Starting phenix.real_space_refine on Thu Sep 26 11:14:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7t_0363/09_2024/6n7t_0363_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7t_0363/09_2024/6n7t_0363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7t_0363/09_2024/6n7t_0363.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7t_0363/09_2024/6n7t_0363.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7t_0363/09_2024/6n7t_0363_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7t_0363/09_2024/6n7t_0363_neut.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 8.47, per 1000 atoms: 0.66 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: 2.98 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.54 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: 3.50 Time building geometry restraints manager: 3.53 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: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.300 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.620 ------------------------------------------------------------------------------- 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= 0.356 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 : 3.57 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.019 0.002 TRP F 329 HIS 0.009 0.002 HIS A 425 PHE 0.013 0.002 PHE A 523 TYR 0.009 0.001 TYR F 411 ARG 0.007 0.001 ARG C 493 *********************** 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 fitting. rotamer outliers: 11 poor density : 333 time to evaluate : 1.454 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: 0.7915 (mt0) REVERT: B 497 ASP cc_start: 0.7987 (m-30) cc_final: 0.7679 (m-30) REVERT: C 425 HIS cc_start: 0.7428 (t-90) cc_final: 0.7012 (t70) REVERT: D 452 PHE cc_start: 0.7352 (t80) cc_final: 0.7106 (t80) REVERT: D 466 LEU cc_start: 0.8692 (mt) cc_final: 0.7922 (mt) REVERT: E 394 TYR cc_start: 0.6906 (t80) cc_final: 0.6660 (t80) REVERT: F 351 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6362 (mt-10) REVERT: F 412 MET cc_start: 0.6288 (ttm) cc_final: 0.6026 (ttt) outliers start: 11 outliers final: 2 residues processed: 343 average time/residue: 0.2596 time to fit residues: 125.2321 Evaluate side-chains 172 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 170 time to evaluate : 1.520 ------------------------------------------------------------------------------- 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 135 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 125 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 145 optimal weight: 9.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN A 468 ASN ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 GLN C 343 GLN C 358 ASN ** C 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 HIS C 475 HIS D 325 GLN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 HIS ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 358 ASN E 475 HIS ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 GLN F 475 HIS F 512 ASN F 536 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 13068 Z= 0.506 Angle : 0.866 9.895 17631 Z= 0.436 Chirality : 0.051 0.186 2006 Planarity : 0.006 0.045 2171 Dihedral : 17.443 175.287 1947 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 3.10 % Allowed : 10.50 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.19), residues: 1558 helix: -1.54 (0.20), residues: 551 sheet: -1.31 (0.29), residues: 307 loop : -2.65 (0.20), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP F 329 HIS 0.009 0.003 HIS E 278 PHE 0.020 0.003 PHE E 378 TYR 0.027 0.003 TYR F 411 ARG 0.008 0.001 ARG A 361 *********************** 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 214 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 172 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 PHE cc_start: 0.7643 (m-10) cc_final: 0.7415 (m-10) REVERT: A 314 SER cc_start: 0.6783 (t) cc_final: 0.6565 (p) REVERT: A 404 ARG cc_start: 0.4749 (OUTLIER) cc_final: 0.4519 (ptt180) REVERT: C 425 HIS cc_start: 0.7955 (t-90) cc_final: 0.7521 (t70) REVERT: C 430 VAL cc_start: 0.7557 (OUTLIER) cc_final: 0.7249 (m) REVERT: D 341 MET cc_start: 0.8114 (mmp) cc_final: 0.7801 (mmp) REVERT: E 278 HIS cc_start: 0.6948 (t-170) cc_final: 0.6344 (t-170) REVERT: E 316 MET cc_start: 0.8531 (mmt) cc_final: 0.7688 (mmt) REVERT: F 308 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8041 (tp) REVERT: F 351 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6775 (mt-10) REVERT: F 381 TRP cc_start: 0.7954 (m-10) cc_final: 0.7694 (m-10) REVERT: F 412 MET cc_start: 0.5623 (ttm) cc_final: 0.5371 (ttt) REVERT: F 532 TYR cc_start: 0.6651 (m-80) cc_final: 0.6393 (m-80) outliers start: 42 outliers final: 22 residues processed: 201 average time/residue: 0.2229 time to fit residues: 67.4913 Evaluate side-chains 167 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 142 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 GLN Chi-restraints excluded: chain A residue 404 ARG Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 447 THR 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 360 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 363 ARG 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 496 SER Chi-restraints excluded: chain F residue 521 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 157 optimal weight: 8.9990 chunk 129 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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** ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13068 Z= 0.166 Angle : 0.579 16.179 17631 Z= 0.288 Chirality : 0.043 0.144 2006 Planarity : 0.003 0.059 2171 Dihedral : 16.443 174.149 1942 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.51 % Allowed : 12.64 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.20), residues: 1558 helix: -0.43 (0.22), residues: 540 sheet: -1.06 (0.29), residues: 315 loop : -2.29 (0.21), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 329 HIS 0.010 0.001 HIS E 357 PHE 0.015 0.001 PHE E 452 TYR 0.019 0.001 TYR A 411 ARG 0.004 0.000 ARG B 274 *********************** 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 207 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 173 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 375 ASN cc_start: 0.7087 (p0) cc_final: 0.6544 (p0) REVERT: C 430 VAL cc_start: 0.7330 (OUTLIER) cc_final: 0.6673 (m) REVERT: E 278 HIS cc_start: 0.6780 (t-170) cc_final: 0.6121 (t-170) REVERT: E 316 MET cc_start: 0.8529 (mmt) cc_final: 0.7881 (mmt) REVERT: E 419 ASP cc_start: 0.6435 (OUTLIER) cc_final: 0.6137 (t0) REVERT: F 351 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6670 (mt-10) REVERT: F 412 MET cc_start: 0.5616 (ttm) cc_final: 0.5359 (ttt) outliers start: 34 outliers final: 18 residues processed: 196 average time/residue: 0.2267 time to fit residues: 68.0251 Evaluate side-chains 162 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 142 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 419 ASP 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 143 optimal weight: 0.9980 chunk 109 optimal weight: 0.0000 chunk 75 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 97 optimal weight: 0.4980 chunk 146 optimal weight: 9.9990 chunk 154 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- 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** ** C 392 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13068 Z= 0.222 Angle : 0.605 12.887 17631 Z= 0.299 Chirality : 0.044 0.219 2006 Planarity : 0.003 0.032 2171 Dihedral : 16.285 177.118 1942 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.66 % Allowed : 13.90 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.21), residues: 1558 helix: 0.01 (0.23), residues: 535 sheet: -0.93 (0.29), residues: 312 loop : -2.10 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 381 HIS 0.010 0.001 HIS E 357 PHE 0.020 0.001 PHE F 523 TYR 0.020 0.001 TYR A 411 ARG 0.005 0.000 ARG F 303 *********************** 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 183 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 147 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7639 (tpp) REVERT: A 512 ASN cc_start: 0.7558 (p0) cc_final: 0.6494 (p0) REVERT: B 316 MET cc_start: 0.7856 (tpp) cc_final: 0.7480 (mmt) REVERT: B 375 ASN cc_start: 0.7162 (p0) cc_final: 0.6623 (p0) REVERT: D 341 MET cc_start: 0.7738 (mmp) cc_final: 0.7333 (mmp) REVERT: E 278 HIS cc_start: 0.6756 (t-170) cc_final: 0.6037 (t-170) REVERT: E 419 ASP cc_start: 0.6490 (OUTLIER) cc_final: 0.6176 (t0) REVERT: F 351 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6567 (mt-10) REVERT: F 381 TRP cc_start: 0.7841 (m-10) cc_final: 0.7451 (m100) REVERT: F 412 MET cc_start: 0.5327 (ttm) cc_final: 0.4962 (ttt) outliers start: 36 outliers final: 27 residues processed: 167 average time/residue: 0.1917 time to fit residues: 50.6783 Evaluate side-chains 165 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 136 time to evaluate : 1.446 ------------------------------------------------------------------------------- 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 429 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 388 ASN Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain 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 510 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain D residue 346 VAL 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 406 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 542 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 131 optimal weight: 0.0040 chunk 106 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 78 optimal weight: 0.6980 chunk 138 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13068 Z= 0.136 Angle : 0.539 11.645 17631 Z= 0.267 Chirality : 0.042 0.179 2006 Planarity : 0.002 0.032 2171 Dihedral : 15.742 176.682 1942 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.44 % Allowed : 15.08 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.21), residues: 1558 helix: 0.49 (0.23), residues: 532 sheet: -0.82 (0.29), residues: 322 loop : -1.92 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 381 HIS 0.011 0.001 HIS E 357 PHE 0.017 0.001 PHE E 452 TYR 0.021 0.001 TYR A 411 ARG 0.006 0.000 ARG F 303 *********************** 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 190 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 157 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7603 (tpp) REVERT: A 467 LYS cc_start: 0.7177 (pttt) cc_final: 0.6936 (pttp) REVERT: B 316 MET cc_start: 0.7704 (tpp) cc_final: 0.7388 (mmt) REVERT: B 344 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8023 (pm20) REVERT: B 375 ASN cc_start: 0.6909 (p0) cc_final: 0.6421 (p0) REVERT: C 504 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7070 (ptm160) REVERT: D 316 MET cc_start: 0.8089 (mtp) cc_final: 0.7872 (mtp) REVERT: E 278 HIS cc_start: 0.6637 (t-170) cc_final: 0.5866 (t-170) REVERT: E 405 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7890 (tt) REVERT: E 419 ASP cc_start: 0.6301 (OUTLIER) cc_final: 0.6005 (t0) REVERT: F 351 GLU cc_start: 0.6839 (mt-10) cc_final: 0.6438 (mt-10) REVERT: F 412 MET cc_start: 0.5537 (ttm) cc_final: 0.5249 (ttt) REVERT: F 532 TYR cc_start: 0.6359 (m-80) cc_final: 0.6100 (m-80) outliers start: 33 outliers final: 21 residues processed: 178 average time/residue: 0.1897 time to fit residues: 53.5692 Evaluate side-chains 164 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 138 time to evaluate : 1.380 ------------------------------------------------------------------------------- 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 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 344 GLU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain C residue 510 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 385 LEU 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 F residue 266 VAL Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 521 CYS Chi-restraints excluded: chain F residue 542 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 10.0000 chunk 139 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 51 optimal weight: 0.0570 chunk 81 optimal weight: 10.0000 overall best weight: 1.5304 ------------------------------------------------------------------------------- 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** ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13068 Z= 0.204 Angle : 0.588 10.670 17631 Z= 0.289 Chirality : 0.043 0.182 2006 Planarity : 0.003 0.031 2171 Dihedral : 15.819 179.743 1942 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.73 % Allowed : 15.67 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.21), residues: 1558 helix: 0.65 (0.24), residues: 531 sheet: -0.76 (0.29), residues: 320 loop : -1.82 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP F 381 HIS 0.011 0.001 HIS E 357 PHE 0.007 0.001 PHE B 321 TYR 0.021 0.001 TYR A 411 ARG 0.012 0.000 ARG B 274 *********************** 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 180 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 143 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 LYS cc_start: 0.7181 (pttt) cc_final: 0.6922 (pttp) REVERT: B 316 MET cc_start: 0.7785 (tpp) cc_final: 0.7399 (mmt) REVERT: B 344 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8089 (pm20) REVERT: B 375 ASN cc_start: 0.7097 (p0) cc_final: 0.6653 (p0) REVERT: C 504 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7410 (ptm160) REVERT: D 341 MET cc_start: 0.7532 (mmp) cc_final: 0.7174 (mmp) REVERT: E 278 HIS cc_start: 0.6717 (t-170) cc_final: 0.5898 (t-170) REVERT: E 405 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7961 (tt) REVERT: E 419 ASP cc_start: 0.6435 (OUTLIER) cc_final: 0.6141 (t0) REVERT: F 351 GLU cc_start: 0.6862 (mt-10) cc_final: 0.6422 (mt-10) REVERT: F 381 TRP cc_start: 0.7603 (m-10) cc_final: 0.7085 (m100) REVERT: F 412 MET cc_start: 0.5429 (ttm) cc_final: 0.5057 (ttt) REVERT: F 532 TYR cc_start: 0.6389 (m-80) cc_final: 0.6102 (m-80) outliers start: 37 outliers final: 27 residues processed: 168 average time/residue: 0.1993 time to fit residues: 52.3429 Evaluate side-chains 167 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 136 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 514 VAL 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 412 MET Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain C residue 510 MET Chi-restraints excluded: chain C residue 514 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 406 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 542 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 113 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 130 optimal weight: 0.3980 chunk 86 optimal weight: 0.7980 chunk 154 optimal weight: 8.9990 chunk 96 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13068 Z= 0.145 Angle : 0.547 10.362 17631 Z= 0.269 Chirality : 0.042 0.169 2006 Planarity : 0.002 0.027 2171 Dihedral : 15.465 177.850 1942 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.37 % Allowed : 16.04 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.21), residues: 1558 helix: 0.85 (0.24), residues: 532 sheet: -0.61 (0.29), residues: 321 loop : -1.76 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 381 HIS 0.009 0.001 HIS E 357 PHE 0.017 0.001 PHE E 452 TYR 0.023 0.001 TYR A 411 ARG 0.008 0.000 ARG B 274 *********************** 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 179 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 147 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 316 MET cc_start: 0.7685 (tpp) cc_final: 0.7363 (mmt) REVERT: B 375 ASN cc_start: 0.6904 (p0) cc_final: 0.6517 (p0) REVERT: C 504 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7307 (ptm160) REVERT: D 341 MET cc_start: 0.7471 (mmp) cc_final: 0.7219 (mmp) REVERT: E 278 HIS cc_start: 0.6651 (t-170) cc_final: 0.5905 (t-170) REVERT: E 405 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7854 (tt) REVERT: E 419 ASP cc_start: 0.6348 (OUTLIER) cc_final: 0.6034 (t0) REVERT: F 351 GLU cc_start: 0.6703 (mt-10) cc_final: 0.6260 (mt-10) REVERT: F 532 TYR cc_start: 0.6357 (m-80) cc_final: 0.6096 (m-80) outliers start: 32 outliers final: 22 residues processed: 171 average time/residue: 0.1903 time to fit residues: 51.5356 Evaluate side-chains 164 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 139 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 425 HIS Chi-restraints excluded: chain A residue 429 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 481 VAL Chi-restraints excluded: chain C residue 322 VAL 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 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 406 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 542 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 8.9990 chunk 61 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 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** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13068 Z= 0.186 Angle : 0.579 10.115 17631 Z= 0.284 Chirality : 0.043 0.166 2006 Planarity : 0.003 0.033 2171 Dihedral : 15.430 175.331 1942 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.59 % Allowed : 16.19 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.22), residues: 1558 helix: 0.87 (0.24), residues: 531 sheet: -0.60 (0.29), residues: 321 loop : -1.68 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 381 HIS 0.008 0.001 HIS E 357 PHE 0.008 0.001 PHE B 382 TYR 0.024 0.001 TYR A 411 ARG 0.007 0.000 ARG B 274 *********************** 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 177 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 142 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.7777 (tpp) cc_final: 0.7568 (tpp) REVERT: B 316 MET cc_start: 0.7806 (tpp) cc_final: 0.7438 (mmt) REVERT: B 375 ASN cc_start: 0.7003 (p0) cc_final: 0.6552 (p0) REVERT: C 504 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7346 (ptm160) REVERT: E 278 HIS cc_start: 0.6689 (t-170) cc_final: 0.5896 (t-170) REVERT: E 405 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7908 (tt) REVERT: E 419 ASP cc_start: 0.6410 (OUTLIER) cc_final: 0.6107 (t0) REVERT: F 351 GLU cc_start: 0.6779 (mt-10) cc_final: 0.6325 (mt-10) REVERT: F 532 TYR cc_start: 0.6490 (m-80) cc_final: 0.6249 (m-80) outliers start: 35 outliers final: 29 residues processed: 169 average time/residue: 0.1999 time to fit residues: 52.9964 Evaluate side-chains 172 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 140 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 425 HIS Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain C residue 322 VAL 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 D residue 385 LEU Chi-restraints excluded: chain D residue 442 ILE 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 406 LEU Chi-restraints excluded: chain E residue 419 ASP Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 465 HIS 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 140 optimal weight: 0.9990 chunk 147 optimal weight: 0.6980 chunk 134 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 HIS ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.4447 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= 0.144 Angle : 0.560 10.036 17631 Z= 0.273 Chirality : 0.042 0.157 2006 Planarity : 0.002 0.038 2171 Dihedral : 15.067 171.924 1942 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.37 % Allowed : 16.41 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.22), residues: 1558 helix: 0.93 (0.24), residues: 537 sheet: -0.46 (0.29), residues: 321 loop : -1.56 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 381 HIS 0.008 0.001 HIS E 357 PHE 0.020 0.001 PHE A 452 TYR 0.024 0.001 TYR A 411 ARG 0.006 0.000 ARG B 274 *********************** 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 185 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 153 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.7630 (tpp) cc_final: 0.7353 (tpp) REVERT: B 316 MET cc_start: 0.7725 (tpp) cc_final: 0.7347 (mmt) REVERT: B 375 ASN cc_start: 0.6882 (p0) cc_final: 0.6606 (m-40) REVERT: C 504 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7183 (ptm160) REVERT: D 308 ILE cc_start: 0.7851 (mp) cc_final: 0.7547 (mt) REVERT: D 484 THR cc_start: 0.7942 (p) cc_final: 0.7727 (p) REVERT: E 316 MET cc_start: 0.8535 (mmm) cc_final: 0.8217 (mmt) REVERT: E 405 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7831 (tt) REVERT: E 419 ASP cc_start: 0.6287 (OUTLIER) cc_final: 0.6014 (t0) outliers start: 32 outliers final: 23 residues processed: 179 average time/residue: 0.1917 time to fit residues: 54.1823 Evaluate side-chains 165 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 139 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 425 HIS 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 449 LEU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain C residue 322 VAL 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 D residue 320 THR Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 419 ASP Chi-restraints excluded: chain E residue 465 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 98 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 100 optimal weight: 0.0170 overall best weight: 1.1020 ------------------------------------------------------------------------------- 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** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13068 Z= 0.168 Angle : 0.569 9.934 17631 Z= 0.279 Chirality : 0.043 0.185 2006 Planarity : 0.003 0.040 2171 Dihedral : 14.976 170.490 1942 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.22 % Allowed : 16.85 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.22), residues: 1558 helix: 0.96 (0.24), residues: 537 sheet: -0.42 (0.29), residues: 321 loop : -1.51 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 381 HIS 0.013 0.001 HIS E 278 PHE 0.019 0.001 PHE A 378 TYR 0.026 0.001 TYR A 411 ARG 0.004 0.000 ARG B 363 ********************** 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 171 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 141 time to evaluate : 1.485 Fit side-chains revert: symmetry clash REVERT: A 316 MET cc_start: 0.7692 (tpp) cc_final: 0.7386 (tpp) REVERT: A 467 LYS cc_start: 0.7183 (pttt) cc_final: 0.6953 (pttp) REVERT: B 316 MET cc_start: 0.7791 (tpp) cc_final: 0.7436 (mmt) REVERT: B 375 ASN cc_start: 0.6957 (p0) cc_final: 0.6628 (m-40) REVERT: C 504 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7961 (ptm160) REVERT: E 316 MET cc_start: 0.8511 (mmm) cc_final: 0.8188 (mmt) REVERT: E 405 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7793 (tt) REVERT: E 419 ASP cc_start: 0.6233 (OUTLIER) cc_final: 0.5908 (t0) REVERT: F 351 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6987 (mt-10) REVERT: F 381 TRP cc_start: 0.7852 (m-10) cc_final: 0.7231 (m100) outliers start: 30 outliers final: 24 residues processed: 166 average time/residue: 0.2019 time to fit residues: 52.4910 Evaluate side-chains 163 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 136 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 425 HIS 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 481 VAL Chi-restraints excluded: chain C residue 322 VAL 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 D residue 295 ILE Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 419 ASP Chi-restraints excluded: chain E residue 514 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 117 optimal weight: 8.9990 chunk 18 optimal weight: 0.0870 chunk 35 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 53 optimal weight: 0.0770 chunk 130 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 chunk 23 optimal weight: 0.0870 chunk 111 optimal weight: 0.9980 overall best weight: 0.3294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.126276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.110936 restraints weight = 33040.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.112951 restraints weight = 20946.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.114299 restraints weight = 14755.004| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.4695 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= 0.122 Angle : 0.541 10.064 17631 Z= 0.263 Chirality : 0.042 0.167 2006 Planarity : 0.002 0.043 2171 Dihedral : 14.558 172.429 1942 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.33 % Allowed : 17.59 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.22), residues: 1558 helix: 1.17 (0.24), residues: 531 sheet: -0.34 (0.30), residues: 326 loop : -1.41 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 381 HIS 0.013 0.001 HIS E 278 PHE 0.018 0.001 PHE E 452 TYR 0.027 0.001 TYR A 411 ARG 0.004 0.000 ARG B 363 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2294.86 seconds wall clock time: 42 minutes 3.85 seconds (2523.85 seconds total)