Starting phenix.real_space_refine on Sat Jun 21 03:29:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hh7_34754/06_2025/8hh7_34754.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hh7_34754/06_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_34754/06_2025/8hh7_34754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hh7_34754/06_2025/8hh7_34754.map" model { file = "/net/cci-nas-00/data/ceres_data/8hh7_34754/06_2025/8hh7_34754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hh7_34754/06_2025/8hh7_34754.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.04, per 1000 atoms: 0.58 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: 5.71 Conformation dependent library (CDL) restraints added in 2.9 seconds 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... Secondary structure from input PDB file: 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: 2.82 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: 10.10 Time building geometry restraints manager: 6.62 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: 3.060 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: 0.860 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 54.410 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.880 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (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 HIS 0.006 0.001 HIS F 363 PHE 0.020 0.001 PHE D 257 TYR 0.018 0.001 TYR A 329 ARG 0.004 0.000 ARG D 240 Details of bonding type rmsd hydrogen bonds : bond 0.13912 ( 1198) hydrogen bonds : angle 6.09104 ( 3390) covalent geometry : bond 0.00435 (24655) covalent geometry : angle 0.58682 (33433) *********************** 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 : 2.566 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: 1.8624 time to fit residues: 257.6122 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 : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 8.9990 chunk 234 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 158 optimal weight: 8.9990 chunk 125 optimal weight: 0.8980 chunk 242 optimal weight: 0.4980 chunk 94 optimal weight: 7.9990 chunk 147 optimal weight: 3.9990 chunk 180 optimal weight: 0.2980 chunk 281 optimal weight: 6.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- 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 = 0.3077 r_free = 0.3077 target = 0.072404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.055223 restraints weight = 46376.778| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 2.30 r_work: 0.2597 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2471 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.0556 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= 0.176 Angle : 0.544 9.059 33433 Z= 0.289 Chirality : 0.046 0.152 3852 Planarity : 0.005 0.047 4362 Dihedral : 7.840 87.196 3546 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.35 % Allowed : 3.39 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.15), residues: 3115 helix: 1.96 (0.15), residues: 1252 sheet: 0.88 (0.21), residues: 559 loop : 0.17 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 363 PHE 0.018 0.001 PHE D 257 TYR 0.015 0.001 TYR A 329 ARG 0.007 0.000 ARG A 89 Details of bonding type rmsd hydrogen bonds : bond 0.05560 ( 1198) hydrogen bonds : angle 5.10142 ( 3390) covalent geometry : bond 0.00427 (24655) covalent geometry : angle 0.54380 (33433) *********************** 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 115 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 2.571 Fit side-chains revert: symmetry clash REVERT: B 390 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.6236 (mpt180) REVERT: C 95 MET cc_start: 0.9352 (tpt) cc_final: 0.9144 (tpt) REVERT: C 189 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8189 (mm-40) outliers start: 9 outliers final: 2 residues processed: 113 average time/residue: 1.7551 time to fit residues: 224.3145 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 : 2.367 ------------------------------------------------------------------------------- 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 292 optimal weight: 5.9990 chunk 222 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 218 optimal weight: 3.9990 chunk 274 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.071828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.054666 restraints weight = 46102.573| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 2.29 r_work: 0.2590 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2464 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 moved from start: 0.0725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 24655 Z= 0.186 Angle : 0.538 8.694 33433 Z= 0.286 Chirality : 0.046 0.168 3852 Planarity : 0.005 0.049 4362 Dihedral : 7.655 95.403 3546 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.90 % Allowed : 4.60 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.15), residues: 3115 helix: 1.96 (0.15), residues: 1238 sheet: 0.75 (0.22), residues: 549 loop : 0.12 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 363 PHE 0.018 0.002 PHE D 257 TYR 0.016 0.001 TYR A 329 ARG 0.006 0.000 ARG A 89 Details of bonding type rmsd hydrogen bonds : bond 0.05577 ( 1198) hydrogen bonds : angle 4.97483 ( 3390) covalent geometry : bond 0.00455 (24655) covalent geometry : angle 0.53822 (33433) *********************** 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 131 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 2.559 Fit side-chains revert: symmetry clash REVERT: B 390 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.6313 (mpt180) outliers start: 23 outliers final: 8 residues processed: 123 average time/residue: 1.5676 time to fit residues: 219.9768 Evaluate side-chains 112 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 2.970 ------------------------------------------------------------------------------- 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 129 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 277 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 238 optimal weight: 9.9990 chunk 30 optimal weight: 0.0070 chunk 245 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 294 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.072314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.055197 restraints weight = 46539.627| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 2.30 r_work: 0.2597 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2471 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 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 : 0.004 0.039 24655 Z= 0.153 Angle : 0.510 8.577 33433 Z= 0.270 Chirality : 0.045 0.163 3852 Planarity : 0.004 0.049 4362 Dihedral : 7.363 97.878 3546 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.70 % Allowed : 5.88 % Favored : 93.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.15), residues: 3115 helix: 2.02 (0.15), residues: 1243 sheet: 0.74 (0.22), residues: 536 loop : 0.10 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 363 PHE 0.018 0.001 PHE D 257 TYR 0.012 0.001 TYR A 329 ARG 0.006 0.000 ARG G 5 Details of bonding type rmsd hydrogen bonds : bond 0.05112 ( 1198) hydrogen bonds : angle 4.85612 ( 3390) covalent geometry : bond 0.00369 (24655) covalent geometry : angle 0.51000 (33433) *********************** 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 128 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 2.479 Fit side-chains revert: symmetry clash REVERT: B 390 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.6299 (mpt180) REVERT: C 95 MET cc_start: 0.9349 (tpt) cc_final: 0.9121 (tpt) outliers start: 18 outliers final: 9 residues processed: 124 average time/residue: 1.6418 time to fit residues: 233.1213 Evaluate side-chains 114 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 3.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 301 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 1 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 187 optimal weight: 2.9990 chunk 276 optimal weight: 0.0470 chunk 236 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 200 optimal weight: 1.9990 chunk 204 optimal weight: 7.9990 chunk 298 optimal weight: 9.9990 chunk 149 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 overall best weight: 1.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.073142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.056254 restraints weight = 46465.514| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 2.28 r_work: 0.2630 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24655 Z= 0.119 Angle : 0.482 8.815 33433 Z= 0.253 Chirality : 0.043 0.158 3852 Planarity : 0.004 0.047 4362 Dihedral : 6.895 96.370 3546 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.82 % Allowed : 6.54 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.15), residues: 3115 helix: 2.16 (0.15), residues: 1242 sheet: 0.75 (0.22), residues: 536 loop : 0.18 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 363 PHE 0.016 0.001 PHE D 257 TYR 0.011 0.001 TYR A 329 ARG 0.008 0.000 ARG A 89 Details of bonding type rmsd hydrogen bonds : bond 0.04524 ( 1198) hydrogen bonds : angle 4.70725 ( 3390) covalent geometry : bond 0.00275 (24655) covalent geometry : angle 0.48225 (33433) *********************** 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 132 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 2.857 Fit side-chains revert: symmetry clash REVERT: A 95 MET cc_start: 0.8764 (tpp) cc_final: 0.8481 (ttp) REVERT: G 182 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8374 (mm-30) outliers start: 21 outliers final: 10 residues processed: 129 average time/residue: 1.6060 time to fit residues: 236.4933 Evaluate side-chains 116 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL 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 359 VAL Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 384 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 58 optimal weight: 6.9990 chunk 170 optimal weight: 9.9990 chunk 214 optimal weight: 3.9990 chunk 257 optimal weight: 1.9990 chunk 224 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 43 optimal weight: 0.0670 chunk 95 optimal weight: 4.9990 chunk 287 optimal weight: 10.0000 chunk 282 optimal weight: 0.9980 chunk 182 optimal weight: 3.9990 overall best weight: 2.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 397 GLN D 173 HIS E 253 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.072147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.055035 restraints weight = 46145.475| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 2.29 r_work: 0.2598 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2473 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9061 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 24655 Z= 0.165 Angle : 0.519 9.904 33433 Z= 0.272 Chirality : 0.045 0.163 3852 Planarity : 0.004 0.049 4362 Dihedral : 7.027 99.174 3546 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.97 % Allowed : 7.28 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.15), residues: 3115 helix: 2.09 (0.15), residues: 1239 sheet: 0.67 (0.22), residues: 551 loop : 0.10 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 363 PHE 0.017 0.001 PHE D 257 TYR 0.010 0.001 TYR A 329 ARG 0.005 0.000 ARG A 89 Details of bonding type rmsd hydrogen bonds : bond 0.05173 ( 1198) hydrogen bonds : angle 4.79772 ( 3390) covalent geometry : bond 0.00399 (24655) covalent geometry : angle 0.51877 (33433) *********************** 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 132 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 2.620 Fit side-chains REVERT: A 95 MET cc_start: 0.8786 (tpp) cc_final: 0.8516 (ttp) outliers start: 25 outliers final: 16 residues processed: 129 average time/residue: 1.8280 time to fit residues: 268.6239 Evaluate side-chains 120 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 2.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 204 optimal weight: 7.9990 chunk 278 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 214 optimal weight: 0.9980 chunk 156 optimal weight: 5.9990 chunk 295 optimal weight: 0.0980 chunk 190 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 256 optimal weight: 5.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.3090 r_free = 0.3090 target = 0.073120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.056026 restraints weight = 46329.805| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 2.30 r_work: 0.2621 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9042 moved from start: 0.0990 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= 0.123 Angle : 0.489 8.950 33433 Z= 0.256 Chirality : 0.043 0.160 3852 Planarity : 0.004 0.048 4362 Dihedral : 6.807 98.110 3546 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.93 % Allowed : 7.83 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.15), residues: 3115 helix: 2.15 (0.15), residues: 1242 sheet: 0.71 (0.22), residues: 551 loop : 0.15 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 363 PHE 0.017 0.001 PHE D 257 TYR 0.009 0.001 TYR A 329 ARG 0.006 0.000 ARG G 5 Details of bonding type rmsd hydrogen bonds : bond 0.04612 ( 1198) hydrogen bonds : angle 4.69379 ( 3390) covalent geometry : bond 0.00285 (24655) covalent geometry : angle 0.48907 (33433) *********************** 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 129 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 2.634 Fit side-chains REVERT: A 95 MET cc_start: 0.8762 (tpp) cc_final: 0.8510 (ttp) REVERT: B 390 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.6534 (mpt180) REVERT: G 139 ARG cc_start: 0.8263 (tpp-160) cc_final: 0.7905 (tpt170) outliers start: 24 outliers final: 17 residues processed: 126 average time/residue: 1.5831 time to fit residues: 229.6774 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 : 2.606 ------------------------------------------------------------------------------- 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 363 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 97 optimal weight: 6.9990 chunk 213 optimal weight: 3.9990 chunk 228 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 85 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 260 optimal weight: 6.9990 chunk 221 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 = 0.3057 r_free = 0.3057 target = 0.071353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.054192 restraints weight = 46314.308| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 2.29 r_work: 0.2580 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2454 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9076 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 24655 Z= 0.205 Angle : 0.548 9.411 33433 Z= 0.287 Chirality : 0.046 0.165 3852 Planarity : 0.005 0.052 4362 Dihedral : 7.127 100.925 3546 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.01 % Allowed : 7.94 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.15), residues: 3115 helix: 2.02 (0.15), residues: 1240 sheet: 0.62 (0.22), residues: 551 loop : 0.01 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 363 PHE 0.019 0.002 PHE D 257 TYR 0.011 0.001 TYR A 251 ARG 0.006 0.000 ARG G 5 Details of bonding type rmsd hydrogen bonds : bond 0.05588 ( 1198) hydrogen bonds : angle 4.86173 ( 3390) covalent geometry : bond 0.00504 (24655) covalent geometry : angle 0.54752 (33433) *********************** 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 133 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 3.175 Fit side-chains REVERT: B 390 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.6518 (mpt180) REVERT: G 139 ARG cc_start: 0.8338 (tpp-160) cc_final: 0.7981 (tpt170) outliers start: 26 outliers final: 18 residues processed: 129 average time/residue: 2.1844 time to fit residues: 324.7373 Evaluate side-chains 124 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 8.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 351 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 363 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 139 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 chunk 225 optimal weight: 0.4980 chunk 117 optimal weight: 5.9990 chunk 303 optimal weight: 6.9990 chunk 251 optimal weight: 0.9990 chunk 246 optimal weight: 0.9980 chunk 238 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 = 0.3104 r_free = 0.3104 target = 0.073848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.057010 restraints weight = 46282.686| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 2.27 r_work: 0.2643 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24655 Z= 0.101 Angle : 0.474 11.266 33433 Z= 0.246 Chirality : 0.043 0.156 3852 Planarity : 0.004 0.046 4362 Dihedral : 6.606 97.017 3546 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.66 % Allowed : 8.33 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.15), residues: 3115 helix: 2.24 (0.15), residues: 1240 sheet: 0.75 (0.22), residues: 549 loop : 0.15 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 363 PHE 0.015 0.001 PHE D 257 TYR 0.009 0.001 TYR A 329 ARG 0.007 0.000 ARG G 5 Details of bonding type rmsd hydrogen bonds : bond 0.04131 ( 1198) hydrogen bonds : angle 4.61099 ( 3390) covalent geometry : bond 0.00220 (24655) covalent geometry : angle 0.47403 (33433) *********************** 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 124 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 2.750 Fit side-chains REVERT: B 390 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.6402 (mpt180) REVERT: C 95 MET cc_start: 0.9291 (tpt) cc_final: 0.9058 (tpt) REVERT: G 139 ARG cc_start: 0.8249 (tpp-160) cc_final: 0.7938 (tpt170) outliers start: 17 outliers final: 14 residues processed: 123 average time/residue: 1.5579 time to fit residues: 219.1716 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 : 2.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 351 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 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 14 optimal weight: 0.0020 chunk 219 optimal weight: 0.1980 chunk 209 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 247 optimal weight: 0.9990 chunk 173 optimal weight: 7.9990 chunk 230 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 279 optimal weight: 2.9990 chunk 186 optimal weight: 0.7980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.075106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.058247 restraints weight = 46183.923| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 2.28 r_work: 0.2669 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24655 Z= 0.089 Angle : 0.462 10.828 33433 Z= 0.238 Chirality : 0.042 0.153 3852 Planarity : 0.004 0.043 4362 Dihedral : 6.298 90.707 3546 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.55 % Allowed : 8.61 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.15), residues: 3115 helix: 2.35 (0.15), residues: 1241 sheet: 0.82 (0.22), residues: 549 loop : 0.26 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS E 363 PHE 0.014 0.001 PHE G 125 TYR 0.008 0.001 TYR A 329 ARG 0.007 0.000 ARG G 5 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 1198) hydrogen bonds : angle 4.50280 ( 3390) covalent geometry : bond 0.00183 (24655) covalent geometry : angle 0.46161 (33433) ********************** 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 128 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 2.754 Fit side-chains REVERT: B 390 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.6467 (mpt180) REVERT: G 139 ARG cc_start: 0.8246 (tpp-160) cc_final: 0.7936 (tpt170) outliers start: 14 outliers final: 12 residues processed: 128 average time/residue: 1.6988 time to fit residues: 247.1965 Evaluate side-chains 115 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 2.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 351 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 D residue 301 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 153 optimal weight: 0.7980 chunk 150 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 192 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 197 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 235 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.073874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.056926 restraints weight = 46461.298| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 2.29 r_work: 0.2639 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.1173 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= 0.118 Angle : 0.484 10.318 33433 Z= 0.250 Chirality : 0.043 0.156 3852 Planarity : 0.004 0.046 4362 Dihedral : 6.366 89.770 3546 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.74 % Allowed : 8.61 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.15), residues: 3115 helix: 2.30 (0.15), residues: 1242 sheet: 0.83 (0.22), residues: 538 loop : 0.25 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 363 PHE 0.015 0.001 PHE D 257 TYR 0.008 0.001 TYR A 329 ARG 0.007 0.000 ARG G 5 Details of bonding type rmsd hydrogen bonds : bond 0.04253 ( 1198) hydrogen bonds : angle 4.55861 ( 3390) covalent geometry : bond 0.00275 (24655) covalent geometry : angle 0.48396 (33433) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16040.18 seconds wall clock time: 286 minutes 8.89 seconds (17168.89 seconds total)