Starting phenix.real_space_refine on Thu Jul 2 23:50:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j0y_61062/07_2026/9j0y_61062.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j0y_61062/07_2026/9j0y_61062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j0y_61062/07_2026/9j0y_61062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j0y_61062/07_2026/9j0y_61062.map" model { file = "/net/cci-nas-00/data/ceres_data/9j0y_61062/07_2026/9j0y_61062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j0y_61062/07_2026/9j0y_61062.cif" } resolution = 3.14 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= 0.041 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: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 52 5.16 5 C 7244 2.51 5 N 1812 2.21 5 O 1824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10936 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2732 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2734 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2732 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2734 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' K': 4} Chain breaks: 4 Time building chain proxies: 2.54, per 1000 atoms: 0.23 Number of scatterers: 10936 At special positions: 0 Unit cell: (99.6, 111.22, 108.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 4 19.00 S 52 16.00 O 1824 8.00 N 1812 7.00 C 7244 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 376.8 milliseconds 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2480 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 6 sheets defined 65.2% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 65 through 70 removed outlier: 3.771A pdb=" N MET A 70 " --> pdb=" O LYS A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 79 removed outlier: 3.700A pdb=" N TRP A 75 " --> pdb=" O PHE A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 88 removed outlier: 4.058A pdb=" N MET A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 99 through 107 removed outlier: 4.519A pdb=" N GLN A 105 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 106 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A 107 " --> pdb=" O VAL A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 164 through 170 removed outlier: 3.659A pdb=" N LEU A 170 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 177 removed outlier: 3.521A pdb=" N LEU A 175 " --> pdb=" O TRP A 172 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 176 " --> pdb=" O ILE A 173 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG A 177 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 189 removed outlier: 3.943A pdb=" N PHE A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU A 189 " --> pdb=" O PHE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 225 removed outlier: 3.591A pdb=" N GLU A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR A 220 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A 223 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 removed outlier: 3.900A pdb=" N GLU A 231 " --> pdb=" O PRO A 228 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N GLY A 232 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 252 removed outlier: 3.661A pdb=" N ILE A 252 " --> pdb=" O PHE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 270 Processing helix chain 'A' and resid 283 through 299 removed outlier: 3.562A pdb=" N PHE A 287 " --> pdb=" O ARG A 283 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 293 " --> pdb=" O MET A 289 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 312 removed outlier: 3.767A pdb=" N ILE A 303 " --> pdb=" O GLY A 299 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 329 removed outlier: 4.003A pdb=" N PHE A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 333 Processing helix chain 'A' and resid 336 through 350 Processing helix chain 'A' and resid 353 through 361 removed outlier: 3.783A pdb=" N THR A 358 " --> pdb=" O HIS A 354 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N VAL A 359 " --> pdb=" O TYR A 355 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET A 360 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 361 " --> pdb=" O ASP A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 376 removed outlier: 3.783A pdb=" N ILE A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 89 removed outlier: 3.767A pdb=" N TYR B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 81 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N THR B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) Proline residue: B 84 - end of helix removed outlier: 3.585A pdb=" N PHE B 89 " --> pdb=" O MET B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 104 Processing helix chain 'B' and resid 107 through 115 removed outlier: 3.973A pdb=" N ASP B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 135 through 143 removed outlier: 3.535A pdb=" N LYS B 141 " --> pdb=" O PHE B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 149 Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 165 through 177 removed outlier: 3.529A pdb=" N LEU B 170 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP B 172 " --> pdb=" O TYR B 169 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B 173 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ARG B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 177 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 190 removed outlier: 3.654A pdb=" N PHE B 184 " --> pdb=" O LYS B 180 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 188 " --> pdb=" O PHE B 184 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS B 190 " --> pdb=" O GLN B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 200 Processing helix chain 'B' and resid 201 through 225 removed outlier: 3.702A pdb=" N THR B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA B 223 " --> pdb=" O PHE B 219 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR B 224 " --> pdb=" O TYR B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 234 removed outlier: 3.931A pdb=" N TYR B 233 " --> pdb=" O ASN B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 270 Processing helix chain 'B' and resid 281 through 311 removed outlier: 3.503A pdb=" N MET B 285 " --> pdb=" O ASN B 281 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 293 " --> pdb=" O MET B 289 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 300 " --> pdb=" O MET B 296 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE B 303 " --> pdb=" O GLY B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 331 removed outlier: 3.702A pdb=" N ARG B 318 " --> pdb=" O SER B 314 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ARG B 320 " --> pdb=" O THR B 316 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA B 321 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN B 324 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER B 328 " --> pdb=" O ASN B 324 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE B 329 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 351 removed outlier: 3.819A pdb=" N GLN B 342 " --> pdb=" O ASP B 338 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR B 344 " --> pdb=" O ARG B 340 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 366 through 376 Processing helix chain 'C' and resid 65 through 70 removed outlier: 3.737A pdb=" N MET C 70 " --> pdb=" O LYS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 74 removed outlier: 3.571A pdb=" N VAL C 74 " --> pdb=" O PHE C 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 71 through 74' Processing helix chain 'C' and resid 77 through 88 removed outlier: 3.928A pdb=" N THR C 83 " --> pdb=" O SER C 79 " (cutoff:3.500A) Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 97 through 103 removed outlier: 3.559A pdb=" N ILE C 102 " --> pdb=" O PHE C 98 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 103 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 115 removed outlier: 3.589A pdb=" N VAL C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 143 removed outlier: 3.945A pdb=" N PHE C 137 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 152 removed outlier: 3.687A pdb=" N PHE C 152 " --> pdb=" O ILE C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 161 removed outlier: 3.666A pdb=" N TYR C 158 " --> pdb=" O TRP C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 177 removed outlier: 3.684A pdb=" N VAL C 167 " --> pdb=" O HIS C 164 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU C 171 " --> pdb=" O ARG C 168 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE C 173 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG C 174 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE C 176 " --> pdb=" O ILE C 173 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG C 177 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 190 removed outlier: 3.804A pdb=" N LYS C 190 " --> pdb=" O GLN C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 225 removed outlier: 3.850A pdb=" N ILE C 201 " --> pdb=" O LEU C 197 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU C 204 " --> pdb=" O ARG C 200 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU C 208 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL C 209 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA C 216 " --> pdb=" O THR C 212 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS C 217 " --> pdb=" O HIS C 213 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N PHE C 219 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA C 223 " --> pdb=" O PHE C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 270 removed outlier: 3.556A pdb=" N PHE C 264 " --> pdb=" O THR C 260 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N THR C 268 " --> pdb=" O PHE C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 311 removed outlier: 3.647A pdb=" N VAL C 292 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL C 297 " --> pdb=" O SER C 293 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU C 302 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE C 303 " --> pdb=" O GLY C 299 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASN C 305 " --> pdb=" O TYR C 301 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU C 309 " --> pdb=" O ASN C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 323 removed outlier: 3.690A pdb=" N ARG C 320 " --> pdb=" O THR C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 331 Processing helix chain 'C' and resid 341 through 352 Processing helix chain 'C' and resid 358 through 363 removed outlier: 4.184A pdb=" N GLN C 362 " --> pdb=" O VAL C 359 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP C 363 " --> pdb=" O MET C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 376 removed outlier: 4.029A pdb=" N ILE C 372 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 89 removed outlier: 4.044A pdb=" N SER D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix removed outlier: 3.515A pdb=" N PHE D 89 " --> pdb=" O MET D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 113 removed outlier: 4.205A pdb=" N PHE D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASP D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 149 Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 164 through 176 removed outlier: 3.594A pdb=" N TRP D 172 " --> pdb=" O TYR D 169 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE D 173 " --> pdb=" O LEU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 187 removed outlier: 4.282A pdb=" N VAL D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 225 removed outlier: 3.578A pdb=" N GLU D 208 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS D 217 " --> pdb=" O HIS D 213 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR D 220 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA D 223 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR D 224 " --> pdb=" O TYR D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 270 Processing helix chain 'D' and resid 282 through 312 removed outlier: 3.552A pdb=" N SER D 293 " --> pdb=" O MET D 289 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL D 297 " --> pdb=" O SER D 293 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA D 308 " --> pdb=" O GLY D 304 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU D 309 " --> pdb=" O ASN D 305 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE D 310 " --> pdb=" O ILE D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 331 removed outlier: 3.779A pdb=" N ASN D 324 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ASP D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER D 328 " --> pdb=" O ASN D 324 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE D 329 " --> pdb=" O ASP D 325 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 338 No H-bonds generated for 'chain 'D' and resid 336 through 338' Processing helix chain 'D' and resid 339 through 350 removed outlier: 3.527A pdb=" N GLY D 345 " --> pdb=" O SER D 341 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N HIS D 346 " --> pdb=" O GLN D 342 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL D 347 " --> pdb=" O ILE D 343 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ARG D 348 " --> pdb=" O THR D 344 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU D 349 " --> pdb=" O GLY D 345 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN D 350 " --> pdb=" O HIS D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 376 removed outlier: 3.866A pdb=" N LYS D 371 " --> pdb=" O SER D 367 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 240 through 241 removed outlier: 3.640A pdb=" N TYR A 244 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 120 through 121 Processing sheet with id=AA3, first strand: chain 'B' and resid 240 through 241 removed outlier: 3.727A pdb=" N TYR B 244 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 240 through 241 Processing sheet with id=AA5, first strand: chain 'D' and resid 120 through 121 removed outlier: 3.958A pdb=" N TYR D 120 " --> pdb=" O VAL D 129 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 240 through 241 437 hydrogen bonds defined for protein. 1188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.48 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3211 1.34 - 1.46: 2460 1.46 - 1.57: 5476 1.57 - 1.69: 1 1.69 - 1.81: 92 Bond restraints: 11240 Sorted by residual: bond pdb=" C ILE B 364 " pdb=" N PRO B 365 " ideal model delta sigma weight residual 1.331 1.370 -0.038 1.21e-02 6.83e+03 1.00e+01 bond pdb=" CB ASP B 352 " pdb=" CG ASP B 352 " ideal model delta sigma weight residual 1.516 1.578 -0.062 2.50e-02 1.60e+03 6.24e+00 bond pdb=" CA THR D 356 " pdb=" C THR D 356 " ideal model delta sigma weight residual 1.522 1.554 -0.031 1.37e-02 5.33e+03 5.21e+00 bond pdb=" CA ASP B 352 " pdb=" CB ASP B 352 " ideal model delta sigma weight residual 1.541 1.564 -0.023 1.20e-02 6.94e+03 3.60e+00 bond pdb=" CB THR B 212 " pdb=" CG2 THR B 212 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.43e+00 ... (remaining 11235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 14737 2.41 - 4.82: 411 4.82 - 7.24: 52 7.24 - 9.65: 16 9.65 - 12.06: 4 Bond angle restraints: 15220 Sorted by residual: angle pdb=" N VAL D 347 " pdb=" CA VAL D 347 " pdb=" C VAL D 347 " ideal model delta sigma weight residual 111.77 105.27 6.50 1.04e+00 9.25e-01 3.91e+01 angle pdb=" N THR D 199 " pdb=" CA THR D 199 " pdb=" C THR D 199 " ideal model delta sigma weight residual 114.09 106.83 7.26 1.55e+00 4.16e-01 2.20e+01 angle pdb=" N ILE D 135 " pdb=" CA ILE D 135 " pdb=" C ILE D 135 " ideal model delta sigma weight residual 113.39 106.58 6.81 1.47e+00 4.63e-01 2.15e+01 angle pdb=" C TYR B 351 " pdb=" N ASP B 352 " pdb=" CA ASP B 352 " ideal model delta sigma weight residual 126.45 134.60 -8.15 1.77e+00 3.19e-01 2.12e+01 angle pdb=" C LEU C 339 " pdb=" N ARG C 340 " pdb=" CA ARG C 340 " ideal model delta sigma weight residual 120.38 126.99 -6.61 1.46e+00 4.69e-01 2.05e+01 ... (remaining 15215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.37: 5534 15.37 - 30.74: 777 30.74 - 46.12: 192 46.12 - 61.49: 29 61.49 - 76.86: 4 Dihedral angle restraints: 6536 sinusoidal: 2664 harmonic: 3872 Sorted by residual: dihedral pdb=" CA ASP A 363 " pdb=" C ASP A 363 " pdb=" N ILE A 364 " pdb=" CA ILE A 364 " ideal model delta harmonic sigma weight residual 180.00 150.39 29.61 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA PHE C 264 " pdb=" C PHE C 264 " pdb=" N ALA C 265 " pdb=" CA ALA C 265 " ideal model delta harmonic sigma weight residual 180.00 151.39 28.61 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA SER D 161 " pdb=" C SER D 161 " pdb=" N GLY D 162 " pdb=" CA GLY D 162 " ideal model delta harmonic sigma weight residual -180.00 -153.84 -26.16 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 6533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 960 0.044 - 0.087: 516 0.087 - 0.131: 137 0.131 - 0.175: 42 0.175 - 0.218: 5 Chirality restraints: 1660 Sorted by residual: chirality pdb=" CB ILE C 236 " pdb=" CA ILE C 236 " pdb=" CG1 ILE C 236 " pdb=" CG2 ILE C 236 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB ILE A 194 " pdb=" CA ILE A 194 " pdb=" CG1 ILE A 194 " pdb=" CG2 ILE A 194 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.88e-01 chirality pdb=" CB ILE A 236 " pdb=" CA ILE A 236 " pdb=" CG1 ILE A 236 " pdb=" CG2 ILE A 236 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.69e-01 ... (remaining 1657 not shown) Planarity restraints: 1860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 93 " -0.040 5.00e-02 4.00e+02 6.07e-02 5.89e+00 pdb=" N PRO B 94 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 94 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 94 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 364 " -0.038 5.00e-02 4.00e+02 5.80e-02 5.39e+00 pdb=" N PRO C 365 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 365 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 365 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 364 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO B 365 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 365 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 365 " -0.030 5.00e-02 4.00e+02 ... (remaining 1857 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.31: 10 2.31 - 3.01: 5440 3.01 - 3.72: 18864 3.72 - 4.43: 29752 4.43 - 5.14: 49348 Nonbonded interactions: 103414 Sorted by model distance: nonbonded pdb=" OE1 GLU C 183 " pdb=" NH1 ARG C 187 " model vdw 1.596 3.120 nonbonded pdb=" CD GLU C 183 " pdb=" NH1 ARG C 187 " model vdw 2.129 3.350 nonbonded pdb=" OE2 GLU C 183 " pdb=" NH1 ARG C 187 " model vdw 2.189 3.120 nonbonded pdb=" O LEU B 349 " pdb=" OG SER B 353 " model vdw 2.236 3.040 nonbonded pdb=" O ASP A 352 " pdb=" OG1 THR A 356 " model vdw 2.261 3.040 ... (remaining 103409 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 52 through 376) selection = (chain 'B' and (resid 52 through 127 or (resid 128 and (name N or name CA or nam \ e C or name O or name CB or name OG1)) or resid 129 through 132 or (resid 133 an \ d (name N or name CA or name C or name O or name CB or name OG1)) or resid 134 t \ hrough 376)) selection = chain 'C' selection = (chain 'D' and (resid 52 through 127 or (resid 128 and (name N or name CA or nam \ e C or name O or name CB or name OG1)) or resid 129 through 132 or (resid 133 an \ d (name N or name CA or name C or name O or name CB or name OG1)) or resid 134 t \ hrough 376)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.610 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 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 : 0.006 0.062 11240 Z= 0.283 Angle : 0.986 12.060 15220 Z= 0.561 Chirality : 0.056 0.218 1660 Planarity : 0.006 0.061 1860 Dihedral : 14.826 76.861 4056 Min Nonbonded Distance : 1.596 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.36 (0.17), residues: 1292 helix: -3.90 (0.11), residues: 799 sheet: -4.04 (1.21), residues: 10 loop : -2.53 (0.24), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 179 TYR 0.028 0.002 TYR D 351 PHE 0.030 0.002 PHE C 264 TRP 0.014 0.002 TRP A 255 HIS 0.014 0.001 HIS C 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.28 (11240) covalent geometry : angle 0.98568 / 0.56 (15220) hydrogen bonds : bond 0.25004 / 15.61 ( 437) hydrogen bonds : angle 8.31461 / 5.44 ( 1188) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.7919 (mm) cc_final: 0.7705 (mp) REVERT: A 121 ARG cc_start: 0.7691 (tpp-160) cc_final: 0.6594 (tpp-160) REVERT: A 166 LEU cc_start: 0.8777 (tt) cc_final: 0.8486 (tp) REVERT: A 196 TYR cc_start: 0.8112 (t80) cc_final: 0.7519 (t80) REVERT: A 323 MET cc_start: 0.5615 (ttm) cc_final: 0.5235 (ptt) REVERT: B 166 LEU cc_start: 0.8378 (tt) cc_final: 0.8140 (mm) REVERT: B 322 LYS cc_start: 0.8569 (mmpt) cc_final: 0.7833 (mttp) REVERT: C 166 LEU cc_start: 0.8416 (tt) cc_final: 0.8160 (mm) REVERT: C 204 LEU cc_start: 0.8472 (mm) cc_final: 0.8120 (mm) REVERT: C 210 TYR cc_start: 0.8492 (t80) cc_final: 0.8270 (t80) REVERT: C 269 MET cc_start: 0.8911 (tmm) cc_final: 0.8624 (ttp) REVERT: D 155 ASP cc_start: 0.7736 (t70) cc_final: 0.7469 (t0) REVERT: D 329 PHE cc_start: 0.6065 (t80) cc_final: 0.5702 (t80) REVERT: D 374 GLN cc_start: 0.5646 (mp-120) cc_final: 0.5236 (pt0) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.1297 time to fit residues: 39.3205 Evaluate side-chains 159 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 0.0670 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 overall best weight: 0.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN A 186 GLN A 278 HIS A 354 HIS B 143 HIS B 230 ASN ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 346 HIS D 230 ASN D 342 GLN D 346 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.179197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.116893 restraints weight = 14505.241| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.85 r_work: 0.3179 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11240 Z= 0.148 Angle : 0.648 9.410 15220 Z= 0.349 Chirality : 0.043 0.165 1660 Planarity : 0.005 0.051 1860 Dihedral : 6.456 32.420 1488 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 1.47 % Allowed : 11.21 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.65 (0.21), residues: 1292 helix: -2.64 (0.15), residues: 822 sheet: -3.48 (1.29), residues: 10 loop : -1.56 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 168 TYR 0.014 0.001 TYR D 351 PHE 0.038 0.001 PHE C 264 TRP 0.016 0.001 TRP A 255 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (11240) covalent geometry : angle 0.64772 / 0.35 (15220) hydrogen bonds : bond 0.05431 / 3.41 ( 437) hydrogen bonds : angle 5.07389 / 3.35 ( 1188) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.8079 (mm) cc_final: 0.7870 (mp) REVERT: A 86 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8555 (tm-30) REVERT: A 114 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8139 (tt) REVERT: A 121 ARG cc_start: 0.7936 (tpp-160) cc_final: 0.6878 (tpp-160) REVERT: A 196 TYR cc_start: 0.8233 (t80) cc_final: 0.7606 (t80) REVERT: A 289 MET cc_start: 0.8919 (mtp) cc_final: 0.8645 (mtp) REVERT: A 309 LEU cc_start: 0.8376 (mp) cc_final: 0.8159 (mm) REVERT: A 323 MET cc_start: 0.5647 (ttm) cc_final: 0.5302 (ptt) REVERT: B 127 ARG cc_start: 0.7568 (mtp-110) cc_final: 0.7017 (ttt90) REVERT: B 146 MET cc_start: 0.8510 (ptt) cc_final: 0.8259 (ptt) REVERT: B 322 LYS cc_start: 0.8632 (mmpt) cc_final: 0.8069 (mttp) REVERT: C 166 LEU cc_start: 0.8528 (tt) cc_final: 0.8196 (mm) REVERT: C 269 MET cc_start: 0.9125 (tmm) cc_final: 0.8878 (ttp) REVERT: C 282 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8630 (mp) REVERT: C 320 ARG cc_start: 0.7984 (mmt180) cc_final: 0.7716 (mtp85) REVERT: D 134 ARG cc_start: 0.7612 (ttp-170) cc_final: 0.7267 (mtp-110) REVERT: D 155 ASP cc_start: 0.8008 (t70) cc_final: 0.7782 (t0) REVERT: D 329 PHE cc_start: 0.6225 (t80) cc_final: 0.5824 (t80) REVERT: D 360 MET cc_start: 0.5708 (mmp) cc_final: 0.3860 (mtt) REVERT: D 374 GLN cc_start: 0.5503 (mp-120) cc_final: 0.5118 (pt0) outliers start: 17 outliers final: 5 residues processed: 196 average time/residue: 0.1254 time to fit residues: 33.4069 Evaluate side-chains 168 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 161 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 145 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 12 optimal weight: 0.0470 chunk 1 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 83 optimal weight: 0.0770 chunk 127 optimal weight: 7.9990 overall best weight: 1.1840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 143 HIS B 342 GLN B 346 HIS C 105 GLN D 59 HIS D 248 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.176225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.114624 restraints weight = 14484.268| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.07 r_work: 0.3108 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 11240 Z= 0.197 Angle : 0.641 8.183 15220 Z= 0.344 Chirality : 0.044 0.151 1660 Planarity : 0.004 0.046 1860 Dihedral : 6.075 29.441 1488 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 2.67 % Allowed : 12.07 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.22), residues: 1292 helix: -2.06 (0.17), residues: 820 sheet: -3.20 (1.42), residues: 10 loop : -1.09 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 193 TYR 0.018 0.002 TYR A 263 PHE 0.015 0.002 PHE B 287 TRP 0.014 0.001 TRP C 255 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (11240) covalent geometry : angle 0.64115 / 0.34 (15220) hydrogen bonds : bond 0.05525 / 3.47 ( 437) hydrogen bonds : angle 4.73977 / 3.14 ( 1188) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.8178 (mm) cc_final: 0.7942 (mp) REVERT: A 86 GLU cc_start: 0.8989 (tm-30) cc_final: 0.8730 (tm-30) REVERT: A 114 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8078 (tt) REVERT: A 121 ARG cc_start: 0.7904 (tpp-160) cc_final: 0.6773 (tpp-160) REVERT: A 289 MET cc_start: 0.8995 (mtp) cc_final: 0.8707 (mtp) REVERT: A 309 LEU cc_start: 0.8408 (mp) cc_final: 0.8148 (mm) REVERT: B 115 GLN cc_start: 0.8301 (mm110) cc_final: 0.7988 (mm-40) REVERT: B 124 GLN cc_start: 0.7966 (mt0) cc_final: 0.7578 (mp10) REVERT: B 127 ARG cc_start: 0.7713 (mtp-110) cc_final: 0.7194 (ttt90) REVERT: B 146 MET cc_start: 0.8535 (ptt) cc_final: 0.8234 (ptt) REVERT: B 322 LYS cc_start: 0.8579 (mmpt) cc_final: 0.8064 (mttp) REVERT: C 282 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8709 (mp) REVERT: D 155 ASP cc_start: 0.8105 (t70) cc_final: 0.7847 (t0) REVERT: D 329 PHE cc_start: 0.6177 (t80) cc_final: 0.5745 (t80) REVERT: D 374 GLN cc_start: 0.5619 (mp-120) cc_final: 0.5330 (pt0) outliers start: 31 outliers final: 18 residues processed: 187 average time/residue: 0.1004 time to fit residues: 26.0470 Evaluate side-chains 179 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 120 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 196 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 18 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 0.0980 chunk 28 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 110 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 143 HIS ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 59 HIS D 248 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.178375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.116354 restraints weight = 14551.992| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.06 r_work: 0.3139 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11240 Z= 0.134 Angle : 0.595 8.229 15220 Z= 0.315 Chirality : 0.042 0.154 1660 Planarity : 0.004 0.042 1860 Dihedral : 5.718 27.061 1488 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 2.41 % Allowed : 14.22 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.23), residues: 1292 helix: -1.59 (0.18), residues: 814 sheet: -2.84 (1.60), residues: 10 loop : -1.01 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 63 TYR 0.012 0.001 TYR D 196 PHE 0.014 0.001 PHE B 319 TRP 0.012 0.001 TRP C 255 HIS 0.010 0.001 HIS D 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (11240) covalent geometry : angle 0.59500 / 0.32 (15220) hydrogen bonds : bond 0.04681 / 2.96 ( 437) hydrogen bonds : angle 4.34985 / 2.88 ( 1188) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.8185 (mm) cc_final: 0.7935 (mp) REVERT: A 86 GLU cc_start: 0.8950 (tm-30) cc_final: 0.8578 (tm-30) REVERT: A 114 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8105 (tt) REVERT: A 121 ARG cc_start: 0.7907 (tpp-160) cc_final: 0.6779 (tpp-160) REVERT: A 289 MET cc_start: 0.9006 (mtp) cc_final: 0.8703 (mtp) REVERT: A 309 LEU cc_start: 0.8362 (mp) cc_final: 0.8095 (mm) REVERT: B 124 GLN cc_start: 0.7934 (mt0) cc_final: 0.7513 (mp10) REVERT: B 146 MET cc_start: 0.8575 (ptt) cc_final: 0.8307 (ptt) REVERT: B 322 LYS cc_start: 0.8616 (mmpt) cc_final: 0.8134 (mttp) REVERT: C 166 LEU cc_start: 0.8516 (tt) cc_final: 0.8172 (mm) REVERT: C 282 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8680 (mp) REVERT: D 319 PHE cc_start: 0.8383 (t80) cc_final: 0.8044 (t80) REVERT: D 329 PHE cc_start: 0.6269 (t80) cc_final: 0.5874 (t80) REVERT: D 356 THR cc_start: 0.5264 (OUTLIER) cc_final: 0.4692 (m) REVERT: D 360 MET cc_start: 0.5899 (mmp) cc_final: 0.3985 (mtt) outliers start: 28 outliers final: 16 residues processed: 191 average time/residue: 0.1011 time to fit residues: 27.0194 Evaluate side-chains 173 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 120 TYR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 356 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 2 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 113 optimal weight: 0.0770 chunk 107 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 143 HIS ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 HIS D 248 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.179335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.116563 restraints weight = 14356.361| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.94 r_work: 0.3158 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11240 Z= 0.131 Angle : 0.585 7.480 15220 Z= 0.311 Chirality : 0.042 0.166 1660 Planarity : 0.003 0.042 1860 Dihedral : 5.486 26.247 1488 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 2.41 % Allowed : 15.52 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.23), residues: 1292 helix: -1.30 (0.18), residues: 803 sheet: -2.55 (1.66), residues: 10 loop : -0.91 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 63 TYR 0.012 0.001 TYR A 263 PHE 0.016 0.001 PHE B 319 TRP 0.011 0.001 TRP A 255 HIS 0.019 0.001 HIS D 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (11240) covalent geometry : angle 0.58465 / 0.31 (15220) hydrogen bonds : bond 0.04508 / 2.86 ( 437) hydrogen bonds : angle 4.18381 / 2.78 ( 1188) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.8293 (mm) cc_final: 0.8018 (mp) REVERT: A 86 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8481 (tm-30) REVERT: A 114 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8310 (tt) REVERT: A 121 ARG cc_start: 0.7935 (tpp-160) cc_final: 0.6840 (tpp-160) REVERT: A 289 MET cc_start: 0.8963 (mtp) cc_final: 0.8649 (mtp) REVERT: A 309 LEU cc_start: 0.8357 (mp) cc_final: 0.8082 (mm) REVERT: B 115 GLN cc_start: 0.7796 (mm-40) cc_final: 0.7570 (mm-40) REVERT: B 124 GLN cc_start: 0.7920 (mt0) cc_final: 0.7551 (mp10) REVERT: B 146 MET cc_start: 0.8600 (ptt) cc_final: 0.8356 (ptt) REVERT: B 322 LYS cc_start: 0.8612 (mmpt) cc_final: 0.8227 (mttp) REVERT: C 63 ARG cc_start: 0.8144 (tpp80) cc_final: 0.7080 (tmt170) REVERT: C 121 ARG cc_start: 0.7689 (ttp80) cc_final: 0.7354 (tmt170) REVERT: C 166 LEU cc_start: 0.8484 (tt) cc_final: 0.8133 (mm) REVERT: C 282 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8687 (mp) REVERT: D 113 VAL cc_start: 0.7942 (t) cc_final: 0.7705 (m) REVERT: D 127 ARG cc_start: 0.7347 (mmm160) cc_final: 0.7112 (mmm160) REVERT: D 130 TYR cc_start: 0.7555 (m-10) cc_final: 0.7116 (m-10) REVERT: D 165 GLU cc_start: 0.8434 (tp30) cc_final: 0.8198 (tp30) REVERT: D 329 PHE cc_start: 0.6285 (t80) cc_final: 0.5878 (t80) outliers start: 28 outliers final: 16 residues processed: 184 average time/residue: 0.1027 time to fit residues: 26.6469 Evaluate side-chains 172 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 170 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 92 optimal weight: 10.0000 chunk 12 optimal weight: 0.2980 chunk 39 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 30 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 115 optimal weight: 0.0470 chunk 37 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 143 HIS ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 HIS D 248 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.178547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.118169 restraints weight = 14335.212| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.09 r_work: 0.3141 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11240 Z= 0.147 Angle : 0.590 7.631 15220 Z= 0.312 Chirality : 0.043 0.189 1660 Planarity : 0.003 0.042 1860 Dihedral : 5.418 26.406 1488 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 2.59 % Allowed : 15.69 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.24), residues: 1292 helix: -1.19 (0.18), residues: 807 sheet: -2.42 (1.68), residues: 10 loop : -0.73 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 168 TYR 0.014 0.001 TYR A 263 PHE 0.014 0.001 PHE B 319 TRP 0.012 0.001 TRP B 255 HIS 0.009 0.001 HIS D 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (11240) covalent geometry : angle 0.59013 / 0.31 (15220) hydrogen bonds : bond 0.04584 / 2.90 ( 437) hydrogen bonds : angle 4.14736 / 2.77 ( 1188) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.8294 (mm) cc_final: 0.7969 (mp) REVERT: A 86 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8526 (tm-30) REVERT: A 114 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8202 (tt) REVERT: A 121 ARG cc_start: 0.7921 (tpp-160) cc_final: 0.6911 (tpp-160) REVERT: A 289 MET cc_start: 0.8979 (mtp) cc_final: 0.8664 (mtp) REVERT: A 309 LEU cc_start: 0.8389 (mp) cc_final: 0.8113 (mm) REVERT: A 350 GLN cc_start: 0.4570 (tm-30) cc_final: 0.4065 (tm-30) REVERT: B 115 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7568 (mm-40) REVERT: B 124 GLN cc_start: 0.7868 (mt0) cc_final: 0.7479 (mp10) REVERT: B 226 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8135 (mp) REVERT: B 322 LYS cc_start: 0.8624 (mmpt) cc_final: 0.8120 (mttp) REVERT: B 326 LEU cc_start: 0.7988 (mp) cc_final: 0.7744 (mp) REVERT: C 121 ARG cc_start: 0.7691 (ttp80) cc_final: 0.7352 (tmt170) REVERT: C 166 LEU cc_start: 0.8516 (tt) cc_final: 0.8161 (mm) REVERT: C 282 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8689 (mp) REVERT: D 113 VAL cc_start: 0.7859 (t) cc_final: 0.7613 (m) REVERT: D 165 GLU cc_start: 0.8427 (tp30) cc_final: 0.8211 (tp30) REVERT: D 329 PHE cc_start: 0.6340 (t80) cc_final: 0.5964 (t80) REVERT: D 360 MET cc_start: 0.5956 (mmp) cc_final: 0.4065 (mtp) outliers start: 30 outliers final: 20 residues processed: 186 average time/residue: 0.1084 time to fit residues: 28.2775 Evaluate side-chains 177 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 170 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 66 optimal weight: 0.0050 chunk 6 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 97 optimal weight: 0.0060 chunk 64 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 overall best weight: 1.3814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 143 HIS ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 248 ASN D 305 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.176138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.112683 restraints weight = 14419.605| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.92 r_work: 0.3111 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11240 Z= 0.214 Angle : 0.637 7.888 15220 Z= 0.337 Chirality : 0.045 0.182 1660 Planarity : 0.004 0.042 1860 Dihedral : 5.511 26.715 1488 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 2.84 % Allowed : 16.55 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.24), residues: 1292 helix: -1.19 (0.18), residues: 810 sheet: -2.28 (1.74), residues: 10 loop : -0.66 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 168 TYR 0.017 0.002 TYR A 263 PHE 0.021 0.002 PHE B 319 TRP 0.012 0.001 TRP A 255 HIS 0.011 0.001 HIS D 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.21 (11240) covalent geometry : angle 0.63663 / 0.34 (15220) hydrogen bonds : bond 0.05166 / 3.27 ( 437) hydrogen bonds : angle 4.30434 / 2.89 ( 1188) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.8401 (mm) cc_final: 0.8071 (mp) REVERT: A 86 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8694 (tm-30) REVERT: A 114 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8276 (tt) REVERT: A 121 ARG cc_start: 0.7920 (tpp-160) cc_final: 0.6884 (tpp-160) REVERT: A 289 MET cc_start: 0.8945 (mtp) cc_final: 0.8670 (mtp) REVERT: A 309 LEU cc_start: 0.8416 (mp) cc_final: 0.8144 (mm) REVERT: B 124 GLN cc_start: 0.7828 (mt0) cc_final: 0.7486 (mp10) REVERT: B 226 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8342 (mp) REVERT: B 322 LYS cc_start: 0.8700 (mmpt) cc_final: 0.8323 (mttp) REVERT: C 121 ARG cc_start: 0.7693 (ttp80) cc_final: 0.7375 (tmt170) REVERT: C 166 LEU cc_start: 0.8564 (tt) cc_final: 0.8194 (mm) REVERT: C 282 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8701 (mp) REVERT: C 354 HIS cc_start: 0.6616 (OUTLIER) cc_final: 0.6261 (m-70) REVERT: D 113 VAL cc_start: 0.7960 (t) cc_final: 0.7726 (m) REVERT: D 165 GLU cc_start: 0.8435 (tp30) cc_final: 0.8216 (tp30) REVERT: D 329 PHE cc_start: 0.6297 (t80) cc_final: 0.5919 (t80) outliers start: 33 outliers final: 19 residues processed: 183 average time/residue: 0.1035 time to fit residues: 26.5399 Evaluate side-chains 177 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 354 HIS Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 170 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 4 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 105 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 143 HIS ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN D 59 HIS D 248 ASN D 305 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.177821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.114955 restraints weight = 14410.781| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.96 r_work: 0.3138 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11240 Z= 0.152 Angle : 0.601 7.756 15220 Z= 0.318 Chirality : 0.043 0.162 1660 Planarity : 0.003 0.042 1860 Dihedral : 5.379 26.397 1488 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 2.59 % Allowed : 17.16 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.24), residues: 1292 helix: -1.03 (0.18), residues: 814 sheet: -2.34 (1.78), residues: 10 loop : -0.63 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 340 TYR 0.013 0.001 TYR A 263 PHE 0.023 0.001 PHE B 319 TRP 0.012 0.001 TRP A 255 HIS 0.004 0.001 HIS C 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (11240) covalent geometry : angle 0.60082 / 0.32 (15220) hydrogen bonds : bond 0.04632 / 2.94 ( 437) hydrogen bonds : angle 4.12303 / 2.75 ( 1188) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.8289 (mm) cc_final: 0.7955 (mp) REVERT: A 72 ILE cc_start: 0.8520 (tt) cc_final: 0.8295 (tt) REVERT: A 86 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8600 (tm-30) REVERT: A 114 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8220 (tt) REVERT: A 121 ARG cc_start: 0.7922 (tpp-160) cc_final: 0.6881 (tpp-160) REVERT: A 289 MET cc_start: 0.8968 (mtp) cc_final: 0.8659 (mtp) REVERT: A 309 LEU cc_start: 0.8397 (mp) cc_final: 0.8125 (mm) REVERT: B 124 GLN cc_start: 0.7841 (mt0) cc_final: 0.7513 (mp10) REVERT: B 226 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8163 (mp) REVERT: B 322 LYS cc_start: 0.8795 (mmpt) cc_final: 0.8297 (mttp) REVERT: C 121 ARG cc_start: 0.7709 (ttp80) cc_final: 0.7385 (tmt170) REVERT: C 166 LEU cc_start: 0.8522 (tt) cc_final: 0.8161 (mm) REVERT: C 282 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8671 (mp) REVERT: D 113 VAL cc_start: 0.7833 (t) cc_final: 0.7581 (m) REVERT: D 296 MET cc_start: 0.8756 (ttp) cc_final: 0.8459 (ttp) REVERT: D 329 PHE cc_start: 0.6319 (t80) cc_final: 0.5865 (t80) outliers start: 30 outliers final: 18 residues processed: 183 average time/residue: 0.1061 time to fit residues: 27.3238 Evaluate side-chains 176 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 170 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 70 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 33 optimal weight: 0.4980 chunk 91 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 117 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 143 HIS ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 HIS D 248 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.178957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.116077 restraints weight = 14344.840| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.91 r_work: 0.3168 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11240 Z= 0.132 Angle : 0.615 9.733 15220 Z= 0.321 Chirality : 0.042 0.172 1660 Planarity : 0.003 0.042 1860 Dihedral : 5.296 26.473 1488 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 1.98 % Allowed : 18.10 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.24), residues: 1292 helix: -0.86 (0.18), residues: 805 sheet: -2.35 (1.72), residues: 10 loop : -0.71 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 340 TYR 0.011 0.001 TYR A 263 PHE 0.015 0.001 PHE B 152 TRP 0.011 0.001 TRP A 255 HIS 0.010 0.001 HIS C 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (11240) covalent geometry : angle 0.61479 / 0.32 (15220) hydrogen bonds : bond 0.04460 / 2.84 ( 437) hydrogen bonds : angle 4.05196 / 2.70 ( 1188) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.8246 (mm) cc_final: 0.7921 (mp) REVERT: A 72 ILE cc_start: 0.8486 (tt) cc_final: 0.8253 (tt) REVERT: A 86 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8532 (tm-30) REVERT: A 114 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8187 (tt) REVERT: A 117 PHE cc_start: 0.8357 (m-10) cc_final: 0.8116 (m-10) REVERT: A 121 ARG cc_start: 0.7907 (tpp-160) cc_final: 0.6882 (tpp-160) REVERT: A 289 MET cc_start: 0.8978 (mtp) cc_final: 0.8665 (mtp) REVERT: A 309 LEU cc_start: 0.8372 (mp) cc_final: 0.8096 (mm) REVERT: B 124 GLN cc_start: 0.7841 (mt0) cc_final: 0.7496 (mp10) REVERT: B 226 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8133 (mp) REVERT: B 322 LYS cc_start: 0.8780 (mmpt) cc_final: 0.8403 (mttp) REVERT: C 121 ARG cc_start: 0.7657 (ttp80) cc_final: 0.7372 (tmt170) REVERT: C 131 LYS cc_start: 0.7292 (tttm) cc_final: 0.7034 (tmtt) REVERT: C 166 LEU cc_start: 0.8473 (tt) cc_final: 0.8117 (mm) REVERT: C 282 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8647 (mp) REVERT: C 323 MET cc_start: 0.6668 (mmm) cc_final: 0.6379 (mmm) REVERT: D 329 PHE cc_start: 0.6270 (t80) cc_final: 0.5800 (t80) REVERT: D 360 MET cc_start: 0.6116 (mmp) cc_final: 0.4274 (mtp) outliers start: 23 outliers final: 18 residues processed: 180 average time/residue: 0.1119 time to fit residues: 28.3506 Evaluate side-chains 177 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 170 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 69 optimal weight: 0.0980 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 143 HIS ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 HIS D 248 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.179586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.116872 restraints weight = 14452.411| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.15 r_work: 0.3153 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11240 Z= 0.129 Angle : 0.612 12.218 15220 Z= 0.318 Chirality : 0.043 0.190 1660 Planarity : 0.003 0.040 1860 Dihedral : 5.186 26.668 1488 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 2.07 % Allowed : 18.28 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.24), residues: 1292 helix: -0.69 (0.18), residues: 802 sheet: -2.18 (1.76), residues: 10 loop : -0.62 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 168 TYR 0.012 0.001 TYR A 263 PHE 0.027 0.001 PHE B 319 TRP 0.011 0.001 TRP C 255 HIS 0.005 0.001 HIS C 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (11240) covalent geometry : angle 0.61245 / 0.32 (15220) hydrogen bonds : bond 0.04351 / 2.76 ( 437) hydrogen bonds : angle 4.05899 / 2.71 ( 1188) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.7349 (tppt) cc_final: 0.7147 (ttpp) REVERT: A 58 ILE cc_start: 0.8242 (mm) cc_final: 0.7920 (mp) REVERT: A 86 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8565 (tm-30) REVERT: A 114 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8203 (tt) REVERT: A 117 PHE cc_start: 0.8322 (m-10) cc_final: 0.8120 (m-10) REVERT: A 289 MET cc_start: 0.8984 (mtp) cc_final: 0.8664 (mtp) REVERT: B 124 GLN cc_start: 0.7882 (mt0) cc_final: 0.7506 (mp10) REVERT: B 322 LYS cc_start: 0.8774 (mmpt) cc_final: 0.8487 (mttp) REVERT: C 121 ARG cc_start: 0.7645 (ttp80) cc_final: 0.7350 (tmt170) REVERT: C 131 LYS cc_start: 0.7286 (tttm) cc_final: 0.7048 (tmtt) REVERT: C 166 LEU cc_start: 0.8505 (tt) cc_final: 0.8148 (mm) REVERT: C 282 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8670 (mp) REVERT: D 165 GLU cc_start: 0.8295 (tp30) cc_final: 0.7805 (tm-30) REVERT: D 329 PHE cc_start: 0.6253 (t80) cc_final: 0.5585 (t80) REVERT: D 360 MET cc_start: 0.6143 (mmp) cc_final: 0.4314 (mtm) outliers start: 24 outliers final: 16 residues processed: 184 average time/residue: 0.1182 time to fit residues: 30.1388 Evaluate side-chains 179 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain D residue 59 HIS Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 170 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 107 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 61 optimal weight: 0.0980 chunk 23 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 96 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 143 HIS ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN D 59 HIS D 248 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.179014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.116701 restraints weight = 14428.999| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.11 r_work: 0.3148 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11240 Z= 0.136 Angle : 0.622 11.756 15220 Z= 0.322 Chirality : 0.043 0.197 1660 Planarity : 0.003 0.040 1860 Dihedral : 5.144 26.390 1488 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 1.90 % Allowed : 18.53 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.24), residues: 1292 helix: -0.61 (0.19), residues: 802 sheet: -2.06 (1.84), residues: 10 loop : -0.55 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 340 TYR 0.012 0.001 TYR A 263 PHE 0.016 0.001 PHE B 152 TRP 0.011 0.001 TRP A 255 HIS 0.005 0.001 HIS D 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (11240) covalent geometry : angle 0.62221 / 0.32 (15220) hydrogen bonds : bond 0.04367 / 2.78 ( 437) hydrogen bonds : angle 4.06825 / 2.72 ( 1188) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3581.97 seconds wall clock time: 61 minutes 55.77 seconds (3715.77 seconds total)