Starting phenix.real_space_refine on Mon Aug 25 01:49:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hh8_34755/08_2025/8hh8_34755.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hh8_34755/08_2025/8hh8_34755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hh8_34755/08_2025/8hh8_34755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hh8_34755/08_2025/8hh8_34755.map" model { file = "/net/cci-nas-00/data/ceres_data/8hh8_34755/08_2025/8hh8_34755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hh8_34755/08_2025/8hh8_34755.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 77 5.16 5 C 15277 2.51 5 N 4214 2.21 5 O 4661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.72, per 1000 atoms: 0.28 Number of scatterers: 24250 At special positions: 0 Unit cell: (127.6, 122.32, 154.88, 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: 2.39 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 20 sheets defined 48.1% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 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: 3.605A 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 252 removed outlier: 3.590A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.645A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 287 through 288 No H-bonds generated for 'chain 'A' and resid 287 through 288' Processing helix chain 'A' and resid 289 through 299 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 351 Processing helix chain 'A' and resid 372 through 391 removed outlier: 3.803A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 397 removed outlier: 4.030A pdb=" N GLN A 397 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 421 removed outlier: 3.550A pdb=" N LYS A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 removed outlier: 3.623A pdb=" N LEU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) 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 removed outlier: 3.550A pdb=" N ASP A 465 " --> pdb=" O TYR A 461 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 479 Processing helix chain 'A' and resid 483 through 498 removed outlier: 3.572A pdb=" N THR A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.569A pdb=" N LEU B 103 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.741A 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: 3.602A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) 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 252 removed outlier: 3.645A pdb=" N LEU B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.668A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 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: 3.700A pdb=" N HIS B 294 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.717A 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 350 Processing helix chain 'B' and resid 372 through 399 removed outlier: 3.979A pdb=" N GLY B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N THR B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 420 removed outlier: 3.543A 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 removed outlier: 3.610A pdb=" N LEU B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 479 Processing helix chain 'B' and resid 483 through 498 Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.678A 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: 3.586A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 216 through 219 removed outlier: 3.551A pdb=" N ASP C 219 " --> pdb=" O GLY C 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 216 through 219' Processing helix chain 'C' and resid 231 through 251 removed outlier: 3.567A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) Proline residue: C 239 - end of helix removed outlier: 3.768A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 287 through 288 No H-bonds generated for 'chain 'C' and resid 287 through 288' Processing helix chain 'C' and resid 289 through 299 removed outlier: 3.599A 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 396 removed outlier: 3.702A pdb=" N GLY C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU C 393 " --> pdb=" O TYR C 389 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA C 396 " --> pdb=" O LEU C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 421 removed outlier: 3.539A pdb=" N LYS C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 442 Processing helix chain 'C' and resid 449 through 451 No H-bonds generated for 'chain 'C' and resid 449 through 451' Processing helix chain 'C' and resid 452 through 467 Processing helix chain 'C' and resid 468 through 479 removed outlier: 3.512A pdb=" N LEU C 472 " --> pdb=" O GLY C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 498 removed outlier: 3.509A pdb=" N THR C 497 " --> pdb=" O ALA C 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'D' and resid 163 through 176 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 242 removed outlier: 4.970A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 269 removed outlier: 3.604A pdb=" N THR D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 4.808A 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 339 Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 360 through 388 removed outlier: 4.179A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 410 removed outlier: 3.831A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 429 through 443 Processing helix chain 'D' and resid 449 through 454 removed outlier: 3.592A pdb=" N ARG D 454 " --> pdb=" O ASP D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 469 removed outlier: 4.038A pdb=" N VAL D 462 " --> pdb=" O ARG D 458 " (cutoff:3.500A) removed outlier: 3.843A 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 243 removed outlier: 5.142A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 removed outlier: 3.824A 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: 3.530A 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 removed outlier: 3.598A pdb=" N LEU E 380 " --> pdb=" O ARG E 376 " (cutoff:3.500A) 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: 3.523A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE E 408 " --> pdb=" O ARG E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 429 through 442 Processing helix chain 'E' and resid 449 through 454 Processing helix chain 'E' and resid 458 through 470 removed outlier: 3.933A pdb=" N VAL E 462 " --> pdb=" O ARG E 458 " (cutoff:3.500A) removed outlier: 4.073A 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: 3.577A 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: 5.199A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 269 removed outlier: 3.964A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) removed outlier: 3.626A 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 322 removed outlier: 3.639A pdb=" N PHE F 322 " --> pdb=" O PRO F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 325 No H-bonds generated for 'chain 'F' and resid 323 through 325' Processing helix chain 'F' and resid 332 through 338 Processing helix chain 'F' and resid 355 through 360 Processing helix chain 'F' and resid 360 through 380 Processing helix chain 'F' and resid 380 through 388 Processing helix chain 'F' and resid 389 through 392 Processing helix chain 'F' and resid 393 through 410 removed outlier: 3.710A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 419 removed outlier: 3.936A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 443 Processing helix chain 'F' and resid 449 through 454 removed outlier: 3.613A pdb=" N ARG F 454 " --> pdb=" O ASP F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 465 removed outlier: 3.527A pdb=" N VAL F 462 " --> pdb=" O ARG F 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 57 removed outlier: 3.711A pdb=" N SER G 30 " --> pdb=" O MET G 26 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) Proline residue: G 44 - end of helix Processing helix chain 'G' and resid 90 through 107 removed outlier: 3.972A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU G 98 " --> pdb=" O ASN G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 129 removed outlier: 3.562A pdb=" N LEU G 123 " --> pdb=" O GLY G 119 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG G 129 " --> pdb=" O PHE G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 162 removed outlier: 3.550A pdb=" N PHE G 160 " --> pdb=" O THR G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 221 removed outlier: 3.941A pdb=" N ASP G 214 " --> pdb=" O GLU G 210 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL G 215 " --> pdb=" O GLU G 211 " (cutoff:3.500A) Proline residue: G 218 - end of helix Processing helix chain 'G' and resid 222 through 227 Processing helix chain 'G' and resid 228 through 283 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 66 removed outlier: 3.892A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 91 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LYS E 17 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N VAL E 6 " --> pdb=" O LYS E 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.050A pdb=" N GLU A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.486A pdb=" N VAL A 108 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE A 192 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N VAL A 259 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE A 194 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR A 260 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 66 removed outlier: 4.404A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU B 76 " --> pdb=" O GLY B 61 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N GLY B 61 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN F 8 " --> pdb=" O ASP F 15 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LYS F 17 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N VAL F 6 " --> pdb=" O LYS F 17 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.198A 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: 6.400A pdb=" N ILE B 192 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N VAL B 259 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE B 194 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR B 260 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 28 through 35 removed outlier: 6.310A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU C 52 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.875A 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: 6.519A pdb=" N ILE C 192 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N VAL C 259 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE C 194 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR C 260 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 10 removed outlier: 5.741A pdb=" N VAL D 6 " --> pdb=" O LYS D 17 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LYS D 17 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN D 8 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLN D 33 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLU D 75 " --> pdb=" O GLN D 33 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB3, first strand: chain 'D' and resid 95 through 96 removed outlier: 3.513A pdb=" N ILE D 182 " --> pdb=" O ASP D 246 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE D 154 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE D 306 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU D 156 " --> pdb=" O ILE D 306 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 134 through 135 removed outlier: 4.219A pdb=" N TYR D 148 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB6, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.371A pdb=" N PHE E 96 " --> pdb=" O PHE E 215 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N GLN E 217 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA E 327 " --> pdb=" O LYS E 153 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.372A pdb=" N TYR E 148 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AB9, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.327A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE F 154 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ILE F 306 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU F 156 " --> pdb=" O ILE F 306 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 134 through 135 removed outlier: 4.201A pdb=" N TYR F 148 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 133 through 137 removed outlier: 8.070A pdb=" N ILE G 134 " --> pdb=" O TYR G 113 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ILE G 115 " --> pdb=" O ILE G 134 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASP G 136 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL G 117 " --> pdb=" O ASP G 136 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N THR G 76 " --> pdb=" O ALA G 114 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE G 116 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N TYR G 78 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ASN G 173 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N MET G 170 " --> pdb=" O LYS G 187 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LYS G 187 " --> pdb=" O MET G 170 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N TYR G 172 " --> pdb=" O GLU G 185 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLU G 185 " --> pdb=" O TYR G 172 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N HIS G 174 " --> pdb=" O VAL G 183 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N VAL G 183 " --> pdb=" O HIS G 174 " (cutoff:3.500A) 1163 hydrogen bonds defined for protein. 3315 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: 5.42 Time building geometry restraints manager: 3.10 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: 8226 1.34 - 1.46: 4591 1.46 - 1.58: 11666 1.58 - 1.70: 18 1.70 - 1.82: 154 Bond restraints: 24655 Sorted by residual: bond pdb=" N THR C 406 " pdb=" CA THR C 406 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.21e-02 6.83e+03 1.05e+01 bond pdb=" O3 PO4 D 603 " pdb=" P PO4 D 603 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.02e+00 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 8.80e+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=" O4 PO4 D 603 " pdb=" P PO4 D 603 " ideal model delta sigma weight residual 1.568 1.510 0.058 2.00e-02 2.50e+03 8.45e+00 ... (remaining 24650 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 32920 1.85 - 3.70: 458 3.70 - 5.55: 46 5.55 - 7.40: 7 7.40 - 9.25: 2 Bond angle restraints: 33433 Sorted by residual: angle pdb=" C LYS C 409 " pdb=" CA LYS C 409 " pdb=" CB LYS C 409 " ideal model delta sigma weight residual 110.79 103.92 6.87 1.66e+00 3.63e-01 1.71e+01 angle pdb=" N LYS C 409 " pdb=" CA LYS C 409 " pdb=" C LYS C 409 " ideal model delta sigma weight residual 111.28 107.40 3.88 1.09e+00 8.42e-01 1.27e+01 angle pdb=" N GLN C 407 " pdb=" CA GLN C 407 " pdb=" C GLN C 407 " ideal model delta sigma weight residual 111.28 107.45 3.83 1.09e+00 8.42e-01 1.23e+01 angle pdb=" C LEU D 455 " pdb=" N VAL D 456 " pdb=" CA VAL D 456 " ideal model delta sigma weight residual 123.08 119.89 3.19 1.01e+00 9.80e-01 9.97e+00 angle pdb=" C ILE G 225 " pdb=" N TYR G 226 " pdb=" CA TYR G 226 " ideal model delta sigma weight residual 122.79 117.44 5.35 1.70e+00 3.46e-01 9.90e+00 ... (remaining 33428 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.31: 14195 22.31 - 44.63: 689 44.63 - 66.94: 129 66.94 - 89.26: 44 89.26 - 111.57: 2 Dihedral angle restraints: 15059 sinusoidal: 6134 harmonic: 8925 Sorted by residual: dihedral pdb=" O1B ADP D 602 " pdb=" O3A ADP D 602 " pdb=" PB ADP D 602 " pdb=" PA ADP D 602 " ideal model delta sinusoidal sigma weight residual -60.00 -171.57 111.57 1 2.00e+01 2.50e-03 3.28e+01 dihedral pdb=" CA GLU G 222 " pdb=" C GLU G 222 " pdb=" N SER G 223 " pdb=" CA SER G 223 " ideal model delta harmonic sigma weight residual 180.00 159.72 20.28 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" C LYS C 409 " pdb=" N LYS C 409 " pdb=" CA LYS C 409 " pdb=" CB LYS C 409 " ideal model delta harmonic sigma weight residual -122.60 -112.97 -9.63 0 2.50e+00 1.60e-01 1.48e+01 ... (remaining 15056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3248 0.059 - 0.117: 552 0.117 - 0.176: 49 0.176 - 0.234: 2 0.234 - 0.293: 1 Chirality restraints: 3852 Sorted by residual: chirality pdb=" CA LYS C 409 " pdb=" N LYS C 409 " pdb=" C LYS C 409 " pdb=" CB LYS C 409 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CG LEU G 194 " pdb=" CB LEU G 194 " pdb=" CD1 LEU G 194 " pdb=" CD2 LEU G 194 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA TYR G 226 " pdb=" N TYR G 226 " pdb=" C TYR G 226 " pdb=" CB TYR G 226 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.99e-01 ... (remaining 3849 not shown) Planarity restraints: 4362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 109 " -0.039 5.00e-02 4.00e+02 5.83e-02 5.44e+00 pdb=" N PRO C 110 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 110 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 110 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 220 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO D 221 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 221 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 221 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 220 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO F 221 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO F 221 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 221 " -0.024 5.00e-02 4.00e+02 ... (remaining 4359 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 113 2.57 - 3.15: 19253 3.15 - 3.73: 36384 3.73 - 4.32: 52466 4.32 - 4.90: 89186 Nonbonded interactions: 197402 Sorted by model distance: nonbonded pdb="MG MG F 601 " pdb=" O3G ATP F 602 " model vdw 1.983 2.170 nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 601 " model vdw 2.010 2.170 nonbonded pdb=" O1G ATP C 600 " pdb="MG MG C 601 " model vdw 2.016 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 601 " model vdw 2.020 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 601 " model vdw 2.058 2.170 ... (remaining 197397 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: 3.360 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 25.900 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24655 Z= 0.148 Angle : 0.556 9.254 33433 Z= 0.319 Chirality : 0.044 0.293 3852 Planarity : 0.004 0.058 4362 Dihedral : 14.033 111.572 9347 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.08 % Allowed : 0.39 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.15), residues: 3115 helix: 1.63 (0.15), residues: 1260 sheet: 0.96 (0.23), residues: 536 loop : -0.12 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 164 TYR 0.025 0.001 TYR G 226 PHE 0.014 0.001 PHE A 463 HIS 0.003 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00297 (24655) covalent geometry : angle 0.55620 (33433) hydrogen bonds : bond 0.15134 ( 1163) hydrogen bonds : angle 6.09360 ( 3315) *********************** 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 140 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: B 465 ASP cc_start: 0.8126 (m-30) cc_final: 0.7818 (m-30) REVERT: E 1 MET cc_start: 0.5116 (ptm) cc_final: 0.4567 (ptm) outliers start: 2 outliers final: 0 residues processed: 140 average time/residue: 0.7901 time to fit residues: 126.1165 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 : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 266 GLN C 189 GLN G 174 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.070200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.051933 restraints weight = 54215.812| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 2.33 r_work: 0.2629 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2504 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 24655 Z= 0.265 Angle : 0.629 9.496 33433 Z= 0.330 Chirality : 0.049 0.283 3852 Planarity : 0.005 0.053 4362 Dihedral : 7.816 83.320 3546 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.97 % Allowed : 5.49 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.15), residues: 3115 helix: 1.29 (0.14), residues: 1272 sheet: 0.55 (0.22), residues: 560 loop : -0.26 (0.17), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 240 TYR 0.025 0.002 TYR A 329 PHE 0.022 0.002 PHE D 257 HIS 0.006 0.001 HIS E 401 Details of bonding type rmsd covalent geometry : bond 0.00636 (24655) covalent geometry : angle 0.62909 (33433) hydrogen bonds : bond 0.06096 ( 1163) hydrogen bonds : angle 5.19470 ( 3315) *********************** 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 127 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 1.083 Fit side-chains REVERT: B 465 ASP cc_start: 0.8467 (m-30) cc_final: 0.8050 (m-30) REVERT: E 1 MET cc_start: 0.5373 (ptm) cc_final: 0.4912 (ptm) REVERT: F 1 MET cc_start: 0.8020 (tpp) cc_final: 0.7812 (tpp) REVERT: G 48 LYS cc_start: 0.5828 (OUTLIER) cc_final: 0.5013 (tmtt) REVERT: G 67 MET cc_start: 0.7440 (ptt) cc_final: 0.6993 (mmp) outliers start: 25 outliers final: 8 residues processed: 115 average time/residue: 0.7383 time to fit residues: 97.8982 Evaluate side-chains 104 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 224 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 111 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 283 optimal weight: 7.9990 chunk 140 optimal weight: 0.7980 chunk 161 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 167 optimal weight: 0.9980 chunk 215 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.072447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.054279 restraints weight = 53740.358| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 2.33 r_work: 0.2684 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2559 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9070 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24655 Z= 0.122 Angle : 0.494 8.791 33433 Z= 0.258 Chirality : 0.043 0.240 3852 Planarity : 0.004 0.045 4362 Dihedral : 7.254 87.226 3546 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.90 % Allowed : 7.09 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.15), residues: 3115 helix: 1.63 (0.15), residues: 1277 sheet: 0.63 (0.22), residues: 547 loop : -0.12 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 240 TYR 0.013 0.001 TYR A 329 PHE 0.014 0.001 PHE D 257 HIS 0.003 0.001 HIS G 107 Details of bonding type rmsd covalent geometry : bond 0.00281 (24655) covalent geometry : angle 0.49407 (33433) hydrogen bonds : bond 0.04482 ( 1163) hydrogen bonds : angle 4.82615 ( 3315) *********************** 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 121 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: B 465 ASP cc_start: 0.8492 (m-30) cc_final: 0.8089 (m-30) REVERT: E 1 MET cc_start: 0.5349 (ptm) cc_final: 0.4893 (ptm) REVERT: G 67 MET cc_start: 0.7451 (ptt) cc_final: 0.6917 (mmt) outliers start: 23 outliers final: 9 residues processed: 113 average time/residue: 0.6294 time to fit residues: 82.6607 Evaluate side-chains 102 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 191 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 201 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 282 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 249 optimal weight: 0.8980 chunk 245 optimal weight: 7.9990 chunk 303 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 217 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.071758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.053552 restraints weight = 53495.499| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 2.33 r_work: 0.2665 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9084 moved from start: 0.1959 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 : 0.512 8.841 33433 Z= 0.266 Chirality : 0.044 0.212 3852 Planarity : 0.004 0.048 4362 Dihedral : 7.075 88.310 3546 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.25 % Allowed : 7.94 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.15), residues: 3115 helix: 1.68 (0.15), residues: 1275 sheet: 0.58 (0.22), residues: 547 loop : -0.13 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 193 TYR 0.014 0.001 TYR A 329 PHE 0.017 0.001 PHE D 257 HIS 0.004 0.001 HIS F 363 Details of bonding type rmsd covalent geometry : bond 0.00364 (24655) covalent geometry : angle 0.51156 (33433) hydrogen bonds : bond 0.04734 ( 1163) hydrogen bonds : angle 4.78083 ( 3315) *********************** 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 127 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: B 465 ASP cc_start: 0.8469 (m-30) cc_final: 0.8037 (m-30) REVERT: E 1 MET cc_start: 0.5319 (ptm) cc_final: 0.4873 (ptm) REVERT: F 1 MET cc_start: 0.8174 (tpp) cc_final: 0.7903 (tpp) REVERT: G 67 MET cc_start: 0.7452 (ptt) cc_final: 0.6885 (mtp) REVERT: G 226 TYR cc_start: 0.8053 (OUTLIER) cc_final: 0.7084 (m-80) outliers start: 32 outliers final: 14 residues processed: 116 average time/residue: 0.5823 time to fit residues: 79.5819 Evaluate side-chains 110 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 226 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 185 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 275 optimal weight: 5.9990 chunk 242 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 186 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.069897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.051693 restraints weight = 53775.283| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 2.32 r_work: 0.2621 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2497 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9124 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 24655 Z= 0.264 Angle : 0.584 9.346 33433 Z= 0.306 Chirality : 0.047 0.176 3852 Planarity : 0.004 0.048 4362 Dihedral : 7.342 93.438 3546 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.29 % Allowed : 8.84 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.15), residues: 3115 helix: 1.44 (0.15), residues: 1273 sheet: 0.50 (0.22), residues: 543 loop : -0.29 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 193 TYR 0.022 0.001 TYR G 226 PHE 0.021 0.002 PHE D 257 HIS 0.010 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00646 (24655) covalent geometry : angle 0.58376 (33433) hydrogen bonds : bond 0.05779 ( 1163) hydrogen bonds : angle 5.01175 ( 3315) *********************** 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: 33 poor density : 99 time to evaluate : 0.950 Fit side-chains REVERT: B 465 ASP cc_start: 0.8560 (m-30) cc_final: 0.8088 (m-30) REVERT: C 375 MET cc_start: 0.9273 (mmt) cc_final: 0.8922 (mmt) REVERT: C 404 LYS cc_start: 0.8548 (mmmt) cc_final: 0.8284 (mtpp) REVERT: E 1 MET cc_start: 0.5495 (ptm) cc_final: 0.5071 (ptm) REVERT: G 48 LYS cc_start: 0.5822 (OUTLIER) cc_final: 0.4803 (tmtt) REVERT: G 67 MET cc_start: 0.7624 (ptt) cc_final: 0.7053 (mtp) REVERT: G 226 TYR cc_start: 0.8126 (OUTLIER) cc_final: 0.7263 (m-80) outliers start: 33 outliers final: 17 residues processed: 123 average time/residue: 0.6273 time to fit residues: 90.6253 Evaluate side-chains 117 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 210 LYS Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 226 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 5 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 291 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 238 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 252 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 240 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3145 r_free = 0.3145 target = 0.069955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.051747 restraints weight = 54112.604| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 2.33 r_work: 0.2622 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2497 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9124 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 24655 Z= 0.242 Angle : 0.571 9.183 33433 Z= 0.298 Chirality : 0.047 0.165 3852 Planarity : 0.004 0.049 4362 Dihedral : 7.333 96.163 3546 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.48 % Allowed : 9.38 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.15), residues: 3115 helix: 1.41 (0.15), residues: 1275 sheet: 0.46 (0.22), residues: 542 loop : -0.31 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 193 TYR 0.021 0.001 TYR G 226 PHE 0.020 0.002 PHE D 257 HIS 0.008 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00591 (24655) covalent geometry : angle 0.57096 (33433) hydrogen bonds : bond 0.05614 ( 1163) hydrogen bonds : angle 5.00591 ( 3315) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 99 time to evaluate : 1.123 Fit side-chains REVERT: B 465 ASP cc_start: 0.8553 (m-30) cc_final: 0.8078 (m-30) REVERT: C 404 LYS cc_start: 0.8494 (mmmt) cc_final: 0.8261 (mtpp) REVERT: E 1 MET cc_start: 0.5447 (ptm) cc_final: 0.5083 (ptm) REVERT: F 1 MET cc_start: 0.8206 (tpp) cc_final: 0.7952 (tpp) REVERT: G 46 MET cc_start: 0.8405 (tpt) cc_final: 0.8180 (tpp) REVERT: G 48 LYS cc_start: 0.5906 (OUTLIER) cc_final: 0.4896 (tmtt) REVERT: G 67 MET cc_start: 0.7606 (ptt) cc_final: 0.7227 (tpt) REVERT: G 68 LEU cc_start: 0.8445 (mm) cc_final: 0.8185 (tm) REVERT: G 226 TYR cc_start: 0.8056 (OUTLIER) cc_final: 0.7266 (m-80) outliers start: 38 outliers final: 21 residues processed: 128 average time/residue: 0.6386 time to fit residues: 96.7571 Evaluate side-chains 121 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 210 LYS Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 226 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 30 optimal weight: 0.8980 chunk 294 optimal weight: 9.9990 chunk 4 optimal weight: 0.6980 chunk 169 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 180 optimal weight: 5.9990 chunk 291 optimal weight: 6.9990 chunk 201 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.071111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.052915 restraints weight = 53771.511| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 2.33 r_work: 0.2649 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9099 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24655 Z= 0.163 Angle : 0.519 9.506 33433 Z= 0.270 Chirality : 0.044 0.147 3852 Planarity : 0.004 0.048 4362 Dihedral : 7.110 94.568 3546 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.05 % Allowed : 10.01 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.15), residues: 3115 helix: 1.59 (0.15), residues: 1275 sheet: 0.55 (0.22), residues: 528 loop : -0.27 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 240 TYR 0.015 0.001 TYR G 226 PHE 0.018 0.001 PHE D 257 HIS 0.007 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00392 (24655) covalent geometry : angle 0.51867 (33433) hydrogen bonds : bond 0.04854 ( 1163) hydrogen bonds : angle 4.84431 ( 3315) *********************** 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 125 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 1.056 Fit side-chains REVERT: B 465 ASP cc_start: 0.8558 (m-30) cc_final: 0.8075 (m-30) REVERT: C 404 LYS cc_start: 0.8495 (mmmt) cc_final: 0.8284 (mtpp) REVERT: E 1 MET cc_start: 0.5381 (ptm) cc_final: 0.5005 (ptm) REVERT: G 46 MET cc_start: 0.8377 (tpt) cc_final: 0.8155 (tpp) REVERT: G 67 MET cc_start: 0.7589 (ptt) cc_final: 0.7241 (tpt) REVERT: G 68 LEU cc_start: 0.8390 (mm) cc_final: 0.8187 (tm) REVERT: G 226 TYR cc_start: 0.7872 (OUTLIER) cc_final: 0.7313 (m-80) outliers start: 27 outliers final: 17 residues processed: 119 average time/residue: 0.6827 time to fit residues: 95.5070 Evaluate side-chains 116 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 226 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 102 optimal weight: 1.9990 chunk 308 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 205 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 chunk 190 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3179 r_free = 0.3179 target = 0.071630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.053511 restraints weight = 53493.130| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 2.32 r_work: 0.2664 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9089 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24655 Z= 0.145 Angle : 0.507 10.101 33433 Z= 0.263 Chirality : 0.044 0.147 3852 Planarity : 0.004 0.047 4362 Dihedral : 6.955 90.690 3546 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.93 % Allowed : 10.28 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.15), residues: 3115 helix: 1.71 (0.15), residues: 1270 sheet: 0.57 (0.22), residues: 528 loop : -0.24 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 240 TYR 0.014 0.001 TYR G 226 PHE 0.017 0.001 PHE D 257 HIS 0.006 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00345 (24655) covalent geometry : angle 0.50749 (33433) hydrogen bonds : bond 0.04576 ( 1163) hydrogen bonds : angle 4.75855 ( 3315) *********************** 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 124 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 1.132 Fit side-chains REVERT: B 465 ASP cc_start: 0.8552 (m-30) cc_final: 0.8073 (m-30) REVERT: E 1 MET cc_start: 0.5319 (ptm) cc_final: 0.4945 (ptm) REVERT: F 1 MET cc_start: 0.8171 (tpp) cc_final: 0.7874 (tpp) REVERT: G 46 MET cc_start: 0.8360 (tpt) cc_final: 0.8148 (tpp) REVERT: G 67 MET cc_start: 0.7601 (ptt) cc_final: 0.7236 (tpt) REVERT: G 226 TYR cc_start: 0.7809 (OUTLIER) cc_final: 0.7266 (m-80) outliers start: 24 outliers final: 18 residues processed: 118 average time/residue: 0.6698 time to fit residues: 92.5957 Evaluate side-chains 117 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain G residue 226 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 263 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 chunk 239 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 154 optimal weight: 0.9980 chunk 57 optimal weight: 0.4980 chunk 110 optimal weight: 6.9990 chunk 269 optimal weight: 1.9990 chunk 25 optimal weight: 0.0870 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.073166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.055063 restraints weight = 53743.273| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.34 r_work: 0.2703 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 24655 Z= 0.104 Angle : 0.474 9.026 33433 Z= 0.244 Chirality : 0.043 0.142 3852 Planarity : 0.004 0.046 4362 Dihedral : 6.631 87.011 3546 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.78 % Allowed : 10.59 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.15), residues: 3115 helix: 1.91 (0.15), residues: 1270 sheet: 0.67 (0.22), residues: 526 loop : -0.15 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 164 TYR 0.010 0.001 TYR G 226 PHE 0.014 0.001 PHE D 125 HIS 0.006 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00233 (24655) covalent geometry : angle 0.47378 (33433) hydrogen bonds : bond 0.03828 ( 1163) hydrogen bonds : angle 4.59001 ( 3315) *********************** 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 121 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: B 465 ASP cc_start: 0.8500 (m-30) cc_final: 0.8042 (m-30) REVERT: E 1 MET cc_start: 0.5313 (ptm) cc_final: 0.4955 (ptm) REVERT: F 1 MET cc_start: 0.8103 (tpp) cc_final: 0.7774 (tpp) REVERT: G 67 MET cc_start: 0.7663 (ptt) cc_final: 0.7354 (tpt) REVERT: G 226 TYR cc_start: 0.7650 (OUTLIER) cc_final: 0.7242 (m-80) outliers start: 20 outliers final: 12 residues processed: 115 average time/residue: 0.6752 time to fit residues: 91.3052 Evaluate side-chains 111 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain G residue 226 TYR Chi-restraints excluded: chain G residue 245 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 134 optimal weight: 0.9990 chunk 180 optimal weight: 8.9990 chunk 229 optimal weight: 6.9990 chunk 168 optimal weight: 0.7980 chunk 118 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 chunk 210 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3204 r_free = 0.3204 target = 0.072884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.054929 restraints weight = 53543.006| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.32 r_work: 0.2701 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 24655 Z= 0.108 Angle : 0.479 9.059 33433 Z= 0.246 Chirality : 0.043 0.143 3852 Planarity : 0.004 0.046 4362 Dihedral : 6.542 85.032 3546 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.58 % Allowed : 10.75 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.15), residues: 3115 helix: 1.97 (0.15), residues: 1269 sheet: 0.66 (0.23), residues: 524 loop : -0.11 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 240 TYR 0.012 0.001 TYR G 226 PHE 0.014 0.001 PHE D 257 HIS 0.005 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00244 (24655) covalent geometry : angle 0.47881 (33433) hydrogen bonds : bond 0.03937 ( 1163) hydrogen bonds : angle 4.55374 ( 3315) ********************** 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 115 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 1.056 Fit side-chains REVERT: B 465 ASP cc_start: 0.8511 (m-30) cc_final: 0.8046 (m-30) REVERT: E 1 MET cc_start: 0.5311 (ptm) cc_final: 0.4922 (ptm) REVERT: F 1 MET cc_start: 0.8113 (tpp) cc_final: 0.7874 (tpp) REVERT: G 67 MET cc_start: 0.7669 (ptt) cc_final: 0.7314 (tpt) REVERT: G 68 LEU cc_start: 0.8436 (tm) cc_final: 0.8184 (mm) REVERT: G 226 TYR cc_start: 0.7716 (OUTLIER) cc_final: 0.7205 (m-80) outliers start: 15 outliers final: 12 residues processed: 112 average time/residue: 0.6639 time to fit residues: 87.7032 Evaluate side-chains 111 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain G residue 226 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 232 optimal weight: 5.9990 chunk 178 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 253 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 284 optimal weight: 6.9990 chunk 275 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 8 GLN E 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.069703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.051522 restraints weight = 53955.002| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 2.32 r_work: 0.2616 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2490 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9129 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 24655 Z= 0.278 Angle : 0.603 10.070 33433 Z= 0.313 Chirality : 0.048 0.189 3852 Planarity : 0.004 0.049 4362 Dihedral : 7.103 88.821 3546 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.78 % Allowed : 10.83 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.15), residues: 3115 helix: 1.56 (0.15), residues: 1268 sheet: 0.53 (0.22), residues: 520 loop : -0.30 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 193 TYR 0.023 0.001 TYR G 226 PHE 0.021 0.002 PHE D 257 HIS 0.007 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00683 (24655) covalent geometry : angle 0.60272 (33433) hydrogen bonds : bond 0.05852 ( 1163) hydrogen bonds : angle 4.97247 ( 3315) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6459.35 seconds wall clock time: 111 minutes 18.64 seconds (6678.64 seconds total)