Starting phenix.real_space_refine on Mon Aug 25 01:41:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hh7_34754/08_2025/8hh7_34754.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hh7_34754/08_2025/8hh7_34754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hh7_34754/08_2025/8hh7_34754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hh7_34754/08_2025/8hh7_34754.map" model { file = "/net/cci-nas-00/data/ceres_data/8hh7_34754/08_2025/8hh7_34754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hh7_34754/08_2025/8hh7_34754.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 16 5.49 5 Mg 5 5.21 5 S 77 5.16 5 C 15277 2.51 5 N 4214 2.21 5 O 4661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24250 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: {'PTRANS': 23, '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: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 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: 4.43, per 1000 atoms: 0.18 Number of scatterers: 24250 At special positions: 0 Unit cell: (126.72, 120.56, 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 16 15.00 Mg 5 11.99 O 4661 8.00 N 4214 7.00 C 15277 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 865.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 135 helices and 19 sheets defined 49.0% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... 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 186 removed outlier: 3.637A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) 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 251 removed outlier: 3.579A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.541A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 289 through 299 removed outlier: 3.545A pdb=" N HIS A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 345 through 352 removed outlier: 3.542A pdb=" N GLY A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.516A pdb=" N ALA A 369 " --> pdb=" O VAL A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 393 removed outlier: 3.953A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 402 removed outlier: 4.440A pdb=" N GLN A 397 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 400 " --> pdb=" O GLN A 397 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP A 401 " --> pdb=" O PHE A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 420 removed outlier: 3.583A pdb=" N LEU A 410 " --> pdb=" O THR A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'A' and resid 449 through 451 No H-bonds generated for 'chain 'A' and resid 449 through 451' Processing helix chain 'A' and resid 452 through 468 Processing helix chain 'A' and resid 468 through 479 Processing helix chain 'A' and resid 483 through 496 Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.770A 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 removed outlier: 3.604A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' 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 251 removed outlier: 3.661A pdb=" N LEU B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.852A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 removed outlier: 3.951A 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 287 through 288 No H-bonds generated for 'chain 'B' and resid 287 through 288' Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.710A pdb=" N HIS B 294 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.670A 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 380 removed outlier: 3.853A pdb=" N VAL B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 397 Processing helix chain 'B' and resid 403 through 420 removed outlier: 3.501A pdb=" N ARG B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 442 Processing helix chain 'B' and resid 449 through 451 No H-bonds generated for 'chain 'B' and resid 449 through 451' Processing helix chain 'B' and resid 452 through 468 Processing helix chain 'B' and resid 468 through 479 Processing helix chain 'B' and resid 483 through 498 removed outlier: 3.582A pdb=" N THR B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.551A 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: 3.538A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 216 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 231 through 251 removed outlier: 3.604A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) Proline residue: C 239 - end of helix removed outlier: 3.783A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 removed outlier: 4.054A pdb=" N GLN C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 289 through 299 removed outlier: 3.778A pdb=" N HIS C 294 " --> pdb=" O ILE C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 309 Processing helix chain 'C' and resid 328 through 336 Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 372 through 380 Processing helix chain 'C' and resid 381 through 397 Processing helix chain 'C' and resid 403 through 420 Processing helix chain 'C' and resid 429 through 442 removed outlier: 3.588A pdb=" N LEU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) 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 468 Processing helix chain 'C' and resid 468 through 479 Processing helix chain 'C' and resid 483 through 498 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'D' and resid 163 through 176 Processing helix chain 'D' and resid 177 through 179 No H-bonds generated for 'chain 'D' and resid 177 through 179' Processing helix chain 'D' and resid 191 through 206 Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 221 through 243 removed outlier: 5.108A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN D 243 " --> pdb=" O PHE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 269 removed outlier: 4.067A pdb=" N THR D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LEU D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 290 Processing helix chain 'D' and resid 309 through 312 Processing helix chain 'D' and resid 315 through 322 Processing helix chain 'D' and resid 323 through 325 No H-bonds generated for 'chain 'D' and resid 323 through 325' Processing helix chain 'D' and resid 332 through 338 removed outlier: 3.689A pdb=" N MET D 338 " --> pdb=" O LYS D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 360 through 388 removed outlier: 3.514A pdb=" N GLN D 381 " --> pdb=" O TYR D 377 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 410 removed outlier: 3.725A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 416 No H-bonds generated for 'chain 'D' and resid 414 through 416' Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 429 through 443 Processing helix chain 'D' and resid 449 through 454 Processing helix chain 'D' and resid 458 through 470 removed outlier: 3.795A pdb=" N VAL D 462 " --> pdb=" O ARG D 458 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 124 through 128 Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 163 through 180 Processing helix chain 'E' and resid 191 through 206 Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 221 through 242 removed outlier: 5.113A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 removed outlier: 3.764A pdb=" N PHE E 257 " --> pdb=" O ASN E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 290 Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 315 through 323 removed outlier: 3.508A pdb=" N SER E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 339 Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 360 through 380 Processing helix chain 'E' and resid 380 through 388 Processing helix chain 'E' and resid 389 through 392 Processing helix chain 'E' and resid 393 through 410 removed outlier: 3.617A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 416 No H-bonds generated for 'chain 'E' and resid 414 through 416' 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 458 through 470 removed outlier: 3.916A pdb=" N VAL E 462 " --> pdb=" O ARG E 458 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 124 through 128 removed outlier: 3.550A pdb=" N LEU F 128 " --> pdb=" O PHE F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 146 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: 5.043A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 269 removed outlier: 3.932A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY F 269 " --> pdb=" O SER F 265 " (cutoff:3.500A) 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 321 removed outlier: 3.598A pdb=" N THR F 321 " --> pdb=" O ALA F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 325 Processing helix chain 'F' and resid 332 through 338 Processing helix chain 'F' and resid 355 through 360 Processing helix chain 'F' and resid 360 through 380 removed outlier: 3.667A pdb=" N LEU F 380 " --> pdb=" O ARG F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 388 Processing helix chain 'F' and resid 393 through 410 removed outlier: 3.777A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 420 removed outlier: 3.568A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 442 Processing helix chain 'F' and resid 449 through 454 removed outlier: 3.611A pdb=" N ARG F 454 " --> pdb=" O ASP F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 469 removed outlier: 3.816A pdb=" N VAL F 462 " --> pdb=" O ARG F 458 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 41 Processing helix chain 'G' and resid 42 through 58 removed outlier: 3.724A pdb=" N LEU G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 107 removed outlier: 3.915A 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 Processing helix chain 'G' and resid 145 through 162 removed outlier: 3.946A pdb=" N ILE G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N GLU G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE G 160 " --> pdb=" O THR G 156 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA G 161 " --> pdb=" O VAL G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 283 removed outlier: 4.000A pdb=" N ASP G 214 " --> pdb=" O GLU G 210 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL G 215 " --> pdb=" O GLU G 211 " (cutoff:3.500A) Proline residue: G 218 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 66 removed outlier: 4.025A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LYS E 17 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 5.724A 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 98 Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.231A pdb=" N ILE A 192 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N VAL A 259 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE A 194 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 66 removed outlier: 4.169A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ARG B 93 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N GLU B 54 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR B 91 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.133A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.379A pdb=" N ILE B 192 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL B 259 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE B 194 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 60 through 66 removed outlier: 4.168A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ARG C 93 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N GLU C 54 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N THR C 91 " --> pdb=" O GLU C 54 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLU D 75 " --> pdb=" O GLN D 33 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLN D 33 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN D 8 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LYS D 17 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL D 6 " --> pdb=" O LYS D 17 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.908A 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: 6.658A pdb=" N SER C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N VAL C 224 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB2, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.239A pdb=" N VAL D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE D 303 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N TYR D 307 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE D 154 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ILE D 306 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LEU D 156 " --> pdb=" O ILE D 306 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 134 through 135 removed outlier: 4.224A pdb=" N TYR D 148 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB5, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.454A pdb=" N PHE E 96 " --> pdb=" O PHE E 215 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N GLN E 217 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.325A pdb=" N TYR E 148 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AB8, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.766A pdb=" N SER F 183 " --> pdb=" O ALA F 212 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N VAL F 214 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N PHE F 185 " --> pdb=" O VAL F 214 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N GLY F 216 " --> pdb=" O PHE F 185 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N GLY F 187 " --> pdb=" O GLY F 216 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE F 154 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE F 306 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU F 156 " --> pdb=" O ILE F 306 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 134 through 135 removed outlier: 4.294A pdb=" N TYR F 148 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 133 through 136 removed outlier: 8.033A pdb=" N ILE G 134 " --> pdb=" O TYR G 113 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE G 115 " --> pdb=" O ILE G 134 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASP G 136 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL G 117 " --> pdb=" O ASP G 136 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N THR G 76 " --> pdb=" O ALA G 114 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE G 116 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N TYR G 78 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASN G 173 " --> pdb=" O ILE G 81 " (cutoff:3.500A) 1198 hydrogen bonds defined for protein. 3390 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.17 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8201 1.34 - 1.45: 2641 1.45 - 1.57: 13638 1.57 - 1.69: 21 1.69 - 1.81: 154 Bond restraints: 24655 Sorted by residual: bond pdb=" O3 PO4 E 501 " pdb=" P PO4 E 501 " ideal model delta sigma weight residual 1.569 1.510 0.059 2.00e-02 2.50e+03 8.59e+00 bond pdb=" O4 PO4 E 501 " pdb=" P PO4 E 501 " ideal model delta sigma weight residual 1.568 1.510 0.058 2.00e-02 2.50e+03 8.51e+00 bond pdb=" O2 PO4 E 501 " pdb=" P PO4 E 501 " ideal model delta sigma weight residual 1.567 1.509 0.058 2.00e-02 2.50e+03 8.27e+00 bond pdb=" O1 PO4 E 501 " pdb=" P PO4 E 501 " ideal model delta sigma weight residual 1.565 1.509 0.056 2.00e-02 2.50e+03 7.74e+00 bond pdb=" O3 PO4 D 503 " pdb=" P PO4 D 503 " ideal model delta sigma weight residual 1.569 1.524 0.045 2.00e-02 2.50e+03 5.11e+00 ... (remaining 24650 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 32882 1.88 - 3.76: 498 3.76 - 5.64: 47 5.64 - 7.53: 5 7.53 - 9.41: 1 Bond angle restraints: 33433 Sorted by residual: angle pdb=" CA GLY B 340 " pdb=" C GLY B 340 " pdb=" N GLN B 341 " ideal model delta sigma weight residual 114.23 117.56 -3.33 8.80e-01 1.29e+00 1.43e+01 angle pdb=" N GLU G 273 " pdb=" CA GLU G 273 " pdb=" CB GLU G 273 " ideal model delta sigma weight residual 110.12 115.12 -5.00 1.47e+00 4.63e-01 1.16e+01 angle pdb=" CA GLN C 407 " pdb=" C GLN C 407 " pdb=" O GLN C 407 " ideal model delta sigma weight residual 120.70 117.28 3.42 1.03e+00 9.43e-01 1.10e+01 angle pdb=" N GLY F 88 " pdb=" CA GLY F 88 " pdb=" C GLY F 88 " ideal model delta sigma weight residual 111.56 114.72 -3.16 1.01e+00 9.80e-01 9.78e+00 angle pdb=" N THR G 138 " pdb=" CA THR G 138 " pdb=" CB THR G 138 " ideal model delta sigma weight residual 113.65 109.31 4.34 1.47e+00 4.63e-01 8.71e+00 ... (remaining 33428 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.83: 14411 24.83 - 49.66: 532 49.66 - 74.49: 97 74.49 - 99.32: 18 99.32 - 124.14: 1 Dihedral angle restraints: 15059 sinusoidal: 6134 harmonic: 8925 Sorted by residual: dihedral pdb=" O1B ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PB ADP D 501 " pdb=" PA ADP D 501 " ideal model delta sinusoidal sigma weight residual 300.00 175.85 124.14 1 2.00e+01 2.50e-03 3.75e+01 dihedral pdb=" CA VAL A 353 " pdb=" C VAL A 353 " pdb=" N ARG A 354 " pdb=" CA ARG A 354 " ideal model delta harmonic sigma weight residual -180.00 -155.96 -24.04 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA PHE G 205 " pdb=" C PHE G 205 " pdb=" N GLU G 206 " pdb=" CA GLU G 206 " ideal model delta harmonic sigma weight residual 180.00 -156.93 -23.07 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 15056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2354 0.035 - 0.069: 1016 0.069 - 0.104: 322 0.104 - 0.139: 153 0.139 - 0.174: 7 Chirality restraints: 3852 Sorted by residual: chirality pdb=" CB THR C 406 " pdb=" CA THR C 406 " pdb=" OG1 THR C 406 " pdb=" CG2 THR C 406 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CG LEU B 52 " pdb=" CB LEU B 52 " pdb=" CD1 LEU B 52 " pdb=" CD2 LEU B 52 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" CA GLU G 273 " pdb=" N GLU G 273 " pdb=" C GLU G 273 " pdb=" CB GLU G 273 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.54e-01 ... (remaining 3849 not shown) Planarity restraints: 4362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA G 269 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.57e+00 pdb=" C ALA G 269 " -0.033 2.00e-02 2.50e+03 pdb=" O ALA G 269 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE G 270 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 220 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO D 221 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 221 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 221 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 341 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO E 342 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO E 342 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 342 " -0.025 5.00e-02 4.00e+02 ... (remaining 4359 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 16 2.23 - 2.90: 8979 2.90 - 3.56: 33912 3.56 - 4.23: 56602 4.23 - 4.90: 99563 Nonbonded interactions: 199072 Sorted by model distance: nonbonded pdb=" CD1 TYR D 307 " pdb=" O2 PO4 D 503 " model vdw 1.560 3.340 nonbonded pdb=" NZ LYS D 164 " pdb=" O1 PO4 D 503 " model vdw 1.649 3.120 nonbonded pdb=" CE1 TYR D 307 " pdb=" O2 PO4 D 503 " model vdw 1.940 3.340 nonbonded pdb=" O1G ATP A 600 " pdb="MG MG A 601 " model vdw 1.952 2.170 nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 601 " model vdw 1.973 2.170 ... (remaining 199067 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 1 through 470) selection = (chain 'E' and resid 1 through 470) selection = (chain 'F' and resid 1 through 470) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.220 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 19.280 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 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 : 0.004 0.061 24655 Z= 0.188 Angle : 0.587 9.406 33433 Z= 0.334 Chirality : 0.046 0.174 3852 Planarity : 0.004 0.046 4362 Dihedral : 13.521 124.144 9347 Min Nonbonded Distance : 1.560 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.04 % Allowed : 0.23 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.15), residues: 3115 helix: 1.89 (0.15), residues: 1264 sheet: 1.08 (0.22), residues: 545 loop : 0.24 (0.17), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 240 TYR 0.018 0.001 TYR A 329 PHE 0.020 0.001 PHE D 257 HIS 0.006 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00435 (24655) covalent geometry : angle 0.58682 (33433) hydrogen bonds : bond 0.13912 ( 1198) hydrogen bonds : angle 6.09104 ( 3390) *********************** 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 123 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.874 Fit side-chains REVERT: C 95 MET cc_start: 0.8894 (tpt) cc_final: 0.8677 (tpt) outliers start: 1 outliers final: 0 residues processed: 123 average time/residue: 0.7742 time to fit residues: 106.5668 Evaluate side-chains 98 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.0670 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 7.9990 overall best weight: 2.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 294 HIS C 425 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.072330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.055147 restraints weight = 46642.584| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 2.30 r_work: 0.2595 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2470 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 moved from start: 0.0571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24655 Z= 0.179 Angle : 0.546 9.044 33433 Z= 0.290 Chirality : 0.046 0.152 3852 Planarity : 0.005 0.047 4362 Dihedral : 7.830 86.574 3546 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.35 % Allowed : 3.43 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.15), residues: 3115 helix: 1.95 (0.15), residues: 1252 sheet: 0.87 (0.21), residues: 559 loop : 0.17 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 89 TYR 0.016 0.001 TYR A 329 PHE 0.018 0.001 PHE D 257 HIS 0.006 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00435 (24655) covalent geometry : angle 0.54618 (33433) hydrogen bonds : bond 0.05560 ( 1198) hydrogen bonds : angle 5.09394 ( 3390) *********************** 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 116 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: B 390 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.6230 (mpt180) REVERT: C 95 MET cc_start: 0.9356 (tpt) cc_final: 0.9148 (tpt) REVERT: C 189 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8189 (mm-40) outliers start: 9 outliers final: 2 residues processed: 114 average time/residue: 0.7340 time to fit residues: 94.9505 Evaluate side-chains 107 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 301 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 111 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 283 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 161 optimal weight: 0.3980 chunk 10 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 294 HIS C 425 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.073378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.056252 restraints weight = 46411.309| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 2.30 r_work: 0.2625 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2500 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.0732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24655 Z= 0.125 Angle : 0.491 8.490 33433 Z= 0.260 Chirality : 0.044 0.159 3852 Planarity : 0.004 0.047 4362 Dihedral : 7.354 88.840 3546 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.55 % Allowed : 4.83 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.15), residues: 3115 helix: 2.09 (0.15), residues: 1240 sheet: 0.83 (0.22), residues: 536 loop : 0.22 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 89 TYR 0.013 0.001 TYR A 329 PHE 0.017 0.001 PHE D 257 HIS 0.004 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00290 (24655) covalent geometry : angle 0.49110 (33433) hydrogen bonds : bond 0.04806 ( 1198) hydrogen bonds : angle 4.85162 ( 3390) *********************** 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 124 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.730 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 3 residues processed: 121 average time/residue: 0.6902 time to fit residues: 94.4644 Evaluate side-chains 107 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain F residue 384 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 201 optimal weight: 0.5980 chunk 124 optimal weight: 7.9990 chunk 282 optimal weight: 7.9990 chunk 43 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 249 optimal weight: 3.9990 chunk 245 optimal weight: 3.9990 chunk 303 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 397 GLN C 425 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.073161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.056043 restraints weight = 46216.606| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 2.30 r_work: 0.2621 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.0816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24655 Z= 0.134 Angle : 0.493 8.532 33433 Z= 0.260 Chirality : 0.044 0.156 3852 Planarity : 0.004 0.047 4362 Dihedral : 7.115 91.981 3546 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.82 % Allowed : 5.18 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.15), residues: 3115 helix: 2.12 (0.15), residues: 1241 sheet: 0.78 (0.22), residues: 546 loop : 0.18 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 5 TYR 0.011 0.001 TYR A 329 PHE 0.017 0.001 PHE D 257 HIS 0.004 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00316 (24655) covalent geometry : angle 0.49328 (33433) hydrogen bonds : bond 0.04789 ( 1198) hydrogen bonds : angle 4.77846 ( 3390) *********************** 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 131 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.631 Fit side-chains REVERT: B 390 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.6520 (mpt180) outliers start: 21 outliers final: 11 residues processed: 126 average time/residue: 0.7358 time to fit residues: 104.6580 Evaluate side-chains 115 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 384 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 185 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 275 optimal weight: 3.9990 chunk 242 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 127 optimal weight: 0.0980 chunk 50 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.073202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.056106 restraints weight = 46044.616| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 2.29 r_work: 0.2622 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2497 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24655 Z= 0.132 Angle : 0.492 8.709 33433 Z= 0.258 Chirality : 0.044 0.161 3852 Planarity : 0.004 0.048 4362 Dihedral : 6.912 94.464 3546 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.86 % Allowed : 6.39 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.15), residues: 3115 helix: 2.16 (0.15), residues: 1240 sheet: 0.76 (0.22), residues: 546 loop : 0.17 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 89 TYR 0.011 0.001 TYR A 329 PHE 0.017 0.001 PHE D 257 HIS 0.004 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00312 (24655) covalent geometry : angle 0.49239 (33433) hydrogen bonds : bond 0.04718 ( 1198) hydrogen bonds : angle 4.72960 ( 3390) *********************** 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 133 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: B 390 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.6506 (mpt180) outliers start: 22 outliers final: 12 residues processed: 127 average time/residue: 0.7428 time to fit residues: 107.1223 Evaluate side-chains 117 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 301 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 5 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 291 optimal weight: 3.9990 chunk 103 optimal weight: 0.2980 chunk 66 optimal weight: 7.9990 chunk 238 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 252 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 240 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 HIS E 253 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.070679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.053495 restraints weight = 46676.036| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 2.30 r_work: 0.2565 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2439 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9089 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 24655 Z= 0.250 Angle : 0.586 10.195 33433 Z= 0.309 Chirality : 0.048 0.177 3852 Planarity : 0.005 0.052 4362 Dihedral : 7.532 103.205 3546 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.13 % Allowed : 6.70 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.15), residues: 3115 helix: 1.88 (0.15), residues: 1241 sheet: 0.63 (0.22), residues: 531 loop : 0.02 (0.16), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 89 TYR 0.012 0.001 TYR B 251 PHE 0.019 0.002 PHE D 125 HIS 0.007 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00620 (24655) covalent geometry : angle 0.58643 (33433) hydrogen bonds : bond 0.06142 ( 1198) hydrogen bonds : angle 4.98839 ( 3390) *********************** 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 137 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.979 Fit side-chains REVERT: B 390 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.6628 (mpt180) REVERT: G 139 ARG cc_start: 0.8232 (tpp-160) cc_final: 0.8023 (tpt170) outliers start: 29 outliers final: 14 residues processed: 132 average time/residue: 0.6590 time to fit residues: 99.5092 Evaluate side-chains 119 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 253 ASN Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 301 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 30 optimal weight: 0.0570 chunk 294 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 180 optimal weight: 0.9980 chunk 291 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 253 ASN G 130 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.074429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.057402 restraints weight = 46099.184| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 2.29 r_work: 0.2648 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24655 Z= 0.099 Angle : 0.470 9.126 33433 Z= 0.245 Chirality : 0.042 0.152 3852 Planarity : 0.004 0.046 4362 Dihedral : 6.723 96.638 3546 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.58 % Allowed : 7.63 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.15), residues: 3115 helix: 2.18 (0.15), residues: 1243 sheet: 0.75 (0.22), residues: 532 loop : 0.16 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 5 TYR 0.010 0.001 TYR A 329 PHE 0.015 0.001 PHE G 125 HIS 0.003 0.000 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00216 (24655) covalent geometry : angle 0.47016 (33433) hydrogen bonds : bond 0.04020 ( 1198) hydrogen bonds : angle 4.62714 ( 3390) *********************** 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 123 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: A 95 MET cc_start: 0.8736 (tpp) cc_final: 0.8420 (ttp) REVERT: C 95 MET cc_start: 0.9282 (tpt) cc_final: 0.9057 (tpt) outliers start: 15 outliers final: 12 residues processed: 123 average time/residue: 0.6271 time to fit residues: 87.9348 Evaluate side-chains 115 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 253 ASN Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 384 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 102 optimal weight: 0.7980 chunk 308 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 157 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 205 optimal weight: 9.9990 chunk 202 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 253 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.073862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.056816 restraints weight = 45956.571| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 2.29 r_work: 0.2640 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24655 Z= 0.110 Angle : 0.474 9.484 33433 Z= 0.247 Chirality : 0.043 0.154 3852 Planarity : 0.004 0.046 4362 Dihedral : 6.614 94.853 3546 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.70 % Allowed : 7.79 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.15), residues: 3115 helix: 2.24 (0.15), residues: 1242 sheet: 0.77 (0.22), residues: 539 loop : 0.20 (0.17), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 5 TYR 0.009 0.001 TYR A 329 PHE 0.016 0.001 PHE D 257 HIS 0.003 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00252 (24655) covalent geometry : angle 0.47431 (33433) hydrogen bonds : bond 0.04295 ( 1198) hydrogen bonds : angle 4.60229 ( 3390) *********************** 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 122 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 95 MET cc_start: 0.8753 (tpp) cc_final: 0.8451 (ttp) REVERT: B 390 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.6400 (mpt180) outliers start: 18 outliers final: 13 residues processed: 120 average time/residue: 0.6875 time to fit residues: 93.9127 Evaluate side-chains 116 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 253 ASN Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 301 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 263 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 239 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 154 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 269 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 253 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.072726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.055813 restraints weight = 46413.206| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 2.28 r_work: 0.2621 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9045 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24655 Z= 0.139 Angle : 0.496 9.516 33433 Z= 0.259 Chirality : 0.044 0.157 3852 Planarity : 0.004 0.049 4362 Dihedral : 6.687 95.760 3546 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.74 % Allowed : 7.83 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.15), residues: 3115 helix: 2.19 (0.15), residues: 1240 sheet: 0.71 (0.22), residues: 539 loop : 0.16 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 5 TYR 0.009 0.001 TYR A 329 PHE 0.017 0.001 PHE D 257 HIS 0.004 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00332 (24655) covalent geometry : angle 0.49593 (33433) hydrogen bonds : bond 0.04709 ( 1198) hydrogen bonds : angle 4.66742 ( 3390) *********************** 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 122 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 1.021 Fit side-chains REVERT: A 95 MET cc_start: 0.8764 (tpp) cc_final: 0.8457 (ttp) REVERT: B 390 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.6455 (mpt180) outliers start: 19 outliers final: 15 residues processed: 121 average time/residue: 0.7287 time to fit residues: 100.1191 Evaluate side-chains 117 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 253 ASN Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 384 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 134 optimal weight: 1.9990 chunk 180 optimal weight: 7.9990 chunk 229 optimal weight: 8.9990 chunk 168 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 104 optimal weight: 0.0980 chunk 210 optimal weight: 0.0060 chunk 86 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 253 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.073726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.056667 restraints weight = 46171.974| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 2.29 r_work: 0.2636 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24655 Z= 0.112 Angle : 0.481 10.114 33433 Z= 0.250 Chirality : 0.043 0.155 3852 Planarity : 0.004 0.048 4362 Dihedral : 6.525 94.341 3546 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.70 % Allowed : 7.94 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.15), residues: 3115 helix: 2.24 (0.15), residues: 1240 sheet: 0.75 (0.22), residues: 537 loop : 0.19 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 5 TYR 0.009 0.001 TYR A 329 PHE 0.016 0.001 PHE D 257 HIS 0.003 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00257 (24655) covalent geometry : angle 0.48056 (33433) hydrogen bonds : bond 0.04356 ( 1198) hydrogen bonds : angle 4.60684 ( 3390) ********************** 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 121 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.934 Fit side-chains REVERT: A 95 MET cc_start: 0.8751 (tpp) cc_final: 0.8451 (ttp) REVERT: B 390 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.6418 (mpt180) REVERT: D 1 MET cc_start: 0.5417 (pp-130) cc_final: 0.5049 (ppp) outliers start: 18 outliers final: 14 residues processed: 120 average time/residue: 0.7032 time to fit residues: 96.5053 Evaluate side-chains 117 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 253 ASN Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 301 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 232 optimal weight: 0.0970 chunk 178 optimal weight: 0.4980 chunk 127 optimal weight: 3.9990 chunk 253 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 284 optimal weight: 4.9990 chunk 275 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 253 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.073392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.056312 restraints weight = 46113.983| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 2.29 r_work: 0.2628 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2504 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24655 Z= 0.126 Angle : 0.488 10.133 33433 Z= 0.254 Chirality : 0.043 0.155 3852 Planarity : 0.004 0.049 4362 Dihedral : 6.530 93.776 3546 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.74 % Allowed : 8.14 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.15), residues: 3115 helix: 2.21 (0.15), residues: 1242 sheet: 0.72 (0.22), residues: 539 loop : 0.19 (0.17), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 5 TYR 0.008 0.001 TYR A 329 PHE 0.016 0.001 PHE D 257 HIS 0.004 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00298 (24655) covalent geometry : angle 0.48778 (33433) hydrogen bonds : bond 0.04513 ( 1198) hydrogen bonds : angle 4.62920 ( 3390) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6518.54 seconds wall clock time: 111 minutes 48.05 seconds (6708.05 seconds total)