Starting phenix.real_space_refine on Fri Mar 15 22:04:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7t_0363/03_2024/6n7t_0363_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7t_0363/03_2024/6n7t_0363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7t_0363/03_2024/6n7t_0363.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7t_0363/03_2024/6n7t_0363.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7t_0363/03_2024/6n7t_0363_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n7t_0363/03_2024/6n7t_0363_neut_updated.pdb" } 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 Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 504": "NH1" <-> "NH2" Residue "C ARG 504": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 370": "NH1" <-> "NH2" Residue "D ARG 504": "NH1" <-> "NH2" Residue "E ARG 274": "NH1" <-> "NH2" Residue "E ARG 363": "NH1" <-> "NH2" Residue "E ARG 370": "NH1" <-> "NH2" Residue "F ARG 274": "NH1" <-> "NH2" Residue "F ARG 363": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 6.46, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 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: 4.95 Conformation dependent library (CDL) restraints added in 2.1 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... running ksdssp... Secondary structure from input PDB file: 58 helices and 6 sheets defined 30.6% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'A' and resid 268 through 271 removed outlier: 3.644A pdb=" N LEU A 271 " --> pdb=" O ALA A 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 268 through 271' Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 318 through 331 removed outlier: 3.544A pdb=" N GLY A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 357 Processing helix chain 'A' and resid 366 through 374 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 378 through 382 Processing helix chain 'A' and resid 403 through 414 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 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 483 through 485 No H-bonds generated for 'chain 'A' and resid 483 through 485' Processing helix chain 'B' and resid 274 through 280 Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 318 through 331 Processing helix chain 'B' and resid 346 through 357 Processing helix chain 'B' and resid 366 through 374 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) Processing helix chain 'B' and resid 377 through 385 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 413 Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 438 through 453 Processing helix chain 'B' and resid 475 through 477 No H-bonds generated for 'chain 'B' and resid 475 through 477' Processing helix chain 'C' and resid 272 through 276 Processing helix chain 'C' and resid 294 through 298 Processing helix chain 'C' and resid 320 through 328 removed outlier: 3.689A pdb=" N GLN C 328 " --> pdb=" O GLN C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 357 removed outlier: 3.690A pdb=" N ALA C 350 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU C 351 " --> pdb=" O GLU C 347 " (cutoff:3.500A) 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 366 through 374 Processing helix chain 'C' and resid 377 through 385 removed outlier: 3.526A pdb=" N LEU C 385 " --> pdb=" O TRP C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 414 removed outlier: 3.782A pdb=" N ALA C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 431 removed outlier: 3.625A pdb=" N VAL C 430 " --> pdb=" O SER C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 456 Processing helix chain 'C' and resid 475 through 477 No H-bonds generated for 'chain 'C' and resid 475 through 477' Processing helix chain 'C' and resid 483 through 485 No H-bonds generated for 'chain 'C' and resid 483 through 485' Processing helix chain 'D' and resid 272 through 276 Processing helix chain 'D' and resid 318 through 331 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) Processing helix chain 'D' and resid 346 through 357 Processing helix chain 'D' and resid 371 through 374 No H-bonds generated for 'chain 'D' and resid 371 through 374' Processing helix chain 'D' and resid 378 through 386 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 414 Processing helix chain 'D' and resid 440 through 456 removed outlier: 3.642A pdb=" N LEU D 445 " --> pdb=" O MET D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 477 No H-bonds generated for 'chain 'D' and resid 475 through 477' Processing helix chain 'D' and resid 491 through 493 No H-bonds generated for 'chain 'D' and resid 491 through 493' Processing helix chain 'E' and resid 273 through 279 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) No H-bonds generated for 'chain 'E' and resid 273 through 279' Processing helix chain 'E' and resid 318 through 328 Processing helix chain 'E' and resid 346 through 357 removed outlier: 3.522A pdb=" N ALA E 350 " --> pdb=" O VAL E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 371 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 386 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 414 Processing helix chain 'E' and resid 440 through 456 removed outlier: 3.911A pdb=" N LEU E 445 " --> pdb=" O MET E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 477 No H-bonds generated for 'chain 'E' and resid 475 through 477' Processing helix chain 'F' and resid 274 through 279 Processing helix chain 'F' and resid 294 through 298 removed outlier: 4.136A pdb=" N LYS F 298 " --> pdb=" O GLY F 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 294 through 298' Processing helix chain 'F' and resid 318 through 330 removed outlier: 3.711A pdb=" N GLN F 324 " --> pdb=" O THR F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 357 Processing helix chain 'F' and resid 366 through 374 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) Processing helix chain 'F' and resid 409 through 414 Processing helix chain 'F' and resid 440 through 453 Processing helix chain 'F' and resid 483 through 485 No H-bonds generated for 'chain 'F' and resid 483 through 485' Processing helix chain 'F' and resid 492 through 495 No H-bonds generated for 'chain 'F' and resid 492 through 495' Processing sheet with id= A, 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: 3.805A pdb=" N LEU A 460 " --> pdb=" O GLU A 306 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 528 through 534 removed outlier: 7.092A pdb=" N VAL B 516 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N TYR B 532 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL B 514 " --> pdb=" O TYR B 532 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE B 499 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR B 498 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU B 460 " --> pdb=" O GLU B 306 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 463 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 542 through 544 removed outlier: 6.842A pdb=" N VAL C 516 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TYR C 532 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL C 514 " --> pdb=" O TYR C 532 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE C 499 " --> pdb=" O LEU C 519 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU C 460 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N VAL C 310 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL C 462 " --> pdb=" O VAL C 310 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 528 through 533 removed outlier: 7.059A pdb=" N VAL D 516 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR D 532 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL D 514 " --> pdb=" O TYR D 532 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE D 499 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR D 498 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SER D 312 " --> pdb=" O CYS D 464 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 528 through 533 removed outlier: 6.774A pdb=" N VAL E 516 " --> pdb=" O ALA E 530 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N TYR E 532 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL E 514 " --> pdb=" O TYR E 532 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE E 499 " --> pdb=" O LEU E 519 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR E 498 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU E 460 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL E 310 " --> pdb=" O LEU E 460 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL E 462 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LYS E 336 " --> pdb=" O ASP E 419 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ILE E 421 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLY E 338 " --> pdb=" O ILE E 421 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LEU E 423 " --> pdb=" O GLY E 338 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA E 340 " --> pdb=" O LEU E 423 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 541 through 545 removed outlier: 3.627A pdb=" N TRP F 541 " --> pdb=" O ASN F 536 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR F 532 " --> pdb=" O SER F 545 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL F 516 " --> pdb=" O ALA F 530 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TYR F 532 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL F 514 " --> pdb=" O TYR F 532 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE F 499 " --> pdb=" O LEU F 519 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE F 308 " --> pdb=" O LEU F 460 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS F 464 " --> pdb=" O VAL F 310 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLY F 338 " --> pdb=" O ILE F 422 " (cutoff:3.500A) 363 hydrogen bonds defined for protein. 1056 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: 3.00 Time building geometry restraints manager: 5.39 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: 98.51 - 105.61: 204 105.61 - 112.72: 6862 112.72 - 119.83: 4570 119.83 - 126.93: 5862 126.93 - 134.04: 133 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: 8059 3.09 - 3.69: 18448 3.69 - 4.30: 27128 4.30 - 4.90: 44941 Nonbonded interactions: 98607 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 98602 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.050 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 33.530 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.710 ------------------------------------------------------------------------------- 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= 0.336 Angle : 0.954 12.157 17631 Z= 0.512 Chirality : 0.056 0.260 2006 Planarity : 0.004 0.051 2171 Dihedral : 15.070 174.962 4930 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.65 % Favored : 94.29 % Rotamer: Outliers : 0.81 % Allowed : 2.96 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.82 (0.17), residues: 1558 helix: -2.95 (0.16), residues: 518 sheet: -0.91 (0.30), residues: 315 loop : -2.93 (0.18), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 329 HIS 0.009 0.002 HIS A 425 PHE 0.013 0.002 PHE A 523 TYR 0.009 0.001 TYR F 411 ARG 0.007 0.001 ARG C 493 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 333 time to evaluate : 1.424 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: 0.2573 time to fit residues: 124.0284 Evaluate side-chains 172 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 170 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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: 9.9990 chunk 67 optimal weight: 0.5980 chunk 41 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 GLN C 343 GLN C 357 HIS ** 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 ** E 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 475 HIS F 512 ASN F 536 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 13068 Z= 0.467 Angle : 0.817 9.272 17631 Z= 0.410 Chirality : 0.049 0.171 2006 Planarity : 0.005 0.043 2171 Dihedral : 17.285 178.029 1947 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.40 % Allowed : 10.27 % Favored : 86.33 % 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: -2.96 (0.19), residues: 1558 helix: -1.49 (0.21), residues: 540 sheet: -1.24 (0.29), residues: 311 loop : -2.65 (0.19), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 381 HIS 0.009 0.003 HIS E 278 PHE 0.020 0.003 PHE E 378 TYR 0.021 0.002 TYR F 411 ARG 0.009 0.001 ARG C 504 *********************** 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 218 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 172 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 SER cc_start: 0.6746 (t) cc_final: 0.6437 (p) REVERT: A 316 MET cc_start: 0.8508 (mmp) cc_final: 0.7953 (mmm) REVERT: A 404 ARG cc_start: 0.4693 (OUTLIER) cc_final: 0.4486 (ptt180) REVERT: C 425 HIS cc_start: 0.8014 (t-90) cc_final: 0.7572 (t70) REVERT: C 430 VAL cc_start: 0.7691 (OUTLIER) cc_final: 0.7434 (m) REVERT: D 341 MET cc_start: 0.8146 (mmp) cc_final: 0.7926 (mmp) REVERT: E 278 HIS cc_start: 0.7022 (t-170) cc_final: 0.6431 (t-170) REVERT: E 316 MET cc_start: 0.8466 (mmt) cc_final: 0.7609 (mmt) REVERT: F 351 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6792 (mt-10) outliers start: 46 outliers final: 21 residues processed: 204 average time/residue: 0.2180 time to fit residues: 67.1295 Evaluate side-chains 166 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 143 time to evaluate : 1.483 ------------------------------------------------------------------------------- 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 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 430 VAL Chi-restraints excluded: chain D residue 296 ASN 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 D residue 379 ASP Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 496 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 chunk 157 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 144 optimal weight: 0.0020 chunk 49 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 357 HIS ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** 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 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13068 Z= 0.140 Angle : 0.537 14.373 17631 Z= 0.268 Chirality : 0.042 0.153 2006 Planarity : 0.003 0.029 2171 Dihedral : 16.238 175.950 1942 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.22 % Allowed : 12.56 % Favored : 85.22 % 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: -2.19 (0.20), residues: 1558 helix: -0.64 (0.22), residues: 540 sheet: -1.00 (0.29), residues: 320 loop : -2.30 (0.20), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 381 HIS 0.010 0.001 HIS E 357 PHE 0.016 0.001 PHE E 452 TYR 0.019 0.001 TYR A 411 ARG 0.007 0.000 ARG D 323 *********************** 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 208 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 178 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 SER cc_start: 0.6690 (t) cc_final: 0.6423 (p) REVERT: A 316 MET cc_start: 0.8066 (mmp) cc_final: 0.7821 (tpp) REVERT: A 467 LYS cc_start: 0.7265 (pttt) cc_final: 0.6825 (pttp) REVERT: C 430 VAL cc_start: 0.7535 (OUTLIER) cc_final: 0.7093 (m) REVERT: D 347 GLU cc_start: 0.7588 (mp0) cc_final: 0.7223 (mp0) REVERT: E 278 HIS cc_start: 0.6732 (t-170) cc_final: 0.6083 (t-170) REVERT: E 468 ASN cc_start: 0.8097 (t0) cc_final: 0.7832 (t0) REVERT: F 331 THR cc_start: 0.6890 (t) cc_final: 0.6622 (t) REVERT: F 351 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6505 (mt-10) REVERT: F 381 TRP cc_start: 0.7641 (m-10) cc_final: 0.7412 (m100) REVERT: F 446 MET cc_start: 0.6529 (mmp) cc_final: 0.6221 (mmp) outliers start: 30 outliers final: 19 residues processed: 198 average time/residue: 0.2201 time to fit residues: 65.9913 Evaluate side-chains 170 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 150 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 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 C residue 322 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 510 MET Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 542 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 chunk 138 optimal weight: 10.0000 chunk 41 optimal weight: 0.3980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3642 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= 0.168 Angle : 0.543 11.406 17631 Z= 0.268 Chirality : 0.042 0.138 2006 Planarity : 0.003 0.055 2171 Dihedral : 15.941 176.849 1942 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.22 % Allowed : 14.19 % 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: -1.78 (0.21), residues: 1558 helix: -0.24 (0.23), residues: 540 sheet: -0.95 (0.29), residues: 321 loop : -2.02 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 381 HIS 0.010 0.001 HIS E 357 PHE 0.018 0.001 PHE F 523 TYR 0.020 0.001 TYR A 411 ARG 0.005 0.000 ARG B 274 *********************** 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 187 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 157 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.8113 (mmp) cc_final: 0.7855 (tpp) REVERT: B 309 MET cc_start: 0.8456 (mmt) cc_final: 0.7973 (mmm) REVERT: C 333 MET cc_start: 0.7411 (mtm) cc_final: 0.7177 (mtm) REVERT: C 430 VAL cc_start: 0.7442 (OUTLIER) cc_final: 0.7160 (m) REVERT: D 308 ILE cc_start: 0.8086 (mp) cc_final: 0.7809 (mt) REVERT: D 341 MET cc_start: 0.7649 (mmp) cc_final: 0.7384 (mmp) REVERT: E 278 HIS cc_start: 0.6747 (t-170) cc_final: 0.5982 (t-170) REVERT: E 468 ASN cc_start: 0.8135 (t0) cc_final: 0.7861 (t0) REVERT: F 308 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7736 (tp) REVERT: F 331 THR cc_start: 0.6899 (t) cc_final: 0.6652 (t) REVERT: F 351 GLU cc_start: 0.6904 (mt-10) cc_final: 0.6318 (mt-10) REVERT: F 532 TYR cc_start: 0.6391 (m-80) cc_final: 0.6110 (m-80) outliers start: 30 outliers final: 25 residues processed: 176 average time/residue: 0.1951 time to fit residues: 54.1090 Evaluate side-chains 172 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 145 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 521 CYS Chi-restraints excluded: chain C residue 322 VAL 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 296 ASN Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 419 ASP Chi-restraints excluded: chain E residue 465 HIS Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 542 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 131 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 78 optimal weight: 0.6980 chunk 138 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 ASN ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13068 Z= 0.141 Angle : 0.524 10.503 17631 Z= 0.259 Chirality : 0.041 0.139 2006 Planarity : 0.003 0.042 2171 Dihedral : 15.624 177.800 1942 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.81 % Allowed : 14.86 % Favored : 82.34 % 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: -1.43 (0.21), residues: 1558 helix: 0.20 (0.23), residues: 525 sheet: -0.78 (0.29), residues: 323 loop : -1.90 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 381 HIS 0.011 0.001 HIS E 357 PHE 0.017 0.001 PHE E 452 TYR 0.021 0.001 TYR A 411 ARG 0.006 0.000 ARG B 274 *********************** 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 194 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 156 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.7885 (mmp) cc_final: 0.7651 (tpp) REVERT: B 309 MET cc_start: 0.8310 (mmt) cc_final: 0.7845 (mmm) REVERT: B 316 MET cc_start: 0.7732 (tpp) cc_final: 0.7425 (mmt) REVERT: C 504 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7811 (ptm160) REVERT: D 308 ILE cc_start: 0.8057 (mp) cc_final: 0.7838 (mt) REVERT: E 278 HIS cc_start: 0.6754 (t-170) cc_final: 0.6007 (t-170) REVERT: E 405 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7917 (tt) REVERT: E 468 ASN cc_start: 0.8226 (t0) cc_final: 0.7951 (t0) REVERT: F 308 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7759 (tp) REVERT: F 331 THR cc_start: 0.6729 (t) cc_final: 0.6527 (t) REVERT: F 351 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6311 (mt-10) REVERT: F 532 TYR cc_start: 0.6339 (m-80) cc_final: 0.6091 (m-80) outliers start: 38 outliers final: 27 residues processed: 181 average time/residue: 0.1974 time to fit residues: 55.7901 Evaluate side-chains 173 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 143 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain C residue 510 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 419 ASP Chi-restraints excluded: chain E residue 465 HIS Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 542 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 30 optimal weight: 0.4980 chunk 90 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 154 optimal weight: 7.9990 chunk 128 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 GLN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 ASN ** 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** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13068 Z= 0.259 Angle : 0.607 10.014 17631 Z= 0.302 Chirality : 0.043 0.143 2006 Planarity : 0.003 0.045 2171 Dihedral : 15.953 179.144 1942 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.03 % Allowed : 15.52 % Favored : 81.45 % 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: -1.51 (0.21), residues: 1558 helix: 0.13 (0.23), residues: 531 sheet: -0.94 (0.29), residues: 322 loop : -1.90 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 381 HIS 0.011 0.002 HIS D 425 PHE 0.014 0.001 PHE F 523 TYR 0.018 0.001 TYR C 411 ARG 0.007 0.001 ARG B 274 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 143 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 375 ASN cc_start: 0.7119 (p0) cc_final: 0.6653 (p0) REVERT: C 504 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8192 (ptm160) REVERT: E 278 HIS cc_start: 0.6842 (t-170) cc_final: 0.6169 (t-170) REVERT: E 316 MET cc_start: 0.8507 (mmm) cc_final: 0.8001 (mmt) REVERT: E 405 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7865 (tt) REVERT: E 510 MET cc_start: 0.6928 (ppp) cc_final: 0.6536 (ptm) REVERT: F 308 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7885 (tp) REVERT: F 309 MET cc_start: 0.7482 (ttp) cc_final: 0.7242 (ttp) REVERT: F 331 THR cc_start: 0.6895 (t) cc_final: 0.6617 (t) REVERT: F 351 GLU cc_start: 0.6942 (mt-10) cc_final: 0.6380 (mt-10) outliers start: 41 outliers final: 34 residues processed: 173 average time/residue: 0.1946 time to fit residues: 52.9259 Evaluate side-chains 173 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 136 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 380 GLN Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 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 442 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain C residue 510 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 526 ASP 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 465 HIS Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 524 THR Chi-restraints excluded: chain F residue 542 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 7.9990 chunk 17 optimal weight: 0.4980 chunk 88 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 154 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 GLN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 ASN ** 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 343 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.4221 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= 0.157 Angle : 0.543 10.421 17631 Z= 0.268 Chirality : 0.041 0.142 2006 Planarity : 0.003 0.050 2171 Dihedral : 15.628 175.967 1942 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.59 % Allowed : 16.48 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.21), residues: 1558 helix: 0.40 (0.24), residues: 530 sheet: -0.83 (0.29), residues: 320 loop : -1.83 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 381 HIS 0.012 0.001 HIS E 357 PHE 0.018 0.001 PHE E 452 TYR 0.024 0.001 TYR A 411 ARG 0.008 0.000 ARG B 274 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 146 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.7835 (mmm) cc_final: 0.7569 (tpp) REVERT: B 316 MET cc_start: 0.7656 (tpp) cc_final: 0.7430 (mmt) REVERT: B 375 ASN cc_start: 0.6890 (p0) cc_final: 0.6397 (p0) REVERT: C 504 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7969 (ptm160) REVERT: D 308 ILE cc_start: 0.8155 (mp) cc_final: 0.7878 (mt) REVERT: E 278 HIS cc_start: 0.6778 (t-170) cc_final: 0.6100 (t-170) REVERT: E 405 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7908 (tt) REVERT: E 468 ASN cc_start: 0.8185 (t0) cc_final: 0.7951 (t0) REVERT: E 510 MET cc_start: 0.6827 (ppp) cc_final: 0.6463 (ptm) REVERT: F 308 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7799 (tp) REVERT: F 309 MET cc_start: 0.7438 (ttp) cc_final: 0.7203 (ttp) REVERT: F 351 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6331 (mt-10) outliers start: 35 outliers final: 29 residues processed: 172 average time/residue: 0.2033 time to fit residues: 53.9580 Evaluate side-chains 169 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 137 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU 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 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 504 ARG Chi-restraints excluded: chain C residue 510 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 533 MET Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 419 ASP Chi-restraints excluded: chain E residue 465 HIS Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 524 THR Chi-restraints excluded: chain F residue 542 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 92 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 GLN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 444 ASN ** C 536 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13068 Z= 0.300 Angle : 0.655 10.079 17631 Z= 0.324 Chirality : 0.044 0.143 2006 Planarity : 0.004 0.053 2171 Dihedral : 16.068 170.163 1942 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 3.18 % Allowed : 16.63 % Favored : 80.19 % 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: -1.57 (0.21), residues: 1558 helix: 0.04 (0.23), residues: 539 sheet: -0.97 (0.29), residues: 316 loop : -1.92 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 381 HIS 0.011 0.002 HIS B 425 PHE 0.012 0.002 PHE F 378 TYR 0.024 0.002 TYR A 411 ARG 0.008 0.001 ARG B 274 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 134 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.7989 (mmm) cc_final: 0.7726 (tpp) REVERT: B 375 ASN cc_start: 0.7210 (p0) cc_final: 0.6776 (p0) REVERT: D 341 MET cc_start: 0.7911 (mmp) cc_final: 0.7098 (mmt) REVERT: E 278 HIS cc_start: 0.6861 (t-170) cc_final: 0.6145 (t-170) REVERT: E 316 MET cc_start: 0.8472 (mmm) cc_final: 0.8029 (mmt) REVERT: E 405 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7838 (tt) REVERT: F 308 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7888 (tp) REVERT: F 309 MET cc_start: 0.7512 (ttp) cc_final: 0.7304 (ttp) REVERT: F 351 GLU cc_start: 0.6945 (mt-10) cc_final: 0.6343 (mt-10) outliers start: 43 outliers final: 35 residues processed: 166 average time/residue: 0.2167 time to fit residues: 56.1799 Evaluate side-chains 169 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 132 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 380 GLN 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 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 426 ILE Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 510 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 526 ASP 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 465 HIS Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 524 THR Chi-restraints excluded: chain F residue 542 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13068 Z= 0.169 Angle : 0.565 10.695 17631 Z= 0.279 Chirality : 0.042 0.145 2006 Planarity : 0.003 0.052 2171 Dihedral : 15.725 169.496 1942 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.66 % Allowed : 17.22 % Favored : 80.12 % 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: -1.27 (0.21), residues: 1558 helix: 0.33 (0.23), residues: 540 sheet: -0.92 (0.29), residues: 318 loop : -1.72 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 329 HIS 0.011 0.001 HIS E 357 PHE 0.018 0.001 PHE E 452 TYR 0.025 0.001 TYR A 411 ARG 0.009 0.000 ARG B 274 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 144 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.8005 (mmm) cc_final: 0.7685 (tpp) REVERT: B 375 ASN cc_start: 0.6991 (p0) cc_final: 0.6591 (p0) REVERT: D 308 ILE cc_start: 0.8197 (mp) cc_final: 0.7943 (mt) REVERT: D 341 MET cc_start: 0.8010 (mmp) cc_final: 0.7350 (mmt) REVERT: E 278 HIS cc_start: 0.6913 (t-170) cc_final: 0.6224 (t-170) REVERT: E 316 MET cc_start: 0.8302 (mmm) cc_final: 0.7924 (mmt) REVERT: E 405 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7704 (tt) REVERT: E 468 ASN cc_start: 0.8246 (t0) cc_final: 0.8044 (t0) REVERT: F 308 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7861 (tp) REVERT: F 309 MET cc_start: 0.7521 (ttp) cc_final: 0.7302 (ttp) REVERT: F 331 THR cc_start: 0.7099 (t) cc_final: 0.6818 (t) REVERT: F 351 GLU cc_start: 0.6778 (mt-10) cc_final: 0.6187 (mt-10) outliers start: 36 outliers final: 31 residues processed: 169 average time/residue: 0.1998 time to fit residues: 52.8285 Evaluate side-chains 171 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 138 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 380 GLN Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain 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 426 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 526 ASP 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 465 HIS Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 524 THR Chi-restraints excluded: chain F residue 542 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 7.9990 chunk 92 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 13 optimal weight: 0.0570 chunk 98 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 overall best weight: 1.2902 ------------------------------------------------------------------------------- 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 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13068 Z= 0.177 Angle : 0.565 10.629 17631 Z= 0.278 Chirality : 0.042 0.142 2006 Planarity : 0.003 0.035 2171 Dihedral : 15.513 168.584 1942 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.59 % Allowed : 17.29 % Favored : 80.12 % 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: 0.43 (0.23), residues: 538 sheet: -0.96 (0.29), residues: 322 loop : -1.70 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 329 HIS 0.011 0.001 HIS E 357 PHE 0.017 0.001 PHE A 452 TYR 0.027 0.001 TYR A 411 ARG 0.011 0.000 ARG B 274 ********************** 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 176 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 141 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.8030 (mmm) cc_final: 0.7681 (tpp) REVERT: B 344 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8230 (pm20) REVERT: B 375 ASN cc_start: 0.7006 (p0) cc_final: 0.6600 (p0) REVERT: D 308 ILE cc_start: 0.8194 (mp) cc_final: 0.7949 (mt) REVERT: D 341 MET cc_start: 0.8057 (mmp) cc_final: 0.7483 (mmt) REVERT: E 278 HIS cc_start: 0.6909 (t-170) cc_final: 0.6229 (t-170) REVERT: E 316 MET cc_start: 0.8289 (mmm) cc_final: 0.7825 (mmt) REVERT: E 405 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7698 (tt) REVERT: E 468 ASN cc_start: 0.8296 (t0) cc_final: 0.8080 (t0) REVERT: F 308 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7839 (tp) REVERT: F 309 MET cc_start: 0.7499 (ttp) cc_final: 0.7287 (ttp) REVERT: F 331 THR cc_start: 0.7206 (t) cc_final: 0.6976 (t) REVERT: F 351 GLU cc_start: 0.6730 (mt-10) cc_final: 0.6126 (mt-10) REVERT: F 439 ARG cc_start: 0.5906 (tmm160) cc_final: 0.5632 (tmm-80) outliers start: 35 outliers final: 29 residues processed: 168 average time/residue: 0.2012 time to fit residues: 52.6680 Evaluate side-chains 170 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 138 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 380 GLN 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 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 426 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 468 ASN 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 F residue 308 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 524 THR Chi-restraints excluded: chain F residue 542 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 127 optimal weight: 0.0270 chunk 53 optimal weight: 0.7980 chunk 130 optimal weight: 0.0270 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.9298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 GLN ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.122621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.107606 restraints weight = 33507.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.109421 restraints weight = 21667.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.110653 restraints weight = 15560.437| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13068 Z= 0.145 Angle : 0.540 10.742 17631 Z= 0.267 Chirality : 0.041 0.141 2006 Planarity : 0.003 0.039 2171 Dihedral : 15.083 167.223 1942 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.14 % Allowed : 17.96 % Favored : 79.90 % 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: -1.07 (0.22), residues: 1558 helix: 0.53 (0.24), residues: 544 sheet: -0.88 (0.29), residues: 327 loop : -1.61 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 329 HIS 0.011 0.001 HIS E 357 PHE 0.020 0.001 PHE E 452 TYR 0.027 0.001 TYR A 411 ARG 0.010 0.000 ARG B 274 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2271.61 seconds wall clock time: 42 minutes 22.24 seconds (2542.24 seconds total)