Starting phenix.real_space_refine on Thu Jul 18 20:30:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ern_19927/07_2024/9ern_19927.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ern_19927/07_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_19927/07_2024/9ern_19927.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ern_19927/07_2024/9ern_19927.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ern_19927/07_2024/9ern_19927.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ern_19927/07_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 4.19, per 1000 atoms: 1.22 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: 1.12 Conformation dependent library (CDL) restraints added in 657.4 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: 0.44 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: 0.72 Time building geometry restraints manager: 1.26 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 2.520 nonbonded pdb=" OG SER C 316 " pdb=" NZ LYS C 370 " model vdw 2.540 2.520 nonbonded pdb=" OG SER E 316 " pdb=" NZ LYS E 370 " model vdw 2.540 2.520 nonbonded pdb=" OG SER A 316 " pdb=" NZ LYS A 370 " model vdw 2.540 2.520 nonbonded pdb=" OG SER B 316 " pdb=" NZ LYS B 370 " model vdw 2.540 2.520 ... (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 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: 7.120 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.740 Find NCS groups from input model: 0.140 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:12.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.810 ------------------------------------------------------------------------------- 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 : 0.366 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: 1.4373 time to fit residues: 209.3060 Evaluate side-chains 113 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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: 4.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 327 ASN B 330 HIS C 330 HIS C 336 GLN C 351 GLN C 362 HIS D 330 HIS E 327 ASN E 336 GLN E 351 GLN E 362 HIS F 351 GLN F 362 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3498 Z= 0.129 Angle : 0.519 3.967 4680 Z= 0.275 Chirality : 0.049 0.137 528 Planarity : 0.004 0.034 594 Dihedral : 4.906 14.922 462 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.01 % Allowed : 15.66 % Favored : 83.33 % 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: -2.13 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 329 PHE 0.009 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 144 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 140 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8712 (ttmt) cc_final: 0.8480 (mtpt) REVERT: A 340 LYS cc_start: 0.8462 (mtpm) cc_final: 0.8157 (mttt) REVERT: A 345 ASP cc_start: 0.8953 (m-30) cc_final: 0.8571 (t0) REVERT: A 375 LYS cc_start: 0.8202 (tttt) cc_final: 0.7904 (tttm) REVERT: B 311 LYS cc_start: 0.8660 (mtmt) cc_final: 0.7099 (pptt) REVERT: B 340 LYS cc_start: 0.8662 (mtpm) cc_final: 0.8326 (mttt) REVERT: C 340 LYS cc_start: 0.8471 (mtpm) cc_final: 0.8083 (mttt) REVERT: C 345 ASP cc_start: 0.8967 (m-30) cc_final: 0.8478 (t0) REVERT: C 375 LYS cc_start: 0.8438 (tttt) cc_final: 0.8189 (tttm) REVERT: D 311 LYS cc_start: 0.8638 (mtmt) cc_final: 0.7237 (pptt) REVERT: D 340 LYS cc_start: 0.8667 (mtpm) cc_final: 0.8315 (mttt) REVERT: E 311 LYS cc_start: 0.7987 (mtmt) cc_final: 0.7514 (mmtt) REVERT: E 340 LYS cc_start: 0.8477 (mtpm) cc_final: 0.8086 (mttt) REVERT: E 349 ARG cc_start: 0.9036 (mtt180) cc_final: 0.7628 (mmp-170) REVERT: F 311 LYS cc_start: 0.7994 (mtmt) cc_final: 0.7548 (mmtt) REVERT: F 340 LYS cc_start: 0.8504 (mtpm) cc_final: 0.8068 (mttt) REVERT: F 349 ARG cc_start: 0.9005 (mtt180) cc_final: 0.7504 (mmp-170) REVERT: F 375 LYS cc_start: 0.8295 (tttt) cc_final: 0.8043 (tttt) outliers start: 4 outliers final: 1 residues processed: 142 average time/residue: 1.2816 time to fit residues: 186.2632 Evaluate side-chains 117 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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: 9.9990 chunk 25 optimal weight: 0.5980 chunk 10 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 41 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS D 362 HIS E 330 HIS E 351 GLN F 330 HIS F 351 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2483 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 : 0.561 6.272 4680 Z= 0.290 Chirality : 0.050 0.130 528 Planarity : 0.004 0.028 594 Dihedral : 4.759 14.844 462 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.78 % Allowed : 20.20 % Favored : 77.02 % 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: -1.88 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 329 PHE 0.009 0.002 PHE A 346 TYR 0.014 0.003 TYR B 310 ARG 0.001 0.000 ARG F 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 134 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8476 (mtpm) cc_final: 0.8166 (mttt) REVERT: A 375 LYS cc_start: 0.8172 (tttt) cc_final: 0.7868 (tttm) REVERT: B 311 LYS cc_start: 0.8606 (mtmt) cc_final: 0.7348 (pptt) REVERT: B 340 LYS cc_start: 0.8664 (mtpm) cc_final: 0.8307 (mttt) REVERT: B 375 LYS cc_start: 0.8679 (tttm) cc_final: 0.8260 (tppp) REVERT: C 340 LYS cc_start: 0.8464 (mtpm) cc_final: 0.8069 (mttt) REVERT: C 345 ASP cc_start: 0.8936 (m-30) cc_final: 0.8425 (t0) REVERT: C 373 THR cc_start: 0.8628 (m) cc_final: 0.8191 (p) REVERT: C 375 LYS cc_start: 0.8477 (tttt) cc_final: 0.8242 (tttm) REVERT: D 311 LYS cc_start: 0.8607 (mtmt) cc_final: 0.7328 (pptt) REVERT: D 340 LYS cc_start: 0.8615 (mtpm) cc_final: 0.8272 (mttt) REVERT: E 311 LYS cc_start: 0.8234 (mtmt) cc_final: 0.7829 (mmtt) REVERT: E 340 LYS cc_start: 0.8508 (mtpm) cc_final: 0.8114 (mttt) REVERT: E 349 ARG cc_start: 0.9035 (mtt180) cc_final: 0.7612 (mmp-170) REVERT: F 311 LYS cc_start: 0.8188 (mtmt) cc_final: 0.7754 (mptt) REVERT: F 331 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8806 (ttmt) REVERT: F 340 LYS cc_start: 0.8501 (mtpm) cc_final: 0.8089 (mttt) REVERT: F 373 THR cc_start: 0.8661 (m) cc_final: 0.8213 (p) outliers start: 11 outliers final: 2 residues processed: 129 average time/residue: 1.3508 time to fit residues: 178.2607 Evaluate side-chains 121 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 118 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 311 LYS 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: 4.9990 chunk 18 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 20 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN E 351 GLN E 368 ASN F 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3498 Z= 0.169 Angle : 0.507 4.022 4680 Z= 0.261 Chirality : 0.049 0.128 528 Planarity : 0.003 0.022 594 Dihedral : 4.547 14.710 462 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.26 % Allowed : 23.74 % 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: -1.75 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (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 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 122 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8433 (mtpm) cc_final: 0.8119 (mttt) REVERT: B 311 LYS cc_start: 0.8595 (mtmt) cc_final: 0.7384 (pptt) REVERT: B 340 LYS cc_start: 0.8668 (mtpm) cc_final: 0.8280 (mttt) REVERT: B 375 LYS cc_start: 0.8580 (tttm) cc_final: 0.8187 (tppp) REVERT: C 340 LYS cc_start: 0.8425 (mtpm) cc_final: 0.8067 (mtmt) REVERT: C 345 ASP cc_start: 0.8975 (m-30) cc_final: 0.8468 (t0) REVERT: C 373 THR cc_start: 0.8612 (m) cc_final: 0.8174 (p) REVERT: C 375 LYS cc_start: 0.8377 (tttt) cc_final: 0.8154 (tttm) REVERT: D 311 LYS cc_start: 0.8606 (mtmt) cc_final: 0.7384 (pptt) REVERT: D 340 LYS cc_start: 0.8565 (mtpm) cc_final: 0.8223 (mttt) REVERT: E 311 LYS cc_start: 0.8281 (mtmt) cc_final: 0.7871 (mmtt) REVERT: E 340 LYS cc_start: 0.8470 (mtpm) cc_final: 0.8078 (mttt) REVERT: E 349 ARG cc_start: 0.9024 (mtt180) cc_final: 0.7590 (mmp-170) REVERT: E 375 LYS cc_start: 0.8385 (tttt) cc_final: 0.7962 (tptm) REVERT: F 311 LYS cc_start: 0.8148 (mtmt) cc_final: 0.7727 (mmtt) REVERT: F 340 LYS cc_start: 0.8485 (mtpm) cc_final: 0.8073 (mttt) REVERT: F 373 THR cc_start: 0.8647 (m) cc_final: 0.8293 (p) REVERT: F 375 LYS cc_start: 0.8346 (tttm) cc_final: 0.8002 (tppp) outliers start: 5 outliers final: 2 residues processed: 118 average time/residue: 1.3522 time to fit residues: 163.2647 Evaluate side-chains 114 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 112 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 311 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 34 optimal weight: 0.0980 chunk 28 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN F 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3498 Z= 0.195 Angle : 0.528 5.701 4680 Z= 0.268 Chirality : 0.049 0.127 528 Planarity : 0.003 0.020 594 Dihedral : 4.567 14.605 462 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.52 % Allowed : 23.99 % 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: -1.69 (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 C 378 TYR 0.011 0.003 TYR B 310 ARG 0.001 0.000 ARG B 379 *********************** 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 121 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 115 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8426 (mtpm) cc_final: 0.8120 (mttt) REVERT: A 345 ASP cc_start: 0.8881 (m-30) cc_final: 0.8393 (t0) REVERT: B 311 LYS cc_start: 0.8602 (mtmt) cc_final: 0.7453 (pptt) REVERT: B 340 LYS cc_start: 0.8670 (mtpm) cc_final: 0.8301 (mtmt) REVERT: B 373 THR cc_start: 0.8950 (m) cc_final: 0.8636 (p) REVERT: B 375 LYS cc_start: 0.8676 (tttm) cc_final: 0.8271 (tppp) REVERT: C 340 LYS cc_start: 0.8423 (mtpm) cc_final: 0.8063 (mtmt) REVERT: C 345 ASP cc_start: 0.8973 (m-30) cc_final: 0.8464 (t0) REVERT: C 373 THR cc_start: 0.8613 (m) cc_final: 0.8183 (p) REVERT: C 375 LYS cc_start: 0.8359 (tttt) cc_final: 0.8146 (tttm) REVERT: D 311 LYS cc_start: 0.8624 (mtmt) cc_final: 0.7430 (pptt) REVERT: D 340 LYS cc_start: 0.8573 (mtpm) cc_final: 0.8227 (mttt) REVERT: E 311 LYS cc_start: 0.8223 (mtmt) cc_final: 0.7792 (mmtt) REVERT: E 340 LYS cc_start: 0.8458 (mtpm) cc_final: 0.8061 (mttt) REVERT: E 349 ARG cc_start: 0.9031 (mtt180) cc_final: 0.7572 (mmp-170) REVERT: E 375 LYS cc_start: 0.8352 (tttt) cc_final: 0.8076 (tttm) REVERT: F 311 LYS cc_start: 0.8179 (mtmt) cc_final: 0.7760 (mmtt) REVERT: F 331 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8821 (ttmt) REVERT: F 340 LYS cc_start: 0.8482 (mtpm) cc_final: 0.8073 (mttt) REVERT: F 373 THR cc_start: 0.8665 (m) cc_final: 0.8317 (p) REVERT: F 375 LYS cc_start: 0.8332 (tttm) cc_final: 0.7987 (tppp) outliers start: 6 outliers final: 1 residues processed: 119 average time/residue: 1.2952 time to fit residues: 157.8022 Evaluate side-chains 116 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 SER 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: 6.9990 chunk 40 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 0.5980 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN F 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3498 Z= 0.156 Angle : 0.512 9.481 4680 Z= 0.253 Chirality : 0.049 0.157 528 Planarity : 0.003 0.020 594 Dihedral : 4.393 14.031 462 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.77 % Allowed : 24.75 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 329 PHE 0.007 0.001 PHE C 378 TYR 0.009 0.002 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 128 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 121 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8419 (mtpm) cc_final: 0.8063 (mttp) REVERT: A 345 ASP cc_start: 0.8903 (m-30) cc_final: 0.8417 (t0) REVERT: B 311 LYS cc_start: 0.8610 (mtmt) cc_final: 0.7489 (pptt) REVERT: B 340 LYS cc_start: 0.8625 (mtpm) cc_final: 0.8282 (mtmt) REVERT: B 373 THR cc_start: 0.8952 (m) cc_final: 0.8635 (p) REVERT: B 375 LYS cc_start: 0.8577 (tttm) cc_final: 0.8197 (tppp) REVERT: C 340 LYS cc_start: 0.8414 (mtpm) cc_final: 0.8050 (mtmt) REVERT: C 345 ASP cc_start: 0.8962 (m-30) cc_final: 0.8471 (t0) REVERT: C 373 THR cc_start: 0.8608 (m) cc_final: 0.8176 (p) REVERT: C 375 LYS cc_start: 0.8345 (tttt) cc_final: 0.8135 (tttm) REVERT: D 311 LYS cc_start: 0.8614 (mtmt) cc_final: 0.7452 (pptt) REVERT: D 340 LYS cc_start: 0.8551 (mtpm) cc_final: 0.8196 (mttt) REVERT: E 311 LYS cc_start: 0.8251 (mtmt) cc_final: 0.7814 (mmtt) REVERT: E 340 LYS cc_start: 0.8452 (mtpm) cc_final: 0.8058 (mttt) REVERT: E 349 ARG cc_start: 0.9015 (mtt180) cc_final: 0.7599 (mmp-170) REVERT: F 311 LYS cc_start: 0.8163 (mtmt) cc_final: 0.7713 (mmtt) REVERT: F 340 LYS cc_start: 0.8467 (mtpm) cc_final: 0.8055 (mttt) REVERT: F 373 THR cc_start: 0.8681 (m) cc_final: 0.8344 (p) REVERT: F 375 LYS cc_start: 0.8321 (tttm) cc_final: 0.7977 (tppp) outliers start: 7 outliers final: 3 residues processed: 124 average time/residue: 1.3971 time to fit residues: 177.3855 Evaluate side-chains 119 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 116 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain B residue 320 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 40 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS F 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 3498 Z= 0.401 Angle : 0.661 10.018 4680 Z= 0.333 Chirality : 0.052 0.187 528 Planarity : 0.003 0.015 594 Dihedral : 4.930 15.805 462 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.02 % Allowed : 25.25 % Favored : 72.73 % 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: -1.73 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 329 PHE 0.010 0.002 PHE F 346 TYR 0.013 0.004 TYR A 310 ARG 0.001 0.000 ARG F 349 *********************** 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: 8 poor density : 115 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8471 (mtpm) cc_final: 0.8088 (mttp) REVERT: B 311 LYS cc_start: 0.8638 (mtmt) cc_final: 0.7542 (pptt) REVERT: B 340 LYS cc_start: 0.8715 (mtpm) cc_final: 0.8309 (mttt) REVERT: B 373 THR cc_start: 0.8958 (m) cc_final: 0.8712 (p) REVERT: B 375 LYS cc_start: 0.8777 (tttm) cc_final: 0.8360 (tppp) REVERT: C 340 LYS cc_start: 0.8488 (mtpm) cc_final: 0.8075 (mtmt) REVERT: C 373 THR cc_start: 0.8668 (m) cc_final: 0.8272 (p) REVERT: C 375 LYS cc_start: 0.8435 (tttt) cc_final: 0.8217 (tttm) REVERT: D 311 LYS cc_start: 0.8682 (mtmt) cc_final: 0.7486 (pptt) REVERT: D 340 LYS cc_start: 0.8613 (mtpm) cc_final: 0.8246 (mttt) REVERT: E 308 ILE cc_start: 0.8439 (mp) cc_final: 0.8235 (mt) REVERT: E 311 LYS cc_start: 0.8368 (mtmt) cc_final: 0.7924 (mmtt) REVERT: E 340 LYS cc_start: 0.8477 (mtpm) cc_final: 0.8091 (mttt) REVERT: E 349 ARG cc_start: 0.9046 (mtt180) cc_final: 0.7632 (mtp180) REVERT: F 311 LYS cc_start: 0.8308 (mtmt) cc_final: 0.7824 (mmtt) REVERT: F 331 LYS cc_start: 0.9018 (mtpp) cc_final: 0.8756 (ttmt) REVERT: F 340 LYS cc_start: 0.8503 (mtpm) cc_final: 0.8112 (mttt) REVERT: F 349 ARG cc_start: 0.9046 (mtt180) cc_final: 0.7319 (tpt90) REVERT: F 375 LYS cc_start: 0.8311 (tttm) cc_final: 0.7953 (tttp) outliers start: 8 outliers final: 4 residues processed: 118 average time/residue: 1.2701 time to fit residues: 153.7596 Evaluate side-chains 118 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 114 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain B residue 320 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 11 optimal weight: 0.0980 chunk 34 optimal weight: 2.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- 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: 0.8873 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3498 Z= 0.299 Angle : 0.606 10.064 4680 Z= 0.303 Chirality : 0.051 0.186 528 Planarity : 0.002 0.014 594 Dihedral : 4.835 15.766 462 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.52 % Allowed : 26.01 % Favored : 72.47 % 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: -1.71 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.007 0.002 PHE A 346 TYR 0.011 0.003 TYR A 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 121 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 115 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8443 (mtpm) cc_final: 0.8053 (mttp) REVERT: B 311 LYS cc_start: 0.8630 (mtmt) cc_final: 0.7528 (pptt) REVERT: B 340 LYS cc_start: 0.8701 (mtpm) cc_final: 0.8306 (mtmt) REVERT: B 373 THR cc_start: 0.8961 (m) cc_final: 0.8698 (p) REVERT: B 375 LYS cc_start: 0.8581 (tttm) cc_final: 0.8228 (tppp) REVERT: C 340 LYS cc_start: 0.8450 (mtpm) cc_final: 0.8041 (mtmt) REVERT: C 373 THR cc_start: 0.8652 (m) cc_final: 0.8252 (p) REVERT: C 375 LYS cc_start: 0.8412 (tttt) cc_final: 0.8203 (tttm) REVERT: D 311 LYS cc_start: 0.8643 (mtmt) cc_final: 0.7491 (pptt) REVERT: D 340 LYS cc_start: 0.8592 (mtpm) cc_final: 0.8228 (mttt) REVERT: E 311 LYS cc_start: 0.8362 (mtmt) cc_final: 0.7914 (mmtt) REVERT: E 340 LYS cc_start: 0.8458 (mtpm) cc_final: 0.8071 (mttt) REVERT: E 349 ARG cc_start: 0.9051 (mtt180) cc_final: 0.7652 (mmp-170) REVERT: F 311 LYS cc_start: 0.8255 (mtmt) cc_final: 0.7785 (mmtt) REVERT: F 340 LYS cc_start: 0.8486 (mtpm) cc_final: 0.8087 (mttt) REVERT: F 349 ARG cc_start: 0.9052 (mtt180) cc_final: 0.7330 (tpt90) REVERT: F 375 LYS cc_start: 0.8293 (tttm) cc_final: 0.7994 (tppp) outliers start: 6 outliers final: 5 residues processed: 117 average time/residue: 1.2580 time to fit residues: 150.8730 Evaluate side-chains 119 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 114 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain B residue 320 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 3498 Z= 0.569 Angle : 0.756 10.538 4680 Z= 0.386 Chirality : 0.055 0.207 528 Planarity : 0.003 0.023 594 Dihedral : 5.268 17.075 462 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.02 % Allowed : 25.76 % Favored : 72.22 % 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: -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 0.001 HIS B 329 PHE 0.012 0.003 PHE E 346 TYR 0.016 0.005 TYR C 310 ARG 0.002 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 120 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8563 (mtpm) cc_final: 0.8126 (mttp) REVERT: A 373 THR cc_start: 0.8656 (m) cc_final: 0.8169 (p) REVERT: B 311 LYS cc_start: 0.8675 (mtmt) cc_final: 0.7588 (pptt) REVERT: B 340 LYS cc_start: 0.8724 (mtpm) cc_final: 0.8305 (mttt) REVERT: B 373 THR cc_start: 0.8975 (m) cc_final: 0.8726 (p) REVERT: C 340 LYS cc_start: 0.8498 (mtpm) cc_final: 0.8071 (mtmt) REVERT: C 373 THR cc_start: 0.8680 (m) cc_final: 0.8247 (p) REVERT: C 375 LYS cc_start: 0.8490 (tttt) cc_final: 0.8266 (tttm) REVERT: D 311 LYS cc_start: 0.8706 (mtmt) cc_final: 0.7532 (pptt) REVERT: D 340 LYS cc_start: 0.8615 (mtpm) cc_final: 0.8258 (mttt) REVERT: E 311 LYS cc_start: 0.8430 (mtmt) cc_final: 0.7984 (mmtt) REVERT: E 340 LYS cc_start: 0.8463 (mtpm) cc_final: 0.8068 (mttt) REVERT: E 349 ARG cc_start: 0.9050 (mtt180) cc_final: 0.7644 (mtp180) REVERT: F 311 LYS cc_start: 0.8366 (mtmt) cc_final: 0.7839 (mmtt) REVERT: F 340 LYS cc_start: 0.8522 (mtpm) cc_final: 0.8128 (mttt) REVERT: F 349 ARG cc_start: 0.9046 (mtt180) cc_final: 0.7323 (tpt90) outliers start: 8 outliers final: 3 residues processed: 113 average time/residue: 1.2244 time to fit residues: 141.8971 Evaluate side-chains 115 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 112 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain B residue 320 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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: 0.8859 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3498 Z= 0.196 Angle : 0.556 9.481 4680 Z= 0.276 Chirality : 0.050 0.161 528 Planarity : 0.002 0.014 594 Dihedral : 4.773 15.318 462 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.01 % Allowed : 26.26 % Favored : 72.73 % 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: -1.62 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 329 PHE 0.006 0.001 PHE C 378 TYR 0.010 0.002 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 117 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 0.427 Fit side-chains REVERT: A 340 LYS cc_start: 0.8419 (mtpm) cc_final: 0.8117 (mttt) REVERT: A 345 ASP cc_start: 0.8916 (m-30) cc_final: 0.8478 (t70) REVERT: A 375 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7848 (tptm) REVERT: B 311 LYS cc_start: 0.8617 (mtmt) cc_final: 0.7548 (pptt) REVERT: B 340 LYS cc_start: 0.8677 (mtpm) cc_final: 0.8280 (mtmt) REVERT: B 373 THR cc_start: 0.8960 (m) cc_final: 0.8688 (p) REVERT: B 375 LYS cc_start: 0.8545 (tttm) cc_final: 0.8173 (tppp) REVERT: C 340 LYS cc_start: 0.8432 (mtpm) cc_final: 0.8027 (mtmt) REVERT: C 373 THR cc_start: 0.8613 (m) cc_final: 0.8219 (p) REVERT: C 375 LYS cc_start: 0.8397 (tttt) cc_final: 0.8180 (tttm) REVERT: D 311 LYS cc_start: 0.8633 (mtmt) cc_final: 0.7520 (pptt) REVERT: D 340 LYS cc_start: 0.8564 (mtpm) cc_final: 0.8203 (mttt) REVERT: E 311 LYS cc_start: 0.8304 (mtmt) cc_final: 0.7860 (mmtt) REVERT: E 340 LYS cc_start: 0.8445 (mtpm) cc_final: 0.8063 (mttt) REVERT: E 349 ARG cc_start: 0.9026 (mtt180) cc_final: 0.7588 (mmp-170) REVERT: E 375 LYS cc_start: 0.8321 (tptm) cc_final: 0.8073 (tptp) REVERT: F 311 LYS cc_start: 0.8224 (mtmt) cc_final: 0.7770 (mmtt) REVERT: F 340 LYS cc_start: 0.8470 (mtpm) cc_final: 0.8067 (mttt) outliers start: 4 outliers final: 1 residues processed: 116 average time/residue: 1.3245 time to fit residues: 157.4922 Evaluate side-chains 113 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain B residue 320 SER 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: 6.9990 chunk 24 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 22 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 25 optimal weight: 0.0010 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 overall best weight: 2.8990 ------------------------------------------------------------------------------- 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 = 0.4170 r_free = 0.4170 target = 0.154247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.112019 restraints weight = 3576.607| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 1.81 r_work: 0.3557 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.3176 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= 0.273 Angle : 0.597 9.828 4680 Z= 0.297 Chirality : 0.050 0.182 528 Planarity : 0.002 0.015 594 Dihedral : 4.840 15.479 462 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.76 % Allowed : 27.27 % Favored : 71.97 % 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: -1.61 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 329 PHE 0.007 0.002 PHE A 346 TYR 0.010 0.003 TYR C 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: 2867.48 seconds wall clock time: 50 minutes 39.07 seconds (3039.07 seconds total)