Starting phenix.real_space_refine on Thu Mar 5 18:21:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hh4_34751/03_2026/8hh4_34751.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hh4_34751/03_2026/8hh4_34751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hh4_34751/03_2026/8hh4_34751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hh4_34751/03_2026/8hh4_34751.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hh4_34751/03_2026/8hh4_34751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hh4_34751/03_2026/8hh4_34751.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 6 5.21 5 S 77 5.16 5 C 15287 2.51 5 N 4219 2.21 5 O 4670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24277 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "C" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 454} Chain: "D" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "E" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "F" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "G" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2218 Classifications: {'peptide': 283} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 272} Chain: "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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" 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: 5.49, per 1000 atoms: 0.23 Number of scatterers: 24277 At special positions: 0 Unit cell: (126.72, 125.84, 154, 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 77 16.00 P 18 15.00 Mg 6 11.99 O 4670 8.00 N 4219 7.00 C 15287 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: 1.80 Conformation dependent library (CDL) restraints added in 1.0 seconds 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 20 sheets defined 48.4% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 78 through 82 removed outlier: 4.183A pdb=" N GLY A 81 " --> pdb=" O PRO A 78 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 82 " --> pdb=" O TYR A 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 78 through 82' Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 185 Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 231 through 252 removed outlier: 3.582A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.732A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 287 through 288 No H-bonds generated for 'chain 'A' and resid 287 through 288' Processing helix chain 'A' and resid 289 through 299 removed outlier: 3.670A pdb=" N HIS A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 372 through 391 removed outlier: 4.563A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 396 Processing helix chain 'A' and resid 402 through 420 removed outlier: 4.330A pdb=" N THR A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ALA A 408 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LYS A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'A' and resid 449 through 468 removed outlier: 4.546A pdb=" N ARG A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ARG A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 479 Processing helix chain 'A' and resid 483 through 498 removed outlier: 3.718A pdb=" N ILE A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.874A pdb=" N ARG B 139 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 231 through 253 removed outlier: 3.562A pdb=" N LEU B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.749A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 removed outlier: 4.062A pdb=" N GLN B 266 " --> pdb=" O ASP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.723A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 345 through 351 Processing helix chain 'B' and resid 372 through 399 removed outlier: 3.880A pdb=" N LYS B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 421 removed outlier: 3.789A pdb=" N THR B 406 " --> pdb=" O LEU B 402 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ALA B 408 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 442 removed outlier: 4.121A pdb=" N LEU B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 removed outlier: 4.237A pdb=" N ASP B 447 " --> pdb=" O PHE B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 468 removed outlier: 3.954A pdb=" N GLU B 457 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS B 458 " --> pdb=" O ARG B 454 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLU B 459 " --> pdb=" O ARG B 455 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 479 Processing helix chain 'B' and resid 484 through 498 Processing helix chain 'C' and resid 78 through 82 removed outlier: 4.312A pdb=" N GLY C 81 " --> pdb=" O PRO C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.687A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.657A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 216 removed outlier: 3.627A pdb=" N HIS C 215 " --> pdb=" O THR C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 231 through 251 removed outlier: 3.719A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) Proline residue: C 239 - end of helix removed outlier: 3.746A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 328 through 338 Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 372 through 393 removed outlier: 3.701A pdb=" N VAL C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR C 389 " --> pdb=" O ASP C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 396 No H-bonds generated for 'chain 'C' and resid 394 through 396' Processing helix chain 'C' and resid 403 through 420 Processing helix chain 'C' and resid 429 through 442 Processing helix chain 'C' and resid 449 through 451 No H-bonds generated for 'chain 'C' and resid 449 through 451' Processing helix chain 'C' and resid 452 through 467 Processing helix chain 'C' and resid 468 through 479 Processing helix chain 'C' and resid 483 through 498 removed outlier: 3.636A pdb=" N THR C 497 " --> pdb=" O ALA C 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 124 through 128 removed outlier: 3.927A pdb=" N LEU D 128 " --> pdb=" O PHE D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 145 Processing helix chain 'D' and resid 163 through 179 Processing helix chain 'D' and resid 191 through 206 Processing helix chain 'D' and resid 221 through 242 removed outlier: 5.018A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 269 removed outlier: 3.828A pdb=" N PHE D 257 " --> pdb=" O ASN D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 277 Processing helix chain 'D' and resid 280 through 291 removed outlier: 4.231A pdb=" N ARG D 291 " --> pdb=" O GLN D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 312 Processing helix chain 'D' and resid 315 through 322 Processing helix chain 'D' and resid 332 through 338 Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 360 through 387 removed outlier: 4.091A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 392 Processing helix chain 'D' and resid 393 through 410 removed outlier: 3.612A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 429 through 442 removed outlier: 4.018A pdb=" N ILE D 440 " --> pdb=" O GLY D 436 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU D 441 " --> pdb=" O PHE D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 453 Processing helix chain 'D' and resid 458 through 469 removed outlier: 3.895A pdb=" N VAL D 462 " --> pdb=" O ARG D 458 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 removed outlier: 3.545A pdb=" N THR E 91 " --> pdb=" O GLY E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 128 removed outlier: 3.604A pdb=" N LEU E 128 " --> pdb=" O PHE E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 145 Processing helix chain 'E' and resid 163 through 180 Processing helix chain 'E' and resid 191 through 206 Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 221 through 242 removed outlier: 4.836A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 removed outlier: 3.903A pdb=" N PHE E 257 " --> pdb=" O ASN E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 277 removed outlier: 3.518A pdb=" N TYR E 277 " --> pdb=" O ALA E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 290 Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 315 through 323 Processing helix chain 'E' and resid 332 through 339 removed outlier: 3.595A pdb=" N ALA E 336 " --> pdb=" O GLU E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 360 through 387 removed outlier: 3.854A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 410 removed outlier: 4.229A pdb=" N VAL E 400 " --> pdb=" O ASP E 396 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 429 through 442 Processing helix chain 'E' and resid 449 through 454 Processing helix chain 'E' and resid 459 through 467 removed outlier: 3.667A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 removed outlier: 3.501A pdb=" N THR F 91 " --> pdb=" O GLY F 88 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU F 92 " --> pdb=" O GLU F 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 88 through 92' Processing helix chain 'F' and resid 124 through 128 removed outlier: 3.599A pdb=" N LEU F 128 " --> pdb=" O PHE F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 145 Processing helix chain 'F' and resid 163 through 176 Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 191 through 206 Processing helix chain 'F' and resid 207 through 209 No H-bonds generated for 'chain 'F' and resid 207 through 209' Processing helix chain 'F' and resid 221 through 242 removed outlier: 5.064A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET F 235 " --> pdb=" O THR F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 266 removed outlier: 4.043A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 269 No H-bonds generated for 'chain 'F' and resid 267 through 269' Processing helix chain 'F' and resid 280 through 290 Processing helix chain 'F' and resid 309 through 312 Processing helix chain 'F' and resid 315 through 322 Processing helix chain 'F' and resid 323 through 325 No H-bonds generated for 'chain 'F' and resid 323 through 325' Processing helix chain 'F' and resid 332 through 337 Processing helix chain 'F' and resid 360 through 388 removed outlier: 3.506A pdb=" N GLN F 381 " --> pdb=" O TYR F 377 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 392 Processing helix chain 'F' and resid 393 through 410 removed outlier: 3.782A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 420 removed outlier: 3.534A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 443 Processing helix chain 'F' and resid 449 through 454 Processing helix chain 'F' and resid 458 through 469 removed outlier: 3.788A pdb=" N VAL F 462 " --> pdb=" O ARG F 458 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 57 removed outlier: 4.001A pdb=" N SER G 30 " --> pdb=" O MET G 26 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER G 41 " --> pdb=" O GLN G 37 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE G 42 " --> pdb=" O ASN G 38 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) Proline residue: G 44 - end of helix Processing helix chain 'G' and resid 90 through 107 removed outlier: 4.207A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 111 No H-bonds generated for 'chain 'G' and resid 109 through 111' Processing helix chain 'G' and resid 119 through 129 removed outlier: 3.683A pdb=" N LEU G 123 " --> pdb=" O GLY G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 162 removed outlier: 3.934A pdb=" N PHE G 160 " --> pdb=" O THR G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 223 removed outlier: 4.729A pdb=" N ASP G 214 " --> pdb=" O GLU G 210 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL G 215 " --> pdb=" O GLU G 211 " (cutoff:3.500A) Proline residue: G 218 - end of helix Processing helix chain 'G' and resid 223 through 284 removed outlier: 4.750A pdb=" N LEU G 230 " --> pdb=" O TYR G 226 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ASP G 231 " --> pdb=" O GLY G 227 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG G 264 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY G 280 " --> pdb=" O GLU G 276 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA G 283 " --> pdb=" O ALA G 279 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU G 284 " --> pdb=" O GLY G 280 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 66 removed outlier: 4.113A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASN A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU A 66 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ALA E 29 " --> pdb=" O THR E 79 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASN E 28 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE E 44 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN E 8 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LYS E 17 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N VAL E 6 " --> pdb=" O LYS E 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.088A pdb=" N GLU A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.572A pdb=" N VAL A 108 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR A 260 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASP A 170 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 66 removed outlier: 4.334A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ARG B 93 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N GLU B 54 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR B 91 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN B 65 " --> pdb=" O GLY B 72 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N THR F 58 " --> pdb=" O LEU F 54 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 99 Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.694A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 28 through 35 removed outlier: 6.600A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.073A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 107 through 108 removed outlier: 3.600A pdb=" N TYR C 260 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 107 through 108 removed outlier: 3.600A pdb=" N TYR C 260 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 4 through 9 removed outlier: 6.643A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASN D 28 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ALA D 81 " --> pdb=" O ALA D 29 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N LYS D 31 " --> pdb=" O THR D 79 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N THR D 79 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N GLN D 33 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ILE D 77 " --> pdb=" O GLN D 33 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL D 76 " --> pdb=" O GLY D 4 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB4, first strand: chain 'D' and resid 95 through 96 removed outlier: 3.918A pdb=" N ILE D 182 " --> pdb=" O ASP D 246 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA D 305 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE D 154 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ILE D 306 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU D 156 " --> pdb=" O ILE D 306 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 134 through 135 removed outlier: 4.389A pdb=" N TYR D 148 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB7, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.319A pdb=" N PHE E 96 " --> pdb=" O PHE E 215 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER E 183 " --> pdb=" O ALA E 212 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N VAL E 214 " --> pdb=" O SER E 183 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N PHE E 185 " --> pdb=" O VAL E 214 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N GLY E 216 " --> pdb=" O PHE E 185 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLY E 187 " --> pdb=" O GLY E 216 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AB9, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.799A pdb=" N PHE F 96 " --> pdb=" O PHE F 215 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE F 154 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ILE F 306 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU F 156 " --> pdb=" O ILE F 306 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 134 through 135 removed outlier: 4.201A pdb=" N TYR F 148 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 133 through 134 removed outlier: 8.803A pdb=" N ILE G 134 " --> pdb=" O TYR G 113 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE G 115 " --> pdb=" O ILE G 134 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N THR G 76 " --> pdb=" O ALA G 114 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE G 116 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N TYR G 78 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLY G 77 " --> pdb=" O TYR G 169 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N TYR G 171 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU G 79 " --> pdb=" O TYR G 171 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ASN G 173 " --> pdb=" O LEU G 79 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N ILE G 81 " --> pdb=" O ASN G 173 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU G 168 " --> pdb=" O LEU G 188 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR G 172 " --> pdb=" O THR G 184 " (cutoff:3.500A) 1201 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: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4179 1.31 - 1.44: 5906 1.44 - 1.56: 14417 1.56 - 1.69: 28 1.69 - 1.81: 154 Bond restraints: 24684 Sorted by residual: bond pdb=" C LYS B 377 " pdb=" O LYS B 377 " ideal model delta sigma weight residual 1.236 1.388 -0.152 1.15e-02 7.56e+03 1.74e+02 bond pdb=" C LYS B 376 " pdb=" O LYS B 376 " ideal model delta sigma weight residual 1.236 1.319 -0.082 1.15e-02 7.56e+03 5.14e+01 bond pdb=" C ARG B 390 " pdb=" O ARG B 390 " ideal model delta sigma weight residual 1.235 1.314 -0.079 1.26e-02 6.30e+03 3.91e+01 bond pdb=" C ARG B 383 " pdb=" O ARG B 383 " ideal model delta sigma weight residual 1.236 1.304 -0.067 1.15e-02 7.56e+03 3.44e+01 bond pdb=" N LYS B 377 " pdb=" CA LYS B 377 " ideal model delta sigma weight residual 1.459 1.518 -0.059 1.19e-02 7.06e+03 2.47e+01 ... (remaining 24679 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 32644 2.15 - 4.30: 713 4.30 - 6.45: 103 6.45 - 8.60: 16 8.60 - 10.76: 3 Bond angle restraints: 33479 Sorted by residual: angle pdb=" C GLY B 380 " pdb=" N THR B 381 " pdb=" CA THR B 381 " ideal model delta sigma weight residual 120.28 110.58 9.70 1.34e+00 5.57e-01 5.24e+01 angle pdb=" N ASP E 390 " pdb=" CA ASP E 390 " pdb=" C ASP E 390 " ideal model delta sigma weight residual 112.92 104.39 8.53 1.23e+00 6.61e-01 4.81e+01 angle pdb=" N GLY F 216 " pdb=" CA GLY F 216 " pdb=" C GLY F 216 " ideal model delta sigma weight residual 112.85 102.09 10.76 1.61e+00 3.86e-01 4.46e+01 angle pdb=" CA LYS B 376 " pdb=" C LYS B 376 " pdb=" N LYS B 377 " ideal model delta sigma weight residual 117.07 124.47 -7.40 1.14e+00 7.69e-01 4.21e+01 angle pdb=" CA MET E 271 " pdb=" C MET E 271 " pdb=" N PRO E 272 " ideal model delta sigma weight residual 117.67 124.04 -6.37 1.01e+00 9.80e-01 3.98e+01 ... (remaining 33474 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.40: 14611 31.40 - 62.79: 432 62.79 - 94.19: 48 94.19 - 125.59: 0 125.59 - 156.99: 2 Dihedral angle restraints: 15093 sinusoidal: 6168 harmonic: 8925 Sorted by residual: dihedral pdb=" O2A ADP D 602 " pdb=" O3A ADP D 602 " pdb=" PA ADP D 602 " pdb=" PB ADP D 602 " ideal model delta sinusoidal sigma weight residual -60.00 96.99 -156.99 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" C5' ADP D 602 " pdb=" O5' ADP D 602 " pdb=" PA ADP D 602 " pdb=" O2A ADP D 602 " ideal model delta sinusoidal sigma weight residual -60.00 71.02 -131.02 1 2.00e+01 2.50e-03 3.98e+01 dihedral pdb=" C ASP E 394 " pdb=" N ASP E 394 " pdb=" CA ASP E 394 " pdb=" CB ASP E 394 " ideal model delta harmonic sigma weight residual -122.60 -136.01 13.41 0 2.50e+00 1.60e-01 2.88e+01 ... (remaining 15090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 3522 0.092 - 0.183: 311 0.183 - 0.274: 16 0.274 - 0.366: 6 0.366 - 0.457: 1 Chirality restraints: 3856 Sorted by residual: chirality pdb=" CA ASP E 394 " pdb=" N ASP E 394 " pdb=" C ASP E 394 " pdb=" CB ASP E 394 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" CA LEU B 402 " pdb=" N LEU B 402 " pdb=" C LEU B 402 " pdb=" CB LEU B 402 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CA LEU E 392 " pdb=" N LEU E 392 " pdb=" C LEU E 392 " pdb=" CB LEU E 392 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 3853 not shown) Planarity restraints: 4363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 374 " -0.021 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C ALA B 374 " 0.075 2.00e-02 2.50e+03 pdb=" O ALA B 374 " -0.028 2.00e-02 2.50e+03 pdb=" N MET B 375 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 389 " -0.021 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" C TYR B 389 " 0.069 2.00e-02 2.50e+03 pdb=" O TYR B 389 " -0.025 2.00e-02 2.50e+03 pdb=" N ARG B 390 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 384 " -0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C LEU B 384 " 0.064 2.00e-02 2.50e+03 pdb=" O LEU B 384 " -0.024 2.00e-02 2.50e+03 pdb=" N ASP B 385 " -0.022 2.00e-02 2.50e+03 ... (remaining 4360 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 97 2.49 - 3.09: 17347 3.09 - 3.70: 35687 3.70 - 4.30: 52988 4.30 - 4.90: 89705 Nonbonded interactions: 195824 Sorted by model distance: nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 601 " model vdw 1.888 2.170 nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 601 " model vdw 1.918 2.170 nonbonded pdb="MG MG F 601 " pdb=" O3G ATP F 602 " model vdw 1.919 2.170 nonbonded pdb="MG MG D 601 " pdb=" O2 PO4 D 603 " model vdw 1.929 2.170 nonbonded pdb="MG MG B 601 " pdb=" O2G ATP B 602 " model vdw 1.980 2.170 ... (remaining 195819 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 24 through 501) selection = (chain 'B' and resid 24 through 501) selection = (chain 'C' and resid 24 through 501) } ncs_group { reference = (chain 'D' and resid 1 through 470) selection = (chain 'E' and resid 1 through 470) selection = (chain 'F' and resid 1 through 470) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 20.880 Find NCS groups from input model: 0.330 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: 0.000 Load rotamer database and sin/cos tables:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 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 : 0.005 0.152 24684 Z= 0.301 Angle : 0.757 10.756 33479 Z= 0.474 Chirality : 0.053 0.457 3856 Planarity : 0.005 0.046 4363 Dihedral : 14.804 156.985 9381 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.21 % Favored : 96.76 % Rotamer: Outliers : 1.64 % Allowed : 0.90 % Favored : 97.47 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.15), residues: 3115 helix: 1.16 (0.15), residues: 1240 sheet: 0.35 (0.22), residues: 528 loop : -0.21 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 455 TYR 0.017 0.001 TYR B 248 PHE 0.016 0.002 PHE A 494 HIS 0.007 0.001 HIS E 401 Details of bonding type rmsd covalent geometry : bond 0.00524 (24684) covalent geometry : angle 0.75733 (33479) hydrogen bonds : bond 0.15491 ( 1184) hydrogen bonds : angle 6.35293 ( 3411) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 223 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8366 (ttp) cc_final: 0.8013 (ttt) REVERT: D 397 LYS cc_start: 0.8704 (mtmm) cc_final: 0.8213 (mtmm) REVERT: E 393 SER cc_start: 0.8051 (OUTLIER) cc_final: 0.7684 (p) REVERT: E 394 ASP cc_start: 0.7486 (p0) cc_final: 0.7099 (p0) REVERT: F 220 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7464 (mm-30) REVERT: G 67 MET cc_start: 0.6841 (OUTLIER) cc_final: 0.6475 (mmt) REVERT: G 193 ASP cc_start: 0.7263 (m-30) cc_final: 0.6920 (t70) REVERT: G 198 LYS cc_start: 0.6233 (OUTLIER) cc_final: 0.5900 (ttpt) REVERT: G 241 MET cc_start: 0.8389 (ttp) cc_final: 0.7966 (ttp) outliers start: 42 outliers final: 11 residues processed: 258 average time/residue: 0.1676 time to fit residues: 66.6804 Evaluate side-chains 149 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 401 HIS Chi-restraints excluded: chain F residue 220 GLU Chi-restraints excluded: chain G residue 65 HIS Chi-restraints excluded: chain G residue 67 MET Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 200 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 HIS E 278 GLN F 28 ASN F 330 ASN G 50 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.079709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.063983 restraints weight = 63972.849| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.58 r_work: 0.2957 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24684 Z= 0.161 Angle : 0.579 8.523 33479 Z= 0.305 Chirality : 0.045 0.239 3856 Planarity : 0.004 0.056 4363 Dihedral : 9.079 163.536 3613 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.05 % Allowed : 5.72 % Favored : 93.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.15), residues: 3115 helix: 1.26 (0.15), residues: 1245 sheet: 0.28 (0.22), residues: 542 loop : -0.16 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 40 TYR 0.019 0.001 TYR B 248 PHE 0.015 0.001 PHE B 456 HIS 0.005 0.001 HIS E 401 Details of bonding type rmsd covalent geometry : bond 0.00372 (24684) covalent geometry : angle 0.57915 (33479) hydrogen bonds : bond 0.04994 ( 1184) hydrogen bonds : angle 5.21737 ( 3411) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 56 ASP cc_start: 0.8043 (t0) cc_final: 0.7649 (t0) REVERT: E 396 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7376 (t0) REVERT: F 43 ASP cc_start: 0.8842 (m-30) cc_final: 0.8467 (m-30) REVERT: G 146 PHE cc_start: 0.6846 (t80) cc_final: 0.6409 (t80) REVERT: G 193 ASP cc_start: 0.7659 (m-30) cc_final: 0.7150 (t70) REVERT: G 198 LYS cc_start: 0.6354 (OUTLIER) cc_final: 0.5881 (ttpt) REVERT: G 241 MET cc_start: 0.8431 (ttp) cc_final: 0.8229 (ttp) outliers start: 27 outliers final: 12 residues processed: 166 average time/residue: 0.1495 time to fit residues: 40.8164 Evaluate side-chains 135 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 200 ARG Chi-restraints excluded: chain G residue 273 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 117 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 176 optimal weight: 0.0370 chunk 23 optimal weight: 6.9990 chunk 284 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 228 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 216 optimal weight: 8.9990 overall best weight: 4.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN F 324 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.078007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.062444 restraints weight = 64429.493| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.57 r_work: 0.2914 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 24684 Z= 0.218 Angle : 0.604 9.363 33479 Z= 0.318 Chirality : 0.047 0.269 3856 Planarity : 0.005 0.074 4363 Dihedral : 8.580 167.045 3593 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.21 % Allowed : 8.18 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.15), residues: 3115 helix: 1.19 (0.15), residues: 1235 sheet: 0.27 (0.22), residues: 526 loop : -0.33 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 365 TYR 0.020 0.002 TYR B 248 PHE 0.016 0.002 PHE F 257 HIS 0.005 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00523 (24684) covalent geometry : angle 0.60356 (33479) hydrogen bonds : bond 0.05351 ( 1184) hydrogen bonds : angle 5.09748 ( 3411) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: E 396 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7374 (t70) REVERT: F 43 ASP cc_start: 0.8830 (m-30) cc_final: 0.8454 (m-30) REVERT: G 193 ASP cc_start: 0.7675 (m-30) cc_final: 0.7229 (t70) REVERT: G 198 LYS cc_start: 0.6456 (OUTLIER) cc_final: 0.5889 (ttpt) REVERT: G 241 MET cc_start: 0.8564 (ttp) cc_final: 0.8348 (ttp) outliers start: 31 outliers final: 21 residues processed: 142 average time/residue: 0.1380 time to fit residues: 33.2063 Evaluate side-chains 138 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 200 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 245 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 295 optimal weight: 5.9990 chunk 196 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 279 optimal weight: 6.9990 chunk 213 optimal weight: 3.9990 chunk 181 optimal weight: 8.9990 chunk 235 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 215 HIS E 365 GLN F 28 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.077619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.061938 restraints weight = 64428.956| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.59 r_work: 0.2905 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 24684 Z= 0.221 Angle : 0.595 7.788 33479 Z= 0.314 Chirality : 0.047 0.214 3856 Planarity : 0.005 0.064 4363 Dihedral : 8.414 168.567 3593 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.06 % Allowed : 9.19 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.15), residues: 3115 helix: 1.20 (0.15), residues: 1229 sheet: 0.15 (0.22), residues: 522 loop : -0.41 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 412 TYR 0.022 0.002 TYR B 248 PHE 0.015 0.002 PHE F 257 HIS 0.005 0.001 HIS D 200 Details of bonding type rmsd covalent geometry : bond 0.00530 (24684) covalent geometry : angle 0.59484 (33479) hydrogen bonds : bond 0.05229 ( 1184) hydrogen bonds : angle 5.05194 ( 3411) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 115 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 95 MET cc_start: 0.9485 (mmm) cc_final: 0.8838 (tpt) REVERT: B 393 GLU cc_start: 0.6469 (OUTLIER) cc_final: 0.6100 (pt0) REVERT: D 56 ASP cc_start: 0.8140 (t0) cc_final: 0.7588 (t0) REVERT: E 396 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7367 (t70) REVERT: E 441 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8397 (mt) REVERT: F 43 ASP cc_start: 0.8833 (m-30) cc_final: 0.8486 (m-30) REVERT: G 165 PHE cc_start: 0.7566 (OUTLIER) cc_final: 0.7158 (m-80) REVERT: G 193 ASP cc_start: 0.7719 (m-30) cc_final: 0.7153 (t70) REVERT: G 198 LYS cc_start: 0.6537 (OUTLIER) cc_final: 0.5949 (ttpt) outliers start: 53 outliers final: 29 residues processed: 159 average time/residue: 0.1308 time to fit residues: 35.7780 Evaluate side-chains 148 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 114 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 200 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 267 optimal weight: 7.9990 chunk 262 optimal weight: 1.9990 chunk 260 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 301 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 228 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.079451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.063967 restraints weight = 63436.871| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.55 r_work: 0.2952 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24684 Z= 0.114 Angle : 0.502 7.781 33479 Z= 0.265 Chirality : 0.043 0.179 3856 Planarity : 0.004 0.058 4363 Dihedral : 7.863 167.103 3592 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.67 % Allowed : 10.48 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.15), residues: 3115 helix: 1.51 (0.15), residues: 1238 sheet: 0.32 (0.22), residues: 520 loop : -0.21 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 40 TYR 0.017 0.001 TYR B 248 PHE 0.012 0.001 PHE A 494 HIS 0.004 0.001 HIS G 65 Details of bonding type rmsd covalent geometry : bond 0.00250 (24684) covalent geometry : angle 0.50240 (33479) hydrogen bonds : bond 0.04120 ( 1184) hydrogen bonds : angle 4.74264 ( 3411) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 125 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ASP cc_start: 0.8110 (m-30) cc_final: 0.7893 (m-30) REVERT: B 95 MET cc_start: 0.9466 (mmm) cc_final: 0.8795 (tpt) REVERT: B 289 ASP cc_start: 0.8041 (t0) cc_final: 0.7815 (t0) REVERT: B 393 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.6130 (pt0) REVERT: D 56 ASP cc_start: 0.8143 (t0) cc_final: 0.7621 (t0) REVERT: F 43 ASP cc_start: 0.8852 (m-30) cc_final: 0.8451 (m-30) REVERT: G 165 PHE cc_start: 0.7582 (OUTLIER) cc_final: 0.7091 (m-80) REVERT: G 193 ASP cc_start: 0.7659 (m-30) cc_final: 0.7224 (t70) REVERT: G 198 LYS cc_start: 0.6651 (OUTLIER) cc_final: 0.6081 (ttpt) outliers start: 43 outliers final: 27 residues processed: 159 average time/residue: 0.1306 time to fit residues: 35.6837 Evaluate side-chains 147 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 3 SER Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 200 ARG Chi-restraints excluded: chain G residue 273 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 165 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 138 optimal weight: 7.9990 chunk 178 optimal weight: 9.9990 chunk 212 optimal weight: 9.9990 chunk 273 optimal weight: 10.0000 chunk 278 optimal weight: 8.9990 chunk 260 optimal weight: 1.9990 chunk 202 optimal weight: 0.9980 chunk 123 optimal weight: 9.9990 chunk 239 optimal weight: 2.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 200 GLN G 65 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.077250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.061636 restraints weight = 64792.098| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.59 r_work: 0.2897 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 24684 Z= 0.237 Angle : 0.597 8.608 33479 Z= 0.313 Chirality : 0.047 0.305 3856 Planarity : 0.005 0.055 4363 Dihedral : 8.099 168.073 3591 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.06 % Allowed : 11.06 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.15), residues: 3115 helix: 1.33 (0.15), residues: 1221 sheet: 0.19 (0.22), residues: 521 loop : -0.41 (0.17), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 93 TYR 0.020 0.002 TYR B 248 PHE 0.017 0.002 PHE F 257 HIS 0.006 0.001 HIS D 200 Details of bonding type rmsd covalent geometry : bond 0.00573 (24684) covalent geometry : angle 0.59738 (33479) hydrogen bonds : bond 0.05217 ( 1184) hydrogen bonds : angle 4.95425 ( 3411) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 117 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 262 ASP cc_start: 0.8240 (m-30) cc_final: 0.8034 (m-30) REVERT: B 393 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.6165 (pt0) REVERT: D 56 ASP cc_start: 0.8142 (t0) cc_final: 0.7598 (t0) REVERT: E 396 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7461 (t70) REVERT: E 441 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8395 (mt) REVERT: F 43 ASP cc_start: 0.8817 (m-30) cc_final: 0.8510 (m-30) REVERT: G 165 PHE cc_start: 0.7500 (OUTLIER) cc_final: 0.6909 (m-80) REVERT: G 193 ASP cc_start: 0.7641 (m-30) cc_final: 0.7190 (t70) REVERT: G 198 LYS cc_start: 0.6529 (OUTLIER) cc_final: 0.5987 (ttpt) outliers start: 53 outliers final: 34 residues processed: 160 average time/residue: 0.1305 time to fit residues: 35.1638 Evaluate side-chains 150 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 111 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 200 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 296 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 233 optimal weight: 7.9990 chunk 226 optimal weight: 10.0000 chunk 146 optimal weight: 7.9990 chunk 305 optimal weight: 9.9990 chunk 303 optimal weight: 6.9990 chunk 175 optimal weight: 0.9980 chunk 283 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 HIS G 65 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.077049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.061572 restraints weight = 64383.286| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.58 r_work: 0.2896 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24684 Z= 0.219 Angle : 0.583 8.636 33479 Z= 0.307 Chirality : 0.046 0.273 3856 Planarity : 0.005 0.050 4363 Dihedral : 8.087 169.620 3591 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.10 % Allowed : 11.88 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.15), residues: 3115 helix: 1.30 (0.15), residues: 1220 sheet: 0.14 (0.22), residues: 519 loop : -0.46 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 93 TYR 0.020 0.001 TYR B 248 PHE 0.015 0.002 PHE A 494 HIS 0.005 0.001 HIS D 200 Details of bonding type rmsd covalent geometry : bond 0.00526 (24684) covalent geometry : angle 0.58317 (33479) hydrogen bonds : bond 0.05103 ( 1184) hydrogen bonds : angle 4.95671 ( 3411) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 111 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: B 357 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.9011 (mp) REVERT: B 393 GLU cc_start: 0.6524 (OUTLIER) cc_final: 0.6162 (pt0) REVERT: D 56 ASP cc_start: 0.8143 (t0) cc_final: 0.7589 (t0) REVERT: E 164 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8153 (mttt) REVERT: E 332 GLU cc_start: 0.7923 (tp30) cc_final: 0.7583 (tm-30) REVERT: E 396 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7536 (t70) REVERT: E 441 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8515 (mt) REVERT: F 43 ASP cc_start: 0.8828 (m-30) cc_final: 0.8522 (m-30) REVERT: G 165 PHE cc_start: 0.7499 (OUTLIER) cc_final: 0.6906 (m-10) REVERT: G 193 ASP cc_start: 0.7616 (m-30) cc_final: 0.7167 (t70) REVERT: G 198 LYS cc_start: 0.6582 (OUTLIER) cc_final: 0.5992 (ttpt) outliers start: 54 outliers final: 38 residues processed: 155 average time/residue: 0.1300 time to fit residues: 34.5835 Evaluate side-chains 153 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 108 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 164 LYS Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 200 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 70 optimal weight: 6.9990 chunk 273 optimal weight: 9.9990 chunk 282 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 272 optimal weight: 0.8980 chunk 227 optimal weight: 3.9990 chunk 163 optimal weight: 0.0980 chunk 237 optimal weight: 4.9990 chunk 275 optimal weight: 0.9990 chunk 242 optimal weight: 6.9990 chunk 217 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 65 HIS ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.078447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.063025 restraints weight = 64015.770| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.55 r_work: 0.2925 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24684 Z= 0.136 Angle : 0.516 7.778 33479 Z= 0.273 Chirality : 0.044 0.251 3856 Planarity : 0.004 0.048 4363 Dihedral : 7.798 169.236 3591 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.87 % Allowed : 12.23 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.15), residues: 3115 helix: 1.53 (0.15), residues: 1224 sheet: 0.31 (0.22), residues: 519 loop : -0.34 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 40 TYR 0.017 0.001 TYR B 248 PHE 0.015 0.001 PHE B 456 HIS 0.004 0.001 HIS E 179 Details of bonding type rmsd covalent geometry : bond 0.00314 (24684) covalent geometry : angle 0.51649 (33479) hydrogen bonds : bond 0.04330 ( 1184) hydrogen bonds : angle 4.75843 ( 3411) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 116 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: A 236 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.8490 (t80) REVERT: A 262 ASP cc_start: 0.8194 (m-30) cc_final: 0.7927 (m-30) REVERT: B 393 GLU cc_start: 0.6434 (OUTLIER) cc_final: 0.6072 (pt0) REVERT: D 56 ASP cc_start: 0.8104 (t0) cc_final: 0.7531 (t0) REVERT: E 164 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8038 (mttt) REVERT: E 396 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7446 (t70) REVERT: E 441 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8482 (mt) REVERT: F 43 ASP cc_start: 0.8853 (m-30) cc_final: 0.8477 (m-30) REVERT: G 165 PHE cc_start: 0.7493 (OUTLIER) cc_final: 0.6870 (m-10) REVERT: G 193 ASP cc_start: 0.7658 (m-30) cc_final: 0.7173 (t70) REVERT: G 198 LYS cc_start: 0.6617 (OUTLIER) cc_final: 0.6024 (ttpt) outliers start: 48 outliers final: 35 residues processed: 153 average time/residue: 0.1291 time to fit residues: 33.6494 Evaluate side-chains 150 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 108 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 164 LYS Chi-restraints excluded: chain E residue 202 MET Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 200 ARG Chi-restraints excluded: chain G residue 273 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 154 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 208 optimal weight: 9.9990 chunk 148 optimal weight: 6.9990 chunk 262 optimal weight: 3.9990 chunk 206 optimal weight: 10.0000 chunk 222 optimal weight: 0.0870 chunk 121 optimal weight: 4.9990 chunk 225 optimal weight: 4.9990 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 GLN G 65 HIS ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.077198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.061821 restraints weight = 64698.250| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.55 r_work: 0.2902 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 24684 Z= 0.212 Angle : 0.579 8.709 33479 Z= 0.304 Chirality : 0.046 0.320 3856 Planarity : 0.004 0.048 4363 Dihedral : 7.951 170.268 3591 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.95 % Allowed : 12.15 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.15), residues: 3115 helix: 1.33 (0.15), residues: 1226 sheet: 0.21 (0.22), residues: 521 loop : -0.43 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 365 TYR 0.019 0.001 TYR B 248 PHE 0.021 0.002 PHE G 42 HIS 0.005 0.001 HIS E 401 Details of bonding type rmsd covalent geometry : bond 0.00511 (24684) covalent geometry : angle 0.57949 (33479) hydrogen bonds : bond 0.04964 ( 1184) hydrogen bonds : angle 4.88987 ( 3411) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 107 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: A 236 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8601 (t80) REVERT: B 357 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.8986 (mp) REVERT: B 393 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.6213 (pt0) REVERT: D 56 ASP cc_start: 0.8155 (t0) cc_final: 0.7597 (t0) REVERT: E 396 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7500 (t70) REVERT: E 441 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8518 (mt) REVERT: F 43 ASP cc_start: 0.8821 (m-30) cc_final: 0.8511 (m-30) REVERT: G 165 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.6837 (m-10) REVERT: G 193 ASP cc_start: 0.7623 (m-30) cc_final: 0.7151 (t70) REVERT: G 198 LYS cc_start: 0.6639 (OUTLIER) cc_final: 0.6043 (ttpt) outliers start: 50 outliers final: 37 residues processed: 148 average time/residue: 0.1313 time to fit residues: 33.4921 Evaluate side-chains 149 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 105 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 200 ARG Chi-restraints excluded: chain G residue 273 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 149 optimal weight: 2.9990 chunk 299 optimal weight: 9.9990 chunk 169 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 301 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 291 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 273 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 chunk 246 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 HIS ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.077352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.061993 restraints weight = 64417.311| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.54 r_work: 0.2906 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 24684 Z= 0.193 Angle : 0.566 9.813 33479 Z= 0.298 Chirality : 0.046 0.304 3856 Planarity : 0.004 0.049 4363 Dihedral : 7.932 171.229 3591 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.83 % Allowed : 12.27 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.15), residues: 3115 helix: 1.36 (0.15), residues: 1223 sheet: 0.20 (0.22), residues: 521 loop : -0.46 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 365 TYR 0.019 0.001 TYR B 248 PHE 0.015 0.002 PHE B 456 HIS 0.005 0.001 HIS E 401 Details of bonding type rmsd covalent geometry : bond 0.00463 (24684) covalent geometry : angle 0.56584 (33479) hydrogen bonds : bond 0.04863 ( 1184) hydrogen bonds : angle 4.87127 ( 3411) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 105 time to evaluate : 0.857 Fit side-chains REVERT: A 236 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8546 (t80) REVERT: B 357 ILE cc_start: 0.9324 (OUTLIER) cc_final: 0.8977 (mp) REVERT: B 393 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.6180 (pt0) REVERT: D 56 ASP cc_start: 0.8121 (t0) cc_final: 0.7568 (t0) REVERT: E 396 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7494 (t70) REVERT: E 441 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8531 (mt) REVERT: F 43 ASP cc_start: 0.8817 (m-30) cc_final: 0.8505 (m-30) REVERT: G 67 MET cc_start: 0.5408 (ppp) cc_final: 0.4410 (mtt) REVERT: G 165 PHE cc_start: 0.7510 (OUTLIER) cc_final: 0.6851 (m-10) REVERT: G 193 ASP cc_start: 0.7604 (m-30) cc_final: 0.7142 (t70) REVERT: G 198 LYS cc_start: 0.6628 (OUTLIER) cc_final: 0.6054 (ttpt) outliers start: 47 outliers final: 37 residues processed: 143 average time/residue: 0.1271 time to fit residues: 31.3805 Evaluate side-chains 148 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 104 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 383 ILE Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 200 ARG Chi-restraints excluded: chain G residue 273 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 298 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 191 optimal weight: 1.9990 chunk 281 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 287 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 222 optimal weight: 0.0270 chunk 238 optimal weight: 10.0000 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 HIS ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.078593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.063153 restraints weight = 63897.191| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.57 r_work: 0.2938 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24684 Z= 0.130 Angle : 0.518 8.595 33479 Z= 0.273 Chirality : 0.044 0.299 3856 Planarity : 0.004 0.048 4363 Dihedral : 7.698 170.493 3591 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.83 % Allowed : 12.31 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.15), residues: 3115 helix: 1.56 (0.15), residues: 1226 sheet: 0.35 (0.22), residues: 519 loop : -0.35 (0.17), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 40 TYR 0.017 0.001 TYR B 248 PHE 0.016 0.001 PHE B 456 HIS 0.004 0.001 HIS E 179 Details of bonding type rmsd covalent geometry : bond 0.00302 (24684) covalent geometry : angle 0.51765 (33479) hydrogen bonds : bond 0.04220 ( 1184) hydrogen bonds : angle 4.71437 ( 3411) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4178.72 seconds wall clock time: 72 minutes 38.34 seconds (4358.34 seconds total)