Starting phenix.real_space_refine on Fri Mar 14 00:35:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ari_11883/03_2025/7ari_11883.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ari_11883/03_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_11883/03_2025/7ari_11883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ari_11883/03_2025/7ari_11883.map" model { file = "/net/cci-nas-00/data/ceres_data/7ari_11883/03_2025/7ari_11883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ari_11883/03_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-5624/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: 6.14, per 1000 atoms: 0.64 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: 2.38 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: 0.91 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: 2.10 Time building geometry restraints manager: 2.81 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: 0.540 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 24.160 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.510 ------------------------------------------------------------------------------- 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 : 0.910 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: 0.2429 time to fit residues: 100.7242 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 : 1.015 ------------------------------------------------------------------------------- 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 = 0.4356 r_free = 0.4356 target = 0.182701 restraints weight = 16491.978| |-----------------------------------------------------------------------------| r_work (start): 0.4346 rms_B_bonded: 3.39 r_work: 0.4112 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 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 : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 51 PHE cc_start: 0.8008 (m-80) cc_final: 0.7727 (m-80) REVERT: C 114 MET cc_start: 0.6904 (pmm) cc_final: 0.5646 (ptp) REVERT: C 201 MET cc_start: 0.7885 (mpp) cc_final: 0.7477 (mmm) REVERT: C 227 ASP cc_start: 0.7372 (p0) cc_final: 0.7049 (p0) REVERT: C 250 ARG cc_start: 0.7063 (OUTLIER) cc_final: 0.4861 (ttp80) REVERT: C 312 MET cc_start: 0.6476 (mmm) cc_final: 0.5715 (mmm) REVERT: E 393 LEU cc_start: 0.8865 (tt) cc_final: 0.8575 (tp) REVERT: F 37 MET cc_start: 0.5570 (ptp) cc_final: 0.5275 (ptp) REVERT: F 110 MET cc_start: 0.9565 (tpp) cc_final: 0.9279 (tpt) REVERT: F 197 THR cc_start: 0.7208 (OUTLIER) cc_final: 0.6948 (t) REVERT: D 38 MET cc_start: 0.7153 (mtp) cc_final: 0.6785 (mtp) REVERT: D 83 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8082 (mp0) REVERT: D 93 TYR cc_start: 0.6860 (m-10) cc_final: 0.6605 (m-80) REVERT: D 127 LEU cc_start: 0.8448 (pp) cc_final: 0.7994 (mt) REVERT: D 185 PHE cc_start: 0.7954 (m-10) cc_final: 0.7704 (m-80) REVERT: D 218 MET cc_start: 0.6918 (tpp) cc_final: 0.6326 (tpp) outliers start: 23 outliers final: 13 residues processed: 230 average time/residue: 0.2002 time to fit residues: 65.2502 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 : 1.024 ------------------------------------------------------------------------------- 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: 9.9990 chunk 27 optimal weight: 0.5980 chunk 83 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 4 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 GLN C 281 ASN 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 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 HIS ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.214787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.151235 restraints weight = 15725.748| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 3.38 r_work: 0.3811 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9696 Z= 0.322 Angle : 0.704 14.841 13128 Z= 0.342 Chirality : 0.046 0.197 1535 Planarity : 0.004 0.043 1687 Dihedral : 4.102 24.861 1334 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.83 % Allowed : 19.10 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.09 (0.19), residues: 1236 helix: -2.21 (0.21), residues: 445 sheet: -2.36 (0.48), residues: 93 loop : -3.24 (0.19), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 396 HIS 0.015 0.002 HIS E 188 PHE 0.019 0.002 PHE E 319 TYR 0.010 0.001 TYR E 322 ARG 0.005 0.001 ARG E 15 *********************** 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: 29 poor density : 196 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 114 MET cc_start: 0.6876 (pmm) cc_final: 0.6061 (ptt) REVERT: C 201 MET cc_start: 0.8127 (mpp) cc_final: 0.7729 (mpp) REVERT: C 251 ASP cc_start: 0.8173 (m-30) cc_final: 0.7848 (m-30) REVERT: C 312 MET cc_start: 0.7533 (mmm) cc_final: 0.6870 (mmm) REVERT: E 48 MET cc_start: 0.8424 (mmt) cc_final: 0.8104 (mmp) REVERT: E 56 ASN cc_start: 0.8423 (p0) cc_final: 0.8066 (p0) REVERT: E 262 TYR cc_start: 0.7947 (OUTLIER) cc_final: 0.7439 (t80) REVERT: E 301 ASP cc_start: 0.8778 (t70) cc_final: 0.8419 (m-30) REVERT: F 37 MET cc_start: 0.5991 (ptp) cc_final: 0.5459 (ptp) REVERT: F 206 LEU cc_start: 0.6539 (tp) cc_final: 0.6237 (tt) REVERT: D 37 MET cc_start: 0.7536 (pmm) cc_final: 0.6765 (pmm) REVERT: D 38 MET cc_start: 0.7091 (mtp) cc_final: 0.6849 (mtp) outliers start: 29 outliers final: 17 residues processed: 215 average time/residue: 0.2100 time to fit residues: 62.9615 Evaluate side-chains 193 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 1.177 ------------------------------------------------------------------------------- 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 28 VAL 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 117 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 56 optimal weight: 30.0000 chunk 11 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 122 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 GLN C 391 GLN E 134 GLN ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 GLN ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.214236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.149113 restraints weight = 15640.963| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 3.43 r_work: 0.3769 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9696 Z= 0.259 Angle : 0.638 11.237 13128 Z= 0.310 Chirality : 0.045 0.231 1535 Planarity : 0.004 0.040 1687 Dihedral : 4.087 23.652 1333 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.41 % Allowed : 21.35 % Favored : 75.24 % 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: -3.59 (0.20), residues: 1236 helix: -1.55 (0.23), residues: 454 sheet: -2.37 (0.55), residues: 74 loop : -3.10 (0.19), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 249 HIS 0.007 0.001 HIS F 96 PHE 0.051 0.002 PHE F 95 TYR 0.015 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 214 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 179 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 MET cc_start: 0.7005 (pmm) cc_final: 0.6247 (ptt) REVERT: C 201 MET cc_start: 0.8219 (mpp) cc_final: 0.7965 (mpp) REVERT: C 250 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.5567 (ttp80) REVERT: C 312 MET cc_start: 0.7600 (mmm) cc_final: 0.6859 (mmm) REVERT: E 301 ASP cc_start: 0.8963 (t70) cc_final: 0.8422 (m-30) REVERT: F 37 MET cc_start: 0.6477 (ptp) cc_final: 0.5779 (ptp) REVERT: D 127 LEU cc_start: 0.8750 (pp) cc_final: 0.8268 (tp) REVERT: D 173 THR cc_start: 0.7917 (m) cc_final: 0.7270 (p) REVERT: D 218 MET cc_start: 0.6489 (tpp) cc_final: 0.6281 (tpp) outliers start: 35 outliers final: 26 residues processed: 206 average time/residue: 0.2077 time to fit residues: 60.8858 Evaluate side-chains 188 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 6 LEU Chi-restraints excluded: chain F residue 41 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 25 LEU Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 175 ASN 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: 4.9990 chunk 99 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 63 optimal weight: 0.0980 chunk 68 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 92 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 GLN E 359 GLN ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.214394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.149477 restraints weight = 15641.100| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 3.47 r_work: 0.3782 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9696 Z= 0.208 Angle : 0.602 10.095 13128 Z= 0.292 Chirality : 0.043 0.162 1535 Planarity : 0.003 0.035 1687 Dihedral : 3.931 21.568 1333 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.41 % Allowed : 22.71 % Favored : 73.88 % 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: -3.09 (0.21), residues: 1236 helix: -1.04 (0.24), residues: 463 sheet: -2.14 (0.57), residues: 75 loop : -2.88 (0.20), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 249 HIS 0.006 0.001 HIS F 96 PHE 0.023 0.001 PHE E 100 TYR 0.010 0.001 TYR E 214 ARG 0.005 0.000 ARG F 179 *********************** 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 209 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 MET cc_start: 0.6913 (pmm) cc_final: 0.6235 (ptt) REVERT: C 201 MET cc_start: 0.8284 (mpp) cc_final: 0.8079 (mpp) REVERT: C 250 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.5625 (ttp80) REVERT: C 312 MET cc_start: 0.7680 (mmm) cc_final: 0.6938 (mmm) REVERT: E 71 VAL cc_start: 0.6828 (OUTLIER) cc_final: 0.6620 (t) REVERT: E 301 ASP cc_start: 0.8933 (t70) cc_final: 0.8462 (m-30) REVERT: F 37 MET cc_start: 0.6577 (ptp) cc_final: 0.5851 (ptp) REVERT: F 71 GLN cc_start: 0.8551 (mm110) cc_final: 0.8351 (mm110) REVERT: F 83 GLU cc_start: 0.8347 (mp0) cc_final: 0.8073 (mp0) REVERT: D 67 ILE cc_start: 0.7707 (tp) cc_final: 0.7484 (tp) REVERT: D 127 LEU cc_start: 0.8817 (pp) cc_final: 0.8283 (mt) REVERT: D 218 MET cc_start: 0.6498 (tpp) cc_final: 0.6295 (tpp) outliers start: 35 outliers final: 22 residues processed: 199 average time/residue: 0.1842 time to fit residues: 53.1291 Evaluate side-chains 184 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 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 F residue 6 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 67 ILE 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 161 VAL 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: 3.9990 chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 5 optimal weight: 0.5980 chunk 50 optimal weight: 20.0000 chunk 3 optimal weight: 0.7980 chunk 49 optimal weight: 30.0000 chunk 67 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 134 GLN ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 GLN ** 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 = 0.4683 r_free = 0.4683 target = 0.215369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.152828 restraints weight = 15709.202| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 3.50 r_work: 0.3779 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.5623 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= 0.162 Angle : 0.572 8.314 13128 Z= 0.276 Chirality : 0.043 0.153 1535 Planarity : 0.003 0.035 1687 Dihedral : 3.741 19.580 1333 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.02 % Allowed : 23.10 % Favored : 73.88 % 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: -2.65 (0.22), residues: 1236 helix: -0.61 (0.24), residues: 467 sheet: -1.78 (0.56), residues: 84 loop : -2.70 (0.21), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 249 HIS 0.004 0.001 HIS F 204 PHE 0.014 0.001 PHE E 319 TYR 0.013 0.001 TYR E 214 ARG 0.004 0.000 ARG D 219 *********************** 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 205 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 51 PHE cc_start: 0.8396 (m-80) cc_final: 0.8115 (m-80) REVERT: C 114 MET cc_start: 0.6855 (pmm) cc_final: 0.6021 (ptt) REVERT: C 250 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.5444 (ttp80) REVERT: C 312 MET cc_start: 0.7725 (mmm) cc_final: 0.6981 (mmm) REVERT: E 71 VAL cc_start: 0.6773 (OUTLIER) cc_final: 0.6558 (t) REVERT: E 301 ASP cc_start: 0.8929 (t70) cc_final: 0.8577 (m-30) REVERT: F 71 GLN cc_start: 0.8579 (mm110) cc_final: 0.8344 (mm110) REVERT: F 83 GLU cc_start: 0.8413 (mp0) cc_final: 0.8151 (mp0) REVERT: D 67 ILE cc_start: 0.7647 (tp) cc_final: 0.7404 (tp) REVERT: D 127 LEU cc_start: 0.8851 (pp) cc_final: 0.8377 (mt) outliers start: 31 outliers final: 22 residues processed: 192 average time/residue: 0.1902 time to fit residues: 52.5053 Evaluate side-chains 186 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 60 LEU 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 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 F residue 6 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 199 PHE Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 201 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 30 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 63 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 317 GLN ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 ASN ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.214786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.151575 restraints weight = 15671.918| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 3.36 r_work: 0.3759 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.5789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9696 Z= 0.175 Angle : 0.592 8.731 13128 Z= 0.283 Chirality : 0.043 0.150 1535 Planarity : 0.003 0.033 1687 Dihedral : 3.704 19.126 1333 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.80 % Allowed : 23.68 % Favored : 72.51 % 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: -2.37 (0.23), residues: 1236 helix: -0.29 (0.25), residues: 465 sheet: -1.81 (0.56), residues: 84 loop : -2.58 (0.21), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 249 HIS 0.004 0.001 HIS F 204 PHE 0.015 0.001 PHE E 319 TYR 0.014 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: 39 poor density : 174 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 51 PHE cc_start: 0.8438 (m-80) cc_final: 0.8183 (m-80) REVERT: C 56 GLN cc_start: 0.8235 (pm20) cc_final: 0.7952 (pm20) REVERT: C 114 MET cc_start: 0.6867 (pmm) cc_final: 0.6069 (ptt) REVERT: C 149 GLN cc_start: 0.6054 (OUTLIER) cc_final: 0.5720 (mt0) REVERT: C 201 MET cc_start: 0.7868 (mpp) cc_final: 0.6561 (mmp) REVERT: C 250 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.5538 (ttp80) REVERT: C 312 MET cc_start: 0.7838 (mmm) cc_final: 0.7063 (mmm) REVERT: E 71 VAL cc_start: 0.6946 (OUTLIER) cc_final: 0.6723 (t) REVERT: E 228 MET cc_start: 0.7332 (ttm) cc_final: 0.7068 (ttm) REVERT: E 301 ASP cc_start: 0.8939 (t70) cc_final: 0.8603 (m-30) REVERT: F 71 GLN cc_start: 0.8569 (mm110) cc_final: 0.8339 (mm110) REVERT: F 83 GLU cc_start: 0.8478 (mp0) cc_final: 0.8201 (mp0) REVERT: D 67 ILE cc_start: 0.7620 (tp) cc_final: 0.7383 (tp) REVERT: D 127 LEU cc_start: 0.8845 (pp) cc_final: 0.8404 (mt) REVERT: D 152 GLN cc_start: 0.8793 (mm-40) cc_final: 0.7815 (tm-30) REVERT: D 156 ILE cc_start: 0.9321 (mt) cc_final: 0.8988 (mp) outliers start: 39 outliers final: 24 residues processed: 200 average time/residue: 0.2256 time to fit residues: 64.9928 Evaluate side-chains 195 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 1.751 ------------------------------------------------------------------------------- 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 250 ARG Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 340 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 201 HIS Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 144 SER 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 161 VAL Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain D residue 201 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 106 optimal weight: 0.2980 chunk 72 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 110 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 14 optimal weight: 20.0000 chunk 71 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 317 GLN ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.214254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.150301 restraints weight = 15939.342| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 3.70 r_work: 0.3754 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.5925 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= 0.162 Angle : 0.584 9.099 13128 Z= 0.279 Chirality : 0.043 0.146 1535 Planarity : 0.003 0.033 1687 Dihedral : 3.615 17.893 1333 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.12 % Allowed : 24.17 % 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: -2.10 (0.23), residues: 1236 helix: 0.02 (0.25), residues: 465 sheet: -1.90 (0.51), residues: 96 loop : -2.46 (0.22), residues: 675 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 0.014 0.001 PHE E 319 TYR 0.014 0.001 TYR E 214 ARG 0.006 0.000 ARG D 219 *********************** 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 211 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 179 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 GLN cc_start: 0.8274 (pm20) cc_final: 0.7948 (pm20) REVERT: C 114 MET cc_start: 0.6855 (pmm) cc_final: 0.6210 (ptt) REVERT: C 149 GLN cc_start: 0.6065 (OUTLIER) cc_final: 0.5098 (mp10) REVERT: C 201 MET cc_start: 0.7938 (mpp) cc_final: 0.6396 (mmp) REVERT: C 312 MET cc_start: 0.7621 (mmm) cc_final: 0.6819 (mmm) REVERT: E 71 VAL cc_start: 0.7221 (OUTLIER) cc_final: 0.6976 (t) REVERT: E 301 ASP cc_start: 0.8890 (t70) cc_final: 0.8569 (m-30) REVERT: F 71 GLN cc_start: 0.8575 (mm110) cc_final: 0.8358 (mm110) REVERT: F 83 GLU cc_start: 0.8476 (mp0) cc_final: 0.8182 (mp0) REVERT: D 11 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7775 (tp) REVERT: D 67 ILE cc_start: 0.7652 (tp) cc_final: 0.7424 (tp) REVERT: D 127 LEU cc_start: 0.8854 (pp) cc_final: 0.8422 (mt) REVERT: D 152 GLN cc_start: 0.8774 (mm-40) cc_final: 0.7801 (tm-30) REVERT: D 156 ILE cc_start: 0.9318 (mt) cc_final: 0.8966 (mp) REVERT: D 185 PHE cc_start: 0.8733 (m-80) cc_final: 0.8489 (m-80) outliers start: 32 outliers final: 21 residues processed: 200 average time/residue: 0.1740 time to fit residues: 50.5940 Evaluate side-chains 196 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 286 LEU Chi-restraints excluded: chain C residue 340 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 160 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 405 ILE 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 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 D residue 11 LEU Chi-restraints excluded: chain D residue 161 VAL 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: 20.0000 chunk 67 optimal weight: 0.5980 chunk 120 optimal weight: 0.9980 chunk 21 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 61 optimal weight: 0.0070 chunk 14 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- 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** D 137 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.212439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.149351 restraints weight = 15623.901| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 3.77 r_work: 0.3725 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.6041 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 : 0.586 9.296 13128 Z= 0.279 Chirality : 0.043 0.151 1535 Planarity : 0.003 0.033 1687 Dihedral : 3.564 17.307 1333 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.83 % Allowed : 25.15 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.94 (0.23), residues: 1236 helix: 0.21 (0.25), residues: 465 sheet: -1.96 (0.51), residues: 95 loop : -2.38 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 249 HIS 0.009 0.001 HIS F 204 PHE 0.030 0.001 PHE F 95 TYR 0.015 0.001 TYR E 214 ARG 0.006 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 203 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 174 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 GLN cc_start: 0.8303 (pm20) cc_final: 0.7982 (pm20) REVERT: C 114 MET cc_start: 0.6897 (pmm) cc_final: 0.6305 (ptt) REVERT: C 149 GLN cc_start: 0.6114 (OUTLIER) cc_final: 0.5079 (mp10) REVERT: C 201 MET cc_start: 0.7979 (mpp) cc_final: 0.6468 (mmp) REVERT: C 296 GLU cc_start: 0.7970 (mp0) cc_final: 0.7758 (mp0) REVERT: C 312 MET cc_start: 0.7860 (mmm) cc_final: 0.7102 (mmm) REVERT: E 71 VAL cc_start: 0.7273 (OUTLIER) cc_final: 0.7022 (t) REVERT: E 301 ASP cc_start: 0.8944 (t70) cc_final: 0.8632 (m-30) REVERT: F 71 GLN cc_start: 0.8621 (mm110) cc_final: 0.8361 (mm110) REVERT: F 83 GLU cc_start: 0.8525 (mp0) cc_final: 0.8210 (mp0) REVERT: D 7 GLN cc_start: 0.8564 (tt0) cc_final: 0.8052 (tp-100) REVERT: D 11 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7776 (tp) REVERT: D 67 ILE cc_start: 0.7667 (tp) cc_final: 0.7436 (tp) REVERT: D 127 LEU cc_start: 0.8847 (pp) cc_final: 0.8452 (mt) REVERT: D 152 GLN cc_start: 0.8796 (mm-40) cc_final: 0.7789 (tm-30) REVERT: D 156 ILE cc_start: 0.9320 (mt) cc_final: 0.8965 (mp) REVERT: D 185 PHE cc_start: 0.8746 (m-80) cc_final: 0.8482 (m-80) outliers start: 29 outliers final: 21 residues processed: 195 average time/residue: 0.1927 time to fit residues: 55.0189 Evaluate side-chains 189 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 286 LEU Chi-restraints excluded: chain C residue 340 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 160 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 6 LEU 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 11 LEU Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 161 VAL 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: 2.9990 chunk 29 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 97 optimal weight: 0.4980 chunk 106 optimal weight: 0.5980 chunk 17 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 121 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** D 215 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.214268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.153954 restraints weight = 15914.434| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 3.68 r_work: 0.3755 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.6148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9696 Z= 0.166 Angle : 0.608 14.321 13128 Z= 0.288 Chirality : 0.043 0.146 1535 Planarity : 0.003 0.033 1687 Dihedral : 3.586 17.998 1333 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.44 % Allowed : 25.83 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.24), residues: 1236 helix: 0.35 (0.25), residues: 459 sheet: -1.90 (0.52), residues: 95 loop : -2.31 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 249 HIS 0.009 0.001 HIS F 204 PHE 0.016 0.001 PHE F 95 TYR 0.016 0.001 TYR E 214 ARG 0.006 0.000 ARG D 219 ********************** 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 190 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 GLN cc_start: 0.8277 (pm20) cc_final: 0.7970 (pm20) REVERT: C 114 MET cc_start: 0.6917 (pmm) cc_final: 0.6355 (ptt) REVERT: C 149 GLN cc_start: 0.6195 (OUTLIER) cc_final: 0.5159 (mp10) REVERT: C 201 MET cc_start: 0.7946 (mpp) cc_final: 0.6458 (mmp) REVERT: C 296 GLU cc_start: 0.7884 (mp0) cc_final: 0.7658 (mp0) REVERT: C 312 MET cc_start: 0.7805 (mmm) cc_final: 0.7040 (mmm) REVERT: C 368 ILE cc_start: 0.9005 (tp) cc_final: 0.8750 (tp) REVERT: E 71 VAL cc_start: 0.7133 (OUTLIER) cc_final: 0.6896 (t) REVERT: E 301 ASP cc_start: 0.8895 (t70) cc_final: 0.8578 (m-30) REVERT: F 71 GLN cc_start: 0.8579 (mm110) cc_final: 0.8366 (mm110) REVERT: F 83 GLU cc_start: 0.8475 (mp0) cc_final: 0.8169 (mp0) REVERT: F 182 ASP cc_start: 0.8181 (p0) cc_final: 0.7947 (p0) REVERT: D 7 GLN cc_start: 0.8480 (tt0) cc_final: 0.7973 (tp-100) REVERT: D 11 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7785 (tp) REVERT: D 67 ILE cc_start: 0.7635 (tp) cc_final: 0.7400 (tp) REVERT: D 127 LEU cc_start: 0.8845 (pp) cc_final: 0.8474 (mt) REVERT: D 152 GLN cc_start: 0.8764 (mm-40) cc_final: 0.7732 (tm-30) REVERT: D 156 ILE cc_start: 0.9317 (mt) cc_final: 0.8956 (mp) REVERT: D 185 PHE cc_start: 0.8706 (m-80) cc_final: 0.8422 (m-80) outliers start: 25 outliers final: 20 residues processed: 183 average time/residue: 0.1791 time to fit residues: 47.8962 Evaluate side-chains 186 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 286 LEU Chi-restraints excluded: chain C residue 340 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 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 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 11 LEU Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain D residue 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 34 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 56 optimal weight: 0.0870 chunk 118 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.8158 ------------------------------------------------------------------------------- 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 = 0.4667 r_free = 0.4667 target = 0.213398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.152318 restraints weight = 15844.984| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 3.62 r_work: 0.3735 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.6279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9696 Z= 0.172 Angle : 0.608 13.873 13128 Z= 0.287 Chirality : 0.043 0.146 1535 Planarity : 0.003 0.034 1687 Dihedral : 3.589 17.252 1333 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.73 % Allowed : 25.44 % 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: -1.68 (0.24), residues: 1236 helix: 0.49 (0.26), residues: 453 sheet: -1.90 (0.52), residues: 95 loop : -2.22 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 249 HIS 0.010 0.001 HIS F 204 PHE 0.038 0.001 PHE F 95 TYR 0.016 0.001 TYR E 214 ARG 0.007 0.000 ARG F 211 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6392.19 seconds wall clock time: 111 minutes 15.46 seconds (6675.46 seconds total)