Starting phenix.real_space_refine on Sun Aug 24 20:01:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tjw_25934/08_2025/7tjw_25934.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tjw_25934/08_2025/7tjw_25934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tjw_25934/08_2025/7tjw_25934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tjw_25934/08_2025/7tjw_25934.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tjw_25934/08_2025/7tjw_25934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tjw_25934/08_2025/7tjw_25934.map" } resolution = 4.0 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= 0.030 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: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 29 5.16 5 C 14226 2.51 5 N 3996 2.21 5 O 4229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22500 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3505 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 457} Chain breaks: 1 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 5, 'GLN:plan1': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 85 Chain: "B" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3430 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 454} Chain breaks: 1 Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 8, 'GLU:plan': 21, 'GLN:plan1': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 133 Chain: "C" Number of atoms: 3648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3648 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 462} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3353 Classifications: {'peptide': 465} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 441} Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 18, 'ASP:plan': 8, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 112 Chain: "E" Number of atoms: 3308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3308 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 444} Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 24, 'GLN:plan1': 5, 'ASP:plan': 5, 'HIS:plan': 1, 'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 158 Chain: "F" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3430 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 444} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 19, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 96 Chain: "G" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1666 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 9, 'TRANS': 249} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 432 Unresolved non-hydrogen dihedrals: 285 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 3, 'ASP:plan': 12, 'GLN:plan1': 6, 'PHE:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 8, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 187 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.43, per 1000 atoms: 0.24 Number of scatterers: 22500 At special positions: 0 Unit cell: (126.665, 126.665, 153.615, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 29 16.00 P 15 15.00 Mg 5 11.99 O 4229 8.00 N 3996 7.00 C 14226 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 947.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5626 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 22 sheets defined 50.8% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 80 through 84 Processing helix chain 'A' and resid 102 through 106 removed outlier: 3.982A pdb=" N LEU A 105 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 176 through 188 removed outlier: 3.776A pdb=" N ALA A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 193 removed outlier: 3.832A pdb=" N ASN A 193 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 241 through 262 removed outlier: 3.596A pdb=" N GLN A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Proline residue: A 249 - end of helix removed outlier: 3.807A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 287 Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 299 through 309 removed outlier: 3.691A pdb=" N LEU A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 335 Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 355 through 361 Processing helix chain 'A' and resid 376 through 380 Processing helix chain 'A' and resid 382 through 403 removed outlier: 4.007A pdb=" N GLN A 387 " --> pdb=" O LYS A 383 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N SER A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LEU A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 402 " --> pdb=" O GLN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 431 Processing helix chain 'A' and resid 439 through 452 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 453 through 458 removed outlier: 4.058A pdb=" N GLY A 457 " --> pdb=" O HIS A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 478 removed outlier: 3.585A pdb=" N LEU A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER A 472 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 489 Processing helix chain 'A' and resid 492 through 509 Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.503A pdb=" N VAL B 84 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 106 Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 176 through 188 removed outlier: 3.851A pdb=" N ALA B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 193 removed outlier: 3.677A pdb=" N ASN B 193 " --> pdb=" O LYS B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 225 Processing helix chain 'B' and resid 226 through 229 Processing helix chain 'B' and resid 241 through 262 removed outlier: 3.584A pdb=" N GLN B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Proline residue: B 249 - end of helix removed outlier: 3.713A pdb=" N TRP B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 removed outlier: 3.579A pdb=" N GLN B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 297 through 298 No H-bonds generated for 'chain 'B' and resid 297 through 298' Processing helix chain 'B' and resid 299 through 309 removed outlier: 3.605A pdb=" N LEU B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 346 Processing helix chain 'B' and resid 355 through 361 Processing helix chain 'B' and resid 376 through 380 Processing helix chain 'B' and resid 382 through 390 Processing helix chain 'B' and resid 391 through 404 Processing helix chain 'B' and resid 414 through 430 removed outlier: 3.895A pdb=" N LEU B 420 " --> pdb=" O THR B 416 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG B 422 " --> pdb=" O GLN B 418 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY B 423 " --> pdb=" O THR B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 453 Proline residue: B 445 - end of helix Processing helix chain 'B' and resid 459 through 461 No H-bonds generated for 'chain 'B' and resid 459 through 461' Processing helix chain 'B' and resid 462 through 477 removed outlier: 3.643A pdb=" N SER B 468 " --> pdb=" O GLY B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 489 removed outlier: 3.691A pdb=" N LEU B 482 " --> pdb=" O HIS B 478 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY B 489 " --> pdb=" O ILE B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 509 Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.630A pdb=" N LEU C 105 " --> pdb=" O GLY C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 159 Processing helix chain 'C' and resid 176 through 188 removed outlier: 3.573A pdb=" N ALA C 181 " --> pdb=" O LYS C 177 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 193 Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 211 through 225 Processing helix chain 'C' and resid 226 through 229 removed outlier: 3.853A pdb=" N LYS C 229 " --> pdb=" O ASP C 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 226 through 229' Processing helix chain 'C' and resid 241 through 263 removed outlier: 3.864A pdb=" N GLN C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Proline residue: C 249 - end of helix removed outlier: 3.523A pdb=" N TRP C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 288 removed outlier: 3.508A pdb=" N ALA C 279 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 296 Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 315 through 319 Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 355 through 361 Processing helix chain 'C' and resid 376 through 380 Processing helix chain 'C' and resid 382 through 390 removed outlier: 3.745A pdb=" N LYS C 386 " --> pdb=" O VAL C 382 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN C 387 " --> pdb=" O LYS C 383 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL C 388 " --> pdb=" O ALA C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 404 removed outlier: 3.508A pdb=" N GLU C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 402 " --> pdb=" O GLN C 398 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA C 404 " --> pdb=" O ARG C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 409 Processing helix chain 'C' and resid 413 through 429 removed outlier: 3.847A pdb=" N GLU C 424 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG C 425 " --> pdb=" O VAL C 421 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C 429 " --> pdb=" O ARG C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 452 Proline residue: C 445 - end of helix Processing helix chain 'C' and resid 459 through 461 No H-bonds generated for 'chain 'C' and resid 459 through 461' Processing helix chain 'C' and resid 462 through 478 removed outlier: 3.777A pdb=" N LEU C 471 " --> pdb=" O GLU C 467 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER C 472 " --> pdb=" O SER C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 488 removed outlier: 3.690A pdb=" N GLU C 484 " --> pdb=" O GLU C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 508 removed outlier: 3.811A pdb=" N ALA C 508 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'D' and resid 162 through 175 Processing helix chain 'D' and resid 190 through 204 Processing helix chain 'D' and resid 225 through 246 removed outlier: 4.631A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 272 Processing helix chain 'D' and resid 277 through 281 Processing helix chain 'D' and resid 282 through 283 No H-bonds generated for 'chain 'D' and resid 282 through 283' Processing helix chain 'D' and resid 284 through 296 removed outlier: 3.943A pdb=" N ARG D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 316 Processing helix chain 'D' and resid 319 through 326 removed outlier: 4.046A pdb=" N THR D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE D 326 " --> pdb=" O PRO D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 329 No H-bonds generated for 'chain 'D' and resid 327 through 329' Processing helix chain 'D' and resid 336 through 342 removed outlier: 3.522A pdb=" N SER D 340 " --> pdb=" O SER D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 364 Processing helix chain 'D' and resid 364 through 392 removed outlier: 3.856A pdb=" N SER D 383 " --> pdb=" O GLN D 379 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE D 390 " --> pdb=" O ASP D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 396 Processing helix chain 'D' and resid 397 through 414 removed outlier: 5.258A pdb=" N THR D 403 " --> pdb=" O GLN D 399 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL D 404 " --> pdb=" O ASP D 400 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU D 405 " --> pdb=" O LYS D 401 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG D 412 " --> pdb=" O ARG D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 423 removed outlier: 4.301A pdb=" N VAL D 423 " --> pdb=" O VAL D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 447 Processing helix chain 'D' and resid 453 through 457 Processing helix chain 'D' and resid 462 through 474 removed outlier: 4.224A pdb=" N GLU D 471 " --> pdb=" O VAL D 467 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS D 472 " --> pdb=" O ALA D 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 138 through 145 Processing helix chain 'E' and resid 162 through 179 Processing helix chain 'E' and resid 190 through 205 Processing helix chain 'E' and resid 225 through 246 removed outlier: 4.782A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LEU E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE E 239 " --> pdb=" O THR E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 272 Processing helix chain 'E' and resid 277 through 281 Processing helix chain 'E' and resid 282 through 283 No H-bonds generated for 'chain 'E' and resid 282 through 283' Processing helix chain 'E' and resid 284 through 294 Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 319 through 327 Processing helix chain 'E' and resid 336 through 342 Processing helix chain 'E' and resid 359 through 392 removed outlier: 7.707A pdb=" N GLN E 365 " --> pdb=" O ALA E 361 " (cutoff:3.500A) removed outlier: 9.562A pdb=" N GLU E 366 " --> pdb=" O VAL E 362 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N HIS E 367 " --> pdb=" O VAL E 363 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER E 383 " --> pdb=" O GLN E 379 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 415 removed outlier: 3.999A pdb=" N ARG E 412 " --> pdb=" O ARG E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 447 removed outlier: 3.605A pdb=" N GLU E 446 " --> pdb=" O LYS E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 475 Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 123 through 127 Processing helix chain 'F' and resid 138 through 145 Processing helix chain 'F' and resid 162 through 175 Processing helix chain 'F' and resid 176 through 178 No H-bonds generated for 'chain 'F' and resid 176 through 178' Processing helix chain 'F' and resid 190 through 203 Processing helix chain 'F' and resid 225 through 246 removed outlier: 3.602A pdb=" N ARG F 231 " --> pdb=" O GLY F 227 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR F 242 " --> pdb=" O THR F 238 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE F 243 " --> pdb=" O ILE F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 273 removed outlier: 4.094A pdb=" N THR F 262 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA F 270 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU F 271 " --> pdb=" O GLU F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 281 Processing helix chain 'F' and resid 284 through 294 removed outlier: 3.882A pdb=" N LEU F 292 " --> pdb=" O ASP F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 297 No H-bonds generated for 'chain 'F' and resid 295 through 297' Processing helix chain 'F' and resid 313 through 316 Processing helix chain 'F' and resid 319 through 328 removed outlier: 4.314A pdb=" N ALA F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N HIS F 328 " --> pdb=" O THR F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 342 removed outlier: 3.676A pdb=" N SER F 340 " --> pdb=" O SER F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 364 removed outlier: 3.690A pdb=" N GLY F 364 " --> pdb=" O ALA F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 391 removed outlier: 5.102A pdb=" N ASP F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ILE F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 396 Processing helix chain 'F' and resid 397 through 414 removed outlier: 3.651A pdb=" N LYS F 409 " --> pdb=" O GLU F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 420 No H-bonds generated for 'chain 'F' and resid 418 through 420' Processing helix chain 'F' and resid 421 through 426 Processing helix chain 'F' and resid 433 through 446 Processing helix chain 'F' and resid 453 through 458 Processing helix chain 'F' and resid 462 through 475 Processing helix chain 'G' and resid 3 through 56 removed outlier: 3.686A pdb=" N ILE G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS G 36 " --> pdb=" O SER G 32 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA G 47 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLU G 48 " --> pdb=" O MET G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 100 removed outlier: 3.922A pdb=" N LEU G 91 " --> pdb=" O ILE G 87 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ALA G 92 " --> pdb=" O HIS G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 119 Processing helix chain 'G' and resid 120 through 121 No H-bonds generated for 'chain 'G' and resid 120 through 121' Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.918A pdb=" N ILE G 126 " --> pdb=" O PRO G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 136 removed outlier: 3.619A pdb=" N LYS G 135 " --> pdb=" O GLY G 132 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP G 136 " --> pdb=" O ILE G 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 132 through 136' Processing helix chain 'G' and resid 139 through 153 removed outlier: 3.570A pdb=" N LYS G 149 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU G 150 " --> pdb=" O ILE G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 159 Processing helix chain 'G' and resid 184 through 191 removed outlier: 3.624A pdb=" N ILE G 188 " --> pdb=" O ASN G 184 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU G 189 " --> pdb=" O ALA G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 198 removed outlier: 3.847A pdb=" N PHE G 197 " --> pdb=" O SER G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 275 removed outlier: 4.231A pdb=" N PHE G 210 " --> pdb=" O PRO G 206 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR G 212 " --> pdb=" O ASP G 208 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR G 213 " --> pdb=" O LEU G 209 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP G 269 " --> pdb=" O ASN G 265 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE G 270 " --> pdb=" O GLU G 266 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 68 removed outlier: 4.316A pdb=" N GLU A 53 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU A 54 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL A 36 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL A 76 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ALA A 65 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LYS E 75 " --> pdb=" O LYS E 40 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LYS E 40 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL E 16 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASP E 22 " --> pdb=" O THR E 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 101 Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.487A pdb=" N VAL A 110 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS A 203 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N VAL A 234 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TYR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ALA A 236 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ALA A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY A 321 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.487A pdb=" N VAL A 110 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS A 203 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N VAL A 234 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TYR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ALA A 236 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ALA A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY A 171 " --> pdb=" O ILE A 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 31 through 37 removed outlier: 5.441A pdb=" N VAL B 33 " --> pdb=" O PHE B 44 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N PHE B 44 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL B 76 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ALA B 65 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLU B 53 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU B 54 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 101 removed outlier: 3.526A pdb=" N GLY B 127 " --> pdb=" O VAL B 101 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 115 through 116 removed outlier: 6.300A pdb=" N TYR B 202 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N VAL B 269 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL B 204 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ASP B 271 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL B 206 " --> pdb=" O ASP B 271 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY B 321 " --> pdb=" O LEU B 314 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 115 through 116 removed outlier: 6.300A pdb=" N TYR B 202 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N VAL B 269 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL B 204 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ASP B 271 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL B 206 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 77 through 78 removed outlier: 6.665A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N HIS D 24 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL D 13 " --> pdb=" O HIS D 24 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ALA C 65 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL C 76 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL C 36 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ARG C 42 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU C 54 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU C 53 " --> pdb=" O ALA C 65 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 98 through 101 Processing sheet with id=AB2, first strand: chain 'C' and resid 109 through 110 removed outlier: 6.644A pdb=" N TYR C 202 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N VAL C 269 " --> pdb=" O TYR C 202 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL C 204 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ASP C 271 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL C 206 " --> pdb=" O ASP C 271 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 109 through 110 removed outlier: 6.644A pdb=" N TYR C 202 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N VAL C 269 " --> pdb=" O TYR C 202 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL C 204 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ASP C 271 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL C 206 " --> pdb=" O ASP C 271 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE C 169 " --> pdb=" O ILE C 329 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N PHE C 353 " --> pdb=" O ASN C 368 " (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: 6.568A pdb=" N SER D 182 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N VAL D 218 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N PHE D 184 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLY D 220 " --> pdb=" O PHE D 184 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N GLY D 186 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL D 183 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY D 157 " --> pdb=" O VAL D 310 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 133 through 134 removed outlier: 4.572A pdb=" N TYR D 147 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB8, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.202A pdb=" N ILE E 96 " --> pdb=" O PHE E 219 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N VAL E 251 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL E 307 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU E 253 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ALA E 309 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE E 255 " --> pdb=" O ALA E 309 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA E 331 " --> pdb=" O LYS E 152 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 10 through 17 removed outlier: 5.464A pdb=" N VAL F 13 " --> pdb=" O HIS F 24 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N HIS F 24 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA F 15 " --> pdb=" O ASP F 22 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ASN F 35 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ALA F 36 " --> pdb=" O THR F 79 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AC2, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.739A pdb=" N SER F 182 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N VAL F 218 " --> pdb=" O SER F 182 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N PHE F 184 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N GLY F 220 " --> pdb=" O PHE F 184 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N GLY F 186 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N PHE F 181 " --> pdb=" O LEU F 252 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N PHE F 254 " --> pdb=" O PHE F 181 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL F 183 " --> pdb=" O PHE F 254 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ASP F 256 " --> pdb=" O VAL F 183 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N THR F 185 " --> pdb=" O ASP F 256 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE F 153 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N VAL F 310 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU F 155 " --> pdb=" O VAL F 310 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 133 through 134 removed outlier: 4.092A pdb=" N TYR F 147 " --> pdb=" O LEU F 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 75 through 76 removed outlier: 6.408A pdb=" N SER G 174 " --> pdb=" O VAL G 170 " (cutoff:3.500A) 1228 hydrogen bonds defined for protein. 3411 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: 4.83 Time building geometry restraints manager: 2.51 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: 7576 1.34 - 1.46: 4121 1.46 - 1.58: 11076 1.58 - 1.69: 21 1.69 - 1.81: 54 Bond restraints: 22848 Sorted by residual: bond pdb=" CB PRO E 8 " pdb=" CG PRO E 8 " ideal model delta sigma weight residual 1.492 1.575 -0.083 5.00e-02 4.00e+02 2.78e+00 bond pdb=" CB ASP C 38 " pdb=" CG ASP C 38 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.65e+00 bond pdb=" C SER G 191 " pdb=" N PRO G 192 " ideal model delta sigma weight residual 1.336 1.348 -0.012 1.20e-02 6.94e+03 1.05e+00 bond pdb=" CG PRO B 365 " pdb=" CD PRO B 365 " ideal model delta sigma weight residual 1.512 1.486 0.026 2.70e-02 1.37e+03 9.43e-01 bond pdb=" CA ILE B 363 " pdb=" CB ILE B 363 " ideal model delta sigma weight residual 1.527 1.539 -0.012 1.31e-02 5.83e+03 9.04e-01 ... (remaining 22843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 30174 1.55 - 3.10: 756 3.10 - 4.66: 151 4.66 - 6.21: 25 6.21 - 7.76: 13 Bond angle restraints: 31119 Sorted by residual: angle pdb=" C ASP D 256 " pdb=" N ASN D 257 " pdb=" CA ASN D 257 " ideal model delta sigma weight residual 121.70 128.54 -6.84 1.80e+00 3.09e-01 1.44e+01 angle pdb=" C ASP F 256 " pdb=" N ASN F 257 " pdb=" CA ASN F 257 " ideal model delta sigma weight residual 121.70 128.44 -6.74 1.80e+00 3.09e-01 1.40e+01 angle pdb=" N VAL A 388 " pdb=" CA VAL A 388 " pdb=" C VAL A 388 " ideal model delta sigma weight residual 113.71 110.82 2.89 9.50e-01 1.11e+00 9.28e+00 angle pdb=" C ASP E 256 " pdb=" N ASN E 257 " pdb=" CA ASN E 257 " ideal model delta sigma weight residual 121.70 127.18 -5.48 1.80e+00 3.09e-01 9.27e+00 angle pdb=" N GLY D 220 " pdb=" CA GLY D 220 " pdb=" C GLY D 220 " ideal model delta sigma weight residual 113.18 106.13 7.05 2.37e+00 1.78e-01 8.85e+00 ... (remaining 31114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 12967 17.99 - 35.98: 623 35.98 - 53.97: 151 53.97 - 71.96: 50 71.96 - 89.95: 26 Dihedral angle restraints: 13817 sinusoidal: 5027 harmonic: 8790 Sorted by residual: dihedral pdb=" CA PHE E 219 " pdb=" C PHE E 219 " pdb=" N GLY E 220 " pdb=" CA GLY E 220 " ideal model delta harmonic sigma weight residual 180.00 151.17 28.83 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA PHE F 219 " pdb=" C PHE F 219 " pdb=" N GLY F 220 " pdb=" CA GLY F 220 " ideal model delta harmonic sigma weight residual 180.00 154.40 25.60 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA GLN A 351 " pdb=" C GLN A 351 " pdb=" N ILE A 352 " pdb=" CA ILE A 352 " ideal model delta harmonic sigma weight residual 180.00 156.52 23.48 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 13814 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3263 0.065 - 0.129: 459 0.129 - 0.194: 23 0.194 - 0.258: 3 0.258 - 0.322: 12 Chirality restraints: 3760 Sorted by residual: chirality pdb=" C2' ATP B 600 " pdb=" C1' ATP B 600 " pdb=" C3' ATP B 600 " pdb=" O2' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.68 -3.00 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C3' ATP B 600 " pdb=" C2' ATP B 600 " pdb=" C4' ATP B 600 " pdb=" O3' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.63 -2.94 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C2' ATP A 600 " pdb=" C1' ATP A 600 " pdb=" C3' ATP A 600 " pdb=" O2' ATP A 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.99 0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 3757 not shown) Planarity restraints: 4009 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 228 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C ALA E 228 " 0.032 2.00e-02 2.50e+03 pdb=" O ALA E 228 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG E 229 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 248 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO C 249 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 249 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 249 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 275 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO E 276 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO E 276 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 276 " 0.024 5.00e-02 4.00e+02 ... (remaining 4006 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.46: 52 2.46 - 3.07: 16477 3.07 - 3.68: 32870 3.68 - 4.29: 49248 4.29 - 4.90: 81793 Nonbonded interactions: 180440 Sorted by model distance: nonbonded pdb=" O3G ATP C 600 " pdb="MG MG C 601 " model vdw 1.855 2.170 nonbonded pdb=" O1B ATP C 600 " pdb="MG MG C 601 " model vdw 1.914 2.170 nonbonded pdb=" O2B ATP A 600 " pdb="MG MG A 601 " model vdw 1.963 2.170 nonbonded pdb=" O3G ATP B 600 " pdb="MG MG B 601 " model vdw 1.971 2.170 nonbonded pdb=" OG1 THR B 178 " pdb="MG MG B 601 " model vdw 2.031 2.170 ... (remaining 180435 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 68 or (resid 69 and ( \ name N or name CA or name C or name O or name CB )) or resid 70 through 80 or (r \ esid 81 and (name N or name CA or name C or name O or name CB )) or resid 82 thr \ ough 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or \ resid 89 through 110 or (resid 111 through 112 and (name N or name CA or name C \ or name O or name CB )) or resid 113 through 117 or (resid 118 and (name N or n \ ame CA or name C or name O or name CB )) or resid 119 or (resid 120 and (name N \ or name CA or name C or name O or name CB )) or resid 121 through 133 or (resid \ 134 through 135 and (name N or name CA or name C or name O or name CB )) or resi \ d 136 through 155 or (resid 156 through 157 and (name N or name CA or name C or \ name O or name CB )) or resid 158 through 164 or (resid 165 and (name N or name \ CA or name C or name O or name CB )) or resid 166 or (resid 167 through 168 and \ (name N or name CA or name C or name O or name CB )) or resid 169 through 195 or \ (resid 196 through 197 and (name N or name CA or name C or name O or name CB )) \ or resid 198 through 239 or (resid 240 through 242 and (name N or name CA or na \ me C or name O or name CB )) or resid 243 through 317 or (resid 318 and (name N \ or name CA or name C or name O or name CB )) or resid 319 through 322 or (resid \ 323 and (name N or name CA or name C or name O or name CB )) or resid 324 throug \ h 329 or (resid 330 and (name N or name CA or name C or name O or name CB )) or \ resid 331 through 334 or (resid 335 and (name N or name CA or name C or name O o \ r name CB )) or resid 336 through 354 or (resid 355 through 357 and (name N or n \ ame CA or name C or name O or name CB )) or resid 358 through 392 or (resid 393 \ and (name N or name CA or name C or name O or name CB )) or resid 394 through 39 \ 7 or (resid 398 and (name N or name CA or name C or name O or name CB )) or resi \ d 399 through 405 or (resid 413 through 420 and (name N or name CA or name C or \ name O or name CB )) or resid 421 through 431 or (resid 432 and (name N or name \ CA or name C or name O or name CB )) or resid 433 or (resid 434 and (name N or n \ ame CA or name C or name O or name CB )) or resid 435 through 440 or (resid 441 \ through 442 and (name N or name CA or name C or name O or name CB )) or resid 44 \ 3 through 461 or (resid 462 and (name N or name CA or name C or name O or name C \ B )) or resid 463 through 464 or (resid 465 through 467 and (name N or name CA o \ r name C or name O or name CB )) or resid 468 through 473 or (resid 474 through \ 475 and (name N or name CA or name C or name O or name CB )) or resid 476 throug \ h 481 or (resid 482 and (name N or name CA or name C or name O or name CB )) or \ resid 483 through 492 or (resid 493 through 497 and (name N or name CA or name C \ or name O or name CB )) or resid 498 through 601)) selection = (chain 'B' and (resid 28 through 51 or (resid 52 through 53 and (name N or name \ CA or name C or name O or name CB )) or resid 54 through 61 or (resid 62 and (na \ me N or name CA or name C or name O or name CB )) or resid 63 through 85 or (res \ id 86 and (name N or name CA or name C or name O or name CB )) or resid 87 throu \ gh 123 or (resid 124 through 126 and (name N or name CA or name C or name O or n \ ame CB )) or resid 127 through 167 or (resid 168 and (name N or name CA or name \ C or name O or name CB )) or resid 169 through 182 or (resid 183 and (name N or \ name CA or name C or name O or name CB )) or resid 184 through 188 or (resid 189 \ and (name N or name CA or name C or name O or name CB )) or resid 190 through 2 \ 75 or (resid 276 through 277 and (name N or name CA or name C or name O or name \ CB )) or resid 278 through 293 or (resid 294 through 295 and (name N or name CA \ or name C or name O or name CB )) or resid 296 through 307 or (resid 308 and (na \ me N or name CA or name C or name O or name CB )) or resid 309 through 334 or (r \ esid 335 and (name N or name CA or name C or name O or name CB )) or resid 336 t \ hrough 382 or (resid 383 through 384 and (name N or name CA or name C or name O \ or name CB )) or resid 385 through 386 or (resid 387 and (name N or name CA or n \ ame C or name O or name CB )) or resid 388 through 427 or (resid 428 and (name N \ or name CA or name C or name O or name CB )) or resid 429 through 465 or (resid \ 466 through 467 and (name N or name CA or name C or name O or name CB )) or res \ id 468 through 486 or (resid 487 through 488 and (name N or name CA or name C or \ name O or name CB )) or resid 489 or (resid 490 and (name N or name CA or name \ C or name O or name CB )) or resid 491 through 494 or (resid 495 through 497 and \ (name N or name CA or name C or name O or name CB )) or resid 498 through 601)) \ selection = (chain 'C' and (resid 28 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 51 or (resid 52 through 53 and (na \ me N or name CA or name C or name O or name CB )) or resid 54 through 61 or (res \ id 62 and (name N or name CA or name C or name O or name CB )) or resid 63 throu \ gh 68 or (resid 69 and (name N or name CA or name C or name O or name CB )) or r \ esid 70 through 80 or (resid 81 and (name N or name CA or name C or name O or na \ me CB )) or resid 82 through 85 or (resid 86 and (name N or name CA or name C or \ name O or name CB )) or resid 87 or (resid 88 and (name N or name CA or name C \ or name O or name CB )) or resid 89 through 110 or (resid 111 through 112 and (n \ ame N or name CA or name C or name O or name CB )) or resid 113 through 117 or ( \ resid 118 and (name N or name CA or name C or name O or name CB )) or resid 119 \ or (resid 120 and (name N or name CA or name C or name O or name CB )) or resid \ 121 through 123 or (resid 124 through 126 and (name N or name CA or name C or na \ me O or name CB )) or resid 127 through 133 or (resid 134 through 135 and (name \ N or name CA or name C or name O or name CB )) or resid 136 through 155 or (resi \ d 156 through 157 and (name N or name CA or name C or name O or name CB )) or re \ sid 158 through 164 or (resid 165 and (name N or name CA or name C or name O or \ name CB )) or resid 166 or (resid 167 through 168 and (name N or name CA or name \ C or name O or name CB )) or resid 169 through 182 or (resid 183 and (name N or \ name CA or name C or name O or name CB )) or resid 184 through 188 or (resid 18 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 190 through \ 195 or (resid 196 through 197 and (name N or name CA or name C or name O or name \ CB )) or resid 198 through 239 or (resid 240 through 242 and (name N or name CA \ or name C or name O or name CB )) or resid 243 through 275 or (resid 276 throug \ h 277 and (name N or name CA or name C or name O or name CB )) or resid 278 thro \ ugh 293 or (resid 294 through 295 and (name N or name CA or name C or name O or \ name CB )) or resid 296 through 307 or (resid 308 and (name N or name CA or name \ C or name O or name CB )) or resid 309 through 316 or (resid 317 through 318 an \ d (name N or name CA or name C or name O or name CB )) or resid 319 through 322 \ or (resid 323 and (name N or name CA or name C or name O or name CB )) or resid \ 324 through 354 or (resid 355 through 357 and (name N or name CA or name C or na \ me O or name CB )) or resid 358 through 382 or (resid 383 through 384 and (name \ N or name CA or name C or name O or name CB )) or resid 385 through 386 or (resi \ d 387 and (name N or name CA or name C or name O or name CB )) or resid 388 thro \ ugh 392 or (resid 393 and (name N or name CA or name C or name O or name CB )) o \ r resid 394 through 397 or (resid 398 and (name N or name CA or name C or name O \ or name CB )) or resid 399 through 400 or (resid 401 and (name N or name CA or \ name C or name O or name CB )) or resid 402 through 405 or (resid 413 through 42 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 421 through \ 423 or (resid 424 and (name N or name CA or name C or name O or name CB )) or re \ sid 425 through 427 or (resid 428 and (name N or name CA or name C or name O or \ name CB )) or resid 429 through 431 or (resid 432 and (name N or name CA or name \ C or name O or name CB )) or resid 433 or (resid 434 and (name N or name CA or \ name C or name O or name CB )) or resid 435 through 440 or (resid 441 through 44 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 443 through \ 458 or (resid 459 and (name N or name CA or name C or name O or name CB )) or re \ sid 460 through 461 or (resid 462 and (name N or name CA or name C or name O or \ name CB )) or resid 463 through 464 or (resid 465 through 467 and (name N or nam \ e CA or name C or name O or name CB )) or resid 468 through 473 or (resid 474 th \ rough 475 and (name N or name CA or name C or name O or name CB )) or resid 476 \ through 479 or (resid 480 and (name N or name CA or name C or name O or name CB \ )) or resid 481 or (resid 482 and (name N or name CA or name C or name O or name \ CB )) or resid 483 or (resid 484 and (name N or name CA or name C or name O or \ name CB )) or resid 485 through 486 or (resid 487 through 488 and (name N or nam \ e CA or name C or name O or name CB )) or resid 489 or (resid 490 and (name N or \ name CA or name C or name O or name CB )) or resid 491 through 492 or (resid 49 \ 3 through 497 and (name N or name CA or name C or name O or name CB )) or resid \ 498 through 499 or (resid 500 and (name N or name CA or name C or name O or name \ CB )) or resid 501 through 601)) } ncs_group { reference = (chain 'D' and (resid 10 through 25 or (resid 26 through 27 and (name N or name \ CA or name C or name O or name CB )) or resid 28 or (resid 29 and (name N or nam \ e CA or name C or name O or name CB )) or resid 30 through 42 or (resid 43 and ( \ name N or name CA or name C or name O or name CB )) or resid 44 through 100 or ( \ resid 101 and (name N or name CA or name C or name O or name CB )) or resid 102 \ through 134 or (resid 135 and (name N or name CA or name C or name O or name CB \ )) or resid 136 through 138 or (resid 139 and (name N or name CA or name C or na \ me O or name CB )) or resid 140 through 162 or (resid 163 and (name N or name CA \ or name C or name O or name CB )) or resid 164 through 168 or (resid 169 and (n \ ame N or name CA or name C or name O or name CB )) or resid 170 through 188 or ( \ resid 189 and (name N or name CA or name C or name O or name CB )) or resid 190 \ through 192 or (resid 193 and (name N or name CA or name C or name O or name CB \ )) or resid 194 through 207 or (resid 208 through 210 and (name N or name CA or \ name C or name O or name CB )) or resid 211 or (resid 212 and (name N or name CA \ or name C or name O or name CB )) or resid 213 through 221 or (resid 222 and (n \ ame N or name CA or name C or name O or name CB )) or resid 223 through 252 or ( \ resid 253 and (name N or name CA or name C or name O or name CB )) or resid 254 \ through 255 or (resid 256 and (name N or name CA or name C or name O or name CB \ )) or resid 257 through 262 or (resid 263 through 264 and (name N or name CA or \ name C or name O or name CB )) or resid 265 through 266 or (resid 267 and (name \ N or name CA or name C or name O or name CB )) or resid 268 through 293 or (resi \ d 294 and (name N or name CA or name C or name O or name CB )) or resid 295 thro \ ugh 300 or (resid 301 and (name N or name CA or name C or name O or name CB )) o \ r resid 302 through 314 or (resid 315 and (name N or name CA or name C or name O \ or name CB )) or resid 316 through 336 or (resid 337 and (name N or name CA or \ name C or name O or name CB )) or resid 338 through 355 or (resid 356 and (name \ N or name CA or name C or name O or name CB )) or resid 357 through 365 or (resi \ d 366 and (name N or name CA or name C or name O or name CB )) or resid 367 thro \ ugh 385 or (resid 386 through 391 and (name N or name CA or name C or name O or \ name CB )) or (resid 392 through 402 and (name N or name CA or name C or name O \ or name CB )) or resid 403 through 404 or (resid 405 and (name N or name CA or n \ ame C or name O or name CB )) or resid 406 through 407 or (resid 408 through 409 \ and (name N or name CA or name C or name O or name CB )) or resid 410 through 4 \ 15 or (resid 416 and (name N or name CA or name C or name O or name CB )) or res \ id 417 through 429 or (resid 430 and (name N or name CA or name C or name O or n \ ame CB )) or resid 431 through 441 or (resid 442 through 443 and (name N or name \ CA or name C or name O or name CB )) or resid 444 through 451 or (resid 452 and \ (name N or name CA or name C or name O or name CB )) or resid 453 through 457 o \ r (resid 458 through 459 and (name N or name CA or name C or name O or name CB ) \ ) or resid 460 through 463 or (resid 464 through 465 and (name N or name CA or n \ ame C or name O or name CB )) or resid 466 through 471 or (resid 472 through 474 \ and (name N or name CA or name C or name O or name CB )))) selection = (chain 'E' and (resid 10 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 55 or (resid 56 and (name N or nam \ e CA or name C or name O or name CB )) or resid 57 through 64 or (resid 65 and ( \ name N or name CA or name C or name O or name CB )) or resid 66 through 89 or (r \ esid 90 and (name N or name CA or name C or name O or name CB )) or resid 91 thr \ ough 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or \ resid 98 through 112 or (resid 113 and (name N or name CA or name C or name O o \ r name CB )) or resid 114 through 162 or (resid 163 and (name N or name CA or na \ me C or name O or name CB )) or resid 164 through 184 or (resid 185 and (name N \ or name CA or name C or name O or name CB )) or resid 186 through 188 or (resid \ 189 and (name N or name CA or name C or name O or name CB )) or resid 190 throug \ h 192 or (resid 193 and (name N or name CA or name C or name O or name CB )) or \ resid 194 through 207 or (resid 208 through 210 and (name N or name CA or name C \ or name O or name CB )) or resid 211 through 221 or (resid 222 and (name N or n \ ame CA or name C or name O or name CB )) or resid 223 or (resid 224 and (name N \ or name CA or name C or name O or name CB )) or resid 225 through 244 or (resid \ 245 through 247 and (name N or name CA or name C or name O or name CB )) or resi \ d 248 through 252 or (resid 253 and (name N or name CA or name C or name O or na \ me CB )) or resid 254 through 255 or (resid 256 and (name N or name CA or name C \ or name O or name CB )) or resid 257 through 266 or (resid 267 and (name N or n \ ame CA or name C or name O or name CB )) or resid 268 through 299 or (resid 300 \ through 301 and (name N or name CA or name C or name O or name CB )) or resid 30 \ 2 through 348 or (resid 349 and (name N or name CA or name C or name O or name C \ B )) or resid 350 or (resid 351 through 352 and (name N or name CA or name C or \ name O or name CB )) or resid 353 through 381 or (resid 382 and (name N or name \ CA or name C or name O or name CB )) or resid 383 or (resid 384 through 391 and \ (name N or name CA or name C or name O or name CB )) or (resid 392 through 402 a \ nd (name N or name CA or name C or name O or name CB )) or resid 403 through 447 \ or (resid 448 and (name N or name CA or name C or name O or name CB )) or resid \ 449 through 464 or (resid 465 and (name N or name CA or name C or name O or nam \ e CB )) or resid 466 through 474)) selection = (chain 'F' and (resid 10 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 or (resid 40 and (name N or name CA or nam \ e C or name O or name CB )) or resid 41 through 55 or (resid 56 and (name N or n \ ame CA or name C or name O or name CB )) or resid 57 through 64 or (resid 65 and \ (name N or name CA or name C or name O or name CB )) or resid 66 through 67 or \ (resid 68 and (name N or name CA or name C or name O or name CB )) or resid 69 t \ hrough 89 or (resid 90 and (name N or name CA or name C or name O or name CB )) \ or resid 91 through 96 or (resid 97 and (name N or name CA or name C or name O o \ r name CB )) or resid 98 through 100 or (resid 101 and (name N or name CA or nam \ e C or name O or name CB )) or resid 102 through 104 or (resid 105 and (name N o \ r name CA or name C or name O or name CB )) or resid 106 through 112 or (resid 1 \ 13 and (name N or name CA or name C or name O or name CB )) or resid 114 through \ 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or r \ esid 133 through 134 or (resid 135 and (name N or name CA or name C or name O or \ name CB )) or resid 136 through 138 or (resid 139 and (name N or name CA or nam \ e C or name O or name CB )) or resid 140 through 141 or (resid 142 and (name N o \ r name CA or name C or name O or name CB )) or resid 143 through 177 or (resid 1 \ 78 and (name N or name CA or name C or name O or name CB )) or resid 179 through \ 184 or (resid 185 and (name N or name CA or name C or name O or name CB )) or r \ esid 186 through 211 or (resid 212 and (name N or name CA or name C or name O or \ name CB )) or resid 213 through 223 or (resid 224 and (name N or name CA or nam \ e C or name O or name CB )) or resid 225 through 244 or (resid 245 through 247 a \ nd (name N or name CA or name C or name O or name CB )) or resid 248 through 262 \ or (resid 263 through 264 and (name N or name CA or name C or name O or name CB \ )) or resid 265 through 299 or (resid 300 through 301 and (name N or name CA or \ name C or name O or name CB )) or resid 302 through 314 or (resid 315 and (name \ N or name CA or name C or name O or name CB )) or resid 316 through 336 or (res \ id 337 and (name N or name CA or name C or name O or name CB )) or resid 338 thr \ ough 348 or (resid 349 and (name N or name CA or name C or name O or name CB )) \ or resid 350 or (resid 351 through 352 and (name N or name CA or name C or name \ O or name CB )) or resid 353 through 355 or (resid 356 and (name N or name CA or \ name C or name O or name CB )) or resid 357 through 365 or (resid 366 and (name \ N or name CA or name C or name O or name CB )) or resid 367 through 381 or (res \ id 382 and (name N or name CA or name C or name O or name CB )) or resid 383 or \ (resid 384 through 391 and (name N or name CA or name C or name O or name CB )) \ or resid 392 or (resid 393 through 402 and (name N or name CA or name C or name \ O or name CB )) or resid 403 through 407 or (resid 408 through 409 and (name N o \ r name CA or name C or name O or name CB )) or resid 410 through 415 or (resid 4 \ 16 and (name N or name CA or name C or name O or name CB )) or resid 417 through \ 429 or (resid 430 and (name N or name CA or name C or name O or name CB )) or r \ esid 431 through 434 or (resid 435 through 436 and (name N or name CA or name C \ or name O or name CB )) or resid 437 through 441 or (resid 442 through 443 and ( \ name N or name CA or name C or name O or name CB )) or resid 444 through 445 or \ (resid 446 and (name N or name CA or name C or name O or name CB )) or resid 447 \ or (resid 448 and (name N or name CA or name C or name O or name CB )) or resid \ 449 through 451 or (resid 452 and (name N or name CA or name C or name O or nam \ e CB )) or resid 453 through 457 or (resid 458 through 459 and (name N or name C \ A or name C or name O or name CB )) or resid 460 through 472 or (resid 473 throu \ gh 474 and (name N or name CA or name C or name O or name CB )))) } 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 group one per residue 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: 1.630 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: 0.030 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.960 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 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: 0.020 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 0.083 22848 Z= 0.136 Angle : 0.639 7.762 31119 Z= 0.353 Chirality : 0.046 0.322 3760 Planarity : 0.004 0.043 4009 Dihedral : 13.065 89.950 8191 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.15), residues: 3077 helix: 0.44 (0.14), residues: 1212 sheet: 0.07 (0.23), residues: 481 loop : 0.05 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 260 TYR 0.022 0.002 TYR D 458 PHE 0.023 0.002 PHE A 506 TRP 0.016 0.003 TRP A 258 HIS 0.008 0.001 HIS E 367 Details of bonding type rmsd covalent geometry : bond 0.00277 (22848) covalent geometry : angle 0.63941 (31119) hydrogen bonds : bond 0.15155 ( 1187) hydrogen bonds : angle 7.16612 ( 3411) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 961 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 961 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ARG cc_start: 0.9084 (mtt180) cc_final: 0.8248 (mtt180) REVERT: A 177 LYS cc_start: 0.9312 (mtmm) cc_final: 0.8992 (mtmm) REVERT: A 187 ASN cc_start: 0.8887 (t0) cc_final: 0.8640 (t0) REVERT: A 191 TRP cc_start: 0.8346 (m-90) cc_final: 0.7881 (m100) REVERT: A 199 LYS cc_start: 0.8234 (mmtt) cc_final: 0.8026 (mmtm) REVERT: A 299 ASP cc_start: 0.8725 (p0) cc_final: 0.8495 (p0) REVERT: A 318 GLU cc_start: 0.8070 (tp30) cc_final: 0.7868 (tp30) REVERT: A 331 THR cc_start: 0.8967 (m) cc_final: 0.8391 (t) REVERT: A 394 LEU cc_start: 0.9043 (mm) cc_final: 0.8524 (mp) REVERT: A 448 TYR cc_start: 0.8540 (t80) cc_final: 0.7899 (t80) REVERT: B 47 ASN cc_start: 0.8913 (m-40) cc_final: 0.8677 (m110) REVERT: B 77 LEU cc_start: 0.8942 (mt) cc_final: 0.8712 (mp) REVERT: B 123 ILE cc_start: 0.8453 (mm) cc_final: 0.8164 (mm) REVERT: B 124 ASP cc_start: 0.7239 (m-30) cc_final: 0.6862 (t0) REVERT: B 149 GLN cc_start: 0.8685 (mm-40) cc_final: 0.8401 (mm-40) REVERT: B 189 LYS cc_start: 0.8837 (ttpt) cc_final: 0.8403 (ttpp) REVERT: B 220 GLN cc_start: 0.8178 (tp40) cc_final: 0.7965 (tp40) REVERT: B 361 LYS cc_start: 0.7997 (tttt) cc_final: 0.7746 (ttpp) REVERT: B 431 LYS cc_start: 0.8409 (mttt) cc_final: 0.7901 (mttp) REVERT: B 487 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7418 (tm-30) REVERT: C 48 ASN cc_start: 0.8834 (m-40) cc_final: 0.8269 (m-40) REVERT: C 56 GLU cc_start: 0.8176 (tt0) cc_final: 0.7698 (tt0) REVERT: C 83 LEU cc_start: 0.8289 (pt) cc_final: 0.7865 (mt) REVERT: C 108 ARG cc_start: 0.8097 (mmm-85) cc_final: 0.7894 (mmm-85) REVERT: C 129 SER cc_start: 0.8799 (t) cc_final: 0.8543 (t) REVERT: C 139 LEU cc_start: 0.8370 (tp) cc_final: 0.8047 (tp) REVERT: C 148 VAL cc_start: 0.9114 (t) cc_final: 0.8776 (p) REVERT: C 149 GLN cc_start: 0.7897 (mt0) cc_final: 0.7672 (mt0) REVERT: C 185 ILE cc_start: 0.8956 (mt) cc_final: 0.8717 (mt) REVERT: C 189 LYS cc_start: 0.8746 (tttt) cc_final: 0.8370 (tttt) REVERT: C 213 SER cc_start: 0.9321 (p) cc_final: 0.9115 (t) REVERT: C 243 PRO cc_start: 0.9529 (Cg_exo) cc_final: 0.9288 (Cg_endo) REVERT: C 294 GLU cc_start: 0.8280 (mt-10) cc_final: 0.8038 (mt-10) REVERT: C 301 PHE cc_start: 0.8831 (t80) cc_final: 0.8243 (t80) REVERT: C 305 SER cc_start: 0.9168 (m) cc_final: 0.8719 (m) REVERT: C 309 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7682 (mm-30) REVERT: C 361 LYS cc_start: 0.8717 (pttt) cc_final: 0.7998 (tptt) REVERT: C 368 ASN cc_start: 0.8465 (t0) cc_final: 0.8192 (t0) REVERT: C 383 LYS cc_start: 0.8788 (tttt) cc_final: 0.8374 (tppt) REVERT: C 395 PHE cc_start: 0.7412 (m-80) cc_final: 0.6604 (m-80) REVERT: D 136 THR cc_start: 0.9027 (p) cc_final: 0.8673 (p) REVERT: D 138 ILE cc_start: 0.9184 (mp) cc_final: 0.8850 (mp) REVERT: D 147 TYR cc_start: 0.8071 (m-10) cc_final: 0.7813 (m-10) REVERT: D 190 ARG cc_start: 0.8180 (mtt90) cc_final: 0.7907 (mtt90) REVERT: D 208 ASN cc_start: 0.8816 (t0) cc_final: 0.8437 (t0) REVERT: D 263 GLN cc_start: 0.7853 (tt0) cc_final: 0.7512 (tt0) REVERT: D 295 ARG cc_start: 0.8959 (mtp85) cc_final: 0.8715 (mtp180) REVERT: D 305 THR cc_start: 0.9406 (m) cc_final: 0.9191 (p) REVERT: D 340 SER cc_start: 0.8173 (p) cc_final: 0.7901 (p) REVERT: D 355 SER cc_start: 0.8824 (t) cc_final: 0.8363 (p) REVERT: D 406 ARG cc_start: 0.6931 (mtt180) cc_final: 0.5680 (ttm-80) REVERT: D 418 PHE cc_start: 0.8969 (m-10) cc_final: 0.8552 (m-80) REVERT: E 16 VAL cc_start: 0.9150 (t) cc_final: 0.8933 (p) REVERT: E 75 LYS cc_start: 0.8789 (mtpt) cc_final: 0.8488 (mtmm) REVERT: E 115 LYS cc_start: 0.8787 (mmmt) cc_final: 0.8444 (mmmm) REVERT: E 126 GLU cc_start: 0.7610 (tt0) cc_final: 0.7019 (pm20) REVERT: E 147 TYR cc_start: 0.8379 (m-10) cc_final: 0.8176 (m-80) REVERT: E 165 VAL cc_start: 0.8725 (t) cc_final: 0.8518 (t) REVERT: E 172 ASN cc_start: 0.7871 (t0) cc_final: 0.7603 (t0) REVERT: E 208 ASN cc_start: 0.7762 (t0) cc_final: 0.7418 (t0) REVERT: E 218 VAL cc_start: 0.9197 (t) cc_final: 0.8865 (m) REVERT: E 231 ARG cc_start: 0.8718 (mmt-90) cc_final: 0.7967 (mmt90) REVERT: E 305 THR cc_start: 0.9299 (m) cc_final: 0.9058 (p) REVERT: F 40 LYS cc_start: 0.9230 (ttmt) cc_final: 0.8970 (ttmm) REVERT: F 90 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7586 (mp0) REVERT: F 95 ILE cc_start: 0.8971 (mt) cc_final: 0.8685 (mt) REVERT: F 111 SER cc_start: 0.7926 (t) cc_final: 0.6406 (t) REVERT: F 123 SER cc_start: 0.8847 (m) cc_final: 0.8629 (p) REVERT: F 149 ARG cc_start: 0.8132 (mmm-85) cc_final: 0.7897 (mtp-110) REVERT: F 174 ILE cc_start: 0.8494 (mt) cc_final: 0.8231 (mt) REVERT: F 201 MET cc_start: 0.8590 (mtt) cc_final: 0.8220 (tpp) REVERT: F 221 GLN cc_start: 0.8423 (mm110) cc_final: 0.7201 (mm110) REVERT: F 224 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7259 (mt-10) REVERT: F 250 ASP cc_start: 0.8283 (m-30) cc_final: 0.7996 (m-30) REVERT: F 295 ARG cc_start: 0.8513 (mmm-85) cc_final: 0.8115 (ttm170) REVERT: F 352 ASP cc_start: 0.8972 (t0) cc_final: 0.8583 (t0) REVERT: F 372 SER cc_start: 0.9075 (m) cc_final: 0.8858 (t) REVERT: G 12 SER cc_start: 0.6802 (t) cc_final: 0.6240 (m) REVERT: G 145 LEU cc_start: 0.6609 (mm) cc_final: 0.5992 (mm) REVERT: G 222 MET cc_start: 0.7744 (mmt) cc_final: 0.7464 (mmm) outliers start: 0 outliers final: 0 residues processed: 961 average time/residue: 0.1498 time to fit residues: 221.7070 Evaluate side-chains 748 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 748 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 GLN A 452 ASN A 454 HIS B 193 ASN ** B 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN C 47 ASN C 225 HIS C 276 GLN ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN D 195 ASN F 118 HIS G 88 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.131662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.112324 restraints weight = 35772.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.115675 restraints weight = 19618.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.117940 restraints weight = 12278.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.119462 restraints weight = 8460.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.120393 restraints weight = 6324.810| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 22848 Z= 0.230 Angle : 0.674 7.623 31119 Z= 0.355 Chirality : 0.048 0.263 3760 Planarity : 0.005 0.050 4009 Dihedral : 8.746 89.746 3488 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.93 % Allowed : 11.84 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.15), residues: 3077 helix: 0.89 (0.15), residues: 1226 sheet: -0.01 (0.22), residues: 488 loop : -0.01 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 173 TYR 0.024 0.002 TYR F 198 PHE 0.023 0.002 PHE B 466 TRP 0.011 0.002 TRP B 191 HIS 0.006 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00527 (22848) covalent geometry : angle 0.67438 (31119) hydrogen bonds : bond 0.04670 ( 1187) hydrogen bonds : angle 5.47340 ( 3411) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 759 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.7781 (t0) cc_final: 0.7031 (p0) REVERT: A 53 GLU cc_start: 0.8727 (tt0) cc_final: 0.8434 (tt0) REVERT: A 139 LEU cc_start: 0.9013 (tp) cc_final: 0.8733 (tt) REVERT: A 149 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8441 (mt0) REVERT: A 163 ARG cc_start: 0.9047 (mtt180) cc_final: 0.8694 (mtt180) REVERT: A 191 TRP cc_start: 0.8288 (m-90) cc_final: 0.7964 (m100) REVERT: A 200 LYS cc_start: 0.8775 (mttt) cc_final: 0.8498 (tppt) REVERT: A 206 VAL cc_start: 0.8886 (t) cc_final: 0.8640 (m) REVERT: A 221 THR cc_start: 0.8900 (OUTLIER) cc_final: 0.8485 (p) REVERT: A 318 GLU cc_start: 0.8098 (tp30) cc_final: 0.7834 (tp30) REVERT: A 355 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7491 (mt-10) REVERT: A 394 LEU cc_start: 0.9102 (mm) cc_final: 0.8803 (mp) REVERT: A 396 LEU cc_start: 0.8973 (mt) cc_final: 0.8750 (mm) REVERT: A 448 TYR cc_start: 0.8392 (t80) cc_final: 0.7765 (t80) REVERT: A 478 HIS cc_start: 0.6227 (m-70) cc_final: 0.6017 (m-70) REVERT: B 124 ASP cc_start: 0.7377 (m-30) cc_final: 0.7034 (t0) REVERT: B 187 ASN cc_start: 0.8652 (t0) cc_final: 0.8376 (t0) REVERT: B 220 GLN cc_start: 0.8344 (tp40) cc_final: 0.7944 (tp40) REVERT: B 257 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8072 (mt-10) REVERT: B 288 ARG cc_start: 0.8208 (ttm110) cc_final: 0.7820 (ttm110) REVERT: B 361 LYS cc_start: 0.8226 (tttt) cc_final: 0.7968 (mtmt) REVERT: B 428 GLN cc_start: 0.8239 (mm110) cc_final: 0.8008 (mm-40) REVERT: B 487 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7456 (tm-30) REVERT: C 43 VAL cc_start: 0.9064 (t) cc_final: 0.8760 (p) REVERT: C 48 ASN cc_start: 0.9002 (m-40) cc_final: 0.8634 (m-40) REVERT: C 83 LEU cc_start: 0.8220 (pt) cc_final: 0.8019 (mt) REVERT: C 108 ARG cc_start: 0.8152 (mmm-85) cc_final: 0.7943 (mmm-85) REVERT: C 139 LEU cc_start: 0.8507 (tp) cc_final: 0.8286 (tp) REVERT: C 148 VAL cc_start: 0.9110 (t) cc_final: 0.8618 (p) REVERT: C 191 TRP cc_start: 0.8602 (m-90) cc_final: 0.8401 (m-90) REVERT: C 192 ASN cc_start: 0.8348 (m-40) cc_final: 0.8100 (m-40) REVERT: C 213 SER cc_start: 0.9277 (p) cc_final: 0.9064 (t) REVERT: C 243 PRO cc_start: 0.9623 (Cg_exo) cc_final: 0.9242 (Cg_endo) REVERT: C 294 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7981 (mt-10) REVERT: C 301 PHE cc_start: 0.8882 (t80) cc_final: 0.8637 (t80) REVERT: C 329 ILE cc_start: 0.9042 (mm) cc_final: 0.8795 (mm) REVERT: C 361 LYS cc_start: 0.8604 (pttt) cc_final: 0.8172 (tptt) REVERT: C 383 LYS cc_start: 0.8739 (tttt) cc_final: 0.8506 (ttmm) REVERT: C 393 LYS cc_start: 0.8089 (tttt) cc_final: 0.7866 (ttpt) REVERT: C 395 PHE cc_start: 0.7487 (m-80) cc_final: 0.6755 (m-80) REVERT: C 441 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7497 (mt-10) REVERT: D 112 LYS cc_start: 0.8650 (mmtt) cc_final: 0.8377 (mmtm) REVERT: D 136 THR cc_start: 0.9149 (p) cc_final: 0.8805 (p) REVERT: D 138 ILE cc_start: 0.9229 (mp) cc_final: 0.9026 (mp) REVERT: D 153 ILE cc_start: 0.8801 (mp) cc_final: 0.8495 (mp) REVERT: D 182 SER cc_start: 0.9431 (m) cc_final: 0.9037 (t) REVERT: D 190 ARG cc_start: 0.8228 (mtt90) cc_final: 0.7967 (mtt90) REVERT: D 208 ASN cc_start: 0.8769 (t0) cc_final: 0.8329 (t0) REVERT: D 252 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.8020 (mp) REVERT: D 284 THR cc_start: 0.8758 (p) cc_final: 0.8144 (m) REVERT: D 288 ASP cc_start: 0.7860 (m-30) cc_final: 0.7326 (m-30) REVERT: E 75 LYS cc_start: 0.8906 (mtpt) cc_final: 0.8398 (mtmm) REVERT: E 89 ARG cc_start: 0.7527 (mtp85) cc_final: 0.7274 (mtp85) REVERT: E 110 LYS cc_start: 0.8573 (ptmm) cc_final: 0.8359 (ptmt) REVERT: E 115 LYS cc_start: 0.9003 (mmmt) cc_final: 0.8758 (mmmt) REVERT: E 141 VAL cc_start: 0.8565 (t) cc_final: 0.8290 (p) REVERT: E 208 ASN cc_start: 0.7792 (t0) cc_final: 0.7443 (t0) REVERT: E 231 ARG cc_start: 0.8749 (mmt-90) cc_final: 0.8213 (mmt90) REVERT: E 368 TYR cc_start: 0.7275 (t80) cc_final: 0.6968 (t80) REVERT: E 433 ARG cc_start: 0.7738 (mmm160) cc_final: 0.6799 (mmp-170) REVERT: F 40 LYS cc_start: 0.9300 (ttmt) cc_final: 0.9000 (ttmm) REVERT: F 77 LEU cc_start: 0.8428 (tp) cc_final: 0.8225 (mt) REVERT: F 95 ILE cc_start: 0.9023 (mt) cc_final: 0.8738 (mt) REVERT: F 149 ARG cc_start: 0.8166 (mmm-85) cc_final: 0.7775 (ttm170) REVERT: F 372 SER cc_start: 0.9165 (m) cc_final: 0.8909 (t) REVERT: F 393 MET cc_start: 0.7478 (tmm) cc_final: 0.7047 (tmm) REVERT: G 12 SER cc_start: 0.6976 (t) cc_final: 0.6455 (m) REVERT: G 145 LEU cc_start: 0.6692 (mm) cc_final: 0.6106 (mm) REVERT: G 234 ARG cc_start: 0.6591 (ttt180) cc_final: 0.6099 (ttt180) outliers start: 86 outliers final: 60 residues processed: 793 average time/residue: 0.1458 time to fit residues: 181.4557 Evaluate side-chains 747 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 684 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 488 LYS Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain E residue 359 ASP Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 99 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 49 optimal weight: 2.9990 chunk 256 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 301 optimal weight: 4.9990 chunk 123 optimal weight: 0.6980 chunk 75 optimal weight: 7.9990 chunk 271 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 304 HIS B 265 HIS C 47 ASN D 35 ASN D 195 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.132284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.112923 restraints weight = 35625.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.116295 restraints weight = 19405.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.118552 restraints weight = 12079.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.120039 restraints weight = 8276.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.121083 restraints weight = 6227.247| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22848 Z= 0.186 Angle : 0.613 8.521 31119 Z= 0.319 Chirality : 0.046 0.254 3760 Planarity : 0.005 0.050 4009 Dihedral : 8.320 87.004 3488 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.62 % Allowed : 14.77 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.15), residues: 3077 helix: 1.14 (0.15), residues: 1232 sheet: 0.08 (0.23), residues: 487 loop : 0.03 (0.18), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 114 TYR 0.023 0.002 TYR D 147 PHE 0.020 0.002 PHE F 441 TRP 0.010 0.002 TRP C 258 HIS 0.005 0.001 HIS C 454 Details of bonding type rmsd covalent geometry : bond 0.00430 (22848) covalent geometry : angle 0.61261 (31119) hydrogen bonds : bond 0.04166 ( 1187) hydrogen bonds : angle 5.14529 ( 3411) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 709 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.7926 (t0) cc_final: 0.7134 (p0) REVERT: A 139 LEU cc_start: 0.8933 (tp) cc_final: 0.8610 (tt) REVERT: A 149 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8375 (mt0) REVERT: A 156 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.8031 (t0) REVERT: A 163 ARG cc_start: 0.9048 (mtt180) cc_final: 0.8659 (mtt180) REVERT: A 173 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7641 (mtm110) REVERT: A 191 TRP cc_start: 0.8382 (m-90) cc_final: 0.8030 (m100) REVERT: A 206 VAL cc_start: 0.8878 (OUTLIER) cc_final: 0.8604 (m) REVERT: A 221 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8432 (p) REVERT: A 330 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8303 (mt-10) REVERT: A 355 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7556 (mt-10) REVERT: A 394 LEU cc_start: 0.9104 (mm) cc_final: 0.8799 (mp) REVERT: A 412 LEU cc_start: 0.7510 (mt) cc_final: 0.7277 (mt) REVERT: B 124 ASP cc_start: 0.7443 (m-30) cc_final: 0.7025 (t0) REVERT: B 187 ASN cc_start: 0.8610 (t0) cc_final: 0.8302 (t0) REVERT: B 219 VAL cc_start: 0.8880 (t) cc_final: 0.8528 (p) REVERT: B 220 GLN cc_start: 0.8365 (tp40) cc_final: 0.7767 (tp40) REVERT: B 288 ARG cc_start: 0.8254 (ttm110) cc_final: 0.7885 (ttm110) REVERT: B 361 LYS cc_start: 0.8139 (tttt) cc_final: 0.7916 (mtmt) REVERT: B 487 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7322 (tm-30) REVERT: B 490 GLU cc_start: 0.8616 (mp0) cc_final: 0.8316 (mp0) REVERT: B 491 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7892 (mt) REVERT: C 83 LEU cc_start: 0.8381 (pt) cc_final: 0.8123 (mt) REVERT: C 118 ASP cc_start: 0.7629 (p0) cc_final: 0.7191 (p0) REVERT: C 148 VAL cc_start: 0.9046 (t) cc_final: 0.8547 (p) REVERT: C 189 LYS cc_start: 0.8535 (tttt) cc_final: 0.8216 (tttt) REVERT: C 192 ASN cc_start: 0.8205 (m-40) cc_final: 0.7875 (m-40) REVERT: C 243 PRO cc_start: 0.9600 (Cg_exo) cc_final: 0.9310 (Cg_endo) REVERT: C 301 PHE cc_start: 0.8978 (t80) cc_final: 0.8583 (t80) REVERT: C 329 ILE cc_start: 0.9128 (mm) cc_final: 0.8901 (mm) REVERT: C 361 LYS cc_start: 0.8567 (pttt) cc_final: 0.8043 (tptt) REVERT: C 383 LYS cc_start: 0.8743 (tttt) cc_final: 0.8493 (ttmm) REVERT: C 393 LYS cc_start: 0.8093 (tttt) cc_final: 0.7840 (ttpt) REVERT: C 395 PHE cc_start: 0.7474 (m-80) cc_final: 0.6706 (m-80) REVERT: C 448 TYR cc_start: 0.7759 (t80) cc_final: 0.7289 (t80) REVERT: D 112 LYS cc_start: 0.8546 (mmtt) cc_final: 0.8341 (mmtm) REVERT: D 182 SER cc_start: 0.9404 (m) cc_final: 0.9145 (t) REVERT: D 208 ASN cc_start: 0.8759 (t0) cc_final: 0.8269 (t0) REVERT: D 284 THR cc_start: 0.8695 (p) cc_final: 0.8303 (p) REVERT: D 373 LYS cc_start: 0.8015 (mttt) cc_final: 0.7672 (mttp) REVERT: E 56 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7287 (tt0) REVERT: E 75 LYS cc_start: 0.8858 (mtpt) cc_final: 0.8405 (mtmm) REVERT: E 89 ARG cc_start: 0.7507 (mtp85) cc_final: 0.7280 (mtp85) REVERT: E 141 VAL cc_start: 0.8310 (t) cc_final: 0.8099 (p) REVERT: E 172 ASN cc_start: 0.7743 (t0) cc_final: 0.7508 (t0) REVERT: E 208 ASN cc_start: 0.7756 (t0) cc_final: 0.7271 (t0) REVERT: E 231 ARG cc_start: 0.8739 (mmt-90) cc_final: 0.8083 (mmt90) REVERT: F 40 LYS cc_start: 0.9281 (ttmt) cc_final: 0.9065 (ttmm) REVERT: F 49 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7588 (mt-10) REVERT: F 95 ILE cc_start: 0.9013 (mt) cc_final: 0.8707 (mt) REVERT: F 149 ARG cc_start: 0.8167 (mmm-85) cc_final: 0.7823 (tpp-160) REVERT: F 199 ARG cc_start: 0.7873 (ttp80) cc_final: 0.7496 (ptm160) REVERT: F 305 THR cc_start: 0.8888 (m) cc_final: 0.8626 (p) REVERT: F 316 ASP cc_start: 0.8563 (t0) cc_final: 0.8067 (t0) REVERT: F 385 GLN cc_start: 0.8522 (pp30) cc_final: 0.8016 (pm20) REVERT: F 386 ASP cc_start: 0.7800 (t70) cc_final: 0.7391 (m-30) REVERT: F 393 MET cc_start: 0.7337 (tmm) cc_final: 0.6918 (tmm) REVERT: F 401 LYS cc_start: 0.8466 (tttt) cc_final: 0.8102 (tttm) REVERT: G 12 SER cc_start: 0.7108 (t) cc_final: 0.6491 (m) REVERT: G 145 LEU cc_start: 0.6719 (mm) cc_final: 0.6147 (mm) REVERT: G 234 ARG cc_start: 0.6464 (ttt180) cc_final: 0.5934 (ttt180) outliers start: 101 outliers final: 73 residues processed: 746 average time/residue: 0.1473 time to fit residues: 173.6059 Evaluate side-chains 756 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 675 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain E residue 359 ASP Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 218 MET Chi-restraints excluded: chain G residue 241 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 68 optimal weight: 0.7980 chunk 26 optimal weight: 0.0980 chunk 180 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 221 optimal weight: 0.0570 chunk 11 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 247 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 217 optimal weight: 7.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 47 ASN C 343 ASN C 432 GLN ** C 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 HIS D 173 ASN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.134587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.115437 restraints weight = 35420.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.118826 restraints weight = 19152.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.121049 restraints weight = 11824.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.122563 restraints weight = 8066.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.123430 restraints weight = 6038.885| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 22848 Z= 0.134 Angle : 0.559 8.310 31119 Z= 0.291 Chirality : 0.044 0.267 3760 Planarity : 0.004 0.048 4009 Dihedral : 7.602 80.179 3488 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.12 % Allowed : 17.38 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.15), residues: 3077 helix: 1.35 (0.15), residues: 1247 sheet: 0.17 (0.23), residues: 484 loop : 0.07 (0.18), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 433 TYR 0.027 0.002 TYR D 147 PHE 0.015 0.001 PHE B 466 TRP 0.009 0.001 TRP C 258 HIS 0.004 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00308 (22848) covalent geometry : angle 0.55888 (31119) hydrogen bonds : bond 0.03630 ( 1187) hydrogen bonds : angle 4.89713 ( 3411) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 720 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8628 (tt0) cc_final: 0.8350 (tt0) REVERT: A 139 LEU cc_start: 0.8882 (tp) cc_final: 0.8509 (tt) REVERT: A 149 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8377 (mt0) REVERT: A 156 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.7873 (t0) REVERT: A 163 ARG cc_start: 0.8979 (mtt180) cc_final: 0.8564 (mtt180) REVERT: A 173 ARG cc_start: 0.8060 (mtm110) cc_final: 0.7428 (mtm110) REVERT: A 191 TRP cc_start: 0.8310 (m-90) cc_final: 0.8009 (m100) REVERT: A 287 LEU cc_start: 0.9151 (mt) cc_final: 0.8918 (mt) REVERT: A 304 HIS cc_start: 0.8663 (OUTLIER) cc_final: 0.6865 (m-70) REVERT: A 318 GLU cc_start: 0.7813 (tp30) cc_final: 0.7585 (tp30) REVERT: A 330 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8166 (mt-10) REVERT: A 349 ASP cc_start: 0.7815 (m-30) cc_final: 0.6974 (m-30) REVERT: A 355 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7527 (mt-10) REVERT: A 394 LEU cc_start: 0.9109 (mm) cc_final: 0.8816 (mp) REVERT: B 124 ASP cc_start: 0.7423 (m-30) cc_final: 0.7009 (t0) REVERT: B 219 VAL cc_start: 0.8813 (t) cc_final: 0.8518 (p) REVERT: B 361 LYS cc_start: 0.8076 (tttt) cc_final: 0.7842 (mtmt) REVERT: B 487 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7289 (tm-30) REVERT: B 491 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7894 (mt) REVERT: C 48 ASN cc_start: 0.8829 (m110) cc_final: 0.8404 (m110) REVERT: C 83 LEU cc_start: 0.8469 (pt) cc_final: 0.8138 (mt) REVERT: C 120 LYS cc_start: 0.8521 (mtmm) cc_final: 0.7539 (mtmm) REVERT: C 148 VAL cc_start: 0.8919 (t) cc_final: 0.8478 (p) REVERT: C 189 LYS cc_start: 0.8507 (tttt) cc_final: 0.8201 (tttt) REVERT: C 192 ASN cc_start: 0.8162 (m-40) cc_final: 0.7851 (m-40) REVERT: C 226 ASP cc_start: 0.8312 (t0) cc_final: 0.8029 (t0) REVERT: C 243 PRO cc_start: 0.9593 (Cg_exo) cc_final: 0.9317 (Cg_endo) REVERT: C 299 ASP cc_start: 0.8286 (p0) cc_final: 0.8069 (p0) REVERT: C 301 PHE cc_start: 0.8915 (t80) cc_final: 0.8368 (t80) REVERT: C 329 ILE cc_start: 0.9167 (mm) cc_final: 0.8946 (mm) REVERT: C 361 LYS cc_start: 0.8501 (pttt) cc_final: 0.8094 (tptt) REVERT: C 383 LYS cc_start: 0.8792 (tttt) cc_final: 0.8493 (ttmm) REVERT: C 393 LYS cc_start: 0.8082 (tttt) cc_final: 0.7855 (ttpt) REVERT: C 395 PHE cc_start: 0.7490 (m-80) cc_final: 0.6676 (m-80) REVERT: C 448 TYR cc_start: 0.7664 (t80) cc_final: 0.7375 (t80) REVERT: D 165 VAL cc_start: 0.9317 (OUTLIER) cc_final: 0.9107 (p) REVERT: D 182 SER cc_start: 0.9437 (m) cc_final: 0.9133 (t) REVERT: D 208 ASN cc_start: 0.8767 (t0) cc_final: 0.8338 (t0) REVERT: D 259 PHE cc_start: 0.8565 (t80) cc_final: 0.8361 (t80) REVERT: D 284 THR cc_start: 0.8718 (p) cc_final: 0.8192 (p) REVERT: D 373 LYS cc_start: 0.8035 (mttt) cc_final: 0.7811 (mmtp) REVERT: D 406 ARG cc_start: 0.6640 (mtt180) cc_final: 0.5892 (ttm-80) REVERT: E 72 ARG cc_start: 0.8968 (mtm-85) cc_final: 0.8617 (mtm-85) REVERT: E 75 LYS cc_start: 0.8718 (mtpt) cc_final: 0.8251 (mtmm) REVERT: E 89 ARG cc_start: 0.7487 (mtp85) cc_final: 0.7282 (mtp85) REVERT: E 104 ASP cc_start: 0.8519 (p0) cc_final: 0.8259 (p0) REVERT: E 127 GLN cc_start: 0.8798 (mm-40) cc_final: 0.7929 (mm-40) REVERT: E 141 VAL cc_start: 0.8492 (t) cc_final: 0.8237 (p) REVERT: E 171 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8232 (mp) REVERT: E 208 ASN cc_start: 0.7876 (t0) cc_final: 0.7511 (t0) REVERT: E 231 ARG cc_start: 0.8648 (mmt-90) cc_final: 0.8158 (mmt90) REVERT: E 411 GLN cc_start: 0.7511 (tm-30) cc_final: 0.7287 (tm-30) REVERT: E 433 ARG cc_start: 0.7430 (mmm160) cc_final: 0.6938 (mmp-170) REVERT: F 40 LYS cc_start: 0.9264 (ttmt) cc_final: 0.9050 (ttmm) REVERT: F 49 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7442 (mt-10) REVERT: F 95 ILE cc_start: 0.8961 (mt) cc_final: 0.8610 (mt) REVERT: F 149 ARG cc_start: 0.8266 (mmm-85) cc_final: 0.7846 (ttm170) REVERT: F 199 ARG cc_start: 0.7720 (ttp80) cc_final: 0.7389 (ptm160) REVERT: F 305 THR cc_start: 0.8949 (m) cc_final: 0.8743 (p) REVERT: F 385 GLN cc_start: 0.8492 (pp30) cc_final: 0.8151 (pm20) REVERT: F 386 ASP cc_start: 0.7746 (t70) cc_final: 0.7297 (m-30) REVERT: F 393 MET cc_start: 0.7396 (tmm) cc_final: 0.6992 (tmm) REVERT: F 401 LYS cc_start: 0.8443 (tttt) cc_final: 0.8132 (tttm) REVERT: F 406 ARG cc_start: 0.8170 (mtp85) cc_final: 0.7856 (mtp85) REVERT: G 12 SER cc_start: 0.7191 (t) cc_final: 0.6542 (m) REVERT: G 145 LEU cc_start: 0.6564 (mm) cc_final: 0.5938 (mm) REVERT: G 218 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.7785 (ttp) REVERT: G 222 MET cc_start: 0.8084 (mmm) cc_final: 0.7775 (mmm) REVERT: G 234 ARG cc_start: 0.6626 (ttt180) cc_final: 0.6236 (ttp-170) outliers start: 90 outliers final: 65 residues processed: 755 average time/residue: 0.1558 time to fit residues: 186.4579 Evaluate side-chains 751 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 678 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 360 TYR Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain E residue 359 ASP Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 218 MET Chi-restraints excluded: chain G residue 241 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 59 optimal weight: 5.9990 chunk 257 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 187 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 152 optimal weight: 0.9990 chunk 211 optimal weight: 0.7980 chunk 255 optimal weight: 0.0070 overall best weight: 1.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 47 ASN D 195 ASN G 265 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.133268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.114025 restraints weight = 35571.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.117354 restraints weight = 19280.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.119567 restraints weight = 11973.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.120989 restraints weight = 8244.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.122091 restraints weight = 6210.947| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22848 Z= 0.174 Angle : 0.581 9.179 31119 Z= 0.302 Chirality : 0.045 0.286 3760 Planarity : 0.004 0.047 4009 Dihedral : 7.622 80.066 3488 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 5.40 % Allowed : 19.02 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.15), residues: 3077 helix: 1.38 (0.15), residues: 1240 sheet: 0.11 (0.24), residues: 472 loop : 0.05 (0.18), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 260 TYR 0.020 0.002 TYR D 147 PHE 0.014 0.002 PHE F 441 TRP 0.008 0.002 TRP C 258 HIS 0.004 0.001 HIS D 24 Details of bonding type rmsd covalent geometry : bond 0.00403 (22848) covalent geometry : angle 0.58081 (31119) hydrogen bonds : bond 0.03751 ( 1187) hydrogen bonds : angle 4.88511 ( 3411) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 692 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ASN cc_start: 0.8010 (OUTLIER) cc_final: 0.7726 (p0) REVERT: A 139 LEU cc_start: 0.8914 (tp) cc_final: 0.8542 (tt) REVERT: A 149 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8126 (mm110) REVERT: A 156 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.7843 (t0) REVERT: A 163 ARG cc_start: 0.9080 (mtt180) cc_final: 0.8722 (mtt180) REVERT: A 191 TRP cc_start: 0.8370 (m-90) cc_final: 0.7993 (m100) REVERT: A 304 HIS cc_start: 0.8654 (OUTLIER) cc_final: 0.6856 (m-70) REVERT: A 318 GLU cc_start: 0.7862 (tp30) cc_final: 0.7638 (tp30) REVERT: A 330 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8102 (mt-10) REVERT: A 349 ASP cc_start: 0.7895 (m-30) cc_final: 0.7109 (m-30) REVERT: A 394 LEU cc_start: 0.9139 (mm) cc_final: 0.8793 (mp) REVERT: A 396 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8295 (mm) REVERT: A 400 ARG cc_start: 0.7405 (mtm110) cc_final: 0.6939 (mtm110) REVERT: B 124 ASP cc_start: 0.7497 (m-30) cc_final: 0.7054 (t0) REVERT: B 187 ASN cc_start: 0.8545 (t0) cc_final: 0.8267 (t0) REVERT: B 191 TRP cc_start: 0.8494 (m-90) cc_final: 0.8080 (m-90) REVERT: B 192 ASN cc_start: 0.8698 (t0) cc_final: 0.8463 (t0) REVERT: B 219 VAL cc_start: 0.8890 (t) cc_final: 0.8587 (p) REVERT: B 361 LYS cc_start: 0.8136 (tttt) cc_final: 0.7884 (mtmt) REVERT: B 473 TYR cc_start: 0.8598 (t80) cc_final: 0.8066 (t80) REVERT: B 487 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7166 (tm-30) REVERT: B 490 GLU cc_start: 0.8614 (mp0) cc_final: 0.8301 (mp0) REVERT: B 491 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7846 (mt) REVERT: C 28 ASN cc_start: 0.7123 (m-40) cc_final: 0.6719 (p0) REVERT: C 47 ASN cc_start: 0.7744 (m-40) cc_final: 0.7467 (m110) REVERT: C 48 ASN cc_start: 0.8885 (m110) cc_final: 0.8652 (m110) REVERT: C 83 LEU cc_start: 0.8511 (pt) cc_final: 0.8165 (mt) REVERT: C 120 LYS cc_start: 0.8343 (mtmm) cc_final: 0.7814 (mtmm) REVERT: C 148 VAL cc_start: 0.8906 (t) cc_final: 0.8410 (p) REVERT: C 188 GLN cc_start: 0.9133 (mm110) cc_final: 0.8874 (mm-40) REVERT: C 189 LYS cc_start: 0.8516 (tttt) cc_final: 0.8201 (tttt) REVERT: C 192 ASN cc_start: 0.8193 (m-40) cc_final: 0.7850 (m-40) REVERT: C 226 ASP cc_start: 0.8315 (t0) cc_final: 0.8011 (t0) REVERT: C 243 PRO cc_start: 0.9531 (Cg_exo) cc_final: 0.9216 (Cg_endo) REVERT: C 299 ASP cc_start: 0.8312 (p0) cc_final: 0.8099 (p0) REVERT: C 301 PHE cc_start: 0.8936 (t80) cc_final: 0.8277 (t80) REVERT: C 329 ILE cc_start: 0.9173 (mm) cc_final: 0.8953 (mm) REVERT: C 361 LYS cc_start: 0.8484 (pttt) cc_final: 0.8093 (tptt) REVERT: C 383 LYS cc_start: 0.8790 (tttt) cc_final: 0.8497 (ttmm) REVERT: C 393 LYS cc_start: 0.8127 (tttt) cc_final: 0.7907 (ttpt) REVERT: C 395 PHE cc_start: 0.7519 (m-80) cc_final: 0.6734 (m-80) REVERT: C 448 TYR cc_start: 0.7663 (t80) cc_final: 0.7359 (t80) REVERT: D 165 VAL cc_start: 0.9350 (OUTLIER) cc_final: 0.9119 (p) REVERT: D 182 SER cc_start: 0.9375 (m) cc_final: 0.9162 (t) REVERT: D 208 ASN cc_start: 0.8800 (t0) cc_final: 0.8321 (t0) REVERT: D 259 PHE cc_start: 0.8610 (t80) cc_final: 0.8372 (t80) REVERT: D 284 THR cc_start: 0.8798 (p) cc_final: 0.7796 (t) REVERT: D 373 LYS cc_start: 0.8063 (mttt) cc_final: 0.7747 (mttp) REVERT: E 56 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7520 (tt0) REVERT: E 72 ARG cc_start: 0.8978 (mtm-85) cc_final: 0.8532 (mtm-85) REVERT: E 75 LYS cc_start: 0.8816 (mtpt) cc_final: 0.8385 (mtmm) REVERT: E 127 GLN cc_start: 0.8698 (mm-40) cc_final: 0.7879 (mm-40) REVERT: E 141 VAL cc_start: 0.8588 (t) cc_final: 0.8380 (p) REVERT: E 171 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8259 (mp) REVERT: E 208 ASN cc_start: 0.7768 (t0) cc_final: 0.7413 (t0) REVERT: E 411 GLN cc_start: 0.7533 (tm-30) cc_final: 0.7295 (tm-30) REVERT: F 40 LYS cc_start: 0.9255 (ttmt) cc_final: 0.9037 (ttmm) REVERT: F 95 ILE cc_start: 0.8965 (mt) cc_final: 0.8649 (mt) REVERT: F 149 ARG cc_start: 0.8308 (mmm-85) cc_final: 0.7909 (ttm170) REVERT: F 199 ARG cc_start: 0.7744 (ttp80) cc_final: 0.7394 (ptm160) REVERT: F 385 GLN cc_start: 0.8520 (pp30) cc_final: 0.8289 (pm20) REVERT: F 386 ASP cc_start: 0.7742 (t70) cc_final: 0.7293 (m-30) REVERT: F 393 MET cc_start: 0.7320 (tmm) cc_final: 0.6961 (tmm) REVERT: F 406 ARG cc_start: 0.8246 (mtp85) cc_final: 0.7915 (mtp85) REVERT: G 12 SER cc_start: 0.7187 (t) cc_final: 0.6529 (m) REVERT: G 145 LEU cc_start: 0.6762 (mm) cc_final: 0.6135 (mm) REVERT: G 222 MET cc_start: 0.8089 (mmm) cc_final: 0.7693 (mmm) REVERT: G 234 ARG cc_start: 0.6618 (ttt180) cc_final: 0.6240 (ttp-170) outliers start: 118 outliers final: 96 residues processed: 741 average time/residue: 0.1571 time to fit residues: 183.8010 Evaluate side-chains 784 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 679 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 360 TYR Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain E residue 345 TYR Chi-restraints excluded: chain E residue 359 ASP Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 308 GLN Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 218 MET Chi-restraints excluded: chain G residue 241 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 172 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 259 optimal weight: 3.9990 chunk 177 optimal weight: 0.4980 chunk 290 optimal weight: 30.0000 chunk 176 optimal weight: 0.6980 chunk 200 optimal weight: 0.0370 chunk 292 optimal weight: 6.9990 chunk 295 optimal weight: 7.9990 chunk 228 optimal weight: 0.6980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 ASN C 188 GLN ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.136733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.117470 restraints weight = 35321.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.120877 restraints weight = 19045.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.123132 restraints weight = 11747.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.124607 restraints weight = 8022.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.125666 restraints weight = 5993.948| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22848 Z= 0.109 Angle : 0.538 7.986 31119 Z= 0.277 Chirality : 0.043 0.291 3760 Planarity : 0.004 0.046 4009 Dihedral : 7.058 77.273 3488 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.84 % Allowed : 21.17 % Favored : 74.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.16), residues: 3077 helix: 1.65 (0.15), residues: 1235 sheet: 0.25 (0.24), residues: 462 loop : 0.16 (0.18), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 433 TYR 0.015 0.001 TYR A 270 PHE 0.016 0.001 PHE F 441 TRP 0.010 0.001 TRP A 258 HIS 0.004 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00245 (22848) covalent geometry : angle 0.53773 (31119) hydrogen bonds : bond 0.03274 ( 1187) hydrogen bonds : angle 4.69598 ( 3411) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 710 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8540 (tt0) cc_final: 0.8247 (tt0) REVERT: A 139 LEU cc_start: 0.8808 (tp) cc_final: 0.8430 (tt) REVERT: A 149 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8296 (mm110) REVERT: A 156 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7770 (t0) REVERT: A 159 VAL cc_start: 0.8913 (OUTLIER) cc_final: 0.8624 (m) REVERT: A 173 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7267 (mtm110) REVERT: A 177 LYS cc_start: 0.9380 (mtmm) cc_final: 0.9101 (mtmm) REVERT: A 191 TRP cc_start: 0.8231 (m-90) cc_final: 0.8014 (m-90) REVERT: A 304 HIS cc_start: 0.8607 (OUTLIER) cc_final: 0.6614 (m-70) REVERT: A 318 GLU cc_start: 0.7727 (tp30) cc_final: 0.7511 (tp30) REVERT: A 330 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8145 (mt-10) REVERT: A 349 ASP cc_start: 0.7708 (m-30) cc_final: 0.6997 (m-30) REVERT: A 394 LEU cc_start: 0.9022 (mm) cc_final: 0.8676 (mt) REVERT: A 400 ARG cc_start: 0.7457 (mtm110) cc_final: 0.7108 (mtm110) REVERT: B 124 ASP cc_start: 0.7435 (m-30) cc_final: 0.7005 (t0) REVERT: B 191 TRP cc_start: 0.8465 (m-90) cc_final: 0.8049 (m-10) REVERT: B 219 VAL cc_start: 0.8846 (t) cc_final: 0.8581 (p) REVERT: B 302 TYR cc_start: 0.9139 (t80) cc_final: 0.8882 (t80) REVERT: B 361 LYS cc_start: 0.8112 (tttt) cc_final: 0.7731 (ttmm) REVERT: B 487 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7547 (tm-30) REVERT: B 490 GLU cc_start: 0.8591 (mp0) cc_final: 0.8276 (mp0) REVERT: C 28 ASN cc_start: 0.7016 (m-40) cc_final: 0.6683 (p0) REVERT: C 83 LEU cc_start: 0.8566 (pt) cc_final: 0.8202 (mt) REVERT: C 85 LYS cc_start: 0.8117 (mtmm) cc_final: 0.7662 (mtpt) REVERT: C 120 LYS cc_start: 0.8295 (mtmm) cc_final: 0.7845 (mtmm) REVERT: C 148 VAL cc_start: 0.8704 (t) cc_final: 0.8224 (p) REVERT: C 189 LYS cc_start: 0.8414 (tttt) cc_final: 0.8089 (tttt) REVERT: C 192 ASN cc_start: 0.8226 (m-40) cc_final: 0.7721 (m-40) REVERT: C 226 ASP cc_start: 0.8112 (t0) cc_final: 0.7732 (t0) REVERT: C 243 PRO cc_start: 0.9512 (Cg_exo) cc_final: 0.9201 (Cg_endo) REVERT: C 301 PHE cc_start: 0.8943 (t80) cc_final: 0.8300 (t80) REVERT: C 329 ILE cc_start: 0.9163 (mm) cc_final: 0.8940 (mm) REVERT: C 361 LYS cc_start: 0.8452 (pttt) cc_final: 0.8065 (tptt) REVERT: C 383 LYS cc_start: 0.8726 (tttt) cc_final: 0.8428 (ttmm) REVERT: C 393 LYS cc_start: 0.8077 (tttt) cc_final: 0.7859 (ttpt) REVERT: C 395 PHE cc_start: 0.7503 (m-80) cc_final: 0.6670 (m-80) REVERT: C 448 TYR cc_start: 0.7505 (t80) cc_final: 0.7166 (t80) REVERT: D 111 SER cc_start: 0.8568 (p) cc_final: 0.8201 (t) REVERT: D 165 VAL cc_start: 0.9357 (t) cc_final: 0.9086 (p) REVERT: D 208 ASN cc_start: 0.8702 (t0) cc_final: 0.8303 (t0) REVERT: D 259 PHE cc_start: 0.8606 (t80) cc_final: 0.8365 (t80) REVERT: D 284 THR cc_start: 0.8651 (p) cc_final: 0.7861 (t) REVERT: D 373 LYS cc_start: 0.8076 (mttt) cc_final: 0.7810 (mmtp) REVERT: D 406 ARG cc_start: 0.6396 (mtt180) cc_final: 0.5672 (ttm-80) REVERT: E 75 LYS cc_start: 0.8732 (mtpt) cc_final: 0.8245 (mtmm) REVERT: E 104 ASP cc_start: 0.8664 (p0) cc_final: 0.8393 (p0) REVERT: E 126 GLU cc_start: 0.7594 (tp30) cc_final: 0.7314 (tp30) REVERT: E 127 GLN cc_start: 0.8501 (mm-40) cc_final: 0.7412 (mm-40) REVERT: E 141 VAL cc_start: 0.8430 (t) cc_final: 0.8147 (p) REVERT: E 208 ASN cc_start: 0.7809 (t0) cc_final: 0.7388 (t0) REVERT: E 382 LYS cc_start: 0.8485 (mtpp) cc_final: 0.8241 (mmtm) REVERT: F 40 LYS cc_start: 0.9227 (ttmt) cc_final: 0.9015 (ttmm) REVERT: F 95 ILE cc_start: 0.8884 (mt) cc_final: 0.8614 (mt) REVERT: F 149 ARG cc_start: 0.8361 (mmm-85) cc_final: 0.7859 (ttm170) REVERT: F 199 ARG cc_start: 0.7714 (ttp80) cc_final: 0.7442 (ptm160) REVERT: F 317 LEU cc_start: 0.9141 (mm) cc_final: 0.8708 (mt) REVERT: F 340 SER cc_start: 0.8521 (OUTLIER) cc_final: 0.7813 (t) REVERT: F 401 LYS cc_start: 0.8306 (tttp) cc_final: 0.7931 (tttp) REVERT: G 12 SER cc_start: 0.7115 (t) cc_final: 0.6436 (m) REVERT: G 222 MET cc_start: 0.8007 (mmm) cc_final: 0.7733 (mmm) REVERT: G 234 ARG cc_start: 0.6612 (ttt180) cc_final: 0.6295 (ttp-170) outliers start: 84 outliers final: 62 residues processed: 744 average time/residue: 0.1557 time to fit residues: 183.0580 Evaluate side-chains 761 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 693 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 360 TYR Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 218 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 24 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 chunk 233 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 277 optimal weight: 4.9990 chunk 182 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN B 193 ASN C 47 ASN ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN D 195 ASN E 411 GLN F 52 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.132862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.113670 restraints weight = 35594.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.116980 restraints weight = 19304.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.119174 restraints weight = 11993.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.120481 restraints weight = 8254.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.121620 restraints weight = 6301.099| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 22848 Z= 0.202 Angle : 0.611 9.090 31119 Z= 0.315 Chirality : 0.046 0.306 3760 Planarity : 0.004 0.046 4009 Dihedral : 7.404 79.339 3488 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 5.08 % Allowed : 20.90 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.16), residues: 3077 helix: 1.54 (0.15), residues: 1238 sheet: 0.06 (0.24), residues: 470 loop : 0.07 (0.18), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 433 TYR 0.020 0.002 TYR A 270 PHE 0.018 0.002 PHE F 441 TRP 0.014 0.002 TRP C 191 HIS 0.004 0.001 HIS D 24 Details of bonding type rmsd covalent geometry : bond 0.00468 (22848) covalent geometry : angle 0.61096 (31119) hydrogen bonds : bond 0.03808 ( 1187) hydrogen bonds : angle 4.88451 ( 3411) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 674 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.8938 (tp) cc_final: 0.8549 (tt) REVERT: A 149 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8032 (mm110) REVERT: A 156 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7841 (t0) REVERT: A 163 ARG cc_start: 0.9072 (mtt180) cc_final: 0.8669 (mtt180) REVERT: A 191 TRP cc_start: 0.8327 (m-90) cc_final: 0.7954 (m100) REVERT: A 304 HIS cc_start: 0.8665 (OUTLIER) cc_final: 0.6806 (m-70) REVERT: A 318 GLU cc_start: 0.7879 (tp30) cc_final: 0.7673 (tp30) REVERT: A 330 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8090 (mt-10) REVERT: A 349 ASP cc_start: 0.7881 (m-30) cc_final: 0.7215 (m-30) REVERT: A 386 LYS cc_start: 0.7817 (pttm) cc_final: 0.7607 (pttm) REVERT: A 394 LEU cc_start: 0.9112 (mm) cc_final: 0.8779 (mt) REVERT: B 124 ASP cc_start: 0.7420 (m-30) cc_final: 0.6965 (t0) REVERT: B 187 ASN cc_start: 0.8551 (t0) cc_final: 0.8268 (t0) REVERT: B 191 TRP cc_start: 0.8556 (m-90) cc_final: 0.8129 (m-10) REVERT: B 219 VAL cc_start: 0.8871 (t) cc_final: 0.8555 (p) REVERT: B 361 LYS cc_start: 0.8130 (tttt) cc_final: 0.7881 (mtmt) REVERT: B 473 TYR cc_start: 0.8641 (t80) cc_final: 0.8091 (t80) REVERT: B 487 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7544 (tm-30) REVERT: B 490 GLU cc_start: 0.8620 (mp0) cc_final: 0.8273 (mp0) REVERT: C 28 ASN cc_start: 0.7201 (m-40) cc_final: 0.6586 (p0) REVERT: C 47 ASN cc_start: 0.7922 (m-40) cc_final: 0.7617 (m110) REVERT: C 83 LEU cc_start: 0.8751 (pt) cc_final: 0.8448 (mt) REVERT: C 148 VAL cc_start: 0.8772 (t) cc_final: 0.8321 (p) REVERT: C 189 LYS cc_start: 0.8474 (tttt) cc_final: 0.8168 (tttt) REVERT: C 192 ASN cc_start: 0.8180 (m-40) cc_final: 0.7834 (m-40) REVERT: C 226 ASP cc_start: 0.8276 (t0) cc_final: 0.7837 (t0) REVERT: C 243 PRO cc_start: 0.9549 (Cg_exo) cc_final: 0.9213 (Cg_endo) REVERT: C 299 ASP cc_start: 0.8348 (p0) cc_final: 0.8143 (p0) REVERT: C 301 PHE cc_start: 0.8982 (t80) cc_final: 0.8368 (t80) REVERT: C 361 LYS cc_start: 0.8491 (pttt) cc_final: 0.8048 (tptt) REVERT: C 383 LYS cc_start: 0.8713 (tttt) cc_final: 0.8422 (ttmm) REVERT: C 393 LYS cc_start: 0.8121 (tttt) cc_final: 0.7912 (ttpt) REVERT: C 395 PHE cc_start: 0.7578 (m-80) cc_final: 0.6811 (m-80) REVERT: C 448 TYR cc_start: 0.7628 (t80) cc_final: 0.7280 (t80) REVERT: C 484 GLU cc_start: 0.8001 (tt0) cc_final: 0.7441 (tm-30) REVERT: D 111 SER cc_start: 0.8586 (p) cc_final: 0.8231 (t) REVERT: D 165 VAL cc_start: 0.9375 (t) cc_final: 0.9126 (p) REVERT: D 208 ASN cc_start: 0.8807 (t0) cc_final: 0.8329 (t0) REVERT: D 284 THR cc_start: 0.8772 (p) cc_final: 0.7872 (t) REVERT: D 373 LYS cc_start: 0.8088 (mttt) cc_final: 0.7792 (mmtp) REVERT: E 56 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7415 (tt0) REVERT: E 75 LYS cc_start: 0.8660 (mtpt) cc_final: 0.8231 (mtmm) REVERT: E 104 ASP cc_start: 0.8763 (p0) cc_final: 0.8452 (p0) REVERT: E 126 GLU cc_start: 0.7713 (tp30) cc_final: 0.7406 (tp30) REVERT: E 127 GLN cc_start: 0.8594 (mm-40) cc_final: 0.7520 (mm-40) REVERT: E 208 ASN cc_start: 0.7991 (t0) cc_final: 0.7605 (t0) REVERT: F 40 LYS cc_start: 0.9271 (ttmt) cc_final: 0.9027 (ttmm) REVERT: F 95 ILE cc_start: 0.8939 (mt) cc_final: 0.8665 (mt) REVERT: F 149 ARG cc_start: 0.8314 (mmm-85) cc_final: 0.7833 (ttm170) REVERT: F 199 ARG cc_start: 0.7746 (ttp80) cc_final: 0.7508 (ptm160) REVERT: F 386 ASP cc_start: 0.7857 (t70) cc_final: 0.7332 (m-30) REVERT: F 414 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8597 (mm) REVERT: G 12 SER cc_start: 0.7167 (t) cc_final: 0.6486 (m) REVERT: G 234 ARG cc_start: 0.6637 (ttt180) cc_final: 0.6287 (ttp-170) outliers start: 111 outliers final: 90 residues processed: 721 average time/residue: 0.1521 time to fit residues: 175.4595 Evaluate side-chains 756 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 661 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 201 MET Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 359 ASP Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 308 GLN Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 372 SER Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 265 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 283 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 265 optimal weight: 0.0030 chunk 116 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 167 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 187 optimal weight: 0.9980 chunk 152 optimal weight: 0.6980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN C 276 GLN D 173 ASN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.136475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.117098 restraints weight = 35123.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.120529 restraints weight = 18883.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.122790 restraints weight = 11658.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.124195 restraints weight = 7963.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.125328 restraints weight = 6016.337| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 22848 Z= 0.116 Angle : 0.567 9.912 31119 Z= 0.290 Chirality : 0.044 0.282 3760 Planarity : 0.004 0.047 4009 Dihedral : 6.936 78.110 3488 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.02 % Allowed : 22.09 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.16), residues: 3077 helix: 1.70 (0.15), residues: 1230 sheet: 0.17 (0.24), residues: 466 loop : 0.15 (0.18), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 408 TYR 0.020 0.001 TYR E 381 PHE 0.016 0.001 PHE E 124 TRP 0.021 0.002 TRP C 191 HIS 0.003 0.001 HIS E 367 Details of bonding type rmsd covalent geometry : bond 0.00267 (22848) covalent geometry : angle 0.56662 (31119) hydrogen bonds : bond 0.03284 ( 1187) hydrogen bonds : angle 4.73151 ( 3411) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 682 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.8840 (tp) cc_final: 0.8476 (tt) REVERT: A 149 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8418 (mt0) REVERT: A 156 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7903 (t0) REVERT: A 159 VAL cc_start: 0.8975 (OUTLIER) cc_final: 0.8660 (m) REVERT: A 173 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7170 (mtm110) REVERT: A 304 HIS cc_start: 0.8585 (OUTLIER) cc_final: 0.6663 (m-70) REVERT: A 330 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8116 (mt-10) REVERT: A 349 ASP cc_start: 0.7689 (m-30) cc_final: 0.7041 (m-30) REVERT: A 385 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8570 (mp) REVERT: A 394 LEU cc_start: 0.9062 (mm) cc_final: 0.8722 (mt) REVERT: A 400 ARG cc_start: 0.7332 (mtm110) cc_final: 0.7102 (mtm110) REVERT: B 124 ASP cc_start: 0.7322 (m-30) cc_final: 0.6878 (t0) REVERT: B 191 TRP cc_start: 0.8309 (m-90) cc_final: 0.7945 (m-10) REVERT: B 219 VAL cc_start: 0.8833 (t) cc_final: 0.8585 (p) REVERT: B 302 TYR cc_start: 0.9153 (t80) cc_final: 0.8913 (t80) REVERT: B 361 LYS cc_start: 0.8104 (tttt) cc_final: 0.7734 (ttmm) REVERT: B 473 TYR cc_start: 0.8559 (t80) cc_final: 0.8001 (t80) REVERT: B 487 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7501 (tm-30) REVERT: B 490 GLU cc_start: 0.8576 (mp0) cc_final: 0.8199 (mp0) REVERT: C 28 ASN cc_start: 0.7180 (m-40) cc_final: 0.6652 (p0) REVERT: C 47 ASN cc_start: 0.7871 (m-40) cc_final: 0.7615 (m110) REVERT: C 83 LEU cc_start: 0.8751 (pt) cc_final: 0.8390 (mt) REVERT: C 85 LYS cc_start: 0.8128 (mtmm) cc_final: 0.7679 (mtpt) REVERT: C 192 ASN cc_start: 0.8059 (m-40) cc_final: 0.7696 (m-40) REVERT: C 226 ASP cc_start: 0.8061 (t0) cc_final: 0.7801 (t0) REVERT: C 243 PRO cc_start: 0.9490 (Cg_exo) cc_final: 0.9171 (Cg_endo) REVERT: C 287 LEU cc_start: 0.8434 (mt) cc_final: 0.8233 (mt) REVERT: C 301 PHE cc_start: 0.8949 (t80) cc_final: 0.8282 (t80) REVERT: C 361 LYS cc_start: 0.8458 (pttt) cc_final: 0.7997 (tptt) REVERT: C 383 LYS cc_start: 0.8724 (tttt) cc_final: 0.8314 (tppt) REVERT: C 393 LYS cc_start: 0.8094 (tttt) cc_final: 0.7863 (ttpt) REVERT: C 395 PHE cc_start: 0.7531 (m-80) cc_final: 0.6715 (m-80) REVERT: C 448 TYR cc_start: 0.7439 (t80) cc_final: 0.7146 (t80) REVERT: D 111 SER cc_start: 0.8591 (p) cc_final: 0.8235 (t) REVERT: D 165 VAL cc_start: 0.9366 (t) cc_final: 0.9103 (p) REVERT: D 208 ASN cc_start: 0.8716 (t0) cc_final: 0.8276 (t0) REVERT: D 284 THR cc_start: 0.8589 (p) cc_final: 0.7856 (t) REVERT: D 340 SER cc_start: 0.8590 (p) cc_final: 0.8252 (t) REVERT: D 373 LYS cc_start: 0.8101 (mttt) cc_final: 0.7812 (mttp) REVERT: E 56 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7401 (tt0) REVERT: E 75 LYS cc_start: 0.8708 (mtpt) cc_final: 0.8366 (mmmm) REVERT: E 89 ARG cc_start: 0.7580 (mtp85) cc_final: 0.7213 (mtp85) REVERT: E 98 VAL cc_start: 0.9334 (t) cc_final: 0.9132 (m) REVERT: E 104 ASP cc_start: 0.8680 (p0) cc_final: 0.8391 (p0) REVERT: E 208 ASN cc_start: 0.7962 (t0) cc_final: 0.7562 (t0) REVERT: E 382 LYS cc_start: 0.8463 (mtpp) cc_final: 0.8194 (mmtm) REVERT: F 40 LYS cc_start: 0.9251 (ttmt) cc_final: 0.9017 (ttmm) REVERT: F 84 SER cc_start: 0.8638 (p) cc_final: 0.8269 (p) REVERT: F 95 ILE cc_start: 0.8872 (mt) cc_final: 0.8612 (mt) REVERT: F 149 ARG cc_start: 0.8278 (mmm-85) cc_final: 0.7609 (tpp-160) REVERT: F 199 ARG cc_start: 0.7705 (ttp80) cc_final: 0.7466 (ptm160) REVERT: F 317 LEU cc_start: 0.9133 (mm) cc_final: 0.8731 (mt) REVERT: F 340 SER cc_start: 0.8550 (OUTLIER) cc_final: 0.7769 (t) REVERT: G 12 SER cc_start: 0.7255 (t) cc_final: 0.6585 (m) REVERT: G 23 MET cc_start: 0.5787 (tmm) cc_final: 0.5297 (tmm) REVERT: G 31 LEU cc_start: 0.8106 (tt) cc_final: 0.7749 (tt) REVERT: G 145 LEU cc_start: 0.6728 (mm) cc_final: 0.6039 (mm) REVERT: G 234 ARG cc_start: 0.6665 (ttt180) cc_final: 0.6347 (ttp-170) outliers start: 88 outliers final: 71 residues processed: 725 average time/residue: 0.1554 time to fit residues: 178.6975 Evaluate side-chains 756 residues out of total 2513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 677 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 360 TYR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 372 SER Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 218 MET Chi-restraints excluded: chain G residue 241 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.4836 > 50: distance: 58 - 79: 29.068 distance: 62 - 87: 21.470 distance: 69 - 79: 31.894 distance: 79 - 80: 40.584 distance: 80 - 81: 47.280 distance: 80 - 83: 51.213 distance: 81 - 82: 14.745 distance: 81 - 87: 34.651 distance: 83 - 84: 16.179 distance: 84 - 85: 17.589 distance: 84 - 86: 40.887 distance: 87 - 88: 15.658 distance: 88 - 89: 42.487 distance: 88 - 91: 15.087 distance: 89 - 90: 40.075 distance: 89 - 92: 47.766 distance: 90 - 117: 26.722 distance: 92 - 93: 25.189 distance: 92 - 98: 28.711 distance: 93 - 94: 13.738 distance: 94 - 95: 40.205 distance: 94 - 99: 31.598 distance: 95 - 122: 42.627 distance: 96 - 97: 23.837 distance: 97 - 98: 25.175 distance: 99 - 100: 46.441 distance: 100 - 101: 30.861 distance: 100 - 103: 12.748 distance: 101 - 110: 40.500 distance: 102 - 127: 35.416 distance: 103 - 104: 16.311 distance: 104 - 105: 5.313 distance: 104 - 106: 8.199 distance: 105 - 107: 27.934 distance: 106 - 108: 14.094 distance: 107 - 109: 7.126 distance: 108 - 109: 8.081 distance: 111 - 112: 16.352 distance: 111 - 114: 37.069 distance: 112 - 113: 17.101 distance: 112 - 117: 26.496 distance: 113 - 133: 44.219 distance: 114 - 115: 47.054 distance: 114 - 116: 43.107 distance: 117 - 118: 14.848 distance: 118 - 119: 39.048 distance: 118 - 121: 11.490 distance: 119 - 120: 31.095 distance: 119 - 122: 22.032 distance: 120 - 141: 46.679 distance: 122 - 123: 47.581 distance: 123 - 124: 25.882 distance: 123 - 126: 36.985 distance: 124 - 125: 25.505 distance: 124 - 127: 24.317 distance: 125 - 145: 35.139 distance: 127 - 128: 8.988 distance: 128 - 129: 31.487 distance: 128 - 131: 13.475 distance: 129 - 130: 30.932 distance: 129 - 133: 21.234 distance: 130 - 153: 20.210 distance: 131 - 132: 41.174 distance: 133 - 134: 24.645 distance: 134 - 135: 5.160 distance: 134 - 137: 23.654 distance: 135 - 136: 22.519 distance: 135 - 141: 44.851 distance: 137 - 138: 4.665 distance: 137 - 139: 24.051 distance: 138 - 140: 16.191 distance: 141 - 142: 14.824 distance: 142 - 143: 19.285 distance: 143 - 144: 16.129 distance: 143 - 145: 15.928 distance: 144 - 167: 33.296