Starting phenix.real_space_refine on Thu Mar 5 17:04:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xko_33258/03_2026/7xko_33258.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xko_33258/03_2026/7xko_33258.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/7xko_33258/03_2026/7xko_33258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xko_33258/03_2026/7xko_33258.map" model { file = "/net/cci-nas-00/data/ceres_data/7xko_33258/03_2026/7xko_33258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xko_33258/03_2026/7xko_33258.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 77 5.16 5 C 15217 2.51 5 N 4187 2.21 5 O 4593 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24075 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 454} Chain: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "C" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 454} Chain: "D" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "E" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "F" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 23, 'TRANS': 446} Chain: "G" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2218 Classifications: {'peptide': 283} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 272} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {' PI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.40, per 1000 atoms: 0.22 Number of scatterers: 24075 At special positions: 0 Unit cell: (129.36, 132, 155.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 P 1 15.00 O 4593 8.00 N 4187 7.00 C 15217 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 1.1 seconds 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5708 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 25 sheets defined 47.2% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 78 through 82 removed outlier: 4.230A pdb=" N GLY A 81 " --> pdb=" O PRO A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 135 through 139 removed outlier: 4.017A pdb=" N ARG A 139 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 185 removed outlier: 3.745A pdb=" N VAL A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 231 through 252 removed outlier: 3.584A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.694A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 372 through 391 removed outlier: 3.706A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 398 removed outlier: 3.648A pdb=" N ALA A 396 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN A 397 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE A 398 " --> pdb=" O PHE A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 421 removed outlier: 3.524A pdb=" N LYS A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'A' and resid 449 through 451 No H-bonds generated for 'chain 'A' and resid 449 through 451' Processing helix chain 'A' and resid 452 through 468 Processing helix chain 'A' and resid 468 through 479 Processing helix chain 'A' and resid 483 through 498 Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 185 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 231 through 253 removed outlier: 3.526A pdb=" N LEU B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.694A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.640A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 338 Processing helix chain 'B' and resid 348 through 352 Processing helix chain 'B' and resid 372 through 392 removed outlier: 4.012A pdb=" N VAL B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLY B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N THR B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 398 removed outlier: 3.632A pdb=" N PHE B 398 " --> pdb=" O PHE B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 421 removed outlier: 4.422A pdb=" N ALA B 408 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS B 421 " --> pdb=" O VAL B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 442 Processing helix chain 'B' and resid 449 through 451 No H-bonds generated for 'chain 'B' and resid 449 through 451' Processing helix chain 'B' and resid 452 through 468 Processing helix chain 'B' and resid 468 through 479 Processing helix chain 'B' and resid 483 through 498 removed outlier: 3.810A pdb=" N LYS B 489 " --> pdb=" O ASP B 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.841A pdb=" N VAL C 178 " --> pdb=" O GLY C 174 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA C 179 " --> pdb=" O LYS C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 216 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 231 through 251 removed outlier: 3.646A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) Proline residue: C 239 - end of helix removed outlier: 3.580A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 removed outlier: 3.896A pdb=" N GLN C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 287 through 288 No H-bonds generated for 'chain 'C' and resid 287 through 288' Processing helix chain 'C' and resid 289 through 299 removed outlier: 3.574A pdb=" N HIS C 294 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 336 Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 372 through 396 removed outlier: 4.269A pdb=" N GLY C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 420 Processing helix chain 'C' and resid 429 through 442 Processing helix chain 'C' and resid 449 through 467 removed outlier: 4.472A pdb=" N ARG C 454 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ARG C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 479 removed outlier: 3.836A pdb=" N LEU C 472 " --> pdb=" O GLY C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 498 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 139 through 145 Processing helix chain 'D' and resid 163 through 179 Processing helix chain 'D' and resid 191 through 206 Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 221 through 242 removed outlier: 3.588A pdb=" N ARG D 227 " --> pdb=" O GLY D 223 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 269 removed outlier: 4.206A pdb=" N PHE D 257 " --> pdb=" O ASN D 253 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 290 Processing helix chain 'D' and resid 308 through 312 removed outlier: 3.523A pdb=" N ASP D 311 " --> pdb=" O VAL D 308 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP D 312 " --> pdb=" O PRO D 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 312' Processing helix chain 'D' and resid 315 through 323 removed outlier: 3.674A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 339 Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 360 through 388 removed outlier: 4.239A pdb=" N LEU D 387 " --> pdb=" O ILE D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 411 removed outlier: 3.889A pdb=" N VAL D 400 " --> pdb=" O ASP D 396 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER D 411 " --> pdb=" O GLN D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 429 through 442 Processing helix chain 'D' and resid 449 through 454 Processing helix chain 'D' and resid 458 through 470 removed outlier: 3.570A pdb=" N VAL D 462 " --> pdb=" O ARG D 458 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 139 through 145 Processing helix chain 'E' and resid 163 through 180 Processing helix chain 'E' and resid 191 through 206 Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 221 through 242 removed outlier: 5.152A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 removed outlier: 3.799A pdb=" N PHE E 257 " --> pdb=" O ASN E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 290 Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 315 through 323 removed outlier: 3.530A pdb=" N SER E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 360 through 388 removed outlier: 4.280A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE E 386 " --> pdb=" O ASP E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 410 removed outlier: 3.554A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 429 through 442 Processing helix chain 'E' and resid 449 through 454 removed outlier: 3.580A pdb=" N ARG E 454 " --> pdb=" O ASP E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 470 removed outlier: 3.597A pdb=" N VAL E 462 " --> pdb=" O ARG E 458 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 139 through 145 Processing helix chain 'F' and resid 163 through 179 Processing helix chain 'F' and resid 191 through 206 Processing helix chain 'F' and resid 207 through 209 No H-bonds generated for 'chain 'F' and resid 207 through 209' Processing helix chain 'F' and resid 221 through 242 removed outlier: 5.210A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 269 removed outlier: 3.543A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 290 Processing helix chain 'F' and resid 308 through 312 removed outlier: 3.621A pdb=" N ASP F 311 " --> pdb=" O VAL F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 323 removed outlier: 3.783A pdb=" N SER F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 339 Processing helix chain 'F' and resid 355 through 360 Processing helix chain 'F' and resid 360 through 387 removed outlier: 4.296A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA F 385 " --> pdb=" O GLN F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 411 removed outlier: 3.981A pdb=" N SER F 411 " --> pdb=" O GLN F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 422 Processing helix chain 'F' and resid 429 through 442 Processing helix chain 'F' and resid 449 through 454 Processing helix chain 'F' and resid 458 through 470 removed outlier: 3.936A pdb=" N VAL F 462 " --> pdb=" O ARG F 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 42 removed outlier: 3.944A pdb=" N GLN G 37 " --> pdb=" O ASN G 33 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASN G 38 " --> pdb=" O ARG G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 54 removed outlier: 3.560A pdb=" N MET G 46 " --> pdb=" O PHE G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 107 removed outlier: 4.525A pdb=" N SER G 93 " --> pdb=" O GLY G 89 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR G 100 " --> pdb=" O LEU G 96 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS G 105 " --> pdb=" O GLN G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 129 removed outlier: 4.206A pdb=" N PHE G 125 " --> pdb=" O VAL G 121 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE G 126 " --> pdb=" O GLY G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 159 removed outlier: 4.072A pdb=" N GLU G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ILE G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 283 Proline residue: G 218 - end of helix removed outlier: 3.612A pdb=" N THR G 257 " --> pdb=" O GLU G 253 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 66 removed outlier: 3.943A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A 91 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ASN A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LEU A 66 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN E 8 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LYS E 17 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N VAL E 6 " --> pdb=" O LYS E 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.281A pdb=" N GLU A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 8.807A pdb=" N ILE A 222 " --> pdb=" O MET A 191 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE A 192 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N VAL A 259 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE A 194 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL A 256 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N LEU A 316 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL A 258 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N PHE A 318 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TYR A 260 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N GLU A 320 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASP A 170 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 66 removed outlier: 4.350A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU B 66 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.752A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.673A pdb=" N SER B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL B 224 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE B 192 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N VAL B 259 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE B 194 " --> pdb=" O VAL B 259 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 318 through 321 removed outlier: 8.385A pdb=" N VAL B 319 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE B 167 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N THR B 321 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY B 169 " --> pdb=" O THR B 321 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 28 through 35 removed outlier: 6.520A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU C 52 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.295A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.147A pdb=" N ILE C 192 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL C 259 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE C 194 " --> pdb=" O VAL C 259 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 318 through 320 removed outlier: 8.088A pdb=" N VAL C 319 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE C 167 " --> pdb=" O VAL C 319 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 3 through 10 removed outlier: 6.641A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLN D 33 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU D 75 " --> pdb=" O GLN D 33 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB5, first strand: chain 'D' and resid 95 through 96 removed outlier: 7.031A pdb=" N SER D 183 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N VAL D 214 " --> pdb=" O SER D 183 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE D 185 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N GLY D 216 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N GLY D 187 " --> pdb=" O GLY D 216 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ILE D 303 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY D 298 " --> pdb=" O THR D 295 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 95 through 96 removed outlier: 7.031A pdb=" N SER D 183 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N VAL D 214 " --> pdb=" O SER D 183 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE D 185 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N GLY D 216 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N GLY D 187 " --> pdb=" O GLY D 216 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ILE D 303 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE D 154 " --> pdb=" O GLN D 304 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 134 through 135 removed outlier: 4.403A pdb=" N TYR D 148 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB9, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.467A pdb=" N PHE E 96 " --> pdb=" O PHE E 215 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N GLN E 217 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL E 184 " --> pdb=" O PHE E 250 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY E 298 " --> pdb=" O THR E 295 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.467A pdb=" N PHE E 96 " --> pdb=" O PHE E 215 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N GLN E 217 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL E 184 " --> pdb=" O PHE E 250 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE E 154 " --> pdb=" O GLN E 304 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LYS E 153 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N THR E 329 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY E 155 " --> pdb=" O THR E 329 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.425A pdb=" N TYR E 148 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AC4, first strand: chain 'F' and resid 94 through 96 removed outlier: 4.020A pdb=" N ARG F 94 " --> pdb=" O THR F 211 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL F 184 " --> pdb=" O PHE F 250 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY F 298 " --> pdb=" O THR F 295 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 94 through 96 removed outlier: 4.020A pdb=" N ARG F 94 " --> pdb=" O THR F 211 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL F 184 " --> pdb=" O PHE F 250 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA F 327 " --> pdb=" O LYS F 153 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 134 through 135 removed outlier: 4.450A pdb=" N TYR F 148 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 133 through 137 removed outlier: 8.142A pdb=" N ILE G 115 " --> pdb=" O ILE G 134 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASP G 136 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL G 117 " --> pdb=" O ASP G 136 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N THR G 76 " --> pdb=" O ALA G 114 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE G 116 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TYR G 78 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR G 169 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASN G 173 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU G 168 " --> pdb=" O LEU G 188 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR G 172 " --> pdb=" O THR G 184 " (cutoff:3.500A) 1149 hydrogen bonds defined for protein. 3306 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: 5.02 Time building geometry restraints manager: 2.60 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: 8210 1.34 - 1.46: 3926 1.46 - 1.57: 12186 1.57 - 1.69: 0 1.69 - 1.81: 154 Bond restraints: 24476 Sorted by residual: bond pdb=" O4 PI D 501 " pdb=" P PI D 501 " ideal model delta sigma weight residual 1.562 1.524 0.038 2.00e-02 2.50e+03 3.69e+00 bond pdb=" O3 PI D 501 " pdb=" P PI D 501 " ideal model delta sigma weight residual 1.562 1.524 0.038 2.00e-02 2.50e+03 3.56e+00 bond pdb=" O1 PI D 501 " pdb=" P PI D 501 " ideal model delta sigma weight residual 1.562 1.524 0.038 2.00e-02 2.50e+03 3.55e+00 bond pdb=" O2 PI D 501 " pdb=" P PI D 501 " ideal model delta sigma weight residual 1.562 1.525 0.037 2.00e-02 2.50e+03 3.51e+00 bond pdb=" CG PRO E 342 " pdb=" CD PRO E 342 " ideal model delta sigma weight residual 1.512 1.478 0.034 2.70e-02 1.37e+03 1.58e+00 ... (remaining 24471 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 32387 1.32 - 2.65: 615 2.65 - 3.97: 125 3.97 - 5.29: 26 5.29 - 6.61: 1 Bond angle restraints: 33154 Sorted by residual: angle pdb=" N THR E 2 " pdb=" CA THR E 2 " pdb=" C THR E 2 " ideal model delta sigma weight residual 113.50 110.43 3.07 1.23e+00 6.61e-01 6.22e+00 angle pdb=" CA GLN B 172 " pdb=" CB GLN B 172 " pdb=" CG GLN B 172 " ideal model delta sigma weight residual 114.10 118.97 -4.87 2.00e+00 2.50e-01 5.93e+00 angle pdb=" N LEU G 87 " pdb=" CA LEU G 87 " pdb=" C LEU G 87 " ideal model delta sigma weight residual 108.58 112.74 -4.16 1.82e+00 3.02e-01 5.22e+00 angle pdb=" N LEU D 455 " pdb=" CA LEU D 455 " pdb=" C LEU D 455 " ideal model delta sigma weight residual 110.61 113.44 -2.83 1.25e+00 6.40e-01 5.12e+00 angle pdb=" CA ILE E 386 " pdb=" C ILE E 386 " pdb=" N LEU E 387 " ideal model delta sigma weight residual 116.60 119.81 -3.21 1.45e+00 4.76e-01 4.89e+00 ... (remaining 33149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 13689 17.82 - 35.63: 969 35.63 - 53.45: 178 53.45 - 71.27: 43 71.27 - 89.09: 25 Dihedral angle restraints: 14904 sinusoidal: 5985 harmonic: 8919 Sorted by residual: dihedral pdb=" CA TYR F 341 " pdb=" C TYR F 341 " pdb=" N PRO F 342 " pdb=" CA PRO F 342 " ideal model delta harmonic sigma weight residual 180.00 141.96 38.04 0 5.00e+00 4.00e-02 5.79e+01 dihedral pdb=" CA ARG B 354 " pdb=" C ARG B 354 " pdb=" N PRO B 355 " pdb=" CA PRO B 355 " ideal model delta harmonic sigma weight residual -180.00 -161.66 -18.34 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA GLN F 217 " pdb=" C GLN F 217 " pdb=" N MET F 218 " pdb=" CA MET F 218 " ideal model delta harmonic sigma weight residual 180.00 -162.19 -17.81 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 14901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2174 0.028 - 0.056: 984 0.056 - 0.084: 364 0.084 - 0.112: 244 0.112 - 0.140: 62 Chirality restraints: 3828 Sorted by residual: chirality pdb=" CB ILE D 386 " pdb=" CA ILE D 386 " pdb=" CG1 ILE D 386 " pdb=" CG2 ILE D 386 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA ILE D 109 " pdb=" N ILE D 109 " pdb=" C ILE D 109 " pdb=" CB ILE D 109 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA ILE B 357 " pdb=" N ILE B 357 " pdb=" C ILE B 357 " pdb=" CB ILE B 357 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 3825 not shown) Planarity restraints: 4355 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 109 " 0.032 5.00e-02 4.00e+02 4.91e-02 3.85e+00 pdb=" N PRO C 110 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 110 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 110 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY F 11 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.51e+00 pdb=" N PRO F 12 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO F 12 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 12 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 220 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.45e+00 pdb=" N PRO D 221 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 221 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 221 " 0.026 5.00e-02 4.00e+02 ... (remaining 4352 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 578 2.71 - 3.26: 24599 3.26 - 3.80: 37767 3.80 - 4.35: 48237 4.35 - 4.90: 82487 Nonbonded interactions: 193668 Sorted by model distance: nonbonded pdb=" O ILE G 103 " pdb=" ND1 HIS G 107 " model vdw 2.161 3.120 nonbonded pdb=" O THR F 137 " pdb=" ND2 ASN F 174 " model vdw 2.252 3.120 nonbonded pdb=" OE1 GLU E 136 " pdb=" OH TYR E 427 " model vdw 2.265 3.040 nonbonded pdb=" O ALA D 29 " pdb=" OG1 THR D 79 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR C 195 " pdb=" OD1 ASP C 261 " model vdw 2.292 3.040 ... (remaining 193663 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 1 through 470) selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.160 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: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.430 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 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 0.120 24477 Z= 0.154 Angle : 0.483 6.615 33154 Z= 0.263 Chirality : 0.043 0.140 3828 Planarity : 0.004 0.049 4355 Dihedral : 13.405 89.085 9196 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.15), residues: 3113 helix: 1.84 (0.15), residues: 1245 sheet: 0.70 (0.23), residues: 508 loop : 0.23 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 94 TYR 0.012 0.001 TYR A 248 PHE 0.013 0.001 PHE D 322 HIS 0.004 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00298 (24476) covalent geometry : angle 0.48271 (33154) hydrogen bonds : bond 0.13054 ( 1130) hydrogen bonds : angle 5.91911 ( 3306) Misc. bond : bond 0.11958 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.793 Fit side-chains REVERT: D 252 ASP cc_start: 0.7469 (p0) cc_final: 0.7183 (p0) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1381 time to fit residues: 25.5885 Evaluate side-chains 93 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 0.0570 chunk 215 optimal weight: 0.0980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.0030 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 30.0000 overall best weight: 2.6312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 401 HIS F 174 ASN ** G 55 ASN ** 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 = 0.3219 r_free = 0.3219 target = 0.060990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.043601 restraints weight = 86436.143| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 3.10 r_work: 0.2611 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.0598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24477 Z= 0.155 Angle : 0.499 6.435 33154 Z= 0.266 Chirality : 0.044 0.141 3828 Planarity : 0.004 0.084 4355 Dihedral : 4.186 34.602 3397 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.43 % Allowed : 3.98 % Favored : 95.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.16), residues: 3113 helix: 1.86 (0.15), residues: 1245 sheet: 0.53 (0.22), residues: 552 loop : 0.26 (0.18), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 94 TYR 0.012 0.001 TYR B 248 PHE 0.013 0.001 PHE B 494 HIS 0.006 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00364 (24476) covalent geometry : angle 0.49949 (33154) hydrogen bonds : bond 0.04184 ( 1130) hydrogen bonds : angle 4.75090 ( 3306) Misc. bond : bond 0.00181 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.878 Fit side-chains REVERT: E 389 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8240 (tpp) outliers start: 11 outliers final: 4 residues processed: 100 average time/residue: 0.1315 time to fit residues: 23.2387 Evaluate side-chains 97 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain E residue 389 MET Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 383 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 256 optimal weight: 3.9990 chunk 190 optimal weight: 9.9990 chunk 141 optimal weight: 0.2980 chunk 162 optimal weight: 6.9990 chunk 274 optimal weight: 20.0000 chunk 260 optimal weight: 1.9990 chunk 221 optimal weight: 6.9990 chunk 182 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.060706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.043351 restraints weight = 86611.735| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 3.10 r_work: 0.2602 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.0757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24477 Z= 0.162 Angle : 0.493 6.262 33154 Z= 0.261 Chirality : 0.044 0.140 3828 Planarity : 0.004 0.073 4355 Dihedral : 4.193 35.971 3397 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.47 % Allowed : 6.20 % Favored : 93.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.15), residues: 3113 helix: 1.84 (0.15), residues: 1249 sheet: 0.46 (0.22), residues: 552 loop : 0.18 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 94 TYR 0.011 0.001 TYR A 329 PHE 0.013 0.001 PHE B 494 HIS 0.004 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00382 (24476) covalent geometry : angle 0.49298 (33154) hydrogen bonds : bond 0.04117 ( 1130) hydrogen bonds : angle 4.59297 ( 3306) Misc. bond : bond 0.00034 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.993 Fit side-chains REVERT: C 157 VAL cc_start: 0.9212 (OUTLIER) cc_final: 0.8983 (m) REVERT: G 241 MET cc_start: 0.6664 (OUTLIER) cc_final: 0.6439 (mmm) outliers start: 12 outliers final: 9 residues processed: 100 average time/residue: 0.1303 time to fit residues: 23.0670 Evaluate side-chains 103 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 241 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 87 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 180 optimal weight: 0.0040 chunk 19 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 overall best weight: 2.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 483 ASN D 423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.060071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.043041 restraints weight = 87129.851| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 3.04 r_work: 0.2597 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24477 Z= 0.166 Angle : 0.493 6.284 33154 Z= 0.261 Chirality : 0.044 0.139 3828 Planarity : 0.004 0.072 4355 Dihedral : 4.199 36.048 3397 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.05 % Allowed : 7.29 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.15), residues: 3113 helix: 1.83 (0.15), residues: 1248 sheet: 0.36 (0.22), residues: 551 loop : 0.13 (0.18), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 94 TYR 0.011 0.001 TYR A 329 PHE 0.013 0.001 PHE B 494 HIS 0.004 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00393 (24476) covalent geometry : angle 0.49341 (33154) hydrogen bonds : bond 0.04094 ( 1130) hydrogen bonds : angle 4.50762 ( 3306) Misc. bond : bond 0.00044 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.932 Fit side-chains REVERT: C 157 VAL cc_start: 0.9219 (OUTLIER) cc_final: 0.8989 (m) REVERT: G 241 MET cc_start: 0.6697 (OUTLIER) cc_final: 0.6476 (mmm) outliers start: 27 outliers final: 15 residues processed: 116 average time/residue: 0.1222 time to fit residues: 25.4466 Evaluate side-chains 110 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 241 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 152 optimal weight: 5.9990 chunk 237 optimal weight: 10.0000 chunk 247 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 249 optimal weight: 9.9990 chunk 167 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 199 optimal weight: 4.9990 chunk 198 optimal weight: 6.9990 chunk 179 optimal weight: 30.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.058479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.041521 restraints weight = 87441.821| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 3.02 r_work: 0.2550 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 24477 Z= 0.312 Angle : 0.617 7.122 33154 Z= 0.324 Chirality : 0.048 0.156 3828 Planarity : 0.005 0.079 4355 Dihedral : 4.617 38.724 3397 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.36 % Allowed : 8.46 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.15), residues: 3113 helix: 1.48 (0.15), residues: 1258 sheet: 0.09 (0.22), residues: 553 loop : -0.11 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 94 TYR 0.015 0.002 TYR C 438 PHE 0.016 0.002 PHE B 494 HIS 0.007 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00740 (24476) covalent geometry : angle 0.61696 (33154) hydrogen bonds : bond 0.05075 ( 1130) hydrogen bonds : angle 4.79230 ( 3306) Misc. bond : bond 0.00075 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 92 time to evaluate : 0.922 Fit side-chains REVERT: C 157 VAL cc_start: 0.9242 (OUTLIER) cc_final: 0.9030 (m) outliers start: 35 outliers final: 25 residues processed: 121 average time/residue: 0.1205 time to fit residues: 26.2485 Evaluate side-chains 117 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 107 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 139 optimal weight: 7.9990 chunk 272 optimal weight: 10.0000 chunk 142 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 302 optimal weight: 0.2980 chunk 61 optimal weight: 2.9990 chunk 284 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 171 optimal weight: 8.9990 chunk 208 optimal weight: 4.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.059959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.042761 restraints weight = 87421.617| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 3.08 r_work: 0.2594 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24477 Z= 0.134 Angle : 0.488 7.818 33154 Z= 0.256 Chirality : 0.044 0.137 3828 Planarity : 0.004 0.069 4355 Dihedral : 4.285 37.123 3397 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.97 % Allowed : 9.43 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.15), residues: 3113 helix: 1.73 (0.15), residues: 1248 sheet: 0.19 (0.22), residues: 551 loop : -0.01 (0.18), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 94 TYR 0.021 0.001 TYR G 78 PHE 0.013 0.001 PHE A 463 HIS 0.003 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00313 (24476) covalent geometry : angle 0.48785 (33154) hydrogen bonds : bond 0.03982 ( 1130) hydrogen bonds : angle 4.49786 ( 3306) Misc. bond : bond 0.00034 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.826 Fit side-chains REVERT: C 157 VAL cc_start: 0.9220 (OUTLIER) cc_final: 0.8993 (m) REVERT: C 191 MET cc_start: 0.9038 (mmt) cc_final: 0.8821 (mmm) outliers start: 25 outliers final: 18 residues processed: 113 average time/residue: 0.1143 time to fit residues: 23.1779 Evaluate side-chains 112 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain G residue 107 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 263 optimal weight: 1.9990 chunk 199 optimal weight: 0.1980 chunk 261 optimal weight: 8.9990 chunk 170 optimal weight: 9.9990 chunk 146 optimal weight: 4.9990 chunk 280 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 227 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.059644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.042667 restraints weight = 87027.653| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 3.04 r_work: 0.2587 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24477 Z= 0.172 Angle : 0.509 9.783 33154 Z= 0.265 Chirality : 0.044 0.152 3828 Planarity : 0.004 0.073 4355 Dihedral : 4.271 37.549 3397 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.17 % Allowed : 9.98 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.15), residues: 3113 helix: 1.72 (0.15), residues: 1250 sheet: 0.15 (0.21), residues: 558 loop : -0.02 (0.18), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 94 TYR 0.019 0.001 TYR G 78 PHE 0.014 0.001 PHE A 463 HIS 0.004 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00405 (24476) covalent geometry : angle 0.50899 (33154) hydrogen bonds : bond 0.04135 ( 1130) hydrogen bonds : angle 4.50330 ( 3306) Misc. bond : bond 0.00043 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.755 Fit side-chains REVERT: C 157 VAL cc_start: 0.9231 (OUTLIER) cc_final: 0.9006 (m) REVERT: C 191 MET cc_start: 0.9046 (mmt) cc_final: 0.8795 (mmm) REVERT: C 375 MET cc_start: 0.8994 (tpt) cc_final: 0.8430 (tpp) outliers start: 30 outliers final: 23 residues processed: 118 average time/residue: 0.1232 time to fit residues: 26.0623 Evaluate side-chains 117 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 107 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 114 optimal weight: 10.0000 chunk 137 optimal weight: 9.9990 chunk 202 optimal weight: 7.9990 chunk 179 optimal weight: 10.0000 chunk 292 optimal weight: 0.0970 chunk 283 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 240 optimal weight: 7.9990 chunk 264 optimal weight: 0.1980 chunk 155 optimal weight: 10.0000 chunk 185 optimal weight: 7.9990 overall best weight: 4.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.058829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.041873 restraints weight = 87360.502| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 3.03 r_work: 0.2560 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 24477 Z= 0.247 Angle : 0.565 8.705 33154 Z= 0.295 Chirality : 0.046 0.180 3828 Planarity : 0.004 0.075 4355 Dihedral : 4.475 38.787 3397 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.33 % Allowed : 9.94 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.15), residues: 3113 helix: 1.57 (0.15), residues: 1251 sheet: 0.04 (0.21), residues: 558 loop : -0.11 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 94 TYR 0.019 0.001 TYR G 78 PHE 0.015 0.001 PHE B 494 HIS 0.005 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00584 (24476) covalent geometry : angle 0.56477 (33154) hydrogen bonds : bond 0.04652 ( 1130) hydrogen bonds : angle 4.65210 ( 3306) Misc. bond : bond 0.00057 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 0.830 Fit side-chains REVERT: A 95 MET cc_start: 0.9121 (tpp) cc_final: 0.8888 (tpt) REVERT: C 157 VAL cc_start: 0.9228 (OUTLIER) cc_final: 0.9015 (m) REVERT: F 469 MET cc_start: 0.7634 (mtt) cc_final: 0.6874 (mtp) outliers start: 34 outliers final: 28 residues processed: 121 average time/residue: 0.1263 time to fit residues: 27.2906 Evaluate side-chains 120 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 107 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 59 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 215 optimal weight: 0.0270 chunk 166 optimal weight: 1.9990 chunk 244 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 218 optimal weight: 2.9990 chunk 296 optimal weight: 0.6980 chunk 254 optimal weight: 8.9990 chunk 186 optimal weight: 9.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.060979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.043906 restraints weight = 86721.690| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 3.08 r_work: 0.2628 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24477 Z= 0.094 Angle : 0.468 11.078 33154 Z= 0.243 Chirality : 0.043 0.174 3828 Planarity : 0.004 0.067 4355 Dihedral : 4.076 35.959 3397 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.01 % Allowed : 10.37 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.15), residues: 3113 helix: 1.88 (0.15), residues: 1249 sheet: 0.23 (0.22), residues: 530 loop : 0.04 (0.17), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 402 TYR 0.014 0.001 TYR G 78 PHE 0.013 0.001 PHE E 257 HIS 0.003 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00207 (24476) covalent geometry : angle 0.46825 (33154) hydrogen bonds : bond 0.03452 ( 1130) hydrogen bonds : angle 4.34210 ( 3306) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.882 Fit side-chains REVERT: C 157 VAL cc_start: 0.9206 (OUTLIER) cc_final: 0.8969 (m) REVERT: C 191 MET cc_start: 0.9070 (mmt) cc_final: 0.8720 (mmm) REVERT: F 469 MET cc_start: 0.7576 (mtt) cc_final: 0.6812 (mtp) outliers start: 26 outliers final: 21 residues processed: 117 average time/residue: 0.1315 time to fit residues: 27.1890 Evaluate side-chains 114 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 236 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 25 optimal weight: 0.0870 chunk 174 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 150 optimal weight: 8.9990 chunk 252 optimal weight: 10.0000 chunk 306 optimal weight: 0.9990 chunk 210 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 284 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.060151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.042940 restraints weight = 87857.044| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 3.09 r_work: 0.2601 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24477 Z= 0.144 Angle : 0.491 10.898 33154 Z= 0.254 Chirality : 0.044 0.169 3828 Planarity : 0.004 0.068 4355 Dihedral : 4.095 36.683 3397 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.90 % Allowed : 10.68 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.15), residues: 3113 helix: 1.84 (0.15), residues: 1258 sheet: 0.20 (0.22), residues: 558 loop : 0.03 (0.18), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 94 TYR 0.016 0.001 TYR G 78 PHE 0.014 0.001 PHE A 463 HIS 0.003 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00339 (24476) covalent geometry : angle 0.49125 (33154) hydrogen bonds : bond 0.03826 ( 1130) hydrogen bonds : angle 4.36982 ( 3306) Misc. bond : bond 0.00036 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6226 Ramachandran restraints generated. 3113 Oldfield, 0 Emsley, 3113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.799 Fit side-chains REVERT: A 95 MET cc_start: 0.9079 (tpp) cc_final: 0.8816 (tpt) REVERT: C 157 VAL cc_start: 0.9237 (OUTLIER) cc_final: 0.9007 (m) REVERT: C 191 MET cc_start: 0.9053 (mmt) cc_final: 0.8714 (mmm) REVERT: C 375 MET cc_start: 0.8942 (tpt) cc_final: 0.8415 (tpp) REVERT: E 389 MET cc_start: 0.8621 (mtp) cc_final: 0.8301 (tpp) REVERT: F 469 MET cc_start: 0.7607 (mtt) cc_final: 0.6857 (mtp) outliers start: 23 outliers final: 22 residues processed: 112 average time/residue: 0.1228 time to fit residues: 24.5214 Evaluate side-chains 116 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain G residue 107 HIS Chi-restraints excluded: chain G residue 236 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 152 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 245 optimal weight: 0.0010 chunk 204 optimal weight: 7.9990 chunk 203 optimal weight: 7.9990 chunk 233 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 193 optimal weight: 10.0000 chunk 191 optimal weight: 7.9990 chunk 273 optimal weight: 0.3980 overall best weight: 1.0390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.061205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.043965 restraints weight = 87041.802| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 3.10 r_work: 0.2632 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24477 Z= 0.094 Angle : 0.461 10.493 33154 Z= 0.238 Chirality : 0.043 0.160 3828 Planarity : 0.004 0.064 4355 Dihedral : 3.948 35.177 3397 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.94 % Allowed : 10.60 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.15), residues: 3113 helix: 1.98 (0.15), residues: 1249 sheet: 0.30 (0.22), residues: 554 loop : 0.08 (0.18), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 3 TYR 0.016 0.001 TYR A 248 PHE 0.013 0.001 PHE B 494 HIS 0.003 0.001 HIS F 401 Details of bonding type rmsd covalent geometry : bond 0.00210 (24476) covalent geometry : angle 0.46126 (33154) hydrogen bonds : bond 0.03368 ( 1130) hydrogen bonds : angle 4.25471 ( 3306) Misc. bond : bond 0.00023 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4246.02 seconds wall clock time: 73 minutes 45.18 seconds (4425.18 seconds total)