Starting phenix.real_space_refine on Wed Jun 11 15:46:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n7t_0363/06_2025/6n7t_0363_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n7t_0363/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6n7t_0363/06_2025/6n7t_0363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n7t_0363/06_2025/6n7t_0363.map" model { file = "/net/cci-nas-00/data/ceres_data/6n7t_0363/06_2025/6n7t_0363_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n7t_0363/06_2025/6n7t_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-5710/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: 8.46, 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: 3.08 Conformation dependent library (CDL) restraints added in 1.7 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: 1.51 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: 3.74 Time building geometry restraints manager: 3.63 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 31.490 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.040 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.310 ------------------------------------------------------------------------------- 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 : 3.57 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 Details of bonding type rmsd hydrogen bonds : bond 0.16558 ( 415) hydrogen bonds : angle 7.22833 ( 1191) covalent geometry : bond 0.00558 (13068) covalent geometry : angle 0.95423 (17631) *********************** 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 : 1.581 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: 0.2675 time to fit residues: 129.4156 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 : 1.419 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.119666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.103748 restraints weight = 33039.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.105619 restraints weight = 21117.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.106829 restraints weight = 15185.614| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 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= 0.336 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 Details of bonding type rmsd hydrogen bonds : bond 0.05098 ( 415) hydrogen bonds : angle 5.82097 ( 1191) covalent geometry : bond 0.00766 (13068) covalent geometry : angle 0.86611 (17631) *********************** 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 to be fit. rotamer outliers: 42 poor density : 172 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 PHE cc_start: 0.7711 (m-10) cc_final: 0.7477 (m-10) REVERT: A 314 SER cc_start: 0.6860 (t) cc_final: 0.6629 (p) REVERT: A 404 ARG cc_start: 0.4587 (OUTLIER) cc_final: 0.4370 (ptt180) REVERT: C 425 HIS cc_start: 0.8003 (t-90) cc_final: 0.7563 (t70) REVERT: C 430 VAL cc_start: 0.7628 (OUTLIER) cc_final: 0.7314 (m) REVERT: D 341 MET cc_start: 0.8189 (mmp) cc_final: 0.7848 (mmp) REVERT: E 278 HIS cc_start: 0.7169 (t-170) cc_final: 0.6564 (t-170) REVERT: E 316 MET cc_start: 0.8526 (mmt) cc_final: 0.7669 (mmt) REVERT: F 308 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8013 (tp) REVERT: F 351 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6812 (mt-10) REVERT: F 381 TRP cc_start: 0.7924 (m-10) cc_final: 0.7636 (m-10) REVERT: F 412 MET cc_start: 0.5609 (ttm) cc_final: 0.5352 (ttt) REVERT: F 532 TYR cc_start: 0.6619 (m-80) cc_final: 0.6359 (m-80) outliers start: 42 outliers final: 22 residues processed: 201 average time/residue: 0.2251 time to fit residues: 68.5709 Evaluate side-chains 167 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 1.624 ------------------------------------------------------------------------------- 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 3 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 11 optimal weight: 0.4980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.124244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.108149 restraints weight = 32197.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.110206 restraints weight = 20903.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.111495 restraints weight = 14744.045| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3438 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= 0.108 Angle : 0.576 16.388 17631 Z= 0.287 Chirality : 0.043 0.145 2006 Planarity : 0.003 0.061 2171 Dihedral : 16.438 174.044 1942 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.37 % Allowed : 12.71 % Favored : 84.92 % 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: -2.08 (0.20), residues: 1558 helix: -0.43 (0.22), residues: 540 sheet: -1.05 (0.29), residues: 315 loop : -2.28 (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 0.018 0.001 TYR A 411 ARG 0.004 0.000 ARG F 323 Details of bonding type rmsd hydrogen bonds : bond 0.02896 ( 415) hydrogen bonds : angle 4.81544 ( 1191) covalent geometry : bond 0.00241 (13068) covalent geometry : angle 0.57648 (17631) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 274 ARG cc_start: 0.6898 (mtm-85) cc_final: 0.6593 (mmp80) REVERT: B 375 ASN cc_start: 0.7041 (p0) cc_final: 0.6432 (p0) REVERT: C 333 MET cc_start: 0.7358 (mtm) cc_final: 0.7150 (mtm) REVERT: C 430 VAL cc_start: 0.7410 (OUTLIER) cc_final: 0.6763 (m) REVERT: E 278 HIS cc_start: 0.7020 (t-170) cc_final: 0.6304 (t-170) REVERT: E 316 MET cc_start: 0.8518 (mmt) cc_final: 0.7851 (mmt) REVERT: E 419 ASP cc_start: 0.6518 (OUTLIER) cc_final: 0.6231 (t0) REVERT: F 351 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6685 (mt-10) REVERT: F 412 MET cc_start: 0.5512 (ttm) cc_final: 0.5244 (ttt) outliers start: 32 outliers final: 17 residues processed: 195 average time/residue: 0.2182 time to fit residues: 64.5328 Evaluate side-chains 160 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 1.571 ------------------------------------------------------------------------------- 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 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 134 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 68 optimal weight: 0.0870 chunk 22 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- 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** ** E 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 = 0.3886 r_free = 0.3886 target = 0.122700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.106547 restraints weight = 32424.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.108567 restraints weight = 20510.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.109896 restraints weight = 14573.783| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13068 Z= 0.130 Angle : 0.586 13.030 17631 Z= 0.289 Chirality : 0.043 0.221 2006 Planarity : 0.003 0.032 2171 Dihedral : 16.183 176.540 1942 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.73 % Allowed : 13.67 % Favored : 83.59 % 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: -1.67 (0.21), residues: 1558 helix: -0.00 (0.23), residues: 543 sheet: -0.95 (0.29), residues: 315 loop : -2.07 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 381 HIS 0.010 0.001 HIS E 357 PHE 0.019 0.001 PHE F 523 TYR 0.020 0.001 TYR A 411 ARG 0.004 0.000 ARG D 439 Details of bonding type rmsd hydrogen bonds : bond 0.02933 ( 415) hydrogen bonds : angle 4.64161 ( 1191) covalent geometry : bond 0.00295 (13068) covalent geometry : angle 0.58559 (17631) *********************** 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 185 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7630 (tpp) REVERT: B 316 MET cc_start: 0.7942 (tpp) cc_final: 0.7579 (mmt) REVERT: B 375 ASN cc_start: 0.7096 (p0) cc_final: 0.6609 (p0) REVERT: C 430 VAL cc_start: 0.7427 (OUTLIER) cc_final: 0.7132 (m) REVERT: D 341 MET cc_start: 0.7766 (mmp) cc_final: 0.7302 (mmp) REVERT: E 278 HIS cc_start: 0.6984 (t-170) cc_final: 0.6225 (t-170) REVERT: E 405 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7974 (tt) REVERT: E 419 ASP cc_start: 0.6564 (OUTLIER) cc_final: 0.6261 (t0) REVERT: F 351 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6572 (mt-10) REVERT: F 381 TRP cc_start: 0.7792 (m-10) cc_final: 0.7380 (m100) outliers start: 37 outliers final: 28 residues processed: 168 average time/residue: 0.1980 time to fit residues: 52.7251 Evaluate side-chains 171 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 1.512 ------------------------------------------------------------------------------- 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 430 VAL 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 D residue 533 MET 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 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 91 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.122727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.106923 restraints weight = 32716.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.108861 restraints weight = 20935.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.110112 restraints weight = 15014.859| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13068 Z= 0.124 Angle : 0.568 11.734 17631 Z= 0.282 Chirality : 0.043 0.188 2006 Planarity : 0.003 0.066 2171 Dihedral : 15.999 177.432 1942 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.81 % Allowed : 14.93 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.39 (0.21), residues: 1558 helix: 0.34 (0.23), residues: 537 sheet: -0.81 (0.29), residues: 314 loop : -1.98 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 381 HIS 0.011 0.001 HIS E 357 PHE 0.016 0.001 PHE E 452 TYR 0.020 0.001 TYR A 411 ARG 0.005 0.000 ARG F 303 Details of bonding type rmsd hydrogen bonds : bond 0.02826 ( 415) hydrogen bonds : angle 4.48736 ( 1191) covalent geometry : bond 0.00283 (13068) covalent geometry : angle 0.56811 (17631) *********************** 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 to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7681 (tpp) REVERT: A 467 LYS cc_start: 0.7189 (pttt) cc_final: 0.6897 (pttp) REVERT: B 316 MET cc_start: 0.7814 (tpp) cc_final: 0.7566 (mmt) REVERT: B 344 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8085 (pm20) REVERT: B 348 GLU cc_start: 0.7088 (tm-30) cc_final: 0.6682 (tm-30) REVERT: B 375 ASN cc_start: 0.7069 (p0) cc_final: 0.6676 (p0) REVERT: C 504 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7063 (ptm160) REVERT: E 278 HIS cc_start: 0.6959 (t-170) cc_final: 0.6132 (t-170) REVERT: E 405 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7954 (tt) REVERT: E 419 ASP cc_start: 0.6555 (OUTLIER) cc_final: 0.6226 (t0) REVERT: F 351 GLU cc_start: 0.6851 (mt-10) cc_final: 0.6467 (mt-10) REVERT: F 381 TRP cc_start: 0.7911 (m-10) cc_final: 0.7694 (m100) REVERT: F 532 TYR cc_start: 0.6355 (m-80) cc_final: 0.6066 (m-80) outliers start: 38 outliers final: 27 residues processed: 174 average time/residue: 0.1922 time to fit residues: 53.5184 Evaluate side-chains 168 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 1.560 ------------------------------------------------------------------------------- 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 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 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 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 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 81 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 133 optimal weight: 0.3980 chunk 119 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 425 HIS ** 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 = 0.3884 r_free = 0.3884 target = 0.122608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.106977 restraints weight = 33965.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.108866 restraints weight = 22170.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.110116 restraints weight = 15994.788| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13068 Z= 0.129 Angle : 0.574 10.793 17631 Z= 0.285 Chirality : 0.043 0.182 2006 Planarity : 0.003 0.068 2171 Dihedral : 15.903 179.249 1942 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.81 % Allowed : 14.93 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.22 (0.21), residues: 1558 helix: 0.57 (0.23), residues: 531 sheet: -0.73 (0.29), residues: 313 loop : -1.92 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 381 HIS 0.009 0.001 HIS E 357 PHE 0.007 0.001 PHE B 382 TYR 0.022 0.001 TYR A 411 ARG 0.005 0.000 ARG B 274 Details of bonding type rmsd hydrogen bonds : bond 0.02908 ( 415) hydrogen bonds : angle 4.46232 ( 1191) covalent geometry : bond 0.00295 (13068) covalent geometry : angle 0.57359 (17631) *********************** 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 182 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 144 time to evaluate : 2.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 344 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8060 (pm20) REVERT: B 375 ASN cc_start: 0.7091 (p0) cc_final: 0.6678 (p0) REVERT: C 504 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7374 (ptm160) REVERT: D 341 MET cc_start: 0.7599 (mmp) cc_final: 0.7262 (mmp) REVERT: E 278 HIS cc_start: 0.6897 (t-170) cc_final: 0.6029 (t-170) REVERT: E 405 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7852 (tt) REVERT: E 419 ASP cc_start: 0.6490 (OUTLIER) cc_final: 0.6169 (t0) REVERT: F 351 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6514 (mt-10) REVERT: F 532 TYR cc_start: 0.6429 (m-80) cc_final: 0.6129 (m-80) outliers start: 38 outliers final: 25 residues processed: 170 average time/residue: 0.1930 time to fit residues: 52.2342 Evaluate side-chains 162 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 1.429 ------------------------------------------------------------------------------- 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 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 504 ARG Chi-restraints excluded: chain C residue 510 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 533 MET 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 542 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 104 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 55 optimal weight: 0.0870 chunk 24 optimal weight: 3.9990 chunk 121 optimal weight: 0.2980 chunk 70 optimal weight: 2.9990 overall best weight: 2.2764 ------------------------------------------------------------------------------- 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** C 392 HIS ** 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** ** 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 = 0.3851 r_free = 0.3851 target = 0.120321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.104851 restraints weight = 33546.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.106654 restraints weight = 21975.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.107843 restraints weight = 15989.488| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.4364 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= 0.180 Angle : 0.634 10.079 17631 Z= 0.316 Chirality : 0.044 0.193 2006 Planarity : 0.004 0.070 2171 Dihedral : 16.094 177.554 1942 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.18 % Allowed : 15.74 % 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: -1.32 (0.21), residues: 1558 helix: 0.42 (0.23), residues: 537 sheet: -0.84 (0.29), residues: 312 loop : -1.91 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F 381 HIS 0.012 0.001 HIS E 357 PHE 0.016 0.002 PHE E 452 TYR 0.023 0.002 TYR A 411 ARG 0.008 0.001 ARG B 274 Details of bonding type rmsd hydrogen bonds : bond 0.03377 ( 415) hydrogen bonds : angle 4.66550 ( 1191) covalent geometry : bond 0.00414 (13068) covalent geometry : angle 0.63367 (17631) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 139 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 309 MET cc_start: 0.8350 (mmt) cc_final: 0.8129 (mmp) REVERT: B 375 ASN cc_start: 0.7250 (p0) cc_final: 0.6813 (p0) REVERT: C 316 MET cc_start: 0.8066 (mmm) cc_final: 0.7856 (tpp) REVERT: C 504 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7312 (ptm160) REVERT: D 341 MET cc_start: 0.7892 (mmp) cc_final: 0.7037 (mmt) REVERT: E 278 HIS cc_start: 0.6983 (t-170) cc_final: 0.6105 (t-170) REVERT: E 316 MET cc_start: 0.8609 (mmm) cc_final: 0.8242 (mmm) REVERT: E 405 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7834 (tt) REVERT: E 419 ASP cc_start: 0.6639 (OUTLIER) cc_final: 0.6321 (t0) REVERT: F 351 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6513 (mt-10) REVERT: F 381 TRP cc_start: 0.7642 (m-10) cc_final: 0.7089 (m100) REVERT: F 532 TYR cc_start: 0.6540 (m-80) cc_final: 0.6322 (m-80) outliers start: 43 outliers final: 36 residues processed: 169 average time/residue: 0.2055 time to fit residues: 54.1500 Evaluate side-chains 172 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 1.527 ------------------------------------------------------------------------------- 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 388 ASN Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain C residue 271 LEU 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 496 SER 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 320 THR Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 441 MET 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 D residue 533 MET Chi-restraints excluded: chain E residue 349 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 91 optimal weight: 5.9990 chunk 19 optimal weight: 0.0980 chunk 87 optimal weight: 0.9980 chunk 123 optimal weight: 0.0470 chunk 80 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- 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** ** 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 = 0.3907 r_free = 0.3907 target = 0.123629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.108173 restraints weight = 33591.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.110057 restraints weight = 22046.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.111331 restraints weight = 15840.965| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 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= 0.093 Angle : 0.547 10.309 17631 Z= 0.270 Chirality : 0.042 0.169 2006 Planarity : 0.003 0.055 2171 Dihedral : 15.456 176.041 1942 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.73 % Allowed : 16.26 % Favored : 81.01 % 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: -0.91 (0.21), residues: 1558 helix: 0.86 (0.24), residues: 532 sheet: -0.63 (0.29), residues: 320 loop : -1.75 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 381 HIS 0.011 0.001 HIS E 357 PHE 0.017 0.001 PHE A 452 TYR 0.022 0.001 TYR A 411 ARG 0.007 0.000 ARG B 274 Details of bonding type rmsd hydrogen bonds : bond 0.02532 ( 415) hydrogen bonds : angle 4.22545 ( 1191) covalent geometry : bond 0.00205 (13068) covalent geometry : angle 0.54724 (17631) *********************** 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 185 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 309 MET cc_start: 0.8366 (mmt) cc_final: 0.8160 (mmp) REVERT: B 375 ASN cc_start: 0.6933 (p0) cc_final: 0.6514 (p0) REVERT: B 445 LEU cc_start: 0.8503 (tp) cc_final: 0.8268 (tp) REVERT: C 504 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.6924 (ptm160) REVERT: D 341 MET cc_start: 0.7614 (mmp) cc_final: 0.6761 (mmt) REVERT: D 484 THR cc_start: 0.7890 (p) cc_final: 0.7679 (p) REVERT: E 278 HIS cc_start: 0.6940 (t-170) cc_final: 0.6118 (t-170) REVERT: E 405 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7729 (tt) REVERT: E 419 ASP cc_start: 0.6384 (OUTLIER) cc_final: 0.6102 (t0) REVERT: F 351 GLU cc_start: 0.6768 (mt-10) cc_final: 0.6347 (mt-10) outliers start: 37 outliers final: 25 residues processed: 176 average time/residue: 0.1951 time to fit residues: 54.6074 Evaluate side-chains 165 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 447 THR 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 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 389 ASP Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 533 MET Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 419 ASP Chi-restraints excluded: chain F residue 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 100 optimal weight: 0.0270 chunk 116 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 overall best weight: 2.1244 ------------------------------------------------------------------------------- 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 357 HIS ** 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 465 HIS ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.120245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.104911 restraints weight = 33963.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.106741 restraints weight = 22121.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.107977 restraints weight = 16012.400| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13068 Z= 0.172 Angle : 0.637 11.382 17631 Z= 0.315 Chirality : 0.044 0.254 2006 Planarity : 0.004 0.071 2171 Dihedral : 15.773 172.817 1942 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.73 % Allowed : 16.63 % Favored : 80.64 % 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: -1.02 (0.21), residues: 1558 helix: 0.67 (0.23), residues: 532 sheet: -0.66 (0.30), residues: 313 loop : -1.73 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 381 HIS 0.012 0.001 HIS D 425 PHE 0.017 0.002 PHE A 378 TYR 0.023 0.002 TYR A 411 ARG 0.009 0.001 ARG B 274 Details of bonding type rmsd hydrogen bonds : bond 0.03309 ( 415) hydrogen bonds : angle 4.59137 ( 1191) covalent geometry : bond 0.00396 (13068) covalent geometry : angle 0.63745 (17631) *********************** 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 175 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 375 ASN cc_start: 0.7192 (p0) cc_final: 0.6769 (p0) REVERT: C 504 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7492 (ptm160) REVERT: D 341 MET cc_start: 0.7766 (mmp) cc_final: 0.6998 (mmt) REVERT: E 278 HIS cc_start: 0.7073 (t-170) cc_final: 0.6200 (t-170) REVERT: E 405 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7847 (tt) REVERT: F 351 GLU cc_start: 0.6812 (mt-10) cc_final: 0.6385 (mt-10) REVERT: F 381 TRP cc_start: 0.7780 (m-10) cc_final: 0.7137 (m100) outliers start: 37 outliers final: 29 residues processed: 163 average time/residue: 0.1929 time to fit residues: 49.7328 Evaluate side-chains 167 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 360 VAL 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 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 442 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 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 442 ILE Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 419 ASP Chi-restraints excluded: chain F residue 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 127 optimal weight: 0.5980 chunk 148 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 465 HIS ** 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 = 0.3871 r_free = 0.3871 target = 0.121250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.106071 restraints weight = 33730.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.107923 restraints weight = 21778.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.109020 restraints weight = 15765.096| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13068 Z= 0.135 Angle : 0.600 9.958 17631 Z= 0.297 Chirality : 0.043 0.172 2006 Planarity : 0.003 0.060 2171 Dihedral : 15.605 170.502 1942 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.14 % Allowed : 17.37 % Favored : 80.49 % 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: -0.97 (0.21), residues: 1558 helix: 0.71 (0.23), residues: 531 sheet: -0.67 (0.30), residues: 312 loop : -1.68 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 381 HIS 0.010 0.001 HIS E 357 PHE 0.016 0.001 PHE A 452 TYR 0.025 0.001 TYR A 411 ARG 0.008 0.000 ARG B 274 Details of bonding type rmsd hydrogen bonds : bond 0.03080 ( 415) hydrogen bonds : angle 4.49238 ( 1191) covalent geometry : bond 0.00312 (13068) covalent geometry : angle 0.60038 (17631) ********************** 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 167 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 467 LYS cc_start: 0.7200 (pttt) cc_final: 0.6953 (pttp) REVERT: B 375 ASN cc_start: 0.7103 (p0) cc_final: 0.6653 (p0) REVERT: C 504 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7304 (ptm160) REVERT: D 341 MET cc_start: 0.7735 (mmp) cc_final: 0.6982 (mmt) REVERT: E 278 HIS cc_start: 0.7034 (t-170) cc_final: 0.6192 (t-170) REVERT: E 405 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7739 (tt) REVERT: F 351 GLU cc_start: 0.6829 (mt-10) cc_final: 0.6414 (mt-10) REVERT: F 381 TRP cc_start: 0.7774 (m-10) cc_final: 0.7150 (m100) outliers start: 29 outliers final: 26 residues processed: 160 average time/residue: 0.2026 time to fit residues: 51.4414 Evaluate side-chains 164 residues out of total 1355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 360 VAL 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 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 389 ASP Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain C residue 510 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain D residue 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 349 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 F residue 310 VAL Chi-restraints excluded: chain F residue 542 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 121 optimal weight: 8.9990 chunk 152 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 chunk 114 optimal weight: 0.1980 chunk 110 optimal weight: 0.0040 chunk 153 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.5994 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.123702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.108589 restraints weight = 33230.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.110475 restraints weight = 21415.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.111736 restraints weight = 15373.452| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13068 Z= 0.093 Angle : 0.554 10.131 17631 Z= 0.273 Chirality : 0.042 0.159 2006 Planarity : 0.003 0.053 2171 Dihedral : 15.087 171.187 1942 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.00 % Allowed : 17.52 % Favored : 80.49 % 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: -0.76 (0.22), residues: 1558 helix: 0.90 (0.24), residues: 538 sheet: -0.56 (0.29), residues: 322 loop : -1.59 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 381 HIS 0.010 0.001 HIS E 357 PHE 0.019 0.001 PHE E 452 TYR 0.025 0.001 TYR A 411 ARG 0.008 0.000 ARG B 274 Details of bonding type rmsd hydrogen bonds : bond 0.02662 ( 415) hydrogen bonds : angle 4.21511 ( 1191) covalent geometry : bond 0.00206 (13068) covalent geometry : angle 0.55414 (17631) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3722.54 seconds wall clock time: 65 minutes 53.97 seconds (3953.97 seconds total)