Starting phenix.real_space_refine on Thu Sep 18 01:32:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n7t_0363/09_2025/6n7t_0363_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n7t_0363/09_2025/6n7t_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 { model { file = "/net/cci-nas-00/data/ceres_data/6n7t_0363/09_2025/6n7t_0363_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n7t_0363/09_2025/6n7t_0363_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6n7t_0363/09_2025/6n7t_0363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n7t_0363/09_2025/6n7t_0363.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 3.70, per 1000 atoms: 0.29 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: 1.04 Conformation dependent library (CDL) restraints added in 585.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.49 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: 1.99 Time building geometry restraints manager: 1.43 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=" C LEU A 542 " pdb=" N GLU A 543 " ideal model delta sigma weight residual 1.327 1.243 0.084 1.71e-02 3.42e+03 2.41e+01 bond pdb=" C6 TTP B 700 " pdb=" N1 TTP B 700 " ideal model delta sigma weight residual 1.337 1.426 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C6 TTP A 700 " pdb=" N1 TTP A 700 " ideal model delta sigma weight residual 1.337 1.426 -0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" C6 TTP D 700 " pdb=" N1 TTP D 700 " ideal model delta sigma weight residual 1.337 1.426 -0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" C6 TTP E 700 " pdb=" N1 TTP E 700 " ideal model delta sigma weight residual 1.337 1.426 -0.089 2.00e-02 2.50e+03 1.99e+01 ... (remaining 13063 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 17165 2.43 - 4.86: 373 4.86 - 7.29: 59 7.29 - 9.73: 26 9.73 - 12.16: 8 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=" N GLY B 490 " pdb=" CA GLY B 490 " pdb=" C GLY B 490 " ideal model delta sigma weight residual 115.80 108.40 7.40 1.74e+00 3.30e-01 1.81e+01 angle pdb=" C LEU A 356 " pdb=" CA LEU A 356 " pdb=" CB LEU A 356 " ideal model delta sigma weight residual 110.09 103.24 6.85 1.67e+00 3.59e-01 1.68e+01 angle pdb=" PA TTP D 700 " pdb=" O3A TTP D 700 " pdb=" PB TTP D 700 " ideal model delta sigma weight residual 120.50 132.66 -12.16 3.00e+00 1.11e-01 1.64e+01 angle pdb=" PB TTP B 700 " pdb=" O3B TTP B 700 " pdb=" PG TTP B 700 " ideal model delta sigma weight residual 120.50 132.61 -12.11 3.00e+00 1.11e-01 1.63e+01 ... (remaining 17626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.99: 7627 34.99 - 69.99: 140 69.99 - 104.98: 18 104.98 - 139.97: 5 139.97 - 174.96: 8 Dihedral angle restraints: 7798 sinusoidal: 3317 harmonic: 4481 Sorted by residual: dihedral pdb=" C2 TTP D 700 " pdb=" C1' TTP D 700 " pdb=" N1 TTP D 700 " pdb=" O4' TTP D 700 " ideal model delta sinusoidal sigma weight residual 301.68 126.72 174.96 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C2 TTP A 700 " pdb=" C1' TTP A 700 " pdb=" N1 TTP A 700 " pdb=" O4' TTP A 700 " ideal model delta sinusoidal sigma weight residual -58.32 111.32 -169.63 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C2 TTP C 700 " pdb=" C1' TTP C 700 " pdb=" N1 TTP C 700 " pdb=" O4' TTP C 700 " ideal model delta sinusoidal sigma weight residual 301.68 132.23 169.45 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 7795 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1446 0.052 - 0.104: 418 0.104 - 0.156: 122 0.156 - 0.208: 11 0.208 - 0.260: 9 Chirality restraints: 2006 Sorted by residual: chirality pdb=" C3' TTP D 700 " pdb=" C2' TTP D 700 " pdb=" C4' TTP D 700 " pdb=" O3' TTP D 700 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C3' TTP E 700 " pdb=" C2' TTP E 700 " pdb=" C4' TTP E 700 " pdb=" O3' TTP E 700 " both_signs ideal model delta sigma weight residual False -2.51 -2.76 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C3' TTP C 700 " pdb=" C2' TTP C 700 " pdb=" C4' TTP C 700 " pdb=" O3' TTP C 700 " both_signs ideal model delta sigma weight residual False -2.51 -2.76 0.25 2.00e-01 2.50e+01 1.58e+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: 0.000 Normalize map: mean=0, sd=1: 1.630 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.450 Find NCS groups from input model: 0.320 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 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 0.089 13068 Z= 0.303 Angle : 0.954 12.157 17631 Z= 0.512 Chirality : 0.056 0.260 2006 Planarity : 0.004 0.051 2171 Dihedral : 15.070 174.962 4930 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 aren 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 covalent geometry : bond 0.00558 (13068) covalent geometry : angle 0.95423 (17631) hydrogen bonds : bond 0.16558 ( 415) hydrogen bonds : angle 7.22833 ( 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 : 0.543 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: 0.7662 (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: 0.7920 (mt) REVERT: E 394 TYR cc_start: 0.6906 (t80) cc_final: 0.6664 (t80) REVERT: F 351 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6361 (mt-10) REVERT: F 412 MET cc_start: 0.6288 (ttm) cc_final: 0.6025 (ttt) outliers start: 11 outliers final: 2 residues processed: 343 average time/residue: 0.1280 time to fit residues: 62.2071 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 : 0.465 ------------------------------------------------------------------------------- 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: 1.9990 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: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 = 0.3965 r_free = 0.3965 target = 0.127694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.110933 restraints weight = 31812.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.113107 restraints weight = 19815.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.114497 restraints weight = 13942.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.115560 restraints weight = 10802.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.116254 restraints weight = 8953.343| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13068 Z= 0.135 Angle : 0.589 6.727 17631 Z= 0.299 Chirality : 0.043 0.139 2006 Planarity : 0.003 0.042 2171 Dihedral : 16.676 169.573 1947 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.44 % Allowed : 9.16 % Favored : 88.40 % 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 aren not related in a simple way. whole: -2.59 (0.19), residues: 1558 helix: -1.26 (0.20), residues: 543 sheet: -0.81 (0.30), residues: 316 loop : -2.51 (0.20), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 504 TYR 0.018 0.001 TYR A 411 PHE 0.014 0.002 PHE F 378 TRP 0.016 0.002 TRP F 381 HIS 0.009 0.001 HIS E 357 Details of bonding type rmsd covalent geometry : bond 0.00304 (13068) covalent geometry : angle 0.58938 (17631) hydrogen bonds : bond 0.03353 ( 415) hydrogen bonds : angle 4.99685 ( 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 230 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.8210 (mmp) cc_final: 0.7755 (tpp) REVERT: A 467 LYS cc_start: 0.7381 (pttt) cc_final: 0.7123 (pttp) REVERT: B 344 GLU cc_start: 0.8185 (mp0) cc_final: 0.7954 (mt-10) REVERT: B 497 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7692 (t0) REVERT: D 341 MET cc_start: 0.7599 (mmp) cc_final: 0.7244 (mmp) REVERT: E 278 HIS cc_start: 0.6976 (t-170) cc_final: 0.6415 (t-170) REVERT: E 464 CYS cc_start: 0.8070 (p) cc_final: 0.7744 (t) REVERT: F 308 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7742 (tp) REVERT: F 351 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6627 (mt-10) REVERT: F 381 TRP cc_start: 0.7778 (m-10) cc_final: 0.7420 (m100) REVERT: F 412 MET cc_start: 0.5555 (ttm) cc_final: 0.5218 (ttt) REVERT: F 532 TYR cc_start: 0.6247 (m-80) cc_final: 0.5933 (m-80) outliers start: 33 outliers final: 19 residues processed: 220 average time/residue: 0.1005 time to fit residues: 33.8583 Evaluate side-chains 181 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 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 E residue 445 LEU Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 360 VAL 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: 5.9990 chunk 23 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 152 optimal weight: 0.0010 chunk 125 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 104 optimal weight: 9.9990 chunk 3 optimal weight: 0.7980 chunk 95 optimal weight: 8.9990 overall best weight: 2.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** D 468 ASN E 425 HIS ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.123318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.107289 restraints weight = 32713.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.109266 restraints weight = 21121.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.110625 restraints weight = 15029.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.111557 restraints weight = 11739.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.112126 restraints weight = 9812.733| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13068 Z= 0.186 Angle : 0.645 14.374 17631 Z= 0.322 Chirality : 0.045 0.149 2006 Planarity : 0.004 0.055 2171 Dihedral : 16.576 177.005 1942 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.03 % Allowed : 11.31 % Favored : 85.66 % 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 aren not related in a simple way. whole: -2.04 (0.20), residues: 1558 helix: -0.45 (0.22), residues: 537 sheet: -0.93 (0.30), residues: 309 loop : -2.24 (0.21), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 276 TYR 0.017 0.002 TYR A 411 PHE 0.014 0.002 PHE E 452 TRP 0.011 0.002 TRP F 381 HIS 0.009 0.002 HIS E 357 Details of bonding type rmsd covalent geometry : bond 0.00424 (13068) covalent geometry : angle 0.64498 (17631) hydrogen bonds : bond 0.03556 ( 415) hydrogen bonds : angle 4.89872 ( 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 204 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 163 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 ASP cc_start: 0.6902 (t0) cc_final: 0.6606 (t0) REVERT: B 344 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8122 (pm20) REVERT: B 375 ASN cc_start: 0.7084 (p0) cc_final: 0.6786 (p0) REVERT: B 497 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7697 (t0) REVERT: C 341 MET cc_start: 0.8090 (mmm) cc_final: 0.7604 (mmm) REVERT: C 430 VAL cc_start: 0.7479 (OUTLIER) cc_final: 0.7187 (m) REVERT: C 504 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7684 (ptm160) REVERT: D 541 TRP cc_start: 0.8149 (m100) cc_final: 0.7909 (m100) REVERT: E 278 HIS cc_start: 0.7078 (t-170) cc_final: 0.6381 (t-170) REVERT: F 351 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6639 (mt-10) REVERT: F 412 MET cc_start: 0.5524 (ttm) cc_final: 0.5128 (ttt) outliers start: 41 outliers final: 24 residues processed: 193 average time/residue: 0.1011 time to fit residues: 29.9454 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 : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 380 GLN Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 462 VAL 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 344 GLU 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 444 ASN Chi-restraints excluded: chain B residue 468 ASN Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain D residue 322 VAL 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 310 VAL 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: 0.5980 chunk 10 optimal weight: 0.0030 chunk 24 optimal weight: 0.0980 chunk 4 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** D 468 ASN ** E 507 GLN ** 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 = 0.3918 r_free = 0.3918 target = 0.125097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.109348 restraints weight = 32227.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.111245 restraints weight = 20382.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.112643 restraints weight = 14573.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.113451 restraints weight = 11312.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.114141 restraints weight = 9520.030| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13068 Z= 0.109 Angle : 0.564 12.092 17631 Z= 0.279 Chirality : 0.042 0.191 2006 Planarity : 0.003 0.067 2171 Dihedral : 16.102 177.473 1942 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.44 % Allowed : 12.56 % Favored : 85.00 % 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 aren not related in a simple way. whole: -1.58 (0.21), residues: 1558 helix: 0.08 (0.23), residues: 533 sheet: -0.86 (0.29), residues: 320 loop : -2.02 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 274 TYR 0.014 0.001 TYR E 394 PHE 0.020 0.001 PHE F 523 TRP 0.023 0.001 TRP F 381 HIS 0.010 0.001 HIS E 357 Details of bonding type rmsd covalent geometry : bond 0.00244 (13068) covalent geometry : angle 0.56444 (17631) hydrogen bonds : bond 0.02723 ( 415) hydrogen bonds : angle 4.48751 ( 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 196 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7672 (tpp) REVERT: A 395 ASP cc_start: 0.6836 (t0) cc_final: 0.6451 (t0) REVERT: A 467 LYS cc_start: 0.7304 (pttt) cc_final: 0.7056 (pttp) REVERT: B 375 ASN cc_start: 0.6965 (p0) cc_final: 0.6707 (p0) REVERT: B 497 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7610 (t0) REVERT: C 312 SER cc_start: 0.8434 (p) cc_final: 0.7551 (m) REVERT: C 341 MET cc_start: 0.7910 (mmm) cc_final: 0.7563 (mmm) REVERT: C 425 HIS cc_start: 0.7906 (t70) cc_final: 0.7609 (t70) REVERT: C 430 VAL cc_start: 0.7278 (OUTLIER) cc_final: 0.6977 (m) REVERT: C 504 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7369 (ptm160) REVERT: D 341 MET cc_start: 0.7665 (mmp) cc_final: 0.7276 (mmp) REVERT: E 278 HIS cc_start: 0.6975 (t-170) cc_final: 0.6255 (t-170) REVERT: E 419 ASP cc_start: 0.6398 (OUTLIER) cc_final: 0.6073 (t0) REVERT: F 351 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6644 (mt-10) REVERT: F 412 MET cc_start: 0.5692 (ttm) cc_final: 0.5247 (ttt) REVERT: F 532 TYR cc_start: 0.6206 (m-80) cc_final: 0.5835 (m-80) outliers start: 33 outliers final: 19 residues processed: 186 average time/residue: 0.1034 time to fit residues: 29.6791 Evaluate side-chains 172 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 430 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 444 ASN Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain C residue 533 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 61 optimal weight: 0.0980 chunk 125 optimal weight: 9.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 ASN ** 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** D 468 ASN ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.122314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.106644 restraints weight = 33076.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.108606 restraints weight = 21047.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.109923 restraints weight = 15009.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.110743 restraints weight = 11699.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.111440 restraints weight = 9813.286| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13068 Z= 0.162 Angle : 0.602 10.820 17631 Z= 0.300 Chirality : 0.044 0.193 2006 Planarity : 0.004 0.064 2171 Dihedral : 16.161 179.582 1942 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.59 % Allowed : 13.30 % Favored : 84.11 % 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 aren not related in a simple way. whole: -1.45 (0.21), residues: 1558 helix: 0.24 (0.23), residues: 534 sheet: -0.87 (0.29), residues: 315 loop : -1.94 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 274 TYR 0.017 0.001 TYR C 411 PHE 0.015 0.002 PHE E 452 TRP 0.017 0.001 TRP F 381 HIS 0.011 0.001 HIS E 357 Details of bonding type rmsd covalent geometry : bond 0.00371 (13068) covalent geometry : angle 0.60212 (17631) hydrogen bonds : bond 0.03142 ( 415) hydrogen bonds : angle 4.54590 ( 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 185 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7757 (tpp) REVERT: A 467 LYS cc_start: 0.7379 (pttt) cc_final: 0.7103 (pttp) REVERT: B 309 MET cc_start: 0.8261 (mmm) cc_final: 0.7995 (mmm) REVERT: B 375 ASN cc_start: 0.7075 (p0) cc_final: 0.6818 (p0) REVERT: B 497 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7586 (t0) REVERT: C 312 SER cc_start: 0.8516 (p) cc_final: 0.7623 (m) REVERT: C 425 HIS cc_start: 0.7939 (t70) cc_final: 0.7700 (t70) REVERT: C 430 VAL cc_start: 0.7505 (OUTLIER) cc_final: 0.7218 (m) REVERT: C 504 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7503 (ptm160) REVERT: E 278 HIS cc_start: 0.7151 (t-170) cc_final: 0.6163 (t-170) REVERT: E 419 ASP cc_start: 0.6574 (OUTLIER) cc_final: 0.6207 (t0) REVERT: F 351 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6285 (mt-10) REVERT: F 381 TRP cc_start: 0.7873 (m-10) cc_final: 0.7650 (m100) REVERT: F 412 MET cc_start: 0.5558 (ttm) cc_final: 0.5107 (ttt) REVERT: F 532 TYR cc_start: 0.6283 (m-80) cc_final: 0.5908 (m-80) outliers start: 35 outliers final: 24 residues processed: 173 average time/residue: 0.0957 time to fit residues: 25.9778 Evaluate side-chains 169 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 430 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 444 ASN Chi-restraints excluded: chain B residue 468 ASN Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 498 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 308 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 524 THR 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: 10.0000 chunk 49 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 146 optimal weight: 8.9990 chunk 153 optimal weight: 8.9990 chunk 38 optimal weight: 0.0980 chunk 103 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 chunk 102 optimal weight: 0.7980 chunk 144 optimal weight: 5.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 GLN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3853 r_free = 0.3853 target = 0.120659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.105308 restraints weight = 33321.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.107121 restraints weight = 21876.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.108343 restraints weight = 15907.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.109178 restraints weight = 12570.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.109724 restraints weight = 10617.008| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13068 Z= 0.199 Angle : 0.654 10.399 17631 Z= 0.325 Chirality : 0.045 0.201 2006 Planarity : 0.004 0.063 2171 Dihedral : 16.322 179.427 1942 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.55 % Allowed : 13.75 % Favored : 82.71 % 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 aren not related in a simple way. whole: -1.52 (0.21), residues: 1558 helix: 0.23 (0.23), residues: 531 sheet: -0.94 (0.29), residues: 312 loop : -2.00 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 274 TYR 0.021 0.002 TYR C 411 PHE 0.014 0.002 PHE F 523 TRP 0.013 0.001 TRP F 381 HIS 0.011 0.001 HIS E 357 Details of bonding type rmsd covalent geometry : bond 0.00456 (13068) covalent geometry : angle 0.65445 (17631) hydrogen bonds : bond 0.03417 ( 415) hydrogen bonds : angle 4.72365 ( 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 193 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 145 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7818 (tpp) REVERT: A 467 LYS cc_start: 0.7292 (pttt) cc_final: 0.6996 (pttp) REVERT: B 309 MET cc_start: 0.8188 (mmm) cc_final: 0.7624 (mmm) REVERT: B 375 ASN cc_start: 0.7231 (p0) cc_final: 0.6981 (p0) REVERT: B 497 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7687 (t0) REVERT: C 312 SER cc_start: 0.8602 (p) cc_final: 0.7651 (m) REVERT: C 430 VAL cc_start: 0.7440 (OUTLIER) cc_final: 0.7207 (m) REVERT: C 504 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7591 (ptm160) REVERT: D 341 MET cc_start: 0.7752 (mmp) cc_final: 0.7443 (mmp) REVERT: E 278 HIS cc_start: 0.7016 (t-170) cc_final: 0.6209 (t-170) REVERT: E 316 MET cc_start: 0.8474 (mmm) cc_final: 0.7977 (mmt) REVERT: E 419 ASP cc_start: 0.6633 (OUTLIER) cc_final: 0.6284 (t0) REVERT: E 510 MET cc_start: 0.6990 (ppp) cc_final: 0.6678 (ptm) REVERT: F 351 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6511 (mt-10) REVERT: F 412 MET cc_start: 0.5462 (ttm) cc_final: 0.5079 (ttt) REVERT: F 532 TYR cc_start: 0.6434 (m-80) cc_final: 0.6063 (m-80) outliers start: 48 outliers final: 36 residues processed: 175 average time/residue: 0.0945 time to fit residues: 26.2478 Evaluate side-chains 180 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 139 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 380 GLN Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 499 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 360 VAL 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 468 ASN Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 442 ILE 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 C residue 533 MET Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 498 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 308 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 521 CYS Chi-restraints excluded: chain F residue 524 THR 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: 6.9990 chunk 31 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 158 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN ** A 465 HIS ** 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** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3855 r_free = 0.3855 target = 0.120685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.105321 restraints weight = 33653.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.107156 restraints weight = 22145.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.108365 restraints weight = 16059.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.109229 restraints weight = 12721.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.109794 restraints weight = 10708.509| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13068 Z= 0.177 Angle : 0.627 10.381 17631 Z= 0.312 Chirality : 0.044 0.194 2006 Planarity : 0.004 0.073 2171 Dihedral : 16.214 179.594 1942 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.47 % Allowed : 14.63 % Favored : 81.89 % 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 aren not related in a simple way. whole: -1.46 (0.21), residues: 1558 helix: 0.28 (0.23), residues: 532 sheet: -0.93 (0.29), residues: 312 loop : -1.96 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 274 TYR 0.019 0.001 TYR C 411 PHE 0.015 0.002 PHE E 452 TRP 0.039 0.002 TRP F 381 HIS 0.010 0.001 HIS A 465 Details of bonding type rmsd covalent geometry : bond 0.00406 (13068) covalent geometry : angle 0.62670 (17631) hydrogen bonds : bond 0.03347 ( 415) hydrogen bonds : angle 4.67888 ( 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 191 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 144 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7869 (tpp) REVERT: A 446 MET cc_start: 0.6891 (OUTLIER) cc_final: 0.6527 (mtp) REVERT: A 467 LYS cc_start: 0.7233 (pttt) cc_final: 0.6947 (pttp) REVERT: B 375 ASN cc_start: 0.7254 (p0) cc_final: 0.6997 (p0) REVERT: B 446 MET cc_start: 0.6081 (OUTLIER) cc_final: 0.5879 (mtp) REVERT: C 312 SER cc_start: 0.8688 (p) cc_final: 0.7826 (m) REVERT: C 504 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7516 (ptm160) REVERT: D 341 MET cc_start: 0.7911 (mmp) cc_final: 0.7087 (mmt) REVERT: E 278 HIS cc_start: 0.7017 (t-170) cc_final: 0.6183 (t-170) REVERT: E 405 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7772 (tt) REVERT: E 419 ASP cc_start: 0.6616 (OUTLIER) cc_final: 0.6264 (t0) REVERT: F 351 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6484 (mt-10) REVERT: F 381 TRP cc_start: 0.7732 (m-10) cc_final: 0.7221 (m100) REVERT: F 412 MET cc_start: 0.5427 (ttm) cc_final: 0.5026 (ttt) REVERT: F 532 TYR cc_start: 0.6295 (m-80) cc_final: 0.6031 (m-80) outliers start: 47 outliers final: 33 residues processed: 172 average time/residue: 0.0886 time to fit residues: 24.4097 Evaluate side-chains 177 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 138 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 380 GLN Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 499 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 360 VAL 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 446 MET Chi-restraints excluded: chain B residue 468 ASN Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 402 THR 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 C residue 533 MET Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 498 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 308 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 521 CYS Chi-restraints excluded: chain F residue 524 THR 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: 0.9980 chunk 89 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 131 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 158 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 HIS ** 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** ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.123272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.107781 restraints weight = 33113.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.109705 restraints weight = 21242.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.111015 restraints weight = 15252.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.111917 restraints weight = 11935.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.112470 restraints weight = 9974.574| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13068 Z= 0.108 Angle : 0.558 10.600 17631 Z= 0.278 Chirality : 0.042 0.178 2006 Planarity : 0.003 0.063 2171 Dihedral : 15.744 179.696 1942 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.29 % Allowed : 15.82 % Favored : 81.89 % 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 aren not related in a simple way. whole: -1.08 (0.21), residues: 1558 helix: 0.71 (0.23), residues: 526 sheet: -0.75 (0.29), residues: 319 loop : -1.81 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 274 TYR 0.012 0.001 TYR C 411 PHE 0.010 0.001 PHE E 382 TRP 0.031 0.001 TRP F 381 HIS 0.009 0.001 HIS E 357 Details of bonding type rmsd covalent geometry : bond 0.00244 (13068) covalent geometry : angle 0.55844 (17631) hydrogen bonds : bond 0.02709 ( 415) hydrogen bonds : angle 4.31746 ( 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 181 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7684 (tpp) REVERT: A 467 LYS cc_start: 0.7266 (pttt) cc_final: 0.7034 (pttp) REVERT: A 512 ASN cc_start: 0.7497 (p0) cc_final: 0.6484 (p0) REVERT: B 375 ASN cc_start: 0.7035 (p0) cc_final: 0.6793 (p0) REVERT: B 497 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7586 (t0) REVERT: C 504 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7312 (ptm160) REVERT: D 341 MET cc_start: 0.7640 (mmp) cc_final: 0.6851 (mmt) REVERT: E 278 HIS cc_start: 0.7031 (t-170) cc_final: 0.6272 (t-170) REVERT: E 316 MET cc_start: 0.8277 (mmm) cc_final: 0.7947 (mmm) REVERT: E 405 LEU cc_start: 0.8220 (mp) cc_final: 0.7742 (tt) REVERT: E 419 ASP cc_start: 0.6376 (OUTLIER) cc_final: 0.6054 (t0) REVERT: F 351 GLU cc_start: 0.6977 (mt-10) cc_final: 0.6458 (mt-10) REVERT: F 412 MET cc_start: 0.5127 (ttm) cc_final: 0.4692 (ttt) REVERT: F 532 TYR cc_start: 0.6305 (m-80) cc_final: 0.6102 (m-80) outliers start: 31 outliers final: 22 residues processed: 170 average time/residue: 0.0948 time to fit residues: 25.5258 Evaluate side-chains 166 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 430 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 468 ASN Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain E residue 419 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 101 optimal weight: 0.3980 chunk 153 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.123862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.108628 restraints weight = 33172.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.110537 restraints weight = 21516.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.111758 restraints weight = 15443.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.112641 restraints weight = 12211.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.113172 restraints weight = 10218.265| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13068 Z= 0.101 Angle : 0.556 10.515 17631 Z= 0.274 Chirality : 0.042 0.172 2006 Planarity : 0.003 0.046 2171 Dihedral : 15.522 178.017 1942 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.07 % Allowed : 16.26 % Favored : 81.67 % 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 aren not related in a simple way. whole: -0.92 (0.22), residues: 1558 helix: 0.82 (0.24), residues: 536 sheet: -0.59 (0.29), residues: 320 loop : -1.77 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 274 TYR 0.010 0.001 TYR C 411 PHE 0.018 0.001 PHE E 452 TRP 0.026 0.001 TRP F 381 HIS 0.008 0.001 HIS E 357 Details of bonding type rmsd covalent geometry : bond 0.00227 (13068) covalent geometry : angle 0.55628 (17631) hydrogen bonds : bond 0.02596 ( 415) hydrogen bonds : angle 4.17603 ( 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 179 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7789 (tpp) REVERT: A 467 LYS cc_start: 0.7267 (pttt) cc_final: 0.7058 (pttp) REVERT: A 512 ASN cc_start: 0.7466 (p0) cc_final: 0.6470 (p0) REVERT: B 375 ASN cc_start: 0.6988 (p0) cc_final: 0.6783 (p0) REVERT: B 497 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7523 (t0) REVERT: C 341 MET cc_start: 0.7365 (mmt) cc_final: 0.7153 (mmt) REVERT: C 389 ASP cc_start: 0.6810 (OUTLIER) cc_final: 0.6577 (m-30) REVERT: C 504 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7168 (ptm160) REVERT: D 341 MET cc_start: 0.7573 (mmp) cc_final: 0.6859 (mmt) REVERT: E 278 HIS cc_start: 0.7026 (t-170) cc_final: 0.6251 (t-170) REVERT: E 316 MET cc_start: 0.8372 (mmm) cc_final: 0.7997 (mmm) REVERT: E 405 LEU cc_start: 0.8182 (mp) cc_final: 0.7651 (tt) REVERT: E 468 ASN cc_start: 0.8015 (t0) cc_final: 0.7780 (t0) REVERT: F 310 VAL cc_start: 0.7863 (OUTLIER) cc_final: 0.7437 (p) REVERT: F 351 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6320 (mt-10) outliers start: 28 outliers final: 21 residues processed: 171 average time/residue: 0.0886 time to fit residues: 24.3049 Evaluate side-chains 171 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 430 VAL 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 468 ASN 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 389 ASP Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 498 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 11 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 91 optimal weight: 0.6980 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.122777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.107604 restraints weight = 33389.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.109466 restraints weight = 21748.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.110695 restraints weight = 15609.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.111591 restraints weight = 12309.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.112196 restraints weight = 10298.935| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13068 Z= 0.126 Angle : 0.575 10.516 17631 Z= 0.283 Chirality : 0.043 0.225 2006 Planarity : 0.003 0.064 2171 Dihedral : 15.530 175.561 1942 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.22 % Allowed : 16.41 % Favored : 81.37 % 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 aren not related in a simple way. whole: -0.94 (0.21), residues: 1558 helix: 0.77 (0.23), residues: 541 sheet: -0.56 (0.29), residues: 320 loop : -1.79 (0.22), residues: 697 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 0.009 0.001 PHE E 382 TRP 0.025 0.001 TRP F 381 HIS 0.008 0.001 HIS D 425 Details of bonding type rmsd covalent geometry : bond 0.00291 (13068) covalent geometry : angle 0.57533 (17631) hydrogen bonds : bond 0.02830 ( 415) hydrogen bonds : angle 4.22912 ( 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 178 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 LYS cc_start: 0.7327 (pttt) cc_final: 0.7098 (pttp) REVERT: B 309 MET cc_start: 0.8521 (mmt) cc_final: 0.7946 (mmm) REVERT: B 375 ASN cc_start: 0.7018 (p0) cc_final: 0.6781 (p0) REVERT: B 497 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7563 (t0) REVERT: C 504 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7239 (ptm160) REVERT: D 341 MET cc_start: 0.7692 (mmp) cc_final: 0.7027 (mmt) REVERT: E 278 HIS cc_start: 0.7082 (t-170) cc_final: 0.6319 (t-170) REVERT: E 316 MET cc_start: 0.8402 (mmm) cc_final: 0.7996 (mmm) REVERT: E 405 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7692 (tt) REVERT: E 468 ASN cc_start: 0.8058 (t0) cc_final: 0.7831 (t0) REVERT: F 351 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6427 (mt-10) outliers start: 30 outliers final: 23 residues processed: 168 average time/residue: 0.0893 time to fit residues: 23.9473 Evaluate side-chains 171 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 514 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 468 ASN 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 389 ASP Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain D residue 295 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain E residue 405 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 92 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 131 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 0.3980 chunk 102 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.124248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.109017 restraints weight = 33300.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.110858 restraints weight = 21669.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.112133 restraints weight = 15703.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.113014 restraints weight = 12302.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.113636 restraints weight = 10305.296| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13068 Z= 0.102 Angle : 0.563 10.686 17631 Z= 0.277 Chirality : 0.042 0.162 2006 Planarity : 0.003 0.062 2171 Dihedral : 15.265 172.125 1942 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.07 % Allowed : 16.63 % Favored : 81.30 % 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 aren not related in a simple way. whole: -0.76 (0.22), residues: 1558 helix: 0.97 (0.24), residues: 536 sheet: -0.47 (0.29), residues: 320 loop : -1.70 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 272 TYR 0.010 0.001 TYR C 411 PHE 0.018 0.001 PHE E 452 TRP 0.022 0.001 TRP F 381 HIS 0.008 0.001 HIS E 357 Details of bonding type rmsd covalent geometry : bond 0.00232 (13068) covalent geometry : angle 0.56290 (17631) hydrogen bonds : bond 0.02652 ( 415) hydrogen bonds : angle 4.13918 ( 1191) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2000.42 seconds wall clock time: 35 minutes 36.92 seconds (2136.92 seconds total)