 109 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8174 (mm) REVERT: C 197 MET cc_start: 0.8201 (ttp) cc_final: 0.7961 (ttm) REVERT: C 320 TYR cc_start: 0.9163 (t80) cc_final: 0.8873 (t80) REVERT: D 178 LEU cc_start: 0.9372 (tp) cc_final: 0.9112 (tt) REVERT: D 213 MET cc_start: 0.9003 (mmm) cc_final: 0.8599 (mmm) REVERT: D 304 MET cc_start: 0.7681 (tpt) cc_final: 0.7269 (mmm) REVERT: D 312 MET cc_start: 0.7297 (ttm) cc_final: 0.6764 (ttm) REVERT: D 314 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.7892 (p) REVERT: E 157 GLU cc_start: 0.8754 (pm20) cc_final: 0.8259 (pm20) REVERT: E 320 TYR cc_start: 0.9265 (m-80) cc_final: 0.8692 (m-80) REVERT: E 332 ASP cc_start: 0.9436 (t70) cc_final: 0.9171 (m-30) REVERT: F 103 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8222 (p) REVERT: F 304 MET cc_start: 0.8667 (ppp) cc_final: 0.8305 (ppp) REVERT: F 320 TYR cc_start: 0.9261 (t80) cc_final: 0.9011 (t80) outliers start: 36 outliers final: 19 residues processed: 174 average time/residue: 0.1183 time to fit residues: 32.9732 Evaluate side-chains 159 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 308 GLN Chi-restraints excluded: chain F residue 319 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 24 optimal weight: 0.9990 chunk 208 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 203 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 206 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 159 optimal weight: 0.2980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 HIS ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN D 86 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.076475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.055492 restraints weight = 76198.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.057311 restraints weight = 39463.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.058509 restraints weight = 26606.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.059302 restraints weight = 20777.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.059760 restraints weight = 17746.609| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16754 Z= 0.154 Angle : 0.631 11.088 22582 Z= 0.317 Chirality : 0.041 0.164 2604 Planarity : 0.003 0.059 2960 Dihedral : 4.058 22.217 2306 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.15 % Allowed : 19.61 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.19), residues: 2090 helix: 1.25 (0.18), residues: 950 sheet: 0.32 (0.27), residues: 452 loop : -1.56 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 268 TYR 0.013 0.002 TYR A 6 PHE 0.012 0.001 PHE A 250 HIS 0.010 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (16754) covalent geometry : angle 0.63052 / 0.32 (22582) hydrogen bonds : bond 0.02854 / 1.92 ( 808) hydrogen bonds : angle 4.57112 / 3.13 ( 2334) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4180 Ramachandran restraints generated. 2090 Oldfield, 0 Emsley, 2090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4180 Ramachandran restraints generated. 2090 Oldfield, 0 Emsley, 2090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8948 (tt) REVERT: A 240 HIS cc_start: 0.8958 (m90) cc_final: 0.8541 (m-70) REVERT: B 157 GLU cc_start: 0.8750 (pm20) cc_final: 0.8185 (pm20) REVERT: B 320 TYR cc_start: 0.9183 (m-80) cc_final: 0.8584 (m-80) REVERT: C 10 MET cc_start: 0.7447 (tmm) cc_final: 0.7132 (ttp) REVERT: C 53 MET cc_start: 0.8962 (ptm) cc_final: 0.8446 (ppp) REVERT: C 103 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8087 (p) REVERT: C 197 MET cc_start: 0.8271 (ttp) cc_final: 0.8026 (ttm) REVERT: D 85 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8558 (m-10) REVERT: D 178 LEU cc_start: 0.9411 (tp) cc_final: 0.9121 (tt) REVERT: D 213 MET cc_start: 0.9016 (mmm) cc_final: 0.8640 (mmm) REVERT: D 240 HIS cc_start: 0.8665 (m170) cc_final: 0.8306 (m90) REVERT: D 304 MET cc_start: 0.7964 (tpt) cc_final: 0.7505 (mmm) REVERT: D 312 MET cc_start: 0.7234 (ttm) cc_final: 0.6712 (ttm) REVERT: D 314 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.7930 (p) REVERT: E 320 TYR cc_start: 0.9259 (m-80) cc_final: 0.8697 (m-80) REVERT: E 332 ASP cc_start: 0.9442 (t70) cc_final: 0.9168 (m-30) REVERT: F 10 MET cc_start: 0.7422 (tmm) cc_final: 0.7099 (ttp) REVERT: F 103 THR cc_start: 0.8865 (OUTLIER) cc_final: 0.8448 (p) REVERT: F 304 MET cc_start: 0.8663 (ppp) cc_final: 0.8315 (ppp) REVERT: F 320 TYR cc_start: 0.9304 (t80) cc_final: 0.9044 (t80) outliers start: 38 outliers final: 28 residues processed: 169 average time/residue: 0.1197 time to fit residues: 32.4559 Evaluate side-chains 169 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 85 PHE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 85 PHE Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 308 GLN Chi-restraints excluded: chain F residue 319 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 31 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 166 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 194 optimal weight: 0.4980 chunk 203 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 139 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 173 GLN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN D 86 GLN D 147 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 GLN ** F 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.075144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.053784 restraints weight = 74762.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.055523 restraints weight = 38662.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.056657 restraints weight = 26025.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.057420 restraints weight = 20343.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.057892 restraints weight = 17366.923| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16754 Z= 0.202 Angle : 0.677 11.437 22582 Z= 0.343 Chirality : 0.042 0.154 2604 Planarity : 0.004 0.057 2960 Dihedral : 4.340 27.117 2306 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.15 % Allowed : 20.01 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.19), residues: 2090 helix: 1.08 (0.18), residues: 948 sheet: 0.08 (0.27), residues: 456 loop : -1.63 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 268 TYR 0.017 0.002 TYR A 6 PHE 0.015 0.001 PHE D 215 HIS 0.009 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 (16754) covalent geometry : angle 0.67684 / 0.34 (22582) hydrogen bonds : bond 0.03145 / 2.13 ( 808) hydrogen bonds : angle 4.82148 / 3.31 ( 2334) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4180 Ramachandran restraints generated. 2090 Oldfield, 0 Emsley, 2090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4180 Ramachandran restraints generated. 2090 Oldfield, 0 Emsley, 2090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.8999 (tt) REVERT: A 240 HIS cc_start: 0.8964 (m90) cc_final: 0.8532 (m-70) REVERT: A 312 MET cc_start: 0.7443 (ttm) cc_final: 0.7021 (ttm) REVERT: A 320 TYR cc_start: 0.9133 (t80) cc_final: 0.8892 (t80) REVERT: B 320 TYR cc_start: 0.9182 (m-80) cc_final: 0.8588 (m-80) REVERT: C 10 MET cc_start: 0.7503 (tmm) cc_final: 0.7247 (ttp) REVERT: C 54 MET cc_start: 0.7494 (ppp) cc_final: 0.6630 (ppp) REVERT: C 103 THR cc_start: 0.8742 (OUTLIER) cc_final: 0.8183 (p) REVERT: C 320 TYR cc_start: 0.9212 (t80) cc_final: 0.8921 (t80) REVERT: D 85 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.8503 (m-10) REVERT: D 178 LEU cc_start: 0.9437 (tp) cc_final: 0.9145 (tt) REVERT: D 213 MET cc_start: 0.9068 (mmm) cc_final: 0.8692 (mmm) REVERT: D 240 HIS cc_start: 0.8675 (m170) cc_final: 0.8330 (m90) REVERT: D 312 MET cc_start: 0.7357 (ttm) cc_final: 0.7015 (ttm) REVERT: D 314 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.7949 (p) REVERT: E 320 TYR cc_start: 0.9299 (m-80) cc_final: 0.8719 (m-80) REVERT: E 332 ASP cc_start: 0.9444 (t70) cc_final: 0.9148 (m-30) REVERT: F 10 MET cc_start: 0.7465 (tmm) cc_final: 0.7187 (ttp) REVERT: F 103 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8451 (p) REVERT: F 209 MET cc_start: 0.9180 (tpp) cc_final: 0.8407 (mmp) REVERT: F 229 ASN cc_start: 0.8702 (p0) cc_final: 0.8449 (p0) REVERT: F 304 MET cc_start: 0.8744 (ppp) cc_final: 0.8412 (ppp) REVERT: F 320 TYR cc_start: 0.9298 (t80) cc_final: 0.9019 (t80) outliers start: 38 outliers final: 31 residues processed: 163 average time/residue: 0.1174 time to fit residues: 30.8076 Evaluate side-chains 167 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 85 PHE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 85 PHE Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 53 MET Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 308 GLN Chi-restraints excluded: chain F residue 319 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 207 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 160 optimal weight: 0.8980 chunk 164 optimal weight: 0.4980 chunk 175 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 173 GLN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 HIS D 69 ASN D 86 GLN D 147 GLN E 173 GLN ** F 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 335 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.076282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.055594 restraints weight = 76198.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.057392 restraints weight = 39193.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.058605 restraints weight = 26277.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.059388 restraints weight = 20432.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.059893 restraints weight = 17424.416| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16754 Z= 0.130 Angle : 0.638 11.472 22582 Z= 0.319 Chirality : 0.042 0.150 2604 Planarity : 0.003 0.046 2960 Dihedral : 4.190 21.207 2306 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.10 % Allowed : 20.41 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.19), residues: 2090 helix: 1.10 (0.18), residues: 948 sheet: 0.16 (0.27), residues: 452 loop : -1.62 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 268 TYR 0.016 0.002 TYR A 320 PHE 0.011 0.001 PHE A 250 HIS 0.013 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (16754) covalent geometry : angle 0.63840 / 0.32 (22582) hydrogen bonds : bond 0.02831 / 1.90 ( 808) hydrogen bonds : angle 4.64341 / 3.18 ( 2334) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3040.11 seconds wall clock time: 53 minutes 20.51 seconds (3200.51 seconds total)