Starting phenix.real_space_refine on Sat Sep 12 01:55:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n7t_0363/09_2026/6n7t_0363_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n7t_0363/09_2026/6n7t_0363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6n7t_0363/09_2026/6n7t_0363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n7t_0363/09_2026/6n7t_0363.map" model { file = "/net/cci-nas-00/data/ceres_data/6n7t_0363/09_2026/6n7t_0363_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n7t_0363/09_2026/6n7t_0363_neut.cif" } resolution = 3.9 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= 0.001 sd= 0.005 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 31 5.49 5 Mg 5 5.21 5 S 78 5.16 5 C 7980 2.51 5 N 2261 2.21 5 O 2535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12890 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2093 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 4, 'TRANS': 266} Chain breaks: 3 Chain: "B" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2111 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 4, 'TRANS': 269} Chain breaks: 3 Chain: "C" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2121 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 4, 'TRANS': 270} Chain breaks: 3 Chain: "D" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2086 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 266} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1995 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 253} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2014 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 4, 'TRANS': 256} Chain breaks: 4 Chain: "T" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 320 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.66, per 1000 atoms: 0.21 Number of scatterers: 12890 At special positions: 0 Unit cell: (86.67, 127.33, 134.82, 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 78 16.00 P 31 15.00 Mg 5 11.99 O 2535 8.00 N 2261 7.00 C 7980 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: 0.91 Conformation dependent library (CDL) restraints added in 446.1 milliseconds 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2868 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 6 sheets defined 36.6% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 269 through 272 Processing helix chain 'A' and resid 273 through 279 Processing helix chain 'A' and resid 292 through 298 removed outlier: 4.232A pdb=" N ASN A 296 " --> pdb=" O CYS A 292 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS A 298 " --> pdb=" O GLY A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 332 removed outlier: 3.544A pdb=" N GLY A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 332 " --> pdb=" O GLN A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 356 Processing helix chain 'A' and resid 365 through 375 removed outlier: 3.503A pdb=" N ILE A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 383 Processing helix chain 'A' and resid 403 through 415 removed outlier: 3.900A pdb=" N LYS A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 439 through 454 Processing helix chain 'A' and resid 482 through 486 removed outlier: 3.600A pdb=" N ASP A 485 " --> pdb=" O SER A 482 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 486 " --> pdb=" O ILE A 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 482 through 486' Processing helix chain 'B' and resid 273 through 280 Processing helix chain 'B' and resid 292 through 298 removed outlier: 4.319A pdb=" N ASN B 296 " --> pdb=" O CYS B 292 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS B 298 " --> pdb=" O GLY B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 332 removed outlier: 3.621A pdb=" N PHE B 321 " --> pdb=" O GLY B 317 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA B 332 " --> pdb=" O GLN B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 358 removed outlier: 3.564A pdb=" N THR B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 375 removed outlier: 3.665A pdb=" N ILE B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU B 374 " --> pdb=" O ARG B 370 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN B 375 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 386 removed outlier: 4.135A pdb=" N GLN B 380 " --> pdb=" O GLY B 376 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU B 384 " --> pdb=" O GLN B 380 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU B 385 " --> pdb=" O TRP B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 414 Processing helix chain 'B' and resid 438 through 454 Processing helix chain 'B' and resid 474 through 478 removed outlier: 3.783A pdb=" N GLY B 478 " --> pdb=" O HIS B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 486 removed outlier: 3.955A pdb=" N ASP B 485 " --> pdb=" O SER B 482 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU B 486 " --> pdb=" O ILE B 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 482 through 486' Processing helix chain 'C' and resid 271 through 277 removed outlier: 3.684A pdb=" N ILE C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 299 Processing helix chain 'C' and resid 319 through 329 removed outlier: 3.689A pdb=" N GLN C 328 " --> pdb=" O GLN C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 358 removed outlier: 3.985A pdb=" N LEU C 353 " --> pdb=" O THR C 349 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY C 355 " --> pdb=" O GLU C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 375 removed outlier: 4.007A pdb=" N LYS C 369 " --> pdb=" O SER C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 386 removed outlier: 4.210A pdb=" N GLN C 380 " --> pdb=" O GLY C 376 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 385 " --> pdb=" O TRP C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 415 removed outlier: 4.349A pdb=" N LEU C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY C 415 " --> pdb=" O TYR C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 432 removed outlier: 3.753A pdb=" N VAL C 430 " --> pdb=" O ILE C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 457 Processing helix chain 'C' and resid 474 through 478 removed outlier: 3.788A pdb=" N GLY C 478 " --> pdb=" O HIS C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 486 removed outlier: 3.594A pdb=" N ASP C 485 " --> pdb=" O SER C 482 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU C 486 " --> pdb=" O ILE C 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 482 through 486' Processing helix chain 'D' and resid 271 through 277 Processing helix chain 'D' and resid 294 through 299 Processing helix chain 'D' and resid 317 through 332 removed outlier: 3.719A pdb=" N GLN D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN D 325 " --> pdb=" O PHE D 321 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA D 332 " --> pdb=" O GLN D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 358 Processing helix chain 'D' and resid 370 through 375 removed outlier: 3.764A pdb=" N GLU D 374 " --> pdb=" O ARG D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 387 removed outlier: 3.518A pdb=" N GLU D 384 " --> pdb=" O GLN D 380 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU D 385 " --> pdb=" O TRP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 415 Processing helix chain 'D' and resid 440 through 457 removed outlier: 3.642A pdb=" N LEU D 445 " --> pdb=" O MET D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 478 removed outlier: 3.503A pdb=" N GLU D 477 " --> pdb=" O ALA D 474 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY D 478 " --> pdb=" O HIS D 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 474 through 478' Processing helix chain 'D' and resid 490 through 494 removed outlier: 4.012A pdb=" N ARG D 493 " --> pdb=" O GLY D 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 280 removed outlier: 4.215A pdb=" N ARG E 276 " --> pdb=" O ARG E 272 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU E 277 " --> pdb=" O GLU E 273 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS E 278 " --> pdb=" O ARG E 274 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU E 279 " --> pdb=" O ILE E 275 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER E 280 " --> pdb=" O ARG E 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 272 through 280' Processing helix chain 'E' and resid 317 through 329 Processing helix chain 'E' and resid 345 through 358 removed outlier: 3.595A pdb=" N THR E 349 " --> pdb=" O SER E 345 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA E 350 " --> pdb=" O VAL E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 372 removed outlier: 3.847A pdb=" N ARG E 370 " --> pdb=" O ASP E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 387 removed outlier: 4.136A pdb=" N LEU E 385 " --> pdb=" O TRP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 415 Processing helix chain 'E' and resid 440 through 457 removed outlier: 3.911A pdb=" N LEU E 445 " --> pdb=" O MET E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 478 removed outlier: 3.716A pdb=" N GLY E 478 " --> pdb=" O HIS E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 279 Processing helix chain 'F' and resid 293 through 299 removed outlier: 3.566A pdb=" N ASP F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS F 298 " --> pdb=" O GLY F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 331 removed outlier: 4.025A pdb=" N PHE F 321 " --> pdb=" O GLY F 317 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN F 324 " --> pdb=" O THR F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 358 removed outlier: 3.782A pdb=" N THR F 349 " --> pdb=" O SER F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 375 removed outlier: 3.793A pdb=" N ILE F 373 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU F 374 " --> pdb=" O ARG F 370 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN F 375 " --> pdb=" O GLU F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 415 Processing helix chain 'F' and resid 439 through 454 Processing helix chain 'F' and resid 491 through 496 removed outlier: 3.980A pdb=" N LEU F 495 " --> pdb=" O ALA F 491 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 267 removed outlier: 3.530A pdb=" N TYR B 394 " --> pdb=" O LEU B 339 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 463 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLU B 306 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL B 462 " --> pdb=" O GLU B 306 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ILE B 308 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR B 498 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE B 499 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL B 514 " --> pdb=" O TYR B 532 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N TYR B 532 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL B 516 " --> pdb=" O ALA B 530 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 542 through 544 removed outlier: 7.082A pdb=" N VAL A 516 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N TYR A 532 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL A 514 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE A 499 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLU A 306 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL A 462 " --> pdb=" O GLU A 306 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ILE A 308 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL A 337 " --> pdb=" O HIS A 392 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N TYR A 394 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 266 through 267 removed outlier: 3.871A pdb=" N VAL B 266 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 393 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE C 308 " --> pdb=" O VAL C 462 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL C 307 " --> pdb=" O THR C 498 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE C 500 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N MET C 309 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LEU C 502 " --> pdb=" O MET C 309 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR C 311 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE C 499 " --> pdb=" O LEU C 519 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL C 514 " --> pdb=" O TYR C 532 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TYR C 532 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL C 516 " --> pdb=" O ALA C 530 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 265 through 267 removed outlier: 3.700A pdb=" N VAL D 266 " --> pdb=" O LEU E 393 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL E 337 " --> pdb=" O HIS E 392 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N TYR E 394 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LYS E 336 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ILE E 308 " --> pdb=" O VAL E 462 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR E 498 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE E 499 " --> pdb=" O LEU E 519 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL E 514 " --> pdb=" O TYR E 532 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N TYR E 532 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL E 516 " --> pdb=" O ALA E 530 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 391 through 392 removed outlier: 6.679A pdb=" N VAL D 337 " --> pdb=" O HIS D 392 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N GLU D 306 " --> pdb=" O LEU D 460 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL D 462 " --> pdb=" O GLU D 306 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ILE D 308 " --> pdb=" O VAL D 462 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL D 307 " --> pdb=" O THR D 498 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ILE D 500 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N MET D 309 " --> pdb=" O ILE D 500 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N LEU D 502 " --> pdb=" O MET D 309 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR D 311 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE D 499 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL D 514 " --> pdb=" O TYR D 532 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR D 532 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL D 516 " --> pdb=" O ALA D 530 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 338 through 340 removed outlier: 6.603A pdb=" N ILE F 421 " --> pdb=" O VAL F 461 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ILE F 463 " --> pdb=" O ILE F 421 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU F 423 " --> pdb=" O ILE F 463 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLU F 306 " --> pdb=" O LEU F 460 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL F 462 " --> pdb=" O GLU F 306 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ILE F 308 " --> pdb=" O VAL F 462 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE F 499 " --> pdb=" O LEU F 519 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL F 514 " --> pdb=" O TYR F 532 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TYR F 532 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL F 516 " --> pdb=" O ALA F 530 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR F 532 " --> pdb=" O SER F 545 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP F 541 " --> pdb=" O ASN F 536 " (cutoff:3.500A) 415 hydrogen bonds defined for protein. 1191 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: 1.37 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2155 1.31 - 1.44: 3233 1.44 - 1.57: 7492 1.57 - 1.70: 56 1.70 - 1.83: 132 Bond restraints: 13068 Sorted by residual: bond pdb=" O3B TTP E 700 " pdb=" PG TTP E 700 " ideal model delta sigma weight residual 1.748 1.593 0.155 2.00e-02 2.50e+03 6.00e+01 bond pdb=" O3B TTP C 700 " pdb=" PG TTP C 700 " ideal model delta sigma weight residual 1.748 1.595 0.153 2.00e-02 2.50e+03 5.88e+01 bond pdb=" O3B TTP B 700 " pdb=" PG TTP B 700 " ideal model delta sigma weight residual 1.748 1.600 0.148 2.00e-02 2.50e+03 5.47e+01 bond pdb=" O3B TTP A 700 " pdb=" PG TTP A 700 " ideal model delta sigma weight residual 1.748 1.600 0.148 2.00e-02 2.50e+03 5.46e+01 bond pdb=" O3B TTP D 700 " pdb=" PG TTP D 700 " ideal model delta sigma weight residual 1.748 1.601 0.147 2.00e-02 2.50e+03 5.43e+01 ... (remaining 13063 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 17276 2.90 - 5.80: 275 5.80 - 8.71: 41 8.71 - 11.61: 18 11.61 - 14.51: 21 Bond angle restraints: 17631 Sorted by residual: angle pdb=" N HIS A 357 " pdb=" CA HIS A 357 " pdb=" C HIS A 357 " ideal model delta sigma weight residual 113.41 102.95 10.46 1.22e+00 6.72e-01 7.35e+01 angle pdb=" O4' DT T 13 " pdb=" C4' DT T 13 " pdb=" C3' DT T 13 " ideal model delta sigma weight residual 106.00 102.99 3.01 6.00e-01 2.78e+00 2.52e+01 angle pdb=" C2 TTP C 700 " pdb=" N3 TTP C 700 " pdb=" C4 TTP C 700 " ideal model delta sigma weight residual 128.28 113.77 14.51 3.00e+00 1.11e-01 2.34e+01 angle pdb=" C2 TTP D 700 " pdb=" N3 TTP D 700 " pdb=" C4 TTP D 700 " ideal model delta sigma weight residual 128.28 113.82 14.46 3.00e+00 1.11e-01 2.32e+01 angle pdb=" C2 TTP E 700 " pdb=" N3 TTP E 700 " pdb=" C4 TTP E 700 " ideal model delta sigma weight residual 128.28 113.83 14.45 3.00e+00 1.11e-01 2.32e+01 ... (remaining 17626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.92: 7619 27.92 - 55.83: 239 55.83 - 83.75: 56 83.75 - 111.66: 3 111.66 - 139.58: 1 Dihedral angle restraints: 7918 sinusoidal: 3437 harmonic: 4481 Sorted by residual: dihedral pdb=" CA ASN F 358 " pdb=" C ASN F 358 " pdb=" N ARG F 359 " pdb=" CA ARG F 359 " ideal model delta harmonic sigma weight residual 180.00 160.67 19.33 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" C4' DT T 5 " pdb=" C3' DT T 5 " pdb=" O3' DT T 5 " pdb=" P DT T 6 " ideal model delta sinusoidal sigma weight residual 220.00 80.42 139.58 1 3.50e+01 8.16e-04 1.38e+01 dihedral pdb=" C LEU A 356 " pdb=" N LEU A 356 " pdb=" CA LEU A 356 " pdb=" CB LEU A 356 " ideal model delta harmonic sigma weight residual -122.60 -113.47 -9.13 0 2.50e+00 1.60e-01 1.33e+01 ... (remaining 7915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1521 0.059 - 0.118: 397 0.118 - 0.176: 75 0.176 - 0.235: 9 0.235 - 0.294: 4 Chirality restraints: 2006 Sorted by residual: chirality pdb=" C4' TTP C 700 " pdb=" C3' TTP C 700 " pdb=" C5' TTP C 700 " pdb=" O4' TTP C 700 " both_signs ideal model delta sigma weight residual False -2.46 -2.75 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C4' TTP B 700 " pdb=" C3' TTP B 700 " pdb=" C5' TTP B 700 " pdb=" O4' TTP B 700 " both_signs ideal model delta sigma weight residual False -2.46 -2.72 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C4' TTP A 700 " pdb=" C3' TTP A 700 " pdb=" C5' TTP A 700 " pdb=" O4' TTP A 700 " both_signs ideal model delta sigma weight residual False -2.46 -2.72 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 2003 not shown) Planarity restraints: 2171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN E 536 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.18e+00 pdb=" C ASN E 536 " 0.043 2.00e-02 2.50e+03 pdb=" O ASN E 536 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS E 537 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 486 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C LEU A 486 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU A 486 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG A 487 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET D 510 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO D 511 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 511 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 511 " 0.028 5.00e-02 4.00e+02 ... (remaining 2168 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 31 2.49 - 3.09: 8034 3.09 - 3.69: 18402 3.69 - 4.30: 27013 4.30 - 4.90: 44919 Nonbonded interactions: 98399 Sorted by model distance: nonbonded pdb=" O1G TTP C 700 " pdb="MG MG C 701 " model vdw 1.883 2.170 nonbonded pdb=" O1G TTP A 700 " pdb="MG MG A 701 " model vdw 2.005 2.170 nonbonded pdb=" O1B TTP A 700 " pdb="MG MG A 701 " model vdw 2.017 2.170 nonbonded pdb=" O2B TTP D 700 " pdb="MG MG D 701 " model vdw 2.044 2.170 nonbonded pdb=" O2B TTP E 700 " pdb="MG MG E 701 " model vdw 2.054 2.170 ... (remaining 98394 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 264 through 373 or resid 377 through 395 or resid 406 thro \ ugh 429 or resid 439 or (resid 440 and (name N or name CA or name C or name O or \ name CB )) or resid 441 through 469 or resid 474 through 506 or resid 510 throu \ gh 545)) selection = (chain 'B' and (resid 264 through 280 or resid 285 through 373 or resid 377 thro \ ugh 395 or resid 406 through 429 or resid 439 or (resid 440 and (name N or name \ CA or name C or name O or name CB )) or resid 441 through 469 or resid 474 throu \ gh 506 or resid 510 through 545)) selection = (chain 'C' and (resid 264 through 280 or resid 285 through 373 or resid 377 thro \ ugh 395 or resid 406 through 429 or resid 439 or (resid 440 and (name N or name \ CA or name C or name O or name CB )) or resid 441 through 469 or resid 474 throu \ gh 545)) selection = (chain 'D' and (resid 264 through 373 or resid 377 through 395 or resid 406 thro \ ugh 429 or resid 439 through 469 or resid 474 through 506 or resid 510 through 5 \ 45)) selection = (chain 'E' and (resid 264 through 395 or resid 406 through 469 or resid 474 thro \ ugh 506 or resid 510 through 545)) selection = (chain 'F' and (resid 264 through 373 or resid 377 through 395 or resid 406 thro \ ugh 429 or resid 439 or (resid 440 and (name N or name CA or name C or name O or \ name CB )) or resid 441 through 506 or resid 510 through 545)) } 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 group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 1.400 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.810 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 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 : 0.006 0.155 13068 Z= 0.354 Angle : 1.090 14.509 17631 Z= 0.570 Chirality : 0.056 0.294 2006 Planarity : 0.004 0.051 2171 Dihedral : 13.886 139.577 5050 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.65 % Favored : 94.29 % Rotamer: Outliers : 0.81 % Allowed : 2.96 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.82 (0.17), residues: 1558 helix: -2.95 (0.16), residues: 518 sheet: -0.91 (0.30), residues: 315 loop : -2.93 (0.18), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 493 TYR 0.009 0.001 TYR F 411 PHE 0.013 0.002 PHE A 523 TRP 0.019 0.002 TRP F 329 HIS 0.009 0.002 HIS A 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.35 (13068) covalent geometry : angle 1.09045 / 0.57 (17631) hydrogen bonds : bond 0.16558 / 11.57 ( 415) hydrogen bonds : angle 7.22833 / 5.22 ( 1191) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 333 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.7965 (mmp) cc_final: 0.7661 (tpp) REVERT: B 328 GLN cc_start: 0.8151 (mm110) cc_final: 0.7916 (mt0) REVERT: C 425 HIS cc_start: 0.7428 (t-90) cc_final: 0.7045 (t70) REVERT: D 452 PHE cc_start: 0.7352 (t80) cc_final: 0.7105 (t80) REVERT: D 466 LEU cc_start: 0.8692 (mt) cc_final: 0.7932 (mt) REVERT: E 394 TYR cc_start: 0.6906 (t80) cc_final: 0.6663 (t80) REVERT: F 351 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6363 (mt-10) REVERT: F 412 MET cc_start: 0.6287 (ttm) cc_final: 0.6025 (ttt) outliers start: 11 outliers final: 2 residues processed: 343 average time/residue: 0.1108 time to fit residues: 54.6555 Evaluate side-chains 172 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 170 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain B residue 504 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 GLN ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 ASN C 465 HIS C 475 HIS D 325 GLN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 HIS E 358 ASN E 475 HIS F 343 GLN F 512 ASN F 536 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.127475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.110709 restraints weight = 31962.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.112794 restraints weight = 20010.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.114317 restraints weight = 14100.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.115335 restraints weight = 10795.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.115936 restraints weight = 8969.925| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13068 Z= 0.151 Angle : 0.596 6.385 17631 Z= 0.311 Chirality : 0.044 0.151 2006 Planarity : 0.004 0.086 2171 Dihedral : 13.886 136.731 2067 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.51 % Allowed : 9.02 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.19), residues: 1558 helix: -1.28 (0.20), residues: 542 sheet: -0.78 (0.30), residues: 313 loop : -2.53 (0.20), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 274 TYR 0.017 0.001 TYR A 411 PHE 0.014 0.002 PHE C 452 TRP 0.020 0.002 TRP F 381 HIS 0.010 0.001 HIS E 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (13068) covalent geometry : angle 0.59564 / 0.31 (17631) hydrogen bonds : bond 0.03499 / 2.38 ( 415) hydrogen bonds : angle 5.10506 / 3.65 ( 1191) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 194 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.8351 (mmp) cc_final: 0.7808 (tpp) REVERT: A 512 ASN cc_start: 0.6502 (p0) cc_final: 0.6147 (p0) REVERT: B 316 MET cc_start: 0.8330 (mmt) cc_final: 0.8105 (tpp) REVERT: B 497 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7719 (t0) REVERT: F 351 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6793 (mt-10) outliers start: 34 outliers final: 19 residues processed: 216 average time/residue: 0.0890 time to fit residues: 29.6035 Evaluate side-chains 180 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 419 ASP Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 496 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 24 optimal weight: 0.0980 chunk 23 optimal weight: 9.9990 chunk 55 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 chunk 152 optimal weight: 0.4980 chunk 125 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 ASN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.126777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.110504 restraints weight = 32204.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.112625 restraints weight = 20435.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.114007 restraints weight = 14354.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.114842 restraints weight = 11212.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.115573 restraints weight = 9453.111| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13068 Z= 0.128 Angle : 0.562 15.182 17631 Z= 0.289 Chirality : 0.043 0.154 2006 Planarity : 0.004 0.077 2171 Dihedral : 13.144 137.805 2062 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.51 % Allowed : 11.46 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.20), residues: 1558 helix: -0.48 (0.22), residues: 540 sheet: -0.73 (0.29), residues: 319 loop : -2.30 (0.21), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 363 TYR 0.018 0.001 TYR A 411 PHE 0.015 0.001 PHE E 452 TRP 0.035 0.001 TRP F 381 HIS 0.010 0.001 HIS E 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (13068) covalent geometry : angle 0.56248 / 0.29 (17631) hydrogen bonds : bond 0.03126 / 2.10 ( 415) hydrogen bonds : angle 4.81028 / 3.41 ( 1191) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.8359 (mmp) cc_final: 0.7893 (tpp) REVERT: B 497 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7701 (t0) REVERT: C 341 MET cc_start: 0.7873 (mmm) cc_final: 0.7352 (mmm) REVERT: C 351 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6524 (tp30) REVERT: C 504 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8256 (ptm160) REVERT: E 464 CYS cc_start: 0.8019 (p) cc_final: 0.7700 (t) REVERT: F 381 TRP cc_start: 0.7489 (m-10) cc_final: 0.7267 (m100) REVERT: F 532 TYR cc_start: 0.6206 (m-80) cc_final: 0.5900 (m-80) outliers start: 34 outliers final: 21 residues processed: 196 average time/residue: 0.0855 time to fit residues: 25.9679 Evaluate side-chains 174 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 419 ASP Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 521 CYS Chi-restraints excluded: chain F residue 542 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 91 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 HIS ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.123647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.107791 restraints weight = 33001.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.109666 restraints weight = 21305.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.110962 restraints weight = 15389.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.111850 restraints weight = 12155.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.112491 restraints weight = 10248.653| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13068 Z= 0.189 Angle : 0.624 11.530 17631 Z= 0.319 Chirality : 0.045 0.208 2006 Planarity : 0.004 0.044 2171 Dihedral : 12.811 138.415 2062 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.33 % Allowed : 12.42 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.20), residues: 1558 helix: -0.21 (0.22), residues: 540 sheet: -0.93 (0.29), residues: 315 loop : -2.16 (0.21), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 522 TYR 0.020 0.002 TYR C 411 PHE 0.012 0.002 PHE B 321 TRP 0.024 0.002 TRP F 381 HIS 0.012 0.002 HIS E 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (13068) covalent geometry : angle 0.62357 / 0.32 (17631) hydrogen bonds : bond 0.03555 / 2.42 ( 415) hydrogen bonds : angle 4.82624 / 3.43 ( 1191) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 162 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 SER cc_start: 0.6866 (t) cc_final: 0.6626 (p) REVERT: A 316 MET cc_start: 0.8525 (mmp) cc_final: 0.8046 (tpp) REVERT: A 395 ASP cc_start: 0.6726 (t0) cc_final: 0.6389 (t0) REVERT: B 375 ASN cc_start: 0.7043 (p0) cc_final: 0.6723 (p0) REVERT: B 497 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7778 (t0) REVERT: C 425 HIS cc_start: 0.7956 (t70) cc_final: 0.7561 (t70) REVERT: C 504 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8441 (ptm160) REVERT: D 316 MET cc_start: 0.8284 (mtp) cc_final: 0.8064 (mtp) REVERT: F 381 TRP cc_start: 0.7744 (m-10) cc_final: 0.7390 (m100) outliers start: 45 outliers final: 27 residues processed: 190 average time/residue: 0.0849 time to fit residues: 25.1178 Evaluate side-chains 173 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain C residue 510 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 419 ASP Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 521 CYS Chi-restraints excluded: chain F residue 542 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 0.2980 chunk 83 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 117 optimal weight: 0.4980 chunk 61 optimal weight: 0.0470 chunk 125 optimal weight: 4.9990 overall best weight: 0.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 357 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.125704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.109704 restraints weight = 32824.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.111724 restraints weight = 21185.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.113014 restraints weight = 15070.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.113989 restraints weight = 11809.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.114639 restraints weight = 9846.735| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13068 Z= 0.094 Angle : 0.533 16.150 17631 Z= 0.270 Chirality : 0.042 0.161 2006 Planarity : 0.003 0.059 2171 Dihedral : 12.281 138.271 2062 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.14 % Allowed : 13.82 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.21), residues: 1558 helix: 0.19 (0.23), residues: 538 sheet: -0.72 (0.29), residues: 320 loop : -2.00 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 274 TYR 0.012 0.001 TYR E 394 PHE 0.022 0.001 PHE F 523 TRP 0.013 0.001 TRP F 381 HIS 0.011 0.001 HIS E 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 (13068) covalent geometry : angle 0.53338 / 0.27 (17631) hydrogen bonds : bond 0.02645 / 1.80 ( 415) hydrogen bonds : angle 4.46971 / 3.17 ( 1191) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 SER cc_start: 0.6868 (t) cc_final: 0.6598 (p) REVERT: A 316 MET cc_start: 0.8416 (mmp) cc_final: 0.7924 (tpp) REVERT: A 395 ASP cc_start: 0.6775 (t0) cc_final: 0.6358 (t0) REVERT: B 316 MET cc_start: 0.7961 (tpp) cc_final: 0.7742 (mmt) REVERT: B 375 ASN cc_start: 0.6812 (p0) cc_final: 0.6490 (p0) REVERT: B 497 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7671 (t0) REVERT: C 504 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8123 (ptm160) REVERT: E 419 ASP cc_start: 0.6401 (OUTLIER) cc_final: 0.6038 (t0) REVERT: F 308 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7499 (tp) REVERT: F 381 TRP cc_start: 0.7672 (m-10) cc_final: 0.7463 (m-10) REVERT: F 532 TYR cc_start: 0.6133 (m-80) cc_final: 0.5850 (m-80) outliers start: 29 outliers final: 19 residues processed: 177 average time/residue: 0.0828 time to fit residues: 23.4728 Evaluate side-chains 166 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 533 MET Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 419 ASP Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 521 CYS Chi-restraints excluded: chain F residue 542 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 109 optimal weight: 0.0070 chunk 49 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 146 optimal weight: 0.1980 chunk 153 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 overall best weight: 1.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.124723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.108881 restraints weight = 32794.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.110855 restraints weight = 21054.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.112188 restraints weight = 15103.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.113123 restraints weight = 11810.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.113772 restraints weight = 9858.152| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13068 Z= 0.109 Angle : 0.519 11.550 17631 Z= 0.267 Chirality : 0.042 0.142 2006 Planarity : 0.003 0.061 2171 Dihedral : 12.231 138.160 2062 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.29 % Allowed : 13.75 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.21), residues: 1558 helix: 0.39 (0.23), residues: 538 sheet: -0.63 (0.29), residues: 320 loop : -1.89 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 303 TYR 0.012 0.001 TYR C 411 PHE 0.015 0.001 PHE F 523 TRP 0.012 0.001 TRP F 381 HIS 0.011 0.001 HIS E 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (13068) covalent geometry : angle 0.51904 / 0.27 (17631) hydrogen bonds : bond 0.02675 / 1.81 ( 415) hydrogen bonds : angle 4.37759 / 3.10 ( 1191) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 SER cc_start: 0.6960 (t) cc_final: 0.6713 (p) REVERT: A 316 MET cc_start: 0.8514 (mmp) cc_final: 0.7973 (tpp) REVERT: A 395 ASP cc_start: 0.6805 (t0) cc_final: 0.6367 (t0) REVERT: B 316 MET cc_start: 0.8006 (tpp) cc_final: 0.7663 (mmt) REVERT: B 375 ASN cc_start: 0.6855 (p0) cc_final: 0.6541 (p0) REVERT: B 497 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7710 (t0) REVERT: C 312 SER cc_start: 0.8411 (p) cc_final: 0.7533 (m) REVERT: C 504 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8184 (ptm160) REVERT: E 419 ASP cc_start: 0.6411 (OUTLIER) cc_final: 0.6071 (t0) REVERT: F 308 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7487 (tp) REVERT: F 333 MET cc_start: 0.6547 (mmm) cc_final: 0.6343 (mmm) REVERT: F 381 TRP cc_start: 0.7788 (m-10) cc_final: 0.7560 (m100) REVERT: F 532 TYR cc_start: 0.6235 (m-80) cc_final: 0.5923 (m-80) outliers start: 31 outliers final: 23 residues processed: 167 average time/residue: 0.0816 time to fit residues: 21.7682 Evaluate side-chains 173 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 419 ASP Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 521 CYS Chi-restraints excluded: chain F residue 542 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 103 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 87 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 107 optimal weight: 0.0970 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.126556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.110798 restraints weight = 32205.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.112767 restraints weight = 20648.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.114129 restraints weight = 14833.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.115065 restraints weight = 11615.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.115681 restraints weight = 9717.838| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13068 Z= 0.091 Angle : 0.501 11.224 17631 Z= 0.257 Chirality : 0.042 0.144 2006 Planarity : 0.003 0.055 2171 Dihedral : 12.101 137.955 2062 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.07 % Allowed : 14.56 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.21), residues: 1558 helix: 0.57 (0.23), residues: 538 sheet: -0.52 (0.29), residues: 320 loop : -1.79 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 274 TYR 0.010 0.001 TYR C 411 PHE 0.018 0.001 PHE E 452 TRP 0.012 0.001 TRP F 381 HIS 0.010 0.001 HIS E 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.09 (13068) covalent geometry : angle 0.50131 / 0.26 (17631) hydrogen bonds : bond 0.02509 / 1.70 ( 415) hydrogen bonds : angle 4.26082 / 3.02 ( 1191) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 SER cc_start: 0.6839 (t) cc_final: 0.6598 (p) REVERT: A 316 MET cc_start: 0.8454 (mmp) cc_final: 0.7925 (tpp) REVERT: A 395 ASP cc_start: 0.6758 (t0) cc_final: 0.6302 (t0) REVERT: B 316 MET cc_start: 0.7880 (tpp) cc_final: 0.7671 (mmt) REVERT: B 375 ASN cc_start: 0.6801 (p0) cc_final: 0.6469 (p0) REVERT: C 504 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7981 (ptm160) REVERT: D 341 MET cc_start: 0.7289 (mmp) cc_final: 0.6848 (mmp) REVERT: E 419 ASP cc_start: 0.6310 (OUTLIER) cc_final: 0.5972 (t0) REVERT: F 308 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7489 (tp) REVERT: F 310 VAL cc_start: 0.7858 (OUTLIER) cc_final: 0.7439 (p) REVERT: F 532 TYR cc_start: 0.6175 (m-80) cc_final: 0.5886 (m-80) outliers start: 28 outliers final: 19 residues processed: 172 average time/residue: 0.0771 time to fit residues: 21.3468 Evaluate side-chains 172 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain E residue 419 ASP Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 542 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 25 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 131 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.125847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.110059 restraints weight = 32533.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.112049 restraints weight = 21028.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.113392 restraints weight = 15068.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.114312 restraints weight = 11818.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.114710 restraints weight = 9894.170| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 13068 Z= 0.104 Angle : 0.506 10.927 17631 Z= 0.261 Chirality : 0.042 0.176 2006 Planarity : 0.003 0.054 2171 Dihedral : 12.118 137.810 2062 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.29 % Allowed : 14.71 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.21), residues: 1558 helix: 0.69 (0.24), residues: 538 sheet: -0.59 (0.29), residues: 324 loop : -1.74 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 274 TYR 0.011 0.001 TYR C 411 PHE 0.010 0.001 PHE A 378 TRP 0.029 0.001 TRP F 381 HIS 0.009 0.001 HIS E 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (13068) covalent geometry : angle 0.50603 / 0.26 (17631) hydrogen bonds : bond 0.02581 / 1.75 ( 415) hydrogen bonds : angle 4.24989 / 3.02 ( 1191) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 SER cc_start: 0.6945 (t) cc_final: 0.6717 (p) REVERT: A 316 MET cc_start: 0.8482 (mmp) cc_final: 0.7908 (tpp) REVERT: A 395 ASP cc_start: 0.6759 (t0) cc_final: 0.6395 (t0) REVERT: B 316 MET cc_start: 0.7884 (tpp) cc_final: 0.7666 (mmt) REVERT: B 375 ASN cc_start: 0.6804 (p0) cc_final: 0.6484 (p0) REVERT: B 497 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7642 (t0) REVERT: C 504 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8128 (ptm160) REVERT: E 419 ASP cc_start: 0.6366 (OUTLIER) cc_final: 0.6034 (t0) REVERT: F 308 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7564 (tp) REVERT: F 532 TYR cc_start: 0.6190 (m-80) cc_final: 0.5911 (m-80) outliers start: 31 outliers final: 24 residues processed: 172 average time/residue: 0.0945 time to fit residues: 25.9977 Evaluate side-chains 172 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain C residue 510 MET Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain E residue 419 ASP Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 542 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 101 optimal weight: 0.8980 chunk 153 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 93 optimal weight: 0.3980 chunk 141 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.125383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.109512 restraints weight = 32325.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.111540 restraints weight = 20408.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.112921 restraints weight = 14479.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.113900 restraints weight = 11262.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.114367 restraints weight = 9350.993| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13068 Z= 0.098 Angle : 0.513 10.869 17631 Z= 0.262 Chirality : 0.042 0.172 2006 Planarity : 0.003 0.057 2171 Dihedral : 12.089 137.670 2062 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.29 % Allowed : 14.71 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.22), residues: 1558 helix: 0.83 (0.24), residues: 533 sheet: -0.55 (0.29), residues: 325 loop : -1.64 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 274 TYR 0.011 0.001 TYR C 411 PHE 0.019 0.001 PHE E 452 TRP 0.041 0.001 TRP F 381 HIS 0.008 0.001 HIS E 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (13068) covalent geometry : angle 0.51296 / 0.26 (17631) hydrogen bonds : bond 0.02555 / 1.72 ( 415) hydrogen bonds : angle 4.21076 / 3.00 ( 1191) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 SER cc_start: 0.7009 (t) cc_final: 0.6776 (p) REVERT: A 316 MET cc_start: 0.8481 (mmp) cc_final: 0.7912 (tpp) REVERT: B 316 MET cc_start: 0.7922 (tpp) cc_final: 0.7691 (mmt) REVERT: B 375 ASN cc_start: 0.6801 (p0) cc_final: 0.6493 (p0) REVERT: B 497 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7594 (t0) REVERT: C 504 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8127 (ptm160) REVERT: E 419 ASP cc_start: 0.6388 (OUTLIER) cc_final: 0.6062 (t0) REVERT: F 308 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7518 (tp) REVERT: F 310 VAL cc_start: 0.7909 (OUTLIER) cc_final: 0.7479 (p) REVERT: F 381 TRP cc_start: 0.7609 (m-10) cc_final: 0.7147 (m100) REVERT: F 532 TYR cc_start: 0.6253 (m-80) cc_final: 0.5964 (m-80) outliers start: 31 outliers final: 23 residues processed: 176 average time/residue: 0.0921 time to fit residues: 26.0663 Evaluate side-chains 173 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain C residue 510 MET Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 419 ASP Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 542 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 11 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 111 optimal weight: 8.9990 chunk 92 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 151 optimal weight: 7.9990 chunk 91 optimal weight: 0.5980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.124016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.108433 restraints weight = 32543.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.110461 restraints weight = 20605.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.111763 restraints weight = 14607.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.112662 restraints weight = 11416.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.113161 restraints weight = 9538.288| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13068 Z= 0.121 Angle : 0.541 10.734 17631 Z= 0.276 Chirality : 0.042 0.167 2006 Planarity : 0.003 0.071 2171 Dihedral : 12.192 137.656 2062 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.29 % Allowed : 15.08 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.22), residues: 1558 helix: 0.83 (0.24), residues: 534 sheet: -0.57 (0.29), residues: 322 loop : -1.64 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 274 TYR 0.013 0.001 TYR C 411 PHE 0.011 0.001 PHE A 378 TRP 0.036 0.001 TRP F 381 HIS 0.014 0.001 HIS E 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (13068) covalent geometry : angle 0.54077 / 0.28 (17631) hydrogen bonds : bond 0.02731 / 1.82 ( 415) hydrogen bonds : angle 4.25057 / 3.02 ( 1191) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 SER cc_start: 0.7015 (t) cc_final: 0.6806 (p) REVERT: A 316 MET cc_start: 0.8526 (mmp) cc_final: 0.7938 (tpp) REVERT: B 316 MET cc_start: 0.7865 (tpp) cc_final: 0.7628 (mmt) REVERT: B 375 ASN cc_start: 0.6877 (p0) cc_final: 0.6606 (p0) REVERT: B 497 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7473 (t0) REVERT: C 504 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8149 (ptm160) REVERT: D 341 MET cc_start: 0.7505 (mmp) cc_final: 0.7281 (mmp) REVERT: E 419 ASP cc_start: 0.6479 (OUTLIER) cc_final: 0.6101 (t0) REVERT: F 308 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7537 (tp) REVERT: F 310 VAL cc_start: 0.7940 (OUTLIER) cc_final: 0.7535 (p) REVERT: F 381 TRP cc_start: 0.7599 (m-10) cc_final: 0.7070 (m100) REVERT: F 532 TYR cc_start: 0.6298 (m-80) cc_final: 0.6010 (m-80) outliers start: 31 outliers final: 24 residues processed: 172 average time/residue: 0.0797 time to fit residues: 22.2008 Evaluate side-chains 174 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain C residue 510 MET Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 419 ASP Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 542 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 92 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 98 optimal weight: 0.3980 chunk 131 optimal weight: 8.9990 chunk 84 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 106 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.124857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.109414 restraints weight = 32559.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.111418 restraints weight = 20335.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.112706 restraints weight = 14502.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.113634 restraints weight = 11292.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.114134 restraints weight = 9468.300| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13068 Z= 0.097 Angle : 0.527 10.741 17631 Z= 0.269 Chirality : 0.042 0.161 2006 Planarity : 0.004 0.113 2171 Dihedral : 12.126 137.514 2062 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.92 % Allowed : 15.59 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.22), residues: 1558 helix: 0.83 (0.24), residues: 541 sheet: -0.49 (0.29), residues: 321 loop : -1.58 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 323 TYR 0.010 0.001 TYR C 411 PHE 0.019 0.001 PHE E 452 TRP 0.031 0.001 TRP F 381 HIS 0.014 0.001 HIS E 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (13068) covalent geometry : angle 0.52726 / 0.27 (17631) hydrogen bonds : bond 0.02569 / 1.69 ( 415) hydrogen bonds : angle 4.20028 / 2.99 ( 1191) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1885.63 seconds wall clock time: 33 minutes 35.49 seconds (2015.49 seconds total)