Starting phenix.real_space_refine on Sat Jun 21 03:47:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hh4_34751/06_2025/8hh4_34751.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hh4_34751/06_2025/8hh4_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hh4_34751/06_2025/8hh4_34751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hh4_34751/06_2025/8hh4_34751.map" model { file = "/net/cci-nas-00/data/ceres_data/8hh4_34751/06_2025/8hh4_34751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hh4_34751/06_2025/8hh4_34751.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.59, per 1000 atoms: 0.60 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: 6.13 Conformation dependent library (CDL) restraints added in 3.1 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: 3.01 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: 8.20 Time building geometry restraints manager: 7.19 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: 3.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.920 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 54.180 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.070 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 HIS 0.007 0.001 HIS E 401 PHE 0.016 0.002 PHE A 494 TYR 0.017 0.001 TYR B 248 ARG 0.004 0.000 ARG B 455 Details of bonding type rmsd hydrogen bonds : bond 0.15491 ( 1184) hydrogen bonds : angle 6.35293 ( 3411) covalent geometry : bond 0.00524 (24684) covalent geometry : angle 0.75733 (33479) *********************** 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 : 2.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8366 (ttp) cc_final: 0.8012 (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: 0.7685 (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: 0.7465 (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: 0.7020 (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: 0.4006 time to fit residues: 159.9369 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 : 3.040 ------------------------------------------------------------------------------- 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 261 optimal weight: 3.9990 chunk 234 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 158 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 242 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 147 optimal weight: 9.9990 chunk 180 optimal weight: 0.9990 chunk 281 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 G 50 GLN 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 = 0.077679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.062064 restraints weight = 64285.090| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.56 r_work: 0.2913 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 24684 Z= 0.272 Angle : 0.669 9.295 33479 Z= 0.352 Chirality : 0.049 0.241 3856 Planarity : 0.005 0.058 4363 Dihedral : 9.320 165.870 3613 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.21 % Allowed : 6.62 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.15), residues: 3115 helix: 1.01 (0.15), residues: 1232 sheet: 0.11 (0.21), residues: 537 loop : -0.39 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 470 PHE 0.017 0.002 PHE A 494 TYR 0.022 0.002 TYR B 248 ARG 0.006 0.001 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.05864 ( 1184) hydrogen bonds : angle 5.39020 ( 3411) covalent geometry : bond 0.00655 (24684) covalent geometry : angle 0.66867 (33479) *********************** 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 168 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 2.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 496 LYS cc_start: 0.8911 (mtpp) cc_final: 0.8703 (mttm) REVERT: E 332 GLU cc_start: 0.8204 (tp30) cc_final: 0.7984 (tp30) REVERT: E 396 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7367 (t70) REVERT: G 148 ASP cc_start: 0.7163 (m-30) cc_final: 0.6926 (p0) REVERT: G 193 ASP cc_start: 0.7623 (m-30) cc_final: 0.7187 (t70) REVERT: G 198 LYS cc_start: 0.6473 (OUTLIER) cc_final: 0.6011 (ttpt) REVERT: G 241 MET cc_start: 0.8479 (ttp) cc_final: 0.8249 (ttp) outliers start: 31 outliers final: 15 residues processed: 162 average time/residue: 0.3472 time to fit residues: 92.9509 Evaluate side-chains 138 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 2.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 392 LEU 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 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 3 SER Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 200 ARG Chi-restraints excluded: chain G residue 201 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 129 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 297 optimal weight: 9.9990 chunk 81 optimal weight: 0.0870 chunk 239 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 283 optimal weight: 8.9990 chunk 128 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN F 324 HIS F 330 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.079594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.064004 restraints weight = 63324.199| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.55 r_work: 0.2957 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1613 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= 0.129 Angle : 0.528 7.416 33479 Z= 0.279 Chirality : 0.044 0.183 3856 Planarity : 0.004 0.076 4363 Dihedral : 8.322 167.040 3593 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.09 % Allowed : 7.98 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.15), residues: 3115 helix: 1.33 (0.15), residues: 1247 sheet: 0.31 (0.22), residues: 526 loop : -0.23 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 65 PHE 0.014 0.001 PHE B 456 TYR 0.021 0.001 TYR G 226 ARG 0.004 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.04452 ( 1184) hydrogen bonds : angle 4.94549 ( 3411) covalent geometry : bond 0.00292 (24684) covalent geometry : angle 0.52776 (33479) *********************** 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 153 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 2.769 Fit side-chains revert: symmetry clash REVERT: B 289 ASP cc_start: 0.8047 (t0) cc_final: 0.7802 (t0) REVERT: B 393 GLU cc_start: 0.6389 (OUTLIER) cc_final: 0.5379 (pt0) REVERT: C 496 LYS cc_start: 0.8859 (mtpp) cc_final: 0.8655 (mttm) REVERT: E 332 GLU cc_start: 0.8153 (tp30) cc_final: 0.7930 (tp30) REVERT: E 396 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7403 (t70) REVERT: F 43 ASP cc_start: 0.8859 (m-30) cc_final: 0.8466 (m-30) REVERT: G 146 PHE cc_start: 0.6803 (t80) cc_final: 0.6539 (t80) REVERT: G 193 ASP cc_start: 0.7639 (m-30) cc_final: 0.7207 (t70) REVERT: G 198 LYS cc_start: 0.6519 (OUTLIER) cc_final: 0.5933 (ttpt) outliers start: 28 outliers final: 17 residues processed: 146 average time/residue: 0.3305 time to fit residues: 81.8455 Evaluate side-chains 136 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 2.860 ------------------------------------------------------------------------------- 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 326 ILE Chi-restraints excluded: chain A residue 435 LEU 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 366 VAL Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 398 LEU 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 301 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 203 optimal weight: 5.9990 chunk 247 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 145 optimal weight: 10.0000 chunk 278 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 134 optimal weight: 0.0470 chunk 137 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 105 optimal weight: 9.9990 overall best weight: 2.1884 ------------------------------------------------------------------------------- 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 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.079272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.063598 restraints weight = 63890.183| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.60 r_work: 0.2942 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24684 Z= 0.139 Angle : 0.521 7.570 33479 Z= 0.274 Chirality : 0.044 0.271 3856 Planarity : 0.004 0.064 4363 Dihedral : 8.009 164.083 3593 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.60 % Allowed : 9.27 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.15), residues: 3115 helix: 1.48 (0.15), residues: 1233 sheet: 0.35 (0.22), residues: 526 loop : -0.19 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 65 PHE 0.014 0.001 PHE A 494 TYR 0.017 0.001 TYR B 248 ARG 0.003 0.000 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.04367 ( 1184) hydrogen bonds : angle 4.80201 ( 3411) covalent geometry : bond 0.00321 (24684) covalent geometry : angle 0.52139 (33479) *********************** 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 164 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 2.994 Fit side-chains revert: symmetry clash REVERT: A 137 MET cc_start: 0.9182 (mmt) cc_final: 0.8968 (mmt) REVERT: B 64 LEU cc_start: 0.9088 (mt) cc_final: 0.8805 (mt) REVERT: B 289 ASP cc_start: 0.8077 (t0) cc_final: 0.7768 (t0) REVERT: D 56 ASP cc_start: 0.8088 (t0) cc_final: 0.7520 (t0) REVERT: E 332 GLU cc_start: 0.8170 (tp30) cc_final: 0.7958 (tp30) REVERT: E 396 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7397 (t70) REVERT: E 441 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8361 (mt) REVERT: F 43 ASP cc_start: 0.8858 (m-30) cc_final: 0.8473 (m-30) REVERT: G 146 PHE cc_start: 0.6755 (t80) cc_final: 0.6546 (t80) REVERT: G 165 PHE cc_start: 0.7572 (OUTLIER) cc_final: 0.7160 (m-80) REVERT: G 193 ASP cc_start: 0.7674 (m-30) cc_final: 0.7232 (t70) REVERT: G 198 LYS cc_start: 0.6620 (OUTLIER) cc_final: 0.6066 (ttpt) outliers start: 41 outliers final: 22 residues processed: 156 average time/residue: 0.3126 time to fit residues: 84.1162 Evaluate side-chains 143 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 2.972 ------------------------------------------------------------------------------- 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 326 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 99 VAL 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 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 D residue 430 VAL Chi-restraints excluded: chain E residue 32 ILE 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 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 197 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 247 optimal weight: 0.0070 chunk 178 optimal weight: 10.0000 chunk 237 optimal weight: 4.9990 chunk 292 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 chunk 279 optimal weight: 6.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.078733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.063187 restraints weight = 64115.733| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.56 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: 0.8640 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24684 Z= 0.159 Angle : 0.529 8.191 33479 Z= 0.278 Chirality : 0.045 0.291 3856 Planarity : 0.004 0.059 4363 Dihedral : 7.900 164.854 3592 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.91 % Allowed : 10.05 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.15), residues: 3115 helix: 1.54 (0.15), residues: 1220 sheet: 0.28 (0.22), residues: 519 loop : -0.24 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 65 PHE 0.014 0.001 PHE A 494 TYR 0.018 0.001 TYR B 248 ARG 0.003 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.04509 ( 1184) hydrogen bonds : angle 4.78390 ( 3411) covalent geometry : bond 0.00377 (24684) covalent geometry : angle 0.52853 (33479) *********************** 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 167 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 118 time to evaluate : 2.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 289 ASP cc_start: 0.8113 (t0) cc_final: 0.7784 (t0) REVERT: D 56 ASP cc_start: 0.8142 (t0) cc_final: 0.7626 (t0) REVERT: E 396 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7484 (t70) REVERT: E 441 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8383 (mt) REVERT: F 43 ASP cc_start: 0.8835 (m-30) cc_final: 0.8453 (m-30) REVERT: G 42 PHE cc_start: 0.4902 (p90) cc_final: 0.4660 (p90) REVERT: G 165 PHE cc_start: 0.7583 (OUTLIER) cc_final: 0.7100 (m-80) REVERT: G 193 ASP cc_start: 0.7690 (m-30) cc_final: 0.7227 (t70) REVERT: G 198 LYS cc_start: 0.6624 (OUTLIER) cc_final: 0.6070 (ttpt) outliers start: 49 outliers final: 28 residues processed: 159 average time/residue: 0.3105 time to fit residues: 84.4939 Evaluate side-chains 146 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 3.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 156 LEU 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 D residue 430 VAL Chi-restraints excluded: chain E residue 32 ILE 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 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 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 265 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 239 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 196 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 72 optimal weight: 0.0670 chunk 149 optimal weight: 3.9990 chunk 186 optimal weight: 0.3980 chunk 176 optimal weight: 0.8980 overall best weight: 1.0722 ------------------------------------------------------------------------------- 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 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.080672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.065134 restraints weight = 63360.780| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.58 r_work: 0.2979 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24684 Z= 0.098 Angle : 0.473 7.735 33479 Z= 0.249 Chirality : 0.043 0.228 3856 Planarity : 0.004 0.055 4363 Dihedral : 7.477 162.886 3591 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.64 % Allowed : 10.67 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.15), residues: 3115 helix: 1.68 (0.15), residues: 1248 sheet: 0.48 (0.22), residues: 518 loop : -0.07 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 179 PHE 0.012 0.001 PHE A 494 TYR 0.020 0.001 TYR G 226 ARG 0.003 0.000 ARG B 412 Details of bonding type rmsd hydrogen bonds : bond 0.03584 ( 1184) hydrogen bonds : angle 4.55662 ( 3411) covalent geometry : bond 0.00210 (24684) covalent geometry : angle 0.47276 (33479) *********************** 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 172 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 130 time to evaluate : 2.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 289 ASP cc_start: 0.8000 (t0) cc_final: 0.7644 (t0) REVERT: B 421 LYS cc_start: 0.8568 (mttt) cc_final: 0.8339 (mttp) REVERT: D 56 ASP cc_start: 0.8080 (t0) cc_final: 0.7526 (t0) REVERT: E 441 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8364 (mt) REVERT: F 43 ASP cc_start: 0.8871 (m-30) cc_final: 0.8475 (m-30) REVERT: F 396 ASP cc_start: 0.8705 (m-30) cc_final: 0.8488 (m-30) REVERT: G 146 PHE cc_start: 0.7019 (t80) cc_final: 0.6342 (m-80) REVERT: G 165 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.6967 (m-80) REVERT: G 193 ASP cc_start: 0.7732 (m-30) cc_final: 0.7254 (t70) REVERT: G 198 LYS cc_start: 0.6529 (OUTLIER) cc_final: 0.5954 (ttpt) outliers start: 42 outliers final: 25 residues processed: 165 average time/residue: 0.3341 time to fit residues: 92.0567 Evaluate side-chains 144 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 156 LEU Chi-restraints excluded: chain B residue 262 ASP 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 D residue 247 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 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 F residue 390 ASP Chi-restraints excluded: chain G residue 73 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 281 optimal weight: 0.9990 chunk 264 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 131 optimal weight: 20.0000 chunk 240 optimal weight: 6.9990 chunk 254 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 200 optimal weight: 0.6980 chunk 182 optimal weight: 8.9990 chunk 271 optimal weight: 9.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 HIS E 365 GLN G 65 HIS ** G 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.077857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.062338 restraints weight = 64449.163| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.57 r_work: 0.2917 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 24684 Z= 0.210 Angle : 0.575 8.092 33479 Z= 0.300 Chirality : 0.046 0.308 3856 Planarity : 0.005 0.084 4363 Dihedral : 7.842 165.362 3591 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.75 % Allowed : 11.06 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.15), residues: 3115 helix: 1.53 (0.15), residues: 1227 sheet: 0.26 (0.22), residues: 531 loop : -0.28 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 200 PHE 0.016 0.002 PHE A 494 TYR 0.018 0.002 TYR B 248 ARG 0.004 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.04875 ( 1184) hydrogen bonds : angle 4.80336 ( 3411) covalent geometry : bond 0.00506 (24684) covalent geometry : angle 0.57456 (33479) *********************** 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 161 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 116 time to evaluate : 2.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 289 ASP cc_start: 0.8200 (t0) cc_final: 0.7939 (t0) REVERT: D 56 ASP cc_start: 0.8097 (t0) cc_final: 0.7569 (t0) REVERT: E 396 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7503 (t70) REVERT: E 441 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8372 (mt) REVERT: F 43 ASP cc_start: 0.8839 (m-30) cc_final: 0.8510 (m-30) REVERT: G 165 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.6872 (m-10) REVERT: G 193 ASP cc_start: 0.7622 (m-30) cc_final: 0.7181 (t70) REVERT: G 198 LYS cc_start: 0.6558 (OUTLIER) cc_final: 0.5958 (ttpt) outliers start: 45 outliers final: 29 residues processed: 154 average time/residue: 0.3090 time to fit residues: 82.4698 Evaluate side-chains 147 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 2.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL 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 156 LEU Chi-restraints excluded: chain B residue 347 ASP 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 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 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 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 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 256 optimal weight: 7.9990 chunk 245 optimal weight: 0.9990 chunk 250 optimal weight: 4.9990 chunk 299 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 159 optimal weight: 8.9990 chunk 173 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 274 optimal weight: 8.9990 chunk 306 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.3330 r_free = 0.3330 target = 0.077207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.061761 restraints weight = 64323.550| |-----------------------------------------------------------------------------| r_work (start): 0.3014 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: 0.8685 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 24684 Z= 0.227 Angle : 0.584 9.515 33479 Z= 0.307 Chirality : 0.047 0.282 3856 Planarity : 0.005 0.068 4363 Dihedral : 7.976 168.711 3591 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.75 % Allowed : 11.41 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.15), residues: 3115 helix: 1.39 (0.15), residues: 1224 sheet: 0.11 (0.21), residues: 530 loop : -0.41 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 200 PHE 0.016 0.002 PHE A 494 TYR 0.020 0.002 TYR B 248 ARG 0.004 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.05051 ( 1184) hydrogen bonds : angle 4.87977 ( 3411) covalent geometry : bond 0.00547 (24684) covalent geometry : angle 0.58428 (33479) *********************** 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 155 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 110 time to evaluate : 2.596 Fit side-chains revert: symmetry clash REVERT: B 289 ASP cc_start: 0.8242 (t0) cc_final: 0.7969 (t0) REVERT: D 56 ASP cc_start: 0.8147 (t0) cc_final: 0.7637 (t0) REVERT: E 396 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7545 (t70) REVERT: E 441 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8427 (mt) REVERT: F 43 ASP cc_start: 0.8809 (m-30) cc_final: 0.8530 (m-30) REVERT: G 165 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.6945 (m-10) REVERT: G 193 ASP cc_start: 0.7580 (m-30) cc_final: 0.7137 (t70) REVERT: G 198 LYS cc_start: 0.6599 (OUTLIER) cc_final: 0.5986 (ttpt) outliers start: 45 outliers final: 33 residues processed: 144 average time/residue: 0.3128 time to fit residues: 77.8086 Evaluate side-chains 146 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 156 LEU 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 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 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 111 ASP Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain G residue 170 MET Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 200 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 7.9990 chunk 247 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 230 optimal weight: 0.6980 chunk 210 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.078834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.063333 restraints weight = 63874.227| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.55 r_work: 0.2937 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24684 Z= 0.125 Angle : 0.505 8.321 33479 Z= 0.266 Chirality : 0.044 0.265 3856 Planarity : 0.004 0.060 4363 Dihedral : 7.660 167.666 3591 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.56 % Allowed : 11.76 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.15), residues: 3115 helix: 1.58 (0.15), residues: 1236 sheet: 0.34 (0.22), residues: 517 loop : -0.25 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 179 PHE 0.019 0.001 PHE G 42 TYR 0.016 0.001 TYR B 248 ARG 0.003 0.000 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 1184) hydrogen bonds : angle 4.66480 ( 3411) covalent geometry : bond 0.00289 (24684) covalent geometry : angle 0.50541 (33479) *********************** 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 156 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 3.143 Fit side-chains revert: symmetry clash REVERT: B 289 ASP cc_start: 0.8092 (t0) cc_final: 0.7734 (t0) REVERT: D 56 ASP cc_start: 0.8136 (t0) cc_final: 0.7551 (t0) REVERT: E 164 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8077 (mttt) REVERT: E 396 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7491 (t70) REVERT: E 441 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8371 (mt) REVERT: F 43 ASP cc_start: 0.8875 (m-30) cc_final: 0.8505 (m-30) REVERT: G 165 PHE cc_start: 0.7533 (OUTLIER) cc_final: 0.6991 (m-10) REVERT: G 193 ASP cc_start: 0.7592 (m-30) cc_final: 0.7169 (t70) REVERT: G 198 LYS cc_start: 0.6543 (OUTLIER) cc_final: 0.5999 (ttpt) outliers start: 40 outliers final: 28 residues processed: 147 average time/residue: 0.3273 time to fit residues: 82.8070 Evaluate side-chains 144 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL 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 156 LEU 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 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 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 F residue 390 ASP Chi-restraints excluded: chain G residue 73 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 220 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 253 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 109 optimal weight: 0.1980 chunk 224 optimal weight: 10.0000 chunk 134 optimal weight: 0.6980 chunk 159 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 = 0.3352 r_free = 0.3352 target = 0.078269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.062824 restraints weight = 63953.895| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.54 r_work: 0.2931 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24684 Z= 0.158 Angle : 0.528 8.731 33479 Z= 0.277 Chirality : 0.044 0.260 3856 Planarity : 0.004 0.071 4363 Dihedral : 7.694 168.095 3591 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.44 % Allowed : 12.03 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.15), residues: 3115 helix: 1.54 (0.15), residues: 1234 sheet: 0.32 (0.22), residues: 517 loop : -0.26 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 401 PHE 0.016 0.001 PHE B 456 TYR 0.016 0.001 TYR B 248 ARG 0.002 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.04395 ( 1184) hydrogen bonds : angle 4.69527 ( 3411) covalent geometry : bond 0.00375 (24684) covalent geometry : angle 0.52813 (33479) ********************** 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 148 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 111 time to evaluate : 2.845 Fit side-chains revert: symmetry clash REVERT: B 289 ASP cc_start: 0.8142 (t0) cc_final: 0.7874 (t0) REVERT: D 56 ASP cc_start: 0.8115 (t0) cc_final: 0.7545 (t0) REVERT: E 396 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7561 (t70) REVERT: E 441 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8388 (mt) REVERT: F 43 ASP cc_start: 0.8840 (m-30) cc_final: 0.8514 (m-30) REVERT: G 165 PHE cc_start: 0.7494 (OUTLIER) cc_final: 0.6850 (m-10) REVERT: G 193 ASP cc_start: 0.7594 (m-30) cc_final: 0.7168 (t70) REVERT: G 198 LYS cc_start: 0.6522 (OUTLIER) cc_final: 0.5966 (ttpt) outliers start: 37 outliers final: 29 residues processed: 141 average time/residue: 0.3495 time to fit residues: 85.8705 Evaluate side-chains 144 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 2.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL 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 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 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 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 F residue 390 ASP Chi-restraints excluded: chain G residue 73 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 64 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 136 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 239 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3337 r_free = 0.3337 target = 0.077566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.062145 restraints weight = 64099.889| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.54 r_work: 0.2917 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2301 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= 0.192 Angle : 0.556 9.461 33479 Z= 0.292 Chirality : 0.045 0.247 3856 Planarity : 0.004 0.065 4363 Dihedral : 7.813 170.034 3591 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.52 % Allowed : 12.11 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.15), residues: 3115 helix: 1.48 (0.15), residues: 1228 sheet: 0.26 (0.22), residues: 517 loop : -0.34 (0.17), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 401 PHE 0.016 0.002 PHE B 456 TYR 0.018 0.001 TYR B 248 ARG 0.003 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.04767 ( 1184) hydrogen bonds : angle 4.78097 ( 3411) covalent geometry : bond 0.00459 (24684) covalent geometry : angle 0.55643 (33479) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11170.55 seconds wall clock time: 201 minutes 40.47 seconds (12100.47 seconds total)