Starting phenix.real_space_refine on Fri Aug 2 15:59:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ern_19927/08_2024/9ern_19927.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ern_19927/08_2024/9ern_19927.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ern_19927/08_2024/9ern_19927.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ern_19927/08_2024/9ern_19927.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ern_19927/08_2024/9ern_19927.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ern_19927/08_2024/9ern_19927.cif" } resolution = 2.5 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= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2160 2.51 5 N 636 2.21 5 O 642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 314": "OD1" <-> "OD2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A ARG 379": "NH1" <-> "NH2" Residue "B ASP 314": "OD1" <-> "OD2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "B ARG 379": "NH1" <-> "NH2" Residue "C ASP 314": "OD1" <-> "OD2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 349": "NH1" <-> "NH2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "C ARG 379": "NH1" <-> "NH2" Residue "D ASP 314": "OD1" <-> "OD2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 349": "NH1" <-> "NH2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "D ARG 379": "NH1" <-> "NH2" Residue "E ASP 314": "OD1" <-> "OD2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 349": "NH1" <-> "NH2" Residue "E GLU 372": "OE1" <-> "OE2" Residue "E ARG 379": "NH1" <-> "NH2" Residue "F ASP 314": "OD1" <-> "OD2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 349": "NH1" <-> "NH2" Residue "F GLU 372": "OE1" <-> "OE2" Residue "F ARG 379": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3444 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 3.13, per 1000 atoms: 0.91 Number of scatterers: 3444 At special positions: 0 Unit cell: (111.24, 136.784, 39.552, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 642 8.00 N 636 7.00 C 2160 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: 1.17 Conformation dependent library (CDL) restraints added in 624.2 milliseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 60.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.532A pdb=" N GLN C 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N TYR D 310 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL C 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.721A pdb=" N VAL C 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 317 through 330 removed outlier: 8.811A pdb=" N VAL C 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 10.768A pdb=" N LYS D 321 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N SER C 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N GLY D 323 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N CYS C 322 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LEU D 325 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N SER C 324 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ASN D 327 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N GLY C 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N HIS D 329 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 9.240A pdb=" N ILE C 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 10.769A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N GLY C 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N CYS A 322 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU C 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N SER A 324 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ASN C 327 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N GLY A 326 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N HIS C 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL E 318 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR A 319 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N SER E 320 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LYS A 321 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N CYS E 322 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY A 323 " --> pdb=" O CYS E 322 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE E 328 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N HIS A 329 " --> pdb=" O ILE E 328 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N HIS E 330 " --> pdb=" O HIS A 329 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 337 through 346 removed outlier: 9.063A pdb=" N VAL C 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 10.291A pdb=" N LYS D 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N VAL C 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 10.293A pdb=" N GLU D 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N SER C 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 9.261A pdb=" N LEU D 344 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS C 343 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N PHE D 346 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ASP C 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 10.291A pdb=" N LYS C 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N VAL A 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 10.292A pdb=" N GLU C 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N SER A 341 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 9.261A pdb=" N LEU C 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LYS A 343 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N PHE C 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLU A 338 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL E 339 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LYS A 340 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N SER E 341 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLU A 342 " --> pdb=" O SER E 341 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LYS E 343 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 350 through 357 removed outlier: 6.567A pdb=" N GLN C 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ILE D 354 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LYS C 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N SER D 356 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLY C 355 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ILE C 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LYS A 353 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N SER C 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLY A 355 " --> pdb=" O SER C 356 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.376A pdb=" N THR A 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 369 through 378 removed outlier: 6.358A pdb=" N LYS A 370 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N THR E 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLU A 372 " --> pdb=" O THR E 373 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N LYS E 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N HIS A 374 " --> pdb=" O LYS E 375 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N THR E 377 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU A 376 " --> pdb=" O THR E 377 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 306 through 310 Processing sheet with id=AA9, first strand: chain 'B' and resid 313 through 314 Processing sheet with id=AB1, first strand: chain 'B' and resid 317 through 330 removed outlier: 6.854A pdb=" N VAL F 318 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR B 319 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N SER F 320 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LYS B 321 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N CYS F 322 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY B 323 " --> pdb=" O CYS F 322 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE F 328 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N HIS B 329 " --> pdb=" O ILE F 328 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N HIS F 330 " --> pdb=" O HIS B 329 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 337 through 346 removed outlier: 6.923A pdb=" N GLU B 338 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL F 339 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LYS B 340 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N SER F 341 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLU B 342 " --> pdb=" O SER F 341 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LYS F 343 " --> pdb=" O GLU B 342 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 350 through 357 Processing sheet with id=AB4, first strand: chain 'B' and resid 360 through 362 removed outlier: 6.376A pdb=" N THR B 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 369 through 378 removed outlier: 6.358A pdb=" N LYS B 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N THR F 373 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLU B 372 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N LYS F 375 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N HIS B 374 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N THR F 377 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU B 376 " --> pdb=" O THR F 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 60 hydrogen bonds defined for protein. 180 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: 0.73 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 796 1.34 - 1.46: 785 1.46 - 1.58: 1911 1.58 - 1.70: 0 1.70 - 1.81: 6 Bond restraints: 3498 Sorted by residual: bond pdb=" CA SER F 316 " pdb=" CB SER F 316 " ideal model delta sigma weight residual 1.529 1.488 0.042 1.64e-02 3.72e+03 6.44e+00 bond pdb=" CA SER D 316 " pdb=" CB SER D 316 " ideal model delta sigma weight residual 1.529 1.488 0.042 1.64e-02 3.72e+03 6.42e+00 bond pdb=" CA SER E 316 " pdb=" CB SER E 316 " ideal model delta sigma weight residual 1.529 1.488 0.042 1.64e-02 3.72e+03 6.42e+00 bond pdb=" CA SER A 316 " pdb=" CB SER A 316 " ideal model delta sigma weight residual 1.529 1.488 0.041 1.64e-02 3.72e+03 6.39e+00 bond pdb=" CA SER B 316 " pdb=" CB SER B 316 " ideal model delta sigma weight residual 1.529 1.488 0.041 1.64e-02 3.72e+03 6.32e+00 ... (remaining 3493 not shown) Histogram of bond angle deviations from ideal: 102.03 - 108.25: 302 108.25 - 114.47: 1894 114.47 - 120.70: 1355 120.70 - 126.92: 1105 126.92 - 133.14: 24 Bond angle restraints: 4680 Sorted by residual: angle pdb=" N GLY E 326 " pdb=" CA GLY E 326 " pdb=" C GLY E 326 " ideal model delta sigma weight residual 110.80 116.87 -6.07 1.41e+00 5.03e-01 1.85e+01 angle pdb=" N GLY C 326 " pdb=" CA GLY C 326 " pdb=" C GLY C 326 " ideal model delta sigma weight residual 110.80 116.85 -6.05 1.41e+00 5.03e-01 1.84e+01 angle pdb=" N GLY B 326 " pdb=" CA GLY B 326 " pdb=" C GLY B 326 " ideal model delta sigma weight residual 110.80 116.85 -6.05 1.41e+00 5.03e-01 1.84e+01 angle pdb=" N GLY A 326 " pdb=" CA GLY A 326 " pdb=" C GLY A 326 " ideal model delta sigma weight residual 110.80 116.85 -6.05 1.41e+00 5.03e-01 1.84e+01 angle pdb=" N GLY D 326 " pdb=" CA GLY D 326 " pdb=" C GLY D 326 " ideal model delta sigma weight residual 110.80 116.84 -6.04 1.41e+00 5.03e-01 1.84e+01 ... (remaining 4675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.49: 1824 11.49 - 22.98: 240 22.98 - 34.47: 42 34.47 - 45.95: 18 45.95 - 57.44: 12 Dihedral angle restraints: 2136 sinusoidal: 894 harmonic: 1242 Sorted by residual: dihedral pdb=" CA VAL C 318 " pdb=" C VAL C 318 " pdb=" N THR C 319 " pdb=" CA THR C 319 " ideal model delta harmonic sigma weight residual -180.00 -155.03 -24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA VAL B 318 " pdb=" C VAL B 318 " pdb=" N THR B 319 " pdb=" CA THR B 319 " ideal model delta harmonic sigma weight residual -180.00 -155.03 -24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA VAL D 318 " pdb=" C VAL D 318 " pdb=" N THR D 319 " pdb=" CA THR D 319 " ideal model delta harmonic sigma weight residual -180.00 -155.06 -24.94 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 2133 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.047: 186 0.047 - 0.092: 211 0.092 - 0.137: 101 0.137 - 0.182: 16 0.182 - 0.226: 14 Chirality restraints: 528 Sorted by residual: chirality pdb=" CB ILE F 328 " pdb=" CA ILE F 328 " pdb=" CG1 ILE F 328 " pdb=" CG2 ILE F 328 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE E 328 " pdb=" CA ILE E 328 " pdb=" CG1 ILE E 328 " pdb=" CG2 ILE E 328 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB ILE B 328 " pdb=" CA ILE B 328 " pdb=" CG1 ILE B 328 " pdb=" CG2 ILE B 328 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 525 not shown) Planarity restraints: 594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " -0.029 2.00e-02 2.50e+03 1.70e-02 5.75e+00 pdb=" CG TYR C 310 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " 0.029 2.00e-02 2.50e+03 1.68e-02 5.65e+00 pdb=" CG TYR F 310 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " -0.029 2.00e-02 2.50e+03 1.68e-02 5.65e+00 pdb=" CG TYR E 310 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " -0.006 2.00e-02 2.50e+03 ... (remaining 591 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 1736 3.01 - 3.48: 2843 3.48 - 3.96: 5484 3.96 - 4.43: 5487 4.43 - 4.90: 10434 Nonbonded interactions: 25984 Sorted by model distance: nonbonded pdb=" OG SER F 316 " pdb=" NZ LYS F 370 " model vdw 2.539 3.120 nonbonded pdb=" OG SER C 316 " pdb=" NZ LYS C 370 " model vdw 2.540 3.120 nonbonded pdb=" OG SER E 316 " pdb=" NZ LYS E 370 " model vdw 2.540 3.120 nonbonded pdb=" OG SER A 316 " pdb=" NZ LYS A 370 " model vdw 2.540 3.120 nonbonded pdb=" OG SER B 316 " pdb=" NZ LYS B 370 " model vdw 2.540 3.120 ... (remaining 25979 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 individual isotropic 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: 3.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.330 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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:10.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 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 : 0.009 0.054 3498 Z= 0.606 Angle : 1.379 6.432 4680 Z= 0.910 Chirality : 0.082 0.226 528 Planarity : 0.008 0.034 594 Dihedral : 11.585 57.442 1344 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.03 % Allowed : 3.03 % Favored : 93.94 % 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: -2.81 (0.30), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.004 HIS B 329 PHE 0.026 0.006 PHE E 346 TYR 0.036 0.011 TYR B 310 ARG 0.001 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 136 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8547 (mtpm) cc_final: 0.8171 (mttp) REVERT: A 345 ASP cc_start: 0.9016 (m-30) cc_final: 0.8507 (t0) REVERT: B 338 GLU cc_start: 0.8830 (tt0) cc_final: 0.8604 (tt0) REVERT: B 340 LYS cc_start: 0.8677 (mtpm) cc_final: 0.8296 (mttp) REVERT: C 340 LYS cc_start: 0.8596 (mtpm) cc_final: 0.8216 (mttt) REVERT: C 373 THR cc_start: 0.8702 (m) cc_final: 0.8133 (p) REVERT: D 317 LYS cc_start: 0.8616 (pttt) cc_final: 0.8393 (ptpt) REVERT: D 340 LYS cc_start: 0.8786 (mtpm) cc_final: 0.8429 (mttt) REVERT: D 373 THR cc_start: 0.8887 (m) cc_final: 0.8472 (p) REVERT: E 340 LYS cc_start: 0.8609 (mtpm) cc_final: 0.8233 (mttp) REVERT: E 348 ASP cc_start: 0.8979 (t0) cc_final: 0.8722 (t0) REVERT: E 349 ARG cc_start: 0.9067 (mtt180) cc_final: 0.7437 (tpt90) REVERT: F 340 LYS cc_start: 0.8596 (mtpm) cc_final: 0.8206 (mttt) REVERT: F 349 ARG cc_start: 0.9046 (mtt180) cc_final: 0.7331 (tpt90) outliers start: 12 outliers final: 0 residues processed: 142 average time/residue: 1.4325 time to fit residues: 207.9180 Evaluate side-chains 113 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS A 336 GLN A 362 HIS B 327 ASN B 330 HIS C 330 HIS C 336 GLN C 351 GLN C 362 HIS D 330 HIS D 362 HIS E 327 ASN E 336 GLN E 351 GLN E 362 HIS F 330 HIS F 351 GLN F 362 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3498 Z= 0.151 Angle : 0.538 3.817 4680 Z= 0.285 Chirality : 0.049 0.136 528 Planarity : 0.004 0.034 594 Dihedral : 4.993 15.377 462 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.77 % Allowed : 14.65 % 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: -2.14 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 329 PHE 0.008 0.001 PHE A 346 TYR 0.015 0.003 TYR B 310 ARG 0.001 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 140 time to evaluate : 0.426 Fit side-chains REVERT: A 340 LYS cc_start: 0.8476 (mtpm) cc_final: 0.8169 (mttt) REVERT: A 345 ASP cc_start: 0.8958 (m-30) cc_final: 0.8571 (t0) REVERT: A 375 LYS cc_start: 0.8205 (tttt) cc_final: 0.7973 (tttm) REVERT: B 311 LYS cc_start: 0.8602 (mtmt) cc_final: 0.7056 (pptt) REVERT: B 340 LYS cc_start: 0.8656 (mtpm) cc_final: 0.8319 (mttt) REVERT: C 340 LYS cc_start: 0.8495 (mtpm) cc_final: 0.8106 (mttt) REVERT: C 345 ASP cc_start: 0.8967 (m-30) cc_final: 0.8453 (t0) REVERT: C 375 LYS cc_start: 0.8435 (tttt) cc_final: 0.8186 (tttm) REVERT: D 311 LYS cc_start: 0.8574 (mtmt) cc_final: 0.7048 (pptt) REVERT: D 340 LYS cc_start: 0.8669 (mtpm) cc_final: 0.8309 (mttt) REVERT: D 373 THR cc_start: 0.8808 (m) cc_final: 0.8592 (p) REVERT: E 311 LYS cc_start: 0.8091 (mtmt) cc_final: 0.7593 (mmtt) REVERT: E 340 LYS cc_start: 0.8529 (mtpm) cc_final: 0.8143 (mttt) REVERT: E 349 ARG cc_start: 0.9044 (mtt180) cc_final: 0.7636 (mmp-170) REVERT: E 375 LYS cc_start: 0.8353 (tttt) cc_final: 0.8061 (tttm) REVERT: F 311 LYS cc_start: 0.8112 (mtmt) cc_final: 0.7640 (mmtt) REVERT: F 340 LYS cc_start: 0.8519 (mtpm) cc_final: 0.8113 (mttt) REVERT: F 349 ARG cc_start: 0.9026 (mtt180) cc_final: 0.7511 (mmp-170) REVERT: F 373 THR cc_start: 0.8625 (m) cc_final: 0.8158 (p) REVERT: F 375 LYS cc_start: 0.8338 (tttt) cc_final: 0.8090 (tttt) outliers start: 7 outliers final: 1 residues processed: 143 average time/residue: 1.2556 time to fit residues: 183.9109 Evaluate side-chains 118 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS E 330 HIS E 351 GLN F 351 GLN F 368 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3498 Z= 0.362 Angle : 0.637 4.674 4680 Z= 0.332 Chirality : 0.051 0.135 528 Planarity : 0.004 0.026 594 Dihedral : 5.069 16.100 462 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 3.03 % Allowed : 18.69 % Favored : 78.28 % 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: -1.96 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 329 PHE 0.010 0.002 PHE A 346 TYR 0.016 0.004 TYR B 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8475 (mtpm) cc_final: 0.8083 (mttp) REVERT: A 375 LYS cc_start: 0.8218 (tttt) cc_final: 0.7960 (tttm) REVERT: B 311 LYS cc_start: 0.8620 (mtmt) cc_final: 0.7378 (pptt) REVERT: B 340 LYS cc_start: 0.8708 (mtpm) cc_final: 0.8308 (mttt) REVERT: C 340 LYS cc_start: 0.8488 (mtpm) cc_final: 0.8081 (mttt) REVERT: C 373 THR cc_start: 0.8610 (m) cc_final: 0.8188 (p) REVERT: C 375 LYS cc_start: 0.8492 (tttt) cc_final: 0.8255 (tttm) REVERT: D 311 LYS cc_start: 0.8619 (mtmt) cc_final: 0.7349 (pptt) REVERT: D 340 LYS cc_start: 0.8639 (mtpm) cc_final: 0.8282 (mttt) REVERT: D 373 THR cc_start: 0.8869 (m) cc_final: 0.8564 (p) REVERT: E 311 LYS cc_start: 0.8334 (mtmt) cc_final: 0.7872 (mmtt) REVERT: E 340 LYS cc_start: 0.8531 (mtpm) cc_final: 0.8125 (mttt) REVERT: E 349 ARG cc_start: 0.9052 (mtt180) cc_final: 0.7652 (mtp180) REVERT: E 375 LYS cc_start: 0.8356 (tttt) cc_final: 0.8065 (tttm) REVERT: F 311 LYS cc_start: 0.8305 (mtmt) cc_final: 0.7795 (mmtt) REVERT: F 331 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8846 (ttmt) REVERT: F 340 LYS cc_start: 0.8534 (mtpm) cc_final: 0.8137 (mttt) REVERT: F 373 THR cc_start: 0.8682 (m) cc_final: 0.8283 (p) REVERT: F 375 LYS cc_start: 0.8348 (tttt) cc_final: 0.8126 (tttt) outliers start: 12 outliers final: 5 residues processed: 131 average time/residue: 1.3250 time to fit residues: 177.6996 Evaluate side-chains 126 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 120 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 331 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 0.0570 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 368 ASN F 351 GLN F 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3498 Z= 0.169 Angle : 0.517 4.277 4680 Z= 0.266 Chirality : 0.049 0.131 528 Planarity : 0.003 0.024 594 Dihedral : 4.691 14.520 462 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.01 % Allowed : 23.74 % Favored : 75.25 % 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: -1.85 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.006 0.001 PHE A 346 TYR 0.011 0.003 TYR B 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 124 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8425 (mtpm) cc_final: 0.8110 (mttt) REVERT: A 375 LYS cc_start: 0.8100 (tttt) cc_final: 0.7823 (tttm) REVERT: B 311 LYS cc_start: 0.8582 (mtmt) cc_final: 0.7394 (pptt) REVERT: B 340 LYS cc_start: 0.8658 (mtpm) cc_final: 0.8266 (mtmt) REVERT: B 375 LYS cc_start: 0.8549 (tttm) cc_final: 0.8178 (tppp) REVERT: C 340 LYS cc_start: 0.8441 (mtpm) cc_final: 0.8042 (mttt) REVERT: C 373 THR cc_start: 0.8604 (m) cc_final: 0.8161 (p) REVERT: C 375 LYS cc_start: 0.8430 (tttt) cc_final: 0.8203 (tttm) REVERT: D 311 LYS cc_start: 0.8599 (mtmt) cc_final: 0.7371 (pptt) REVERT: D 340 LYS cc_start: 0.8565 (mtpm) cc_final: 0.8218 (mttt) REVERT: D 373 THR cc_start: 0.8800 (m) cc_final: 0.8528 (p) REVERT: E 311 LYS cc_start: 0.8313 (mtmt) cc_final: 0.7868 (mmtt) REVERT: E 340 LYS cc_start: 0.8505 (mtpm) cc_final: 0.8110 (mttp) REVERT: E 349 ARG cc_start: 0.9027 (mtt180) cc_final: 0.7574 (mmp-170) REVERT: E 375 LYS cc_start: 0.8368 (tttt) cc_final: 0.8101 (tttm) REVERT: F 311 LYS cc_start: 0.8202 (mtmt) cc_final: 0.7754 (mmtt) REVERT: F 340 LYS cc_start: 0.8496 (mtpm) cc_final: 0.8096 (mttt) REVERT: F 373 THR cc_start: 0.8715 (m) cc_final: 0.8397 (p) outliers start: 4 outliers final: 1 residues processed: 125 average time/residue: 1.3345 time to fit residues: 170.7270 Evaluate side-chains 119 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 118 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.2980 chunk 16 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN F 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3498 Z= 0.289 Angle : 0.589 4.888 4680 Z= 0.300 Chirality : 0.050 0.129 528 Planarity : 0.003 0.021 594 Dihedral : 4.892 15.892 462 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.27 % Allowed : 23.48 % Favored : 74.24 % 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: -1.81 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 329 PHE 0.008 0.002 PHE A 346 TYR 0.012 0.003 TYR B 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8444 (mtpm) cc_final: 0.8067 (mttt) REVERT: A 375 LYS cc_start: 0.8118 (tttt) cc_final: 0.7813 (tttm) REVERT: B 311 LYS cc_start: 0.8620 (mtmt) cc_final: 0.7451 (pptt) REVERT: B 340 LYS cc_start: 0.8705 (mtpm) cc_final: 0.8303 (mtmt) REVERT: B 373 THR cc_start: 0.8939 (m) cc_final: 0.8632 (p) REVERT: B 375 LYS cc_start: 0.8677 (tttm) cc_final: 0.8310 (tppp) REVERT: C 340 LYS cc_start: 0.8480 (mtpm) cc_final: 0.8065 (mtmt) REVERT: C 373 THR cc_start: 0.8644 (m) cc_final: 0.8215 (p) REVERT: C 375 LYS cc_start: 0.8409 (tttt) cc_final: 0.8197 (tttm) REVERT: D 311 LYS cc_start: 0.8639 (mtmt) cc_final: 0.7440 (pptt) REVERT: D 340 LYS cc_start: 0.8599 (mtpm) cc_final: 0.8234 (mttt) REVERT: D 373 THR cc_start: 0.8812 (m) cc_final: 0.8532 (p) REVERT: D 375 LYS cc_start: 0.8810 (tttt) cc_final: 0.8586 (tttm) REVERT: E 311 LYS cc_start: 0.8338 (mtmt) cc_final: 0.7879 (mmtt) REVERT: E 331 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8818 (mtmm) REVERT: E 340 LYS cc_start: 0.8500 (mtpm) cc_final: 0.8106 (mttp) REVERT: E 349 ARG cc_start: 0.9053 (mtt180) cc_final: 0.7662 (mtp180) REVERT: E 375 LYS cc_start: 0.8352 (tttt) cc_final: 0.8081 (tttm) REVERT: F 311 LYS cc_start: 0.8293 (mtmt) cc_final: 0.7814 (mmtt) REVERT: F 331 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8845 (ttmt) REVERT: F 340 LYS cc_start: 0.8501 (mtpm) cc_final: 0.8110 (mttt) REVERT: F 349 ARG cc_start: 0.9053 (mtt180) cc_final: 0.7323 (tpt90) REVERT: F 373 THR cc_start: 0.8701 (m) cc_final: 0.8381 (p) outliers start: 9 outliers final: 1 residues processed: 124 average time/residue: 1.3321 time to fit residues: 169.0912 Evaluate side-chains 120 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 117 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain F residue 331 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 0.0670 chunk 21 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 overall best weight: 2.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN F 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3498 Z= 0.249 Angle : 0.583 10.108 4680 Z= 0.290 Chirality : 0.050 0.173 528 Planarity : 0.003 0.019 594 Dihedral : 4.804 15.748 462 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.27 % Allowed : 22.73 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.76 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 329 PHE 0.008 0.002 PHE F 378 TYR 0.011 0.003 TYR B 310 ARG 0.001 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8428 (mtpm) cc_final: 0.8053 (mttt) REVERT: B 311 LYS cc_start: 0.8594 (mtmt) cc_final: 0.7459 (pptt) REVERT: B 340 LYS cc_start: 0.8686 (mtpm) cc_final: 0.8284 (mtmt) REVERT: B 375 LYS cc_start: 0.8584 (tttm) cc_final: 0.8255 (tppp) REVERT: C 340 LYS cc_start: 0.8458 (mtpm) cc_final: 0.8046 (mtmt) REVERT: C 373 THR cc_start: 0.8619 (m) cc_final: 0.8190 (p) REVERT: C 375 LYS cc_start: 0.8355 (tttt) cc_final: 0.8148 (tttm) REVERT: D 311 LYS cc_start: 0.8618 (mtmt) cc_final: 0.7442 (pptt) REVERT: D 314 ASP cc_start: 0.8543 (t0) cc_final: 0.8293 (t0) REVERT: D 340 LYS cc_start: 0.8580 (mtpm) cc_final: 0.8214 (mttt) REVERT: D 373 THR cc_start: 0.8817 (m) cc_final: 0.8548 (p) REVERT: D 375 LYS cc_start: 0.8804 (tttt) cc_final: 0.8582 (tttm) REVERT: E 311 LYS cc_start: 0.8334 (mtmt) cc_final: 0.7877 (mmtt) REVERT: E 331 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8809 (mtmm) REVERT: E 340 LYS cc_start: 0.8480 (mtpm) cc_final: 0.8090 (mttt) REVERT: E 349 ARG cc_start: 0.9037 (mtt180) cc_final: 0.7604 (mmp-170) REVERT: E 375 LYS cc_start: 0.8354 (tttt) cc_final: 0.8088 (tttm) REVERT: F 311 LYS cc_start: 0.8295 (mtmt) cc_final: 0.7796 (mmtt) REVERT: F 340 LYS cc_start: 0.8496 (mtpm) cc_final: 0.8110 (mttt) REVERT: F 349 ARG cc_start: 0.9055 (mtt180) cc_final: 0.7327 (tpt90) REVERT: F 373 THR cc_start: 0.8717 (m) cc_final: 0.8386 (p) REVERT: F 375 LYS cc_start: 0.8338 (tttm) cc_final: 0.8033 (tppp) outliers start: 9 outliers final: 1 residues processed: 123 average time/residue: 1.3949 time to fit residues: 175.5863 Evaluate side-chains 114 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 112 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain E residue 331 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 3498 Z= 0.400 Angle : 0.673 10.475 4680 Z= 0.338 Chirality : 0.052 0.187 528 Planarity : 0.003 0.016 594 Dihedral : 5.047 15.991 462 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.01 % Allowed : 25.00 % Favored : 73.99 % 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: -1.80 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 329 PHE 0.009 0.002 PHE E 346 TYR 0.013 0.004 TYR C 310 ARG 0.002 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 119 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8505 (mtpm) cc_final: 0.8073 (mttp) REVERT: B 311 LYS cc_start: 0.8633 (mtmt) cc_final: 0.7548 (pptt) REVERT: B 340 LYS cc_start: 0.8724 (mtpm) cc_final: 0.8294 (mttt) REVERT: B 373 THR cc_start: 0.8950 (m) cc_final: 0.8637 (p) REVERT: B 375 LYS cc_start: 0.8686 (tttm) cc_final: 0.8314 (tppp) REVERT: C 340 LYS cc_start: 0.8490 (mtpm) cc_final: 0.8064 (mtmt) REVERT: C 373 THR cc_start: 0.8648 (m) cc_final: 0.8235 (p) REVERT: C 375 LYS cc_start: 0.8435 (tttt) cc_final: 0.8218 (tttm) REVERT: D 311 LYS cc_start: 0.8680 (mtmt) cc_final: 0.7492 (pptt) REVERT: D 340 LYS cc_start: 0.8604 (mtpm) cc_final: 0.8234 (mttt) REVERT: D 373 THR cc_start: 0.8845 (m) cc_final: 0.8564 (p) REVERT: E 311 LYS cc_start: 0.8418 (mtmt) cc_final: 0.7968 (mmtt) REVERT: E 331 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8840 (mtmm) REVERT: E 340 LYS cc_start: 0.8498 (mtpm) cc_final: 0.8108 (mttt) REVERT: E 349 ARG cc_start: 0.9057 (mtt180) cc_final: 0.7641 (mtp180) REVERT: E 375 LYS cc_start: 0.8350 (tttt) cc_final: 0.8081 (tttm) REVERT: F 311 LYS cc_start: 0.8343 (mtmt) cc_final: 0.7823 (mmtt) REVERT: F 340 LYS cc_start: 0.8500 (mtpm) cc_final: 0.8113 (mttt) REVERT: F 349 ARG cc_start: 0.9056 (mtt180) cc_final: 0.7321 (tpt90) REVERT: F 373 THR cc_start: 0.8707 (m) cc_final: 0.8369 (p) outliers start: 4 outliers final: 1 residues processed: 122 average time/residue: 1.3152 time to fit residues: 164.3381 Evaluate side-chains 120 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 118 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain E residue 331 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 11 optimal weight: 0.0060 chunk 34 optimal weight: 0.9990 overall best weight: 1.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3498 Z= 0.185 Angle : 0.552 9.759 4680 Z= 0.273 Chirality : 0.050 0.168 528 Planarity : 0.002 0.015 594 Dihedral : 4.688 14.859 462 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.01 % Allowed : 25.00 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 329 PHE 0.007 0.001 PHE F 378 TYR 0.010 0.002 TYR B 310 ARG 0.001 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8403 (mtpm) cc_final: 0.8092 (mttt) REVERT: B 311 LYS cc_start: 0.8598 (mtmt) cc_final: 0.7526 (pptt) REVERT: B 340 LYS cc_start: 0.8650 (mtpm) cc_final: 0.8255 (mtmt) REVERT: B 375 LYS cc_start: 0.8559 (tttm) cc_final: 0.8214 (tppp) REVERT: C 340 LYS cc_start: 0.8432 (mtpm) cc_final: 0.8009 (mttt) REVERT: C 373 THR cc_start: 0.8613 (m) cc_final: 0.8177 (p) REVERT: C 375 LYS cc_start: 0.8347 (tttt) cc_final: 0.8143 (tttm) REVERT: D 311 LYS cc_start: 0.8623 (mtmt) cc_final: 0.7487 (pptt) REVERT: D 314 ASP cc_start: 0.8533 (t0) cc_final: 0.8249 (t0) REVERT: D 340 LYS cc_start: 0.8569 (mtpm) cc_final: 0.8194 (mttt) REVERT: D 373 THR cc_start: 0.8794 (m) cc_final: 0.8563 (p) REVERT: D 375 LYS cc_start: 0.8795 (tttt) cc_final: 0.8576 (tttm) REVERT: E 311 LYS cc_start: 0.8373 (mtmt) cc_final: 0.7904 (mmtt) REVERT: E 331 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8831 (mtmm) REVERT: E 340 LYS cc_start: 0.8484 (mtpm) cc_final: 0.8088 (mttp) REVERT: E 349 ARG cc_start: 0.9037 (mtt180) cc_final: 0.7590 (mmp-170) REVERT: E 375 LYS cc_start: 0.8325 (tttt) cc_final: 0.7950 (tptm) REVERT: F 311 LYS cc_start: 0.8296 (mtmt) cc_final: 0.7809 (mmtt) REVERT: F 340 LYS cc_start: 0.8474 (mtpm) cc_final: 0.8083 (mttt) REVERT: F 373 THR cc_start: 0.8724 (m) cc_final: 0.8399 (p) outliers start: 4 outliers final: 1 residues processed: 114 average time/residue: 1.2873 time to fit residues: 150.4071 Evaluate side-chains 113 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain E residue 331 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 0.0770 chunk 41 optimal weight: 7.9990 chunk 38 optimal weight: 0.0470 chunk 33 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 overall best weight: 2.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3498 Z= 0.220 Angle : 0.567 9.767 4680 Z= 0.280 Chirality : 0.050 0.170 528 Planarity : 0.002 0.013 594 Dihedral : 4.685 14.813 462 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.76 % Allowed : 24.49 % Favored : 74.75 % 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 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 329 PHE 0.008 0.002 PHE F 378 TYR 0.010 0.003 TYR B 310 ARG 0.001 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 110 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8410 (mtpm) cc_final: 0.8103 (mttt) REVERT: B 311 LYS cc_start: 0.8623 (mtmt) cc_final: 0.7563 (pptt) REVERT: B 340 LYS cc_start: 0.8667 (mtpm) cc_final: 0.8268 (mtmt) REVERT: B 373 THR cc_start: 0.8943 (m) cc_final: 0.8629 (p) REVERT: B 375 LYS cc_start: 0.8570 (tttm) cc_final: 0.8234 (tppp) REVERT: C 340 LYS cc_start: 0.8434 (mtpm) cc_final: 0.8008 (mttt) REVERT: C 373 THR cc_start: 0.8621 (m) cc_final: 0.8188 (p) REVERT: C 375 LYS cc_start: 0.8347 (tttt) cc_final: 0.8141 (tttm) REVERT: D 311 LYS cc_start: 0.8636 (mtmt) cc_final: 0.7477 (pptt) REVERT: D 340 LYS cc_start: 0.8566 (mtpm) cc_final: 0.8196 (mttt) REVERT: D 373 THR cc_start: 0.8811 (m) cc_final: 0.8553 (p) REVERT: D 375 LYS cc_start: 0.8799 (tttt) cc_final: 0.8579 (tttm) REVERT: E 311 LYS cc_start: 0.8434 (mtmt) cc_final: 0.7975 (mmtt) REVERT: E 331 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8817 (mtmm) REVERT: E 340 LYS cc_start: 0.8469 (mtpm) cc_final: 0.8077 (mttp) REVERT: E 349 ARG cc_start: 0.9041 (mtt180) cc_final: 0.7613 (mmp-170) REVERT: E 375 LYS cc_start: 0.8327 (tttt) cc_final: 0.8069 (tttm) REVERT: F 311 LYS cc_start: 0.8310 (mtmt) cc_final: 0.7817 (mmtt) REVERT: F 340 LYS cc_start: 0.8477 (mtpm) cc_final: 0.8090 (mttt) REVERT: F 373 THR cc_start: 0.8726 (m) cc_final: 0.8411 (p) REVERT: F 375 LYS cc_start: 0.8286 (tttm) cc_final: 0.7992 (tppp) outliers start: 3 outliers final: 1 residues processed: 112 average time/residue: 1.3372 time to fit residues: 153.3653 Evaluate side-chains 112 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain E residue 331 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3498 Z= 0.264 Angle : 0.593 9.946 4680 Z= 0.294 Chirality : 0.050 0.176 528 Planarity : 0.002 0.014 594 Dihedral : 4.789 15.138 462 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.76 % Allowed : 24.49 % Favored : 74.75 % 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: -1.68 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 329 PHE 0.008 0.002 PHE F 378 TYR 0.011 0.003 TYR B 310 ARG 0.001 0.000 ARG B 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 113 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8428 (mtpm) cc_final: 0.8051 (mttt) REVERT: B 311 LYS cc_start: 0.8643 (mtmt) cc_final: 0.7579 (pptt) REVERT: B 340 LYS cc_start: 0.8697 (mtpm) cc_final: 0.8293 (mtmt) REVERT: B 373 THR cc_start: 0.8942 (m) cc_final: 0.8627 (p) REVERT: B 375 LYS cc_start: 0.8577 (tttm) cc_final: 0.8240 (tppp) REVERT: C 340 LYS cc_start: 0.8451 (mtpm) cc_final: 0.8037 (mtmt) REVERT: C 373 THR cc_start: 0.8632 (m) cc_final: 0.8204 (p) REVERT: C 375 LYS cc_start: 0.8353 (tttt) cc_final: 0.8149 (tttm) REVERT: D 311 LYS cc_start: 0.8667 (mtmt) cc_final: 0.7512 (pptt) REVERT: D 314 ASP cc_start: 0.8492 (t0) cc_final: 0.8247 (t0) REVERT: D 340 LYS cc_start: 0.8579 (mtpm) cc_final: 0.8210 (mttt) REVERT: D 373 THR cc_start: 0.8791 (m) cc_final: 0.8530 (p) REVERT: D 375 LYS cc_start: 0.8804 (tttt) cc_final: 0.8583 (tttm) REVERT: E 311 LYS cc_start: 0.8439 (mtmt) cc_final: 0.7979 (mmtt) REVERT: E 331 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8818 (mtmm) REVERT: E 340 LYS cc_start: 0.8474 (mtpm) cc_final: 0.8085 (mttp) REVERT: E 349 ARG cc_start: 0.9044 (mtt180) cc_final: 0.7609 (mmp-170) REVERT: E 375 LYS cc_start: 0.8321 (tttt) cc_final: 0.8069 (tttm) REVERT: F 311 LYS cc_start: 0.8313 (mtmt) cc_final: 0.7815 (mmtt) REVERT: F 340 LYS cc_start: 0.8485 (mtpm) cc_final: 0.8100 (mttt) REVERT: F 349 ARG cc_start: 0.9061 (mtt180) cc_final: 0.7323 (tpt90) REVERT: F 373 THR cc_start: 0.8725 (m) cc_final: 0.8401 (p) REVERT: F 375 LYS cc_start: 0.8277 (tttm) cc_final: 0.7994 (tppp) outliers start: 3 outliers final: 1 residues processed: 115 average time/residue: 1.3076 time to fit residues: 154.1299 Evaluate side-chains 113 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain E residue 331 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.153470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.111314 restraints weight = 3596.774| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.82 r_work: 0.3547 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3498 Z= 0.364 Angle : 0.649 10.187 4680 Z= 0.325 Chirality : 0.052 0.187 528 Planarity : 0.003 0.017 594 Dihedral : 4.979 16.354 462 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.01 % Allowed : 24.49 % Favored : 74.49 % 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: -1.72 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 329 PHE 0.009 0.002 PHE E 346 TYR 0.012 0.004 TYR B 310 ARG 0.002 0.000 ARG B 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2912.51 seconds wall clock time: 51 minutes 19.78 seconds (3079.78 seconds total)