Starting phenix.real_space_refine on Thu Feb 13 21:08:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ari_11883/02_2025/7ari_11883.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ari_11883/02_2025/7ari_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_11883/02_2025/7ari_11883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ari_11883/02_2025/7ari_11883.map" model { file = "/net/cci-nas-00/data/ceres_data/7ari_11883/02_2025/7ari_11883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ari_11883/02_2025/7ari_11883.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.85, per 1000 atoms: 0.61 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: 2.27 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.95 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: 2.36 Time building geometry restraints manager: 2.63 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.940 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.840 ------------------------------------------------------------------------------- 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= 0.216 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.005 0.001 TRP C 28 HIS 0.005 0.001 HIS F 96 PHE 0.017 0.001 PHE D 199 TYR 0.008 0.000 TYR F 15 ARG 0.004 0.000 ARG C 177 *********************** 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 : 1.040 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: 0.8295 (mm) cc_final: 0.8069 (mp) REVERT: C 312 MET cc_start: 0.5563 (mmm) cc_final: 0.4940 (mmm) REVERT: E 78 TRP cc_start: 0.4585 (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: 0.6157 (mtp) REVERT: D 94 GLN cc_start: 0.6221 (pt0) cc_final: 0.5281 (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: 0.9067 (mp) REVERT: D 185 PHE cc_start: 0.7621 (m-10) cc_final: 0.7325 (m-80) outliers start: 7 outliers final: 3 residues processed: 313 average time/residue: 0.2527 time to fit residues: 104.8202 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 : 1.084 ------------------------------------------------------------------------------- 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 103 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 49 optimal weight: 0.0470 chunk 96 optimal weight: 5.9990 chunk 37 optimal weight: 0.0980 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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 26 HIS F 27 ASN F 94 GLN F 204 HIS ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 HIS D 107 ASN D 180 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.232197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.182710 restraints weight = 16491.979| |-----------------------------------------------------------------------------| r_work (start): 0.4346 rms_B_bonded: 3.38 r_work: 0.4113 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2684 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= 0.154 Angle : 0.592 13.535 13128 Z= 0.285 Chirality : 0.042 0.127 1535 Planarity : 0.004 0.041 1687 Dihedral : 3.950 53.460 1337 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.24 % Allowed : 16.67 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.80 (0.18), residues: 1236 helix: -3.16 (0.17), residues: 426 sheet: -2.21 (0.54), residues: 78 loop : -3.48 (0.17), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 249 HIS 0.009 0.001 HIS E 376 PHE 0.023 0.002 PHE F 185 TYR 0.007 0.001 TYR E 397 ARG 0.007 0.000 ARG F 125 *********************** 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 238 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 215 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 51 PHE cc_start: 0.8005 (m-80) cc_final: 0.7741 (m-80) REVERT: C 114 MET cc_start: 0.6911 (pmm) cc_final: 0.5661 (ptp) REVERT: C 201 MET cc_start: 0.7891 (mpp) cc_final: 0.7481 (mmm) REVERT: C 227 ASP cc_start: 0.7379 (p0) cc_final: 0.7056 (p0) REVERT: C 250 ARG cc_start: 0.7072 (OUTLIER) cc_final: 0.4879 (ttp80) REVERT: C 312 MET cc_start: 0.6485 (mmm) cc_final: 0.5723 (mmm) REVERT: E 393 LEU cc_start: 0.8871 (tt) cc_final: 0.8580 (tp) REVERT: F 37 MET cc_start: 0.5562 (ptp) cc_final: 0.5270 (ptp) REVERT: F 110 MET cc_start: 0.9562 (tpp) cc_final: 0.9275 (tpt) REVERT: F 197 THR cc_start: 0.7190 (OUTLIER) cc_final: 0.6931 (t) REVERT: D 38 MET cc_start: 0.7159 (mtp) cc_final: 0.6795 (mtp) REVERT: D 83 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8092 (mp0) REVERT: D 93 TYR cc_start: 0.6860 (m-10) cc_final: 0.6606 (m-80) REVERT: D 127 LEU cc_start: 0.8431 (pp) cc_final: 0.7981 (mt) REVERT: D 185 PHE cc_start: 0.7932 (m-10) cc_final: 0.7688 (m-80) REVERT: D 218 MET cc_start: 0.6927 (tpp) cc_final: 0.6333 (tpp) outliers start: 23 outliers final: 13 residues processed: 230 average time/residue: 0.2200 time to fit residues: 71.6489 Evaluate side-chains 203 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 188 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 ILE 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 288 LEU 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 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 88 optimal weight: 6.9990 chunk 19 optimal weight: 0.0870 chunk 27 optimal weight: 0.2980 chunk 83 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 281 ASN C 317 GLN E 174 ASN E 181 GLN ** F 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 HIS F 204 HIS F 215 GLN D 175 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.221234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.164604 restraints weight = 16034.806| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 3.50 r_work: 0.3929 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9696 Z= 0.209 Angle : 0.603 11.648 13128 Z= 0.288 Chirality : 0.044 0.155 1535 Planarity : 0.004 0.038 1687 Dihedral : 3.554 18.536 1334 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.53 % Allowed : 18.32 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.19), residues: 1236 helix: -1.95 (0.21), residues: 426 sheet: -2.34 (0.49), residues: 94 loop : -3.24 (0.18), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 249 HIS 0.025 0.002 HIS E 188 PHE 0.017 0.002 PHE F 95 TYR 0.010 0.001 TYR E 397 ARG 0.004 0.000 ARG F 179 *********************** 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 225 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 114 MET cc_start: 0.7044 (pmm) cc_final: 0.5561 (ptp) REVERT: C 201 MET cc_start: 0.8062 (mpp) cc_final: 0.7521 (mpp) REVERT: C 227 ASP cc_start: 0.7612 (p0) cc_final: 0.7319 (p0) REVERT: C 312 MET cc_start: 0.7216 (mmm) cc_final: 0.6617 (mmm) REVERT: E 301 ASP cc_start: 0.8650 (t70) cc_final: 0.8389 (m-30) REVERT: F 37 MET cc_start: 0.5809 (ptp) cc_final: 0.5492 (ptp) REVERT: F 52 LEU cc_start: 0.9385 (mm) cc_final: 0.9045 (mm) REVERT: F 197 THR cc_start: 0.7350 (OUTLIER) cc_final: 0.7078 (t) REVERT: F 206 LEU cc_start: 0.6043 (tp) cc_final: 0.5513 (tt) REVERT: D 38 MET cc_start: 0.7070 (mtp) cc_final: 0.6720 (mtp) REVERT: D 83 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8315 (mp0) REVERT: D 127 LEU cc_start: 0.8660 (pp) cc_final: 0.8132 (mt) outliers start: 26 outliers final: 15 residues processed: 216 average time/residue: 0.2115 time to fit residues: 65.0333 Evaluate side-chains 194 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 126 THR 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 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 88 LYS Chi-restraints excluded: chain D residue 175 ASN 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 117 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 GLN ** E 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 GLN F 152 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.216382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.153627 restraints weight = 15644.521| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 3.62 r_work: 0.3784 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9696 Z= 0.252 Angle : 0.653 9.770 13128 Z= 0.318 Chirality : 0.046 0.237 1535 Planarity : 0.004 0.043 1687 Dihedral : 4.054 21.611 1333 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.41 % Allowed : 20.76 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.20), residues: 1236 helix: -1.46 (0.23), residues: 459 sheet: -2.23 (0.51), residues: 84 loop : -3.13 (0.19), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 396 HIS 0.006 0.001 HIS F 26 PHE 0.020 0.002 PHE F 185 TYR 0.013 0.001 TYR E 214 ARG 0.005 0.001 ARG F 179 *********************** 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 219 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 MET cc_start: 0.6934 (pmm) cc_final: 0.6144 (ptt) REVERT: C 201 MET cc_start: 0.8154 (mpp) cc_final: 0.7846 (mpp) REVERT: C 250 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.5503 (ttp80) REVERT: C 312 MET cc_start: 0.7666 (mmm) cc_final: 0.6836 (mmm) REVERT: C 315 MET cc_start: 0.6765 (ptt) cc_final: 0.6384 (ptm) REVERT: E 56 ASN cc_start: 0.8511 (p0) cc_final: 0.8308 (p0) REVERT: E 301 ASP cc_start: 0.8917 (t70) cc_final: 0.8524 (m-30) REVERT: F 37 MET cc_start: 0.6451 (ptp) cc_final: 0.5790 (ptp) REVERT: F 71 GLN cc_start: 0.8562 (mm110) cc_final: 0.8327 (mm110) REVERT: F 218 MET cc_start: 0.7116 (tpt) cc_final: 0.6896 (tpp) REVERT: D 38 MET cc_start: 0.7347 (mtp) cc_final: 0.7123 (mtp) REVERT: D 129 MET cc_start: 0.9228 (tpp) cc_final: 0.9023 (tpp) REVERT: D 173 THR cc_start: 0.7965 (m) cc_final: 0.7247 (p) outliers start: 35 outliers final: 22 residues processed: 208 average time/residue: 0.2134 time to fit residues: 62.2948 Evaluate side-chains 184 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 250 ARG Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 367 VAL 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 201 HIS Chi-restraints excluded: chain E residue 262 TYR Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 277 VAL 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 F residue 199 PHE 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 199 PHE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 95 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 chunk 24 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 317 GLN C 391 GLN E 359 GLN ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.217174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.155663 restraints weight = 15729.864| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 3.55 r_work: 0.3820 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.5127 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= 0.172 Angle : 0.572 12.429 13128 Z= 0.275 Chirality : 0.043 0.150 1535 Planarity : 0.003 0.035 1687 Dihedral : 3.730 19.279 1333 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.83 % Allowed : 22.12 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.22), residues: 1236 helix: -0.78 (0.25), residues: 450 sheet: -2.22 (0.55), residues: 75 loop : -2.85 (0.20), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 249 HIS 0.006 0.001 HIS F 96 PHE 0.025 0.001 PHE F 95 TYR 0.010 0.001 TYR E 214 ARG 0.003 0.000 ARG D 219 *********************** 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 205 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 51 PHE cc_start: 0.8278 (m-10) cc_final: 0.7983 (m-80) REVERT: C 114 MET cc_start: 0.6801 (pmm) cc_final: 0.6097 (ptt) REVERT: C 201 MET cc_start: 0.8199 (mpp) cc_final: 0.7972 (mpp) REVERT: C 312 MET cc_start: 0.7515 (mmm) cc_final: 0.6754 (mmm) REVERT: E 71 VAL cc_start: 0.6823 (OUTLIER) cc_final: 0.6602 (t) REVERT: E 301 ASP cc_start: 0.8873 (t70) cc_final: 0.8503 (m-30) REVERT: F 37 MET cc_start: 0.6380 (ptp) cc_final: 0.5702 (ptp) REVERT: D 127 LEU cc_start: 0.8695 (pp) cc_final: 0.8219 (mt) outliers start: 29 outliers final: 20 residues processed: 194 average time/residue: 0.1868 time to fit residues: 52.4386 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 : 1.091 ------------------------------------------------------------------------------- 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 375 ILE 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 195 LEU Chi-restraints excluded: chain E residue 201 HIS 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 67 ILE Chi-restraints excluded: chain F residue 135 LEU 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 88 LYS 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 116 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 55 optimal weight: 0.0980 chunk 89 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 67 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 27 ASN ** 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 = 0.4700 r_free = 0.4700 target = 0.217064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.153280 restraints weight = 15769.716| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 3.54 r_work: 0.3837 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.5274 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= 0.153 Angle : 0.560 10.565 13128 Z= 0.266 Chirality : 0.042 0.150 1535 Planarity : 0.003 0.034 1687 Dihedral : 3.596 18.466 1333 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.92 % Allowed : 22.81 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.22), residues: 1236 helix: -0.42 (0.25), residues: 457 sheet: -2.03 (0.54), residues: 86 loop : -2.71 (0.20), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 249 HIS 0.004 0.001 HIS F 96 PHE 0.013 0.001 PHE E 319 TYR 0.010 0.001 TYR E 397 ARG 0.005 0.000 ARG F 179 *********************** 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 203 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 51 PHE cc_start: 0.8252 (m-10) cc_final: 0.7840 (m-80) REVERT: C 114 MET cc_start: 0.6755 (pmm) cc_final: 0.6043 (ptt) REVERT: C 201 MET cc_start: 0.8173 (mpp) cc_final: 0.7967 (mpp) REVERT: C 312 MET cc_start: 0.7484 (mmm) cc_final: 0.6627 (mmm) REVERT: E 71 VAL cc_start: 0.6844 (OUTLIER) cc_final: 0.6620 (t) REVERT: E 98 ILE cc_start: 0.8586 (pt) cc_final: 0.8295 (pt) REVERT: E 301 ASP cc_start: 0.8805 (t70) cc_final: 0.8490 (m-30) REVERT: F 71 GLN cc_start: 0.8573 (mm110) cc_final: 0.8319 (mm110) REVERT: D 67 ILE cc_start: 0.7529 (tp) cc_final: 0.7110 (tp) REVERT: D 127 LEU cc_start: 0.8748 (pp) cc_final: 0.8223 (mt) REVERT: D 173 THR cc_start: 0.7848 (m) cc_final: 0.7271 (p) REVERT: D 218 MET cc_start: 0.6439 (tpp) cc_final: 0.6003 (tpp) outliers start: 30 outliers final: 20 residues processed: 192 average time/residue: 0.1781 time to fit residues: 50.2382 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 : 1.081 ------------------------------------------------------------------------------- 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 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 71 VAL Chi-restraints excluded: chain E residue 195 LEU 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 E residue 277 VAL Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 67 ILE 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 88 LYS 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 30 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 51 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 1 optimal weight: 0.0270 chunk 63 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.216828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.157487 restraints weight = 15828.058| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 3.66 r_work: 0.3810 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.5483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9696 Z= 0.160 Angle : 0.576 9.939 13128 Z= 0.273 Chirality : 0.043 0.171 1535 Planarity : 0.003 0.032 1687 Dihedral : 3.574 18.038 1333 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.02 % Allowed : 24.27 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.23), residues: 1236 helix: -0.22 (0.25), residues: 462 sheet: -1.97 (0.54), residues: 86 loop : -2.57 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 249 HIS 0.004 0.001 HIS F 204 PHE 0.028 0.001 PHE F 95 TYR 0.012 0.001 TYR E 214 ARG 0.007 0.000 ARG F 211 *********************** 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 213 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 51 PHE cc_start: 0.8237 (m-80) cc_final: 0.7842 (m-80) REVERT: C 56 GLN cc_start: 0.8190 (pm20) cc_final: 0.7956 (pm20) REVERT: C 114 MET cc_start: 0.6808 (pmm) cc_final: 0.6167 (ptt) REVERT: C 312 MET cc_start: 0.7636 (mmm) cc_final: 0.6754 (mmm) REVERT: E 71 VAL cc_start: 0.6822 (OUTLIER) cc_final: 0.6605 (t) REVERT: E 228 MET cc_start: 0.7200 (ttm) cc_final: 0.6883 (ttm) REVERT: E 301 ASP cc_start: 0.8854 (t70) cc_final: 0.8544 (m-30) REVERT: F 71 GLN cc_start: 0.8566 (mm110) cc_final: 0.8323 (mm110) REVERT: F 182 ASP cc_start: 0.8308 (p0) cc_final: 0.8059 (p0) REVERT: D 67 ILE cc_start: 0.7616 (tp) cc_final: 0.7233 (tp) REVERT: D 127 LEU cc_start: 0.8740 (pp) cc_final: 0.8192 (mt) REVERT: D 218 MET cc_start: 0.6358 (tpp) cc_final: 0.5940 (tpp) outliers start: 31 outliers final: 21 residues processed: 201 average time/residue: 0.1832 time to fit residues: 53.7994 Evaluate side-chains 191 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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 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 71 VAL 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 44 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 67 ILE 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 88 LYS 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 106 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 61 optimal weight: 20.0000 chunk 78 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 chunk 71 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 27 ASN ** 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 = 0.4692 r_free = 0.4692 target = 0.215914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.152659 restraints weight = 15930.305| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 3.37 r_work: 0.3802 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.5714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9696 Z= 0.172 Angle : 0.590 9.624 13128 Z= 0.279 Chirality : 0.043 0.146 1535 Planarity : 0.003 0.031 1687 Dihedral : 3.645 17.969 1333 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.83 % Allowed : 25.34 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.23), residues: 1236 helix: -0.06 (0.25), residues: 461 sheet: -1.92 (0.55), residues: 86 loop : -2.48 (0.21), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 249 HIS 0.003 0.001 HIS F 204 PHE 0.014 0.001 PHE E 319 TYR 0.013 0.001 TYR E 214 ARG 0.005 0.000 ARG F 211 *********************** 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 200 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 51 PHE cc_start: 0.8283 (m-80) cc_final: 0.7880 (m-80) REVERT: C 56 GLN cc_start: 0.8189 (pm20) cc_final: 0.7935 (pm20) REVERT: C 114 MET cc_start: 0.6798 (pmm) cc_final: 0.6189 (ptt) REVERT: C 201 MET cc_start: 0.7752 (mpp) cc_final: 0.6421 (mmp) REVERT: C 250 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.5485 (ttp80) REVERT: C 312 MET cc_start: 0.7747 (mmm) cc_final: 0.6860 (mmm) REVERT: E 71 VAL cc_start: 0.6768 (OUTLIER) cc_final: 0.6544 (t) REVERT: E 228 MET cc_start: 0.7408 (ttm) cc_final: 0.7074 (ttm) REVERT: E 301 ASP cc_start: 0.8875 (t70) cc_final: 0.8565 (m-30) REVERT: F 71 GLN cc_start: 0.8572 (mm110) cc_final: 0.8349 (mm110) REVERT: D 67 ILE cc_start: 0.7644 (tp) cc_final: 0.7257 (tp) REVERT: D 127 LEU cc_start: 0.8774 (pp) cc_final: 0.8271 (mt) REVERT: D 212 MET cc_start: 0.5363 (ttp) cc_final: 0.5141 (tmm) REVERT: D 218 MET cc_start: 0.6393 (tpp) cc_final: 0.5960 (tpp) outliers start: 29 outliers final: 21 residues processed: 189 average time/residue: 0.1925 time to fit residues: 52.7289 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 : 1.195 ------------------------------------------------------------------------------- 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 250 ARG 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 71 VAL 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 44 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 67 ILE 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 88 LYS Chi-restraints excluded: chain D residue 201 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 15 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 61 optimal weight: 0.0030 chunk 14 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 339 GLN ** F 27 ASN ** 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 = 0.4676 r_free = 0.4676 target = 0.213807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.148417 restraints weight = 15337.483| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 3.58 r_work: 0.3754 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.5960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9696 Z= 0.181 Angle : 0.609 9.556 13128 Z= 0.289 Chirality : 0.043 0.148 1535 Planarity : 0.003 0.033 1687 Dihedral : 3.662 18.133 1333 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.83 % Allowed : 25.73 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.23), residues: 1236 helix: 0.12 (0.26), residues: 456 sheet: -1.91 (0.56), residues: 85 loop : -2.36 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 249 HIS 0.005 0.001 HIS F 204 PHE 0.015 0.001 PHE E 319 TYR 0.013 0.001 TYR E 214 ARG 0.007 0.000 ARG D 219 *********************** 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 200 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 48 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7829 (mmm) REVERT: C 56 GLN cc_start: 0.8246 (pm20) cc_final: 0.7958 (pm20) REVERT: C 114 MET cc_start: 0.6888 (pmm) cc_final: 0.6324 (ptt) REVERT: C 149 GLN cc_start: 0.6189 (OUTLIER) cc_final: 0.5593 (pp30) REVERT: C 201 MET cc_start: 0.7852 (mpp) cc_final: 0.6365 (mmp) REVERT: C 312 MET cc_start: 0.7691 (mmm) cc_final: 0.6825 (mmm) REVERT: E 71 VAL cc_start: 0.7177 (OUTLIER) cc_final: 0.6948 (t) REVERT: E 228 MET cc_start: 0.7429 (ttm) cc_final: 0.7116 (ttm) REVERT: E 301 ASP cc_start: 0.8922 (t70) cc_final: 0.8600 (m-30) REVERT: F 71 GLN cc_start: 0.8620 (mm110) cc_final: 0.8341 (mm110) REVERT: D 37 MET cc_start: 0.7503 (pmm) cc_final: 0.7122 (pmm) REVERT: D 67 ILE cc_start: 0.7702 (tp) cc_final: 0.7338 (tp) REVERT: D 127 LEU cc_start: 0.8773 (pp) cc_final: 0.8334 (mt) REVERT: D 218 MET cc_start: 0.6388 (tpp) cc_final: 0.5954 (tpp) outliers start: 29 outliers final: 20 residues processed: 189 average time/residue: 0.1943 time to fit residues: 53.8895 Evaluate side-chains 187 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 1.186 ------------------------------------------------------------------------------- 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 149 GLN 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 71 VAL 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 44 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 199 PHE 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 94 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 chunk 104 optimal weight: 0.9980 chunk 97 optimal weight: 0.2980 chunk 106 optimal weight: 0.0170 chunk 17 optimal weight: 10.0000 chunk 44 optimal weight: 0.6980 chunk 121 optimal weight: 0.0980 chunk 57 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.2818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 ASN D 94 GLN D 215 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.215926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.155018 restraints weight = 16045.385| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 3.59 r_work: 0.3803 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.5972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 9696 Z= 0.155 Angle : 0.625 13.622 13128 Z= 0.294 Chirality : 0.043 0.143 1535 Planarity : 0.003 0.030 1687 Dihedral : 3.591 16.655 1333 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.14 % Allowed : 27.19 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.23), residues: 1236 helix: 0.37 (0.26), residues: 454 sheet: -1.90 (0.56), residues: 85 loop : -2.31 (0.21), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 249 HIS 0.005 0.001 HIS F 204 PHE 0.016 0.001 PHE F 30 TYR 0.014 0.001 TYR E 214 ARG 0.007 0.000 ARG F 211 ********************** 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 194 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: C 56 GLN cc_start: 0.8248 (pm20) cc_final: 0.7963 (pm20) REVERT: C 114 MET cc_start: 0.6788 (pmm) cc_final: 0.6151 (ptt) REVERT: C 149 GLN cc_start: 0.6143 (OUTLIER) cc_final: 0.5536 (pp30) REVERT: C 201 MET cc_start: 0.7830 (mpp) cc_final: 0.6379 (mmp) REVERT: C 312 MET cc_start: 0.7521 (mmm) cc_final: 0.6638 (mmm) REVERT: C 368 ILE cc_start: 0.9035 (tp) cc_final: 0.8784 (tp) REVERT: E 71 VAL cc_start: 0.7222 (OUTLIER) cc_final: 0.6973 (t) REVERT: E 228 MET cc_start: 0.7424 (ttm) cc_final: 0.7133 (ttm) REVERT: E 301 ASP cc_start: 0.8822 (t70) cc_final: 0.8550 (m-30) REVERT: F 37 MET cc_start: 0.5419 (mtm) cc_final: 0.5211 (mmm) REVERT: F 65 ASP cc_start: 0.5503 (t0) cc_final: 0.5092 (m-30) REVERT: F 71 GLN cc_start: 0.8604 (mm110) cc_final: 0.8368 (mm110) REVERT: D 37 MET cc_start: 0.7314 (pmm) cc_final: 0.7009 (pmm) REVERT: D 67 ILE cc_start: 0.7639 (tp) cc_final: 0.7268 (tp) REVERT: D 83 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8279 (mp0) REVERT: D 127 LEU cc_start: 0.8737 (pp) cc_final: 0.8384 (mt) REVERT: D 171 GLU cc_start: 0.7330 (tm-30) cc_final: 0.6969 (tm-30) REVERT: D 173 THR cc_start: 0.7532 (m) cc_final: 0.7225 (p) REVERT: D 218 MET cc_start: 0.6278 (tpp) cc_final: 0.5832 (tpp) outliers start: 22 outliers final: 16 residues processed: 187 average time/residue: 0.1843 time to fit residues: 50.3115 Evaluate side-chains 180 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 149 GLN Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 378 LEU 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 E residue 389 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain D residue 88 LYS 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 34 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 63 optimal weight: 0.0980 chunk 68 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 56 optimal weight: 40.0000 chunk 118 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 ASN 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 = 0.213572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.149416 restraints weight = 15825.778| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 3.80 r_work: 0.3729 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.6179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9696 Z= 0.189 Angle : 0.645 12.086 13128 Z= 0.304 Chirality : 0.044 0.150 1535 Planarity : 0.003 0.031 1687 Dihedral : 3.691 20.650 1333 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.83 % Allowed : 26.22 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.24), residues: 1236 helix: 0.34 (0.25), residues: 456 sheet: -1.78 (0.53), residues: 95 loop : -2.26 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 249 HIS 0.004 0.001 HIS F 204 PHE 0.016 0.001 PHE F 30 TYR 0.014 0.001 TYR E 214 ARG 0.006 0.000 ARG D 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5776.91 seconds wall clock time: 102 minutes 38.98 seconds (6158.98 seconds total)