Starting phenix.real_space_refine on Tue Mar 3 23:56:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ari_11883/03_2026/7ari_11883.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ari_11883/03_2026/7ari_11883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ari_11883/03_2026/7ari_11883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ari_11883/03_2026/7ari_11883.map" model { file = "/net/cci-nas-00/data/ceres_data/7ari_11883/03_2026/7ari_11883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ari_11883/03_2026/7ari_11883.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 6071 2.51 5 N 1683 2.21 5 O 1732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9538 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 2977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 2977 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Chain: "E" Number of atoms: 3159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3159 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 14, 'TRANS': 394} Chain: "F" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1707 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 8, 'TRANS': 214} Chain: "D" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1695 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 8, 'TRANS': 212} Time building chain proxies: 2.27, per 1000 atoms: 0.24 Number of scatterers: 9538 At special positions: 0 Unit cell: (121.68, 147.03, 117.624, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1732 8.00 N 1683 7.00 C 6071 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: 0.69 Conformation dependent library (CDL) restraints added in 354.1 milliseconds 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2278 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 10 sheets defined 38.4% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'C' and resid 7 through 14 removed outlier: 3.609A pdb=" N ARG C 12 " --> pdb=" O PHE C 8 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR C 13 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET C 14 " --> pdb=" O GLY C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 55 removed outlier: 3.854A pdb=" N VAL C 26 " --> pdb=" O PHE C 22 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER C 27 " --> pdb=" O GLY C 23 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TRP C 28 " --> pdb=" O ARG C 24 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE C 51 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU C 52 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 155 removed outlier: 3.793A pdb=" N GLN C 153 " --> pdb=" O GLN C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 236 removed outlier: 3.914A pdb=" N SER C 236 " --> pdb=" O ASP C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 258 removed outlier: 4.348A pdb=" N PHE C 257 " --> pdb=" O GLY C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 269 Processing helix chain 'C' and resid 273 through 279 Processing helix chain 'C' and resid 279 through 288 removed outlier: 3.571A pdb=" N LEU C 288 " --> pdb=" O THR C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 303 removed outlier: 4.033A pdb=" N VAL C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLN C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 324 removed outlier: 3.804A pdb=" N MET C 311 " --> pdb=" O PRO C 307 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET C 312 " --> pdb=" O ARG C 308 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE C 314 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET C 315 " --> pdb=" O MET C 311 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL C 316 " --> pdb=" O MET C 312 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE C 324 " --> pdb=" O SER C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 336 removed outlier: 3.599A pdb=" N LEU C 336 " --> pdb=" O LEU C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 364 removed outlier: 3.525A pdb=" N GLN C 364 " --> pdb=" O GLU C 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 361 through 364' Processing helix chain 'C' and resid 365 through 380 removed outlier: 4.168A pdb=" N VAL C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA C 372 " --> pdb=" O ILE C 368 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C 375 " --> pdb=" O VAL C 371 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU C 377 " --> pdb=" O MET C 373 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR C 380 " --> pdb=" O ALA C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 387 removed outlier: 3.574A pdb=" N ALA C 387 " --> pdb=" O PRO C 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 44 removed outlier: 3.723A pdb=" N ILE E 26 " --> pdb=" O MET E 22 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE E 29 " --> pdb=" O LEU E 25 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY E 37 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.747A pdb=" N MET E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU E 52 " --> pdb=" O MET E 48 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG E 53 " --> pdb=" O ASN E 49 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU E 55 " --> pdb=" O PHE E 51 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN E 56 " --> pdb=" O GLU E 52 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 85 removed outlier: 3.862A pdb=" N VAL E 85 " --> pdb=" O ALA E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 258 removed outlier: 4.022A pdb=" N THR E 257 " --> pdb=" O SER E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 272 Processing helix chain 'E' and resid 277 through 284 removed outlier: 3.651A pdb=" N GLY E 281 " --> pdb=" O VAL E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 292 Processing helix chain 'E' and resid 292 through 297 removed outlier: 4.166A pdb=" N LYS E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP E 297 " --> pdb=" O MET E 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 292 through 297' Processing helix chain 'E' and resid 298 through 308 removed outlier: 3.562A pdb=" N ALA E 303 " --> pdb=" O SER E 299 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU E 305 " --> pdb=" O ASP E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 343 removed outlier: 3.586A pdb=" N ARG E 316 " --> pdb=" O ASP E 312 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE E 319 " --> pdb=" O ILE E 315 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL E 320 " --> pdb=" O ARG E 316 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TRP E 321 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS E 333 " --> pdb=" O PHE E 329 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLY E 334 " --> pdb=" O GLY E 330 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL E 335 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE E 336 " --> pdb=" O LEU E 332 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL E 341 " --> pdb=" O ILE E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 352 removed outlier: 3.810A pdb=" N ILE E 348 " --> pdb=" O GLN E 344 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU E 350 " --> pdb=" O THR E 346 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE E 352 " --> pdb=" O ILE E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 395 removed outlier: 3.743A pdb=" N TYR E 382 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL E 383 " --> pdb=" O ASP E 379 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU E 384 " --> pdb=" O VAL E 380 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR E 386 " --> pdb=" O TYR E 382 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU E 388 " --> pdb=" O LEU E 384 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU E 393 " --> pdb=" O LEU E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 402 Processing helix chain 'F' and resid 47 through 57 removed outlier: 3.825A pdb=" N HIS F 53 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY F 57 " --> pdb=" O HIS F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 88 removed outlier: 3.768A pdb=" N GLN F 87 " --> pdb=" O GLU F 83 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS F 88 " --> pdb=" O LEU F 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 83 through 88' Processing helix chain 'F' and resid 103 through 109 removed outlier: 3.848A pdb=" N VAL F 108 " --> pdb=" O ALA F 104 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA F 109 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 115 removed outlier: 3.801A pdb=" N ILE F 114 " --> pdb=" O MET F 110 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY F 115 " --> pdb=" O PRO F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 131 removed outlier: 3.964A pdb=" N ASN F 123 " --> pdb=" O PRO F 119 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER F 124 " --> pdb=" O ALA F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 139 removed outlier: 3.658A pdb=" N ALA F 139 " --> pdb=" O ASP F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 160 removed outlier: 3.749A pdb=" N ILE F 156 " --> pdb=" O GLN F 152 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA F 157 " --> pdb=" O ARG F 153 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG F 158 " --> pdb=" O VAL F 154 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA F 159 " --> pdb=" O ALA F 155 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LEU F 160 " --> pdb=" O ILE F 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 152 through 160' Processing helix chain 'F' and resid 178 through 195 removed outlier: 4.280A pdb=" N ASP F 182 " --> pdb=" O ALA F 178 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER F 183 " --> pdb=" O ARG F 179 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE F 184 " --> pdb=" O ASN F 180 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE F 185 " --> pdb=" O ALA F 181 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN F 186 " --> pdb=" O ASP F 182 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU F 187 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN F 192 " --> pdb=" O LEU F 188 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG F 193 " --> pdb=" O GLY F 189 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU F 194 " --> pdb=" O GLU F 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 57 removed outlier: 3.524A pdb=" N LEU D 52 " --> pdb=" O LYS D 48 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS D 53 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU D 54 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY D 57 " --> pdb=" O HIS D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 88 removed outlier: 3.719A pdb=" N GLU D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS D 88 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 109 removed outlier: 3.613A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 115 removed outlier: 3.688A pdb=" N GLY D 115 " --> pdb=" O PRO D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 131 removed outlier: 3.678A pdb=" N ASN D 123 " --> pdb=" O PRO D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 158 removed outlier: 3.880A pdb=" N GLN D 152 " --> pdb=" O GLY D 148 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ARG D 153 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL D 154 " --> pdb=" O GLU D 150 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 194 removed outlier: 4.083A pdb=" N ASP D 182 " --> pdb=" O ALA D 178 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER D 183 " --> pdb=" O ARG D 179 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN D 186 " --> pdb=" O ASP D 182 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU D 187 " --> pdb=" O SER D 183 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG D 193 " --> pdb=" O GLY D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 222 removed outlier: 3.788A pdb=" N GLY D 221 " --> pdb=" O MET D 218 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 66 through 67 removed outlier: 4.277A pdb=" N ALA C 66 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU C 224 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY C 221 " --> pdb=" O ILE C 96 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 180 through 183 removed outlier: 4.296A pdb=" N SER C 180 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL C 166 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ARG C 163 " --> pdb=" O GLN C 104 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN C 104 " --> pdb=" O ARG C 163 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA C 110 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N MET C 201 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL C 113 " --> pdb=" O MET C 201 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N VAL C 203 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LEU C 115 " --> pdb=" O VAL C 203 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 143 through 147 removed outlier: 4.019A pdb=" N ILE C 187 " --> pdb=" O VAL C 144 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N LEU C 146 " --> pdb=" O ILE C 187 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR C 189 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 115 through 116 Processing sheet with id=AA5, first strand: chain 'E' and resid 147 through 150 removed outlier: 6.059A pdb=" N ILE E 148 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE E 192 " --> pdb=" O ILE E 148 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE E 150 " --> pdb=" O ILE E 192 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU E 187 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL E 166 " --> pdb=" O LEU E 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'F' and resid 31 through 32 removed outlier: 4.083A pdb=" N LEU F 6 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN F 7 " --> pdb=" O ILE F 67 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE F 67 " --> pdb=" O GLN F 7 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP F 9 " --> pdb=" O ASP F 65 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP F 65 " --> pdb=" O ASP F 9 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 38 through 41 removed outlier: 6.162A pdb=" N MET F 38 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N THR F 203 " --> pdb=" O MET F 38 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE F 40 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL F 167 " --> pdb=" O LEU F 200 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N VAL F 202 " --> pdb=" O VAL F 167 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ALA F 169 " --> pdb=" O VAL F 202 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLY F 90 " --> pdb=" O LEU F 168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 217 through 218 removed outlier: 3.868A pdb=" N GLU F 217 " --> pdb=" O THR F 224 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 6 through 7 removed outlier: 4.134A pdb=" N LEU D 6 " --> pdb=" O VAL D 32 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 39 through 41 removed outlier: 6.558A pdb=" N ILE D 40 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLY D 90 " --> pdb=" O LEU D 168 " (cutoff:3.500A) 208 hydrogen bonds defined for protein. 609 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: 1.14 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3186 1.34 - 1.46: 1687 1.46 - 1.58: 4725 1.58 - 1.69: 0 1.69 - 1.81: 98 Bond restraints: 9696 Sorted by residual: bond pdb=" N VAL C 38 " pdb=" CA VAL C 38 " ideal model delta sigma weight residual 1.462 1.496 -0.034 1.14e-02 7.69e+03 8.88e+00 bond pdb=" N ILE C 32 " pdb=" CA ILE C 32 " ideal model delta sigma weight residual 1.462 1.496 -0.034 1.17e-02 7.31e+03 8.52e+00 bond pdb=" N VAL C 26 " pdb=" CA VAL C 26 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.30e-02 5.92e+03 8.47e+00 bond pdb=" N ILE C 34 " pdb=" CA ILE C 34 " ideal model delta sigma weight residual 1.460 1.493 -0.034 1.21e-02 6.83e+03 7.69e+00 bond pdb=" N PHE C 25 " pdb=" CA PHE C 25 " ideal model delta sigma weight residual 1.459 1.490 -0.030 1.20e-02 6.94e+03 6.40e+00 ... (remaining 9691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 12653 1.85 - 3.70: 381 3.70 - 5.54: 64 5.54 - 7.39: 26 7.39 - 9.24: 4 Bond angle restraints: 13128 Sorted by residual: angle pdb=" C PHE F 95 " pdb=" N HIS F 96 " pdb=" CA HIS F 96 " ideal model delta sigma weight residual 122.82 128.73 -5.91 1.42e+00 4.96e-01 1.73e+01 angle pdb=" C LEU E 158 " pdb=" N LYS E 159 " pdb=" CA LYS E 159 " ideal model delta sigma weight residual 122.46 128.07 -5.61 1.41e+00 5.03e-01 1.58e+01 angle pdb=" CA LYS E 159 " pdb=" CB LYS E 159 " pdb=" CG LYS E 159 " ideal model delta sigma weight residual 114.10 121.54 -7.44 2.00e+00 2.50e-01 1.39e+01 angle pdb=" C LEU C 55 " pdb=" N GLN C 56 " pdb=" CA GLN C 56 " ideal model delta sigma weight residual 122.61 128.15 -5.54 1.56e+00 4.11e-01 1.26e+01 angle pdb=" N VAL E 295 " pdb=" CA VAL E 295 " pdb=" C VAL E 295 " ideal model delta sigma weight residual 111.90 109.03 2.87 8.10e-01 1.52e+00 1.25e+01 ... (remaining 13123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 5322 17.94 - 35.89: 449 35.89 - 53.83: 83 53.83 - 71.77: 19 71.77 - 89.72: 6 Dihedral angle restraints: 5879 sinusoidal: 2338 harmonic: 3541 Sorted by residual: dihedral pdb=" C THR C 35 " pdb=" N THR C 35 " pdb=" CA THR C 35 " pdb=" CB THR C 35 " ideal model delta harmonic sigma weight residual -122.00 -130.43 8.43 0 2.50e+00 1.60e-01 1.14e+01 dihedral pdb=" CA ASP F 182 " pdb=" CB ASP F 182 " pdb=" CG ASP F 182 " pdb=" OD1 ASP F 182 " ideal model delta sinusoidal sigma weight residual -30.00 -85.69 55.69 1 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CB GLU D 217 " pdb=" CG GLU D 217 " pdb=" CD GLU D 217 " pdb=" OE1 GLU D 217 " ideal model delta sinusoidal sigma weight residual 0.00 85.10 -85.10 1 3.00e+01 1.11e-03 9.75e+00 ... (remaining 5876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1094 0.045 - 0.090: 314 0.090 - 0.135: 106 0.135 - 0.180: 13 0.180 - 0.225: 8 Chirality restraints: 1535 Sorted by residual: chirality pdb=" CB VAL C 196 " pdb=" CA VAL C 196 " pdb=" CG1 VAL C 196 " pdb=" CG2 VAL C 196 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB THR C 126 " pdb=" CA THR C 126 " pdb=" OG1 THR C 126 " pdb=" CG2 THR C 126 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA THR C 35 " pdb=" N THR C 35 " pdb=" C THR C 35 " pdb=" CB THR C 35 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1532 not shown) Planarity restraints: 1687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 346 " 0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO E 347 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO E 347 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 347 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 255 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.50e+00 pdb=" C GLU C 255 " -0.037 2.00e-02 2.50e+03 pdb=" O GLU C 255 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU C 256 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE E 170 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO E 171 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO E 171 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 171 " 0.027 5.00e-02 4.00e+02 ... (remaining 1684 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 3060 2.85 - 3.36: 8029 3.36 - 3.88: 14701 3.88 - 4.39: 16373 4.39 - 4.90: 27778 Nonbonded interactions: 69941 Sorted by model distance: nonbonded pdb=" O VAL C 232 " pdb=" OG SER C 236 " model vdw 2.339 3.040 nonbonded pdb=" O CYS D 12 " pdb=" OG SER D 63 " model vdw 2.339 3.040 nonbonded pdb=" O SER E 6 " pdb=" OG SER E 6 " model vdw 2.427 3.040 nonbonded pdb=" O ALA C 66 " pdb=" NH1 ARG C 223 " model vdw 2.430 3.120 nonbonded pdb=" O SER E 395 " pdb=" OG SER E 395 " model vdw 2.432 3.040 ... (remaining 69936 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 'D' selection = (chain 'F' and resid 3 through 223) } 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: 0.450 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.520 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 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 : 0.003 0.038 9696 Z= 0.194 Angle : 0.778 9.240 13128 Z= 0.430 Chirality : 0.049 0.225 1535 Planarity : 0.005 0.057 1687 Dihedral : 13.730 89.717 3601 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.68 % Allowed : 8.58 % Favored : 90.74 % 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: -5.94 (0.15), residues: 1236 helix: -4.98 (0.07), residues: 373 sheet: -2.46 (0.60), residues: 59 loop : -3.78 (0.15), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 177 TYR 0.008 0.000 TYR F 15 PHE 0.017 0.001 PHE D 199 TRP 0.005 0.001 TRP C 28 HIS 0.005 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9696) covalent geometry : angle 0.77817 (13128) hydrogen bonds : bond 0.34845 ( 208) hydrogen bonds : angle 9.83657 ( 609) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 310 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 MET cc_start: 0.6783 (pmm) cc_final: 0.5107 (ptp) REVERT: C 212 MET cc_start: 0.4068 (mtt) cc_final: 0.3833 (mtp) REVERT: C 227 ASP cc_start: 0.7255 (p0) cc_final: 0.6941 (p0) REVERT: C 286 LEU cc_start: 0.8294 (mm) cc_final: 0.8068 (mp) REVERT: C 312 MET cc_start: 0.5564 (mmm) cc_final: 0.4940 (mmm) REVERT: E 78 TRP cc_start: 0.4586 (p-90) cc_final: 0.4109 (p-90) REVERT: E 228 MET cc_start: 0.7074 (ttm) cc_final: 0.6865 (ttm) REVERT: F 52 LEU cc_start: 0.9206 (mm) cc_final: 0.8986 (mm) REVERT: F 71 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8292 (mm110) REVERT: F 123 ASN cc_start: 0.8599 (t0) cc_final: 0.8304 (t0) REVERT: D 38 MET cc_start: 0.6466 (mtp) cc_final: 0.6186 (mtp) REVERT: D 94 GLN cc_start: 0.6222 (pt0) cc_final: 0.5282 (pt0) REVERT: D 130 LEU cc_start: 0.8977 (mt) cc_final: 0.8699 (mt) REVERT: D 156 ILE cc_start: 0.9275 (mt) cc_final: 0.9068 (mp) REVERT: D 185 PHE cc_start: 0.7622 (m-10) cc_final: 0.7327 (m-80) outliers start: 7 outliers final: 3 residues processed: 313 average time/residue: 0.1092 time to fit residues: 45.8835 Evaluate side-chains 196 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 193 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 35 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.0470 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.0070 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN C 149 GLN C 157 ASN C 204 ASN C 317 GLN C 339 GLN C 341 ASN C 391 GLN E 134 GLN E 146 GLN E 188 HIS E 194 GLN E 198 GLN E 359 GLN E 376 HIS F 10 ASN F 26 HIS F 94 GLN F 204 HIS F 215 GLN D 53 HIS D 107 ASN D 180 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.232637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.191528 restraints weight = 16694.663| |-----------------------------------------------------------------------------| r_work (start): 0.4463 rms_B_bonded: 4.24 r_work: 0.4135 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9696 Z= 0.104 Angle : 0.587 12.987 13128 Z= 0.284 Chirality : 0.041 0.127 1535 Planarity : 0.004 0.041 1687 Dihedral : 3.916 53.082 1337 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.05 % Allowed : 16.76 % Favored : 81.19 % 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: -4.86 (0.17), residues: 1236 helix: -3.23 (0.17), residues: 424 sheet: -2.24 (0.54), residues: 78 loop : -3.50 (0.17), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 125 TYR 0.009 0.001 TYR F 15 PHE 0.022 0.001 PHE F 185 TRP 0.012 0.001 TRP C 249 HIS 0.007 0.001 HIS E 376 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 9696) covalent geometry : angle 0.58735 (13128) hydrogen bonds : bond 0.04697 ( 208) hydrogen bonds : angle 4.89777 ( 609) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 213 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 51 PHE cc_start: 0.7948 (m-80) cc_final: 0.7635 (m-80) REVERT: C 114 MET cc_start: 0.6886 (pmm) cc_final: 0.5526 (ptp) REVERT: C 195 GLU cc_start: 0.4241 (tt0) cc_final: 0.4013 (tt0) REVERT: C 201 MET cc_start: 0.7834 (mpp) cc_final: 0.7411 (mmm) REVERT: C 227 ASP cc_start: 0.7344 (p0) cc_final: 0.7013 (p0) REVERT: C 250 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.4874 (ttp80) REVERT: C 312 MET cc_start: 0.6486 (mmm) cc_final: 0.5677 (mmm) REVERT: E 393 LEU cc_start: 0.8859 (tt) cc_final: 0.8566 (tp) REVERT: F 110 MET cc_start: 0.9590 (tpp) cc_final: 0.9322 (tpt) REVERT: F 197 THR cc_start: 0.7177 (OUTLIER) cc_final: 0.6917 (t) REVERT: D 38 MET cc_start: 0.7372 (mtp) cc_final: 0.6818 (mtp) REVERT: D 83 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8093 (mp0) REVERT: D 93 TYR cc_start: 0.6901 (m-10) cc_final: 0.6668 (m-80) REVERT: D 127 LEU cc_start: 0.8485 (pp) cc_final: 0.8002 (mt) REVERT: D 185 PHE cc_start: 0.7970 (m-10) cc_final: 0.7711 (m-80) REVERT: D 218 MET cc_start: 0.6820 (tpp) cc_final: 0.6236 (tpp) outliers start: 21 outliers final: 12 residues processed: 225 average time/residue: 0.0863 time to fit residues: 27.6991 Evaluate side-chains 200 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 262 TYR Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 201 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 57 optimal weight: 0.0980 chunk 60 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 1 optimal weight: 0.0970 chunk 18 optimal weight: 10.0000 chunk 25 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 117 optimal weight: 0.1980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 317 GLN E 174 ASN E 181 GLN F 26 HIS F 97 HIS F 204 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.229823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.188208 restraints weight = 16366.563| |-----------------------------------------------------------------------------| r_work (start): 0.4421 rms_B_bonded: 4.36 r_work: 0.4093 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9696 Z= 0.095 Angle : 0.542 10.577 13128 Z= 0.256 Chirality : 0.042 0.148 1535 Planarity : 0.003 0.039 1687 Dihedral : 3.299 18.741 1334 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.24 % Allowed : 18.91 % Favored : 78.85 % 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: -3.98 (0.19), residues: 1236 helix: -2.02 (0.21), residues: 427 sheet: -2.13 (0.55), residues: 79 loop : -3.25 (0.18), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 179 TYR 0.011 0.001 TYR E 397 PHE 0.016 0.001 PHE F 95 TRP 0.013 0.001 TRP C 249 HIS 0.019 0.001 HIS E 188 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 9696) covalent geometry : angle 0.54215 (13128) hydrogen bonds : bond 0.03415 ( 208) hydrogen bonds : angle 4.35292 ( 609) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 51 PHE cc_start: 0.8078 (m-80) cc_final: 0.7772 (m-80) REVERT: C 114 MET cc_start: 0.6806 (pmm) cc_final: 0.5168 (ptp) REVERT: C 201 MET cc_start: 0.7904 (mpp) cc_final: 0.7389 (mpp) REVERT: C 227 ASP cc_start: 0.7379 (p0) cc_final: 0.7045 (p0) REVERT: C 312 MET cc_start: 0.6667 (mmm) cc_final: 0.5873 (mmm) REVERT: C 317 GLN cc_start: 0.7170 (tt0) cc_final: 0.6936 (tt0) REVERT: E 393 LEU cc_start: 0.8969 (tt) cc_final: 0.8681 (tp) REVERT: F 37 MET cc_start: 0.5307 (ptp) cc_final: 0.5063 (ptp) REVERT: F 110 MET cc_start: 0.9611 (tpp) cc_final: 0.9311 (tpt) REVERT: F 197 THR cc_start: 0.7211 (OUTLIER) cc_final: 0.6930 (t) REVERT: D 38 MET cc_start: 0.7350 (mtp) cc_final: 0.6948 (mtp) REVERT: D 83 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8300 (mp0) REVERT: D 127 LEU cc_start: 0.8554 (pp) cc_final: 0.8068 (mt) REVERT: D 152 GLN cc_start: 0.8763 (tm-30) cc_final: 0.8106 (tm-30) REVERT: D 212 MET cc_start: 0.5731 (tmm) cc_final: 0.5393 (ttp) outliers start: 23 outliers final: 13 residues processed: 210 average time/residue: 0.0787 time to fit residues: 24.2733 Evaluate side-chains 198 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 184 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 257 PHE Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 262 TYR Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 201 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 66 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 106 optimal weight: 0.2980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 GLN F 71 GLN ** F 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.212290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.147480 restraints weight = 15653.641| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 3.37 r_work: 0.3754 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.5042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9696 Z= 0.223 Angle : 0.717 8.976 13128 Z= 0.354 Chirality : 0.048 0.192 1535 Planarity : 0.004 0.051 1687 Dihedral : 4.332 25.330 1333 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.92 % Allowed : 19.69 % Favored : 77.39 % 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: -3.80 (0.20), residues: 1236 helix: -1.77 (0.22), residues: 452 sheet: -2.35 (0.51), residues: 85 loop : -3.20 (0.19), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 53 TYR 0.013 0.002 TYR E 322 PHE 0.021 0.002 PHE E 319 TRP 0.019 0.002 TRP E 396 HIS 0.007 0.001 HIS E 376 Details of bonding type rmsd covalent geometry : bond 0.00532 ( 9696) covalent geometry : angle 0.71716 (13128) hydrogen bonds : bond 0.04927 ( 208) hydrogen bonds : angle 4.72433 ( 609) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 197 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.8180 (tpt-90) cc_final: 0.7883 (tpp-160) REVERT: C 48 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7919 (mmt) REVERT: C 114 MET cc_start: 0.6967 (pmm) cc_final: 0.6202 (ptt) REVERT: C 201 MET cc_start: 0.8170 (mpp) cc_final: 0.7863 (mpp) REVERT: C 250 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.5557 (ttp80) REVERT: C 312 MET cc_start: 0.7715 (mmm) cc_final: 0.7114 (mmm) REVERT: E 48 MET cc_start: 0.8530 (mmt) cc_final: 0.8241 (mmt) REVERT: E 56 ASN cc_start: 0.8647 (p0) cc_final: 0.8274 (p0) REVERT: E 262 TYR cc_start: 0.8040 (OUTLIER) cc_final: 0.7542 (t80) REVERT: E 301 ASP cc_start: 0.8801 (t70) cc_final: 0.8550 (m-30) REVERT: F 37 MET cc_start: 0.6271 (ptp) cc_final: 0.5849 (ptp) REVERT: D 37 MET cc_start: 0.7587 (pmm) cc_final: 0.7278 (pmm) REVERT: D 173 THR cc_start: 0.7857 (m) cc_final: 0.7206 (p) outliers start: 30 outliers final: 18 residues processed: 217 average time/residue: 0.0959 time to fit residues: 28.7121 Evaluate side-chains 187 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 262 TYR Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 193 ARG Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain D residue 201 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 56 optimal weight: 2.9990 chunk 75 optimal weight: 0.0050 chunk 49 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 89 optimal weight: 0.4980 chunk 61 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 GLN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 359 GLN F 137 HIS ** F 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 GLN D 215 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.216018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.157456 restraints weight = 15770.616| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 3.31 r_work: 0.3830 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9696 Z= 0.099 Angle : 0.594 12.408 13128 Z= 0.279 Chirality : 0.043 0.172 1535 Planarity : 0.003 0.036 1687 Dihedral : 3.705 20.515 1333 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.83 % Allowed : 22.42 % Favored : 74.76 % 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: -3.10 (0.21), residues: 1236 helix: -0.90 (0.24), residues: 444 sheet: -2.28 (0.56), residues: 75 loop : -2.94 (0.19), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 125 TYR 0.014 0.001 TYR E 397 PHE 0.014 0.001 PHE E 319 TRP 0.014 0.001 TRP C 249 HIS 0.005 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 9696) covalent geometry : angle 0.59366 (13128) hydrogen bonds : bond 0.02974 ( 208) hydrogen bonds : angle 4.07772 ( 609) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 188 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 MET cc_start: 0.6845 (pmm) cc_final: 0.5957 (ptt) REVERT: C 201 MET cc_start: 0.8143 (mpp) cc_final: 0.7875 (mpp) REVERT: C 312 MET cc_start: 0.7670 (mmm) cc_final: 0.7071 (mmm) REVERT: E 71 VAL cc_start: 0.6768 (OUTLIER) cc_final: 0.6546 (t) REVERT: E 228 MET cc_start: 0.7185 (ttm) cc_final: 0.6911 (ttm) REVERT: E 301 ASP cc_start: 0.8880 (t70) cc_final: 0.8554 (m-30) REVERT: F 71 GLN cc_start: 0.8544 (mm110) cc_final: 0.8272 (mm110) REVERT: F 206 LEU cc_start: 0.6843 (tp) cc_final: 0.6529 (tp) REVERT: D 7 GLN cc_start: 0.7389 (tp40) cc_final: 0.7133 (tp-100) REVERT: D 11 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7500 (tp) REVERT: D 127 LEU cc_start: 0.8678 (pp) cc_final: 0.8250 (tp) REVERT: D 173 THR cc_start: 0.7715 (m) cc_final: 0.7040 (p) outliers start: 29 outliers final: 20 residues processed: 204 average time/residue: 0.0800 time to fit residues: 23.9668 Evaluate side-chains 192 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 199 PHE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 65 optimal weight: 0.7980 chunk 68 optimal weight: 0.0970 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 102 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 chunk 64 optimal weight: 0.0570 chunk 52 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 GLN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.215844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.154403 restraints weight = 15708.198| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 3.38 r_work: 0.3839 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9696 Z= 0.097 Angle : 0.576 10.516 13128 Z= 0.273 Chirality : 0.043 0.156 1535 Planarity : 0.003 0.034 1687 Dihedral : 3.571 18.369 1333 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.92 % Allowed : 23.10 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.22), residues: 1236 helix: -0.45 (0.25), residues: 450 sheet: -2.27 (0.52), residues: 86 loop : -2.74 (0.20), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 214 TYR 0.010 0.001 TYR E 397 PHE 0.029 0.001 PHE F 95 TRP 0.014 0.001 TRP C 249 HIS 0.004 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 9696) covalent geometry : angle 0.57633 (13128) hydrogen bonds : bond 0.02946 ( 208) hydrogen bonds : angle 3.93715 ( 609) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 51 PHE cc_start: 0.8270 (m-80) cc_final: 0.8032 (m-80) REVERT: C 114 MET cc_start: 0.6866 (pmm) cc_final: 0.6057 (ptt) REVERT: C 212 MET cc_start: 0.5112 (ptp) cc_final: 0.4643 (pmm) REVERT: C 312 MET cc_start: 0.7603 (mmm) cc_final: 0.6688 (mmm) REVERT: C 315 MET cc_start: 0.6508 (OUTLIER) cc_final: 0.6037 (ptm) REVERT: E 71 VAL cc_start: 0.6815 (OUTLIER) cc_final: 0.6597 (t) REVERT: E 98 ILE cc_start: 0.8591 (pt) cc_final: 0.8312 (pt) REVERT: E 228 MET cc_start: 0.7180 (ttm) cc_final: 0.6907 (ttm) REVERT: E 301 ASP cc_start: 0.8840 (t70) cc_final: 0.8525 (m-30) REVERT: F 71 GLN cc_start: 0.8559 (mm110) cc_final: 0.8259 (mm-40) REVERT: F 206 LEU cc_start: 0.6776 (tp) cc_final: 0.6421 (tp) REVERT: D 7 GLN cc_start: 0.7563 (tp40) cc_final: 0.7238 (tp-100) REVERT: D 127 LEU cc_start: 0.8721 (pp) cc_final: 0.8172 (mt) REVERT: D 218 MET cc_start: 0.6427 (tpp) cc_final: 0.5997 (tpp) outliers start: 30 outliers final: 21 residues processed: 190 average time/residue: 0.0749 time to fit residues: 21.1209 Evaluate side-chains 193 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 199 PHE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 23 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 0.3980 chunk 60 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 105 optimal weight: 0.0870 chunk 74 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.213207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.150645 restraints weight = 15560.410| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 3.55 r_work: 0.3783 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.5543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9696 Z= 0.118 Angle : 0.606 9.775 13128 Z= 0.285 Chirality : 0.043 0.164 1535 Planarity : 0.003 0.033 1687 Dihedral : 3.627 19.085 1333 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.31 % Allowed : 23.78 % Favored : 72.90 % 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: -2.46 (0.22), residues: 1236 helix: -0.36 (0.25), residues: 460 sheet: -2.12 (0.54), residues: 86 loop : -2.58 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 211 TYR 0.007 0.001 TYR E 397 PHE 0.015 0.001 PHE E 319 TRP 0.012 0.001 TRP C 249 HIS 0.004 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9696) covalent geometry : angle 0.60555 (13128) hydrogen bonds : bond 0.03196 ( 208) hydrogen bonds : angle 3.92143 ( 609) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8290 (mp) REVERT: C 48 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7796 (mmm) REVERT: C 51 PHE cc_start: 0.8412 (m-80) cc_final: 0.8206 (m-80) REVERT: C 56 GLN cc_start: 0.8243 (pm20) cc_final: 0.7995 (pm20) REVERT: C 114 MET cc_start: 0.6888 (pmm) cc_final: 0.6281 (ptt) REVERT: C 201 MET cc_start: 0.7723 (mpp) cc_final: 0.6737 (mmp) REVERT: C 212 MET cc_start: 0.5536 (ptp) cc_final: 0.4885 (pmm) REVERT: C 296 GLU cc_start: 0.7851 (mp0) cc_final: 0.7591 (mp0) REVERT: C 312 MET cc_start: 0.7627 (mmm) cc_final: 0.6910 (mmm) REVERT: E 228 MET cc_start: 0.7172 (ttm) cc_final: 0.6877 (ttm) REVERT: E 301 ASP cc_start: 0.8907 (t70) cc_final: 0.8596 (m-30) REVERT: F 71 GLN cc_start: 0.8583 (mm110) cc_final: 0.8271 (mm-40) REVERT: F 182 ASP cc_start: 0.8195 (p0) cc_final: 0.7949 (p0) REVERT: F 206 LEU cc_start: 0.6872 (tp) cc_final: 0.6506 (tp) REVERT: D 7 GLN cc_start: 0.7594 (tp40) cc_final: 0.7255 (tp-100) REVERT: D 127 LEU cc_start: 0.8797 (pp) cc_final: 0.8283 (mt) REVERT: D 218 MET cc_start: 0.6387 (tpp) cc_final: 0.5961 (tpp) outliers start: 34 outliers final: 21 residues processed: 198 average time/residue: 0.0726 time to fit residues: 21.6052 Evaluate side-chains 189 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 199 PHE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 68 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 69 optimal weight: 0.6980 chunk 117 optimal weight: 0.4980 chunk 20 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.215012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.150137 restraints weight = 15738.308| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 3.85 r_work: 0.3771 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.5760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9696 Z= 0.112 Angle : 0.592 9.539 13128 Z= 0.280 Chirality : 0.043 0.139 1535 Planarity : 0.003 0.033 1687 Dihedral : 3.649 18.617 1333 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.83 % Allowed : 25.05 % Favored : 72.12 % 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: -2.22 (0.23), residues: 1236 helix: -0.11 (0.25), residues: 460 sheet: -2.02 (0.55), residues: 85 loop : -2.48 (0.21), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 211 TYR 0.008 0.001 TYR E 397 PHE 0.014 0.001 PHE E 319 TRP 0.017 0.001 TRP C 249 HIS 0.004 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9696) covalent geometry : angle 0.59220 (13128) hydrogen bonds : bond 0.03109 ( 208) hydrogen bonds : angle 3.89257 ( 609) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 48 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7809 (mmm) REVERT: C 51 PHE cc_start: 0.8414 (m-80) cc_final: 0.8181 (m-80) REVERT: C 56 GLN cc_start: 0.8227 (pm20) cc_final: 0.7962 (pm20) REVERT: C 114 MET cc_start: 0.6894 (pmm) cc_final: 0.6276 (ptt) REVERT: C 201 MET cc_start: 0.7778 (mpp) cc_final: 0.6902 (mmp) REVERT: C 212 MET cc_start: 0.5394 (ptp) cc_final: 0.4817 (pmm) REVERT: C 249 TRP cc_start: 0.4756 (p-90) cc_final: 0.4250 (p-90) REVERT: C 296 GLU cc_start: 0.7820 (mp0) cc_final: 0.7592 (mp0) REVERT: C 312 MET cc_start: 0.7811 (mmm) cc_final: 0.7069 (mmm) REVERT: C 368 ILE cc_start: 0.9033 (tp) cc_final: 0.8772 (tp) REVERT: E 228 MET cc_start: 0.7373 (ttm) cc_final: 0.7070 (ttm) REVERT: E 301 ASP cc_start: 0.8922 (t70) cc_final: 0.8610 (m-30) REVERT: F 37 MET cc_start: 0.6305 (mtp) cc_final: 0.6020 (mtp) REVERT: F 71 GLN cc_start: 0.8584 (mm110) cc_final: 0.8293 (mm110) REVERT: F 206 LEU cc_start: 0.7067 (tp) cc_final: 0.6609 (tp) REVERT: D 11 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7675 (tp) REVERT: D 127 LEU cc_start: 0.8832 (pp) cc_final: 0.8362 (mt) REVERT: D 218 MET cc_start: 0.6305 (tpp) cc_final: 0.5879 (tpp) outliers start: 29 outliers final: 23 residues processed: 188 average time/residue: 0.0802 time to fit residues: 22.3519 Evaluate side-chains 189 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 55 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 76 optimal weight: 0.0170 chunk 78 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 26 optimal weight: 0.4980 overall best weight: 1.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 317 GLN E 134 GLN ** F 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 ASN D 215 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.208203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.141491 restraints weight = 15603.780| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 3.04 r_work: 0.3715 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.6215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9696 Z= 0.153 Angle : 0.671 9.215 13128 Z= 0.320 Chirality : 0.045 0.142 1535 Planarity : 0.003 0.032 1687 Dihedral : 4.007 22.375 1333 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.92 % Allowed : 24.66 % Favored : 72.42 % 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: -2.14 (0.23), residues: 1236 helix: -0.07 (0.25), residues: 456 sheet: -2.08 (0.49), residues: 107 loop : -2.36 (0.22), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 219 TYR 0.007 0.001 TYR E 258 PHE 0.017 0.002 PHE E 319 TRP 0.007 0.001 TRP E 165 HIS 0.004 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 9696) covalent geometry : angle 0.67090 (13128) hydrogen bonds : bond 0.03842 ( 208) hydrogen bonds : angle 4.15182 ( 609) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.8216 (tpt-90) cc_final: 0.7989 (tpp-160) REVERT: C 114 MET cc_start: 0.7052 (pmm) cc_final: 0.6436 (ptt) REVERT: C 201 MET cc_start: 0.7923 (mpp) cc_final: 0.7134 (mmp) REVERT: C 312 MET cc_start: 0.7821 (mmm) cc_final: 0.7090 (mmm) REVERT: E 228 MET cc_start: 0.7455 (ttm) cc_final: 0.7166 (ttm) REVERT: E 301 ASP cc_start: 0.8917 (t70) cc_final: 0.8471 (m-30) REVERT: F 71 GLN cc_start: 0.8612 (mm110) cc_final: 0.8310 (mm-40) REVERT: D 11 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7729 (tp) REVERT: D 127 LEU cc_start: 0.8833 (pp) cc_final: 0.8406 (mt) REVERT: D 152 GLN cc_start: 0.8903 (mm-40) cc_final: 0.8287 (tm-30) REVERT: D 171 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7365 (tt0) REVERT: D 212 MET cc_start: 0.5936 (tmm) cc_final: 0.5085 (tmm) outliers start: 30 outliers final: 20 residues processed: 193 average time/residue: 0.0847 time to fit residues: 23.7886 Evaluate side-chains 181 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 199 PHE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 112 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 chunk 90 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 14 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.211614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.150459 restraints weight = 15719.558| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 4.06 r_work: 0.3741 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.6295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9696 Z= 0.123 Angle : 0.663 14.226 13128 Z= 0.310 Chirality : 0.044 0.140 1535 Planarity : 0.003 0.033 1687 Dihedral : 3.876 20.571 1333 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.14 % Allowed : 25.83 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.03 (0.23), residues: 1236 helix: 0.03 (0.25), residues: 460 sheet: -2.09 (0.49), residues: 107 loop : -2.31 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 219 TYR 0.006 0.001 TYR E 397 PHE 0.015 0.001 PHE E 319 TRP 0.017 0.001 TRP C 249 HIS 0.004 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9696) covalent geometry : angle 0.66321 (13128) hydrogen bonds : bond 0.03359 ( 208) hydrogen bonds : angle 4.08049 ( 609) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7953 (mmm) REVERT: C 56 GLN cc_start: 0.8237 (pm20) cc_final: 0.7949 (pm20) REVERT: C 114 MET cc_start: 0.7002 (pmm) cc_final: 0.6358 (ptt) REVERT: C 201 MET cc_start: 0.7900 (mpp) cc_final: 0.7183 (mmp) REVERT: C 212 MET cc_start: 0.5644 (ptp) cc_final: 0.5107 (pmm) REVERT: C 312 MET cc_start: 0.7949 (mmm) cc_final: 0.7236 (mmm) REVERT: E 301 ASP cc_start: 0.8887 (t70) cc_final: 0.8458 (m-30) REVERT: F 44 SER cc_start: 0.7355 (OUTLIER) cc_final: 0.7056 (p) REVERT: F 71 GLN cc_start: 0.8598 (mm110) cc_final: 0.8332 (mm-40) REVERT: F 179 ARG cc_start: 0.8215 (tpm170) cc_final: 0.7994 (tpm170) REVERT: F 199 PHE cc_start: 0.7868 (OUTLIER) cc_final: 0.7348 (p90) REVERT: D 127 LEU cc_start: 0.8815 (pp) cc_final: 0.8413 (mt) REVERT: D 212 MET cc_start: 0.5339 (tmm) cc_final: 0.4917 (tmm) outliers start: 22 outliers final: 15 residues processed: 183 average time/residue: 0.0791 time to fit residues: 21.4126 Evaluate side-chains 178 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 199 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 37 optimal weight: 0.7980 chunk 61 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 92 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.209106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.147453 restraints weight = 15598.120| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 3.93 r_work: 0.3693 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.6650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9696 Z= 0.156 Angle : 0.687 14.608 13128 Z= 0.325 Chirality : 0.045 0.147 1535 Planarity : 0.003 0.034 1687 Dihedral : 4.075 22.707 1333 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.14 % Allowed : 25.93 % Favored : 71.93 % 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: -2.08 (0.23), residues: 1236 helix: -0.05 (0.25), residues: 464 sheet: -2.16 (0.49), residues: 105 loop : -2.31 (0.22), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 219 TYR 0.007 0.001 TYR E 258 PHE 0.016 0.002 PHE E 319 TRP 0.012 0.001 TRP C 249 HIS 0.004 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 9696) covalent geometry : angle 0.68672 (13128) hydrogen bonds : bond 0.03761 ( 208) hydrogen bonds : angle 4.18611 ( 609) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2728.03 seconds wall clock time: 47 minutes 6.36 seconds (2826.36 seconds total)