Starting phenix.real_space_refine on Mon Jan 13 18:05:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ern_19927/01_2025/9ern_19927.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ern_19927/01_2025/9ern_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/cci-nas-00/data/ceres_data/9ern_19927/01_2025/9ern_19927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ern_19927/01_2025/9ern_19927.map" model { file = "/net/cci-nas-00/data/ceres_data/9ern_19927/01_2025/9ern_19927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ern_19927/01_2025/9ern_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. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 3444 Number of models: 1 Model: "" Number of chains: 1 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} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 2.70, per 1000 atoms: 0.78 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 387.6 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: 0.45 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: 0.89 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: 0.00 - 1.29: 3298 1.29 - 2.57: 1073 2.57 - 3.86: 247 3.86 - 5.15: 50 5.15 - 6.43: 12 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 2.780 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.510 Find NCS groups from input model: 0.070 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:11.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.260 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.445 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: 1.4691 time to fit residues: 213.2542 Evaluate side-chains 113 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.161241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.119570 restraints weight = 3532.500| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 1.79 r_work: 0.3639 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 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 to be fit. rotamer outliers: 7 poor density : 140 time to evaluate : 0.410 Fit side-chains REVERT: A 340 LYS cc_start: 0.8410 (mtpm) cc_final: 0.8102 (mttt) REVERT: A 375 LYS cc_start: 0.8029 (tttt) cc_final: 0.7669 (tttm) REVERT: B 311 LYS cc_start: 0.8425 (mtmt) cc_final: 0.6777 (pptt) REVERT: B 338 GLU cc_start: 0.8561 (tt0) cc_final: 0.8324 (tt0) REVERT: B 340 LYS cc_start: 0.8636 (mtpm) cc_final: 0.8255 (mttt) REVERT: B 347 LYS cc_start: 0.8883 (mptt) cc_final: 0.8652 (mptp) REVERT: C 340 LYS cc_start: 0.8436 (mtpm) cc_final: 0.8031 (mttt) REVERT: C 345 ASP cc_start: 0.8393 (m-30) cc_final: 0.8009 (t0) REVERT: C 375 LYS cc_start: 0.8215 (tttt) cc_final: 0.7853 (tttm) REVERT: D 311 LYS cc_start: 0.8365 (mtmt) cc_final: 0.6756 (pptt) REVERT: D 317 LYS cc_start: 0.8537 (pttt) cc_final: 0.8275 (ptpt) REVERT: D 321 LYS cc_start: 0.8581 (ttpt) cc_final: 0.8331 (mtmm) REVERT: D 340 LYS cc_start: 0.8610 (mtpm) cc_final: 0.8261 (mttt) REVERT: D 373 THR cc_start: 0.8639 (m) cc_final: 0.8437 (p) REVERT: D 375 LYS cc_start: 0.8681 (tttt) cc_final: 0.8476 (tttt) REVERT: E 311 LYS cc_start: 0.7939 (mtmt) cc_final: 0.7479 (mmtt) REVERT: E 340 LYS cc_start: 0.8416 (mtpm) cc_final: 0.8055 (mttt) REVERT: E 349 ARG cc_start: 0.8726 (mtt180) cc_final: 0.7288 (mmp-170) REVERT: E 375 LYS cc_start: 0.8124 (tttt) cc_final: 0.7691 (tttm) REVERT: F 311 LYS cc_start: 0.7903 (mtmt) cc_final: 0.7442 (mmtt) REVERT: F 340 LYS cc_start: 0.8424 (mtpm) cc_final: 0.7970 (mttt) REVERT: F 347 LYS cc_start: 0.8768 (mptt) cc_final: 0.8521 (mptp) REVERT: F 349 ARG cc_start: 0.8723 (mtt180) cc_final: 0.7123 (mmp-170) REVERT: F 373 THR cc_start: 0.8402 (m) cc_final: 0.7897 (p) REVERT: F 375 LYS cc_start: 0.8059 (tttt) cc_final: 0.7723 (tttt) outliers start: 7 outliers final: 1 residues processed: 143 average time/residue: 1.4247 time to fit residues: 208.4167 Evaluate side-chains 120 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 19 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 E 368 ASN F 351 GLN F 368 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.155516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.113339 restraints weight = 3543.376| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.81 r_work: 0.3569 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3498 Z= 0.318 Angle : 0.616 4.275 4680 Z= 0.321 Chirality : 0.051 0.131 528 Planarity : 0.004 0.027 594 Dihedral : 4.995 15.733 462 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.27 % Allowed : 19.44 % 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 0.011 0.002 PHE A 346 TYR 0.015 0.004 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 136 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8393 (mtpm) cc_final: 0.8065 (mttt) REVERT: A 375 LYS cc_start: 0.8030 (tttt) cc_final: 0.7585 (tttm) REVERT: B 311 LYS cc_start: 0.8457 (mtmt) cc_final: 0.7117 (pptt) REVERT: B 317 LYS cc_start: 0.8675 (ptpt) cc_final: 0.8470 (ptpt) REVERT: B 338 GLU cc_start: 0.8548 (tt0) cc_final: 0.8239 (tt0) REVERT: B 340 LYS cc_start: 0.8693 (mtpm) cc_final: 0.8240 (mttt) REVERT: B 375 LYS cc_start: 0.8441 (tttm) cc_final: 0.7890 (tppp) REVERT: C 340 LYS cc_start: 0.8411 (mtpm) cc_final: 0.7990 (mttt) REVERT: C 373 THR cc_start: 0.8446 (m) cc_final: 0.8023 (p) REVERT: C 375 LYS cc_start: 0.8304 (tttt) cc_final: 0.7952 (tttm) REVERT: D 311 LYS cc_start: 0.8394 (mtmt) cc_final: 0.7103 (pptt) REVERT: D 317 LYS cc_start: 0.8595 (pttt) cc_final: 0.8320 (ptpt) REVERT: D 340 LYS cc_start: 0.8561 (mtpm) cc_final: 0.8210 (mttt) REVERT: D 373 THR cc_start: 0.8677 (m) cc_final: 0.8390 (p) REVERT: E 311 LYS cc_start: 0.8158 (mtmt) cc_final: 0.7718 (mmtt) REVERT: E 340 LYS cc_start: 0.8422 (mtpm) cc_final: 0.8034 (mttt) REVERT: E 349 ARG cc_start: 0.8726 (mtt180) cc_final: 0.7295 (mtp180) REVERT: E 375 LYS cc_start: 0.8157 (tttt) cc_final: 0.7732 (tttm) REVERT: F 311 LYS cc_start: 0.8069 (mtmt) cc_final: 0.7599 (mmtt) REVERT: F 331 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8810 (ttmt) REVERT: F 340 LYS cc_start: 0.8411 (mtpm) cc_final: 0.7977 (mttt) REVERT: F 347 LYS cc_start: 0.8804 (mptt) cc_final: 0.8542 (mptp) REVERT: F 373 THR cc_start: 0.8457 (m) cc_final: 0.8061 (p) REVERT: F 375 LYS cc_start: 0.8084 (tttt) cc_final: 0.7756 (tttt) outliers start: 9 outliers final: 5 residues processed: 132 average time/residue: 1.4746 time to fit residues: 198.9778 Evaluate side-chains 127 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 121 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 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 26 optimal weight: 8.9990 chunk 13 optimal weight: 0.3980 chunk 7 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 GLN F 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.154830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.112850 restraints weight = 3599.473| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.82 r_work: 0.3558 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2763 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= 0.307 Angle : 0.597 4.444 4680 Z= 0.309 Chirality : 0.050 0.131 528 Planarity : 0.003 0.021 594 Dihedral : 4.946 15.659 462 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.53 % Allowed : 21.21 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.009 0.002 PHE A 346 TYR 0.014 0.004 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 132 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8384 (mtpm) cc_final: 0.8065 (mttt) REVERT: A 375 LYS cc_start: 0.7979 (tttt) cc_final: 0.7556 (tttm) REVERT: B 311 LYS cc_start: 0.8424 (mtmt) cc_final: 0.7218 (pptt) REVERT: B 338 GLU cc_start: 0.8555 (tt0) cc_final: 0.8308 (tt0) REVERT: B 340 LYS cc_start: 0.8693 (mtpm) cc_final: 0.8230 (mttt) REVERT: B 375 LYS cc_start: 0.8363 (tttm) cc_final: 0.7880 (tppp) REVERT: C 340 LYS cc_start: 0.8440 (mtpm) cc_final: 0.7986 (mttt) REVERT: C 373 THR cc_start: 0.8460 (m) cc_final: 0.8034 (p) REVERT: C 375 LYS cc_start: 0.8296 (tttt) cc_final: 0.7962 (tttm) REVERT: D 311 LYS cc_start: 0.8408 (mtmt) cc_final: 0.7177 (pptt) REVERT: D 340 LYS cc_start: 0.8544 (mtpm) cc_final: 0.8189 (mttt) REVERT: D 373 THR cc_start: 0.8676 (m) cc_final: 0.8390 (p) REVERT: E 311 LYS cc_start: 0.8173 (mtmt) cc_final: 0.7801 (mmtt) REVERT: E 317 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8152 (ptpp) REVERT: E 340 LYS cc_start: 0.8409 (mtpm) cc_final: 0.8037 (mttt) REVERT: E 349 ARG cc_start: 0.8753 (mtt180) cc_final: 0.7286 (mtp180) REVERT: E 375 LYS cc_start: 0.8159 (tttt) cc_final: 0.7738 (tttm) REVERT: F 311 LYS cc_start: 0.8008 (mtmt) cc_final: 0.7577 (mmtt) REVERT: F 331 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8826 (ttmt) REVERT: F 340 LYS cc_start: 0.8390 (mtpm) cc_final: 0.7961 (mttt) REVERT: F 347 LYS cc_start: 0.8783 (mptt) cc_final: 0.8518 (mptp) REVERT: F 349 ARG cc_start: 0.8734 (mtt180) cc_final: 0.6988 (tpt90) REVERT: F 373 THR cc_start: 0.8487 (m) cc_final: 0.8121 (p) REVERT: F 375 LYS cc_start: 0.8053 (tttt) cc_final: 0.7846 (tttm) outliers start: 10 outliers final: 2 residues processed: 126 average time/residue: 1.3763 time to fit residues: 177.4878 Evaluate side-chains 125 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 121 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain E residue 317 LYS Chi-restraints excluded: chain F residue 331 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 6 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.151975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.110054 restraints weight = 3618.712| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.82 r_work: 0.3525 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 3498 Z= 0.465 Angle : 0.689 6.136 4680 Z= 0.356 Chirality : 0.053 0.138 528 Planarity : 0.003 0.015 594 Dihedral : 5.203 16.332 462 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.78 % Allowed : 21.46 % Favored : 75.76 % 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: -1.84 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 329 PHE 0.011 0.002 PHE A 346 TYR 0.015 0.004 TYR C 310 ARG 0.001 0.000 ARG F 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 135 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8609 (mtmt) REVERT: A 340 LYS cc_start: 0.8457 (mtpm) cc_final: 0.8014 (mttp) REVERT: A 375 LYS cc_start: 0.8018 (tttt) cc_final: 0.7641 (tttm) REVERT: B 311 LYS cc_start: 0.8458 (mtmt) cc_final: 0.7398 (pptt) REVERT: B 340 LYS cc_start: 0.8683 (mtpm) cc_final: 0.8245 (mttt) REVERT: B 373 THR cc_start: 0.8820 (m) cc_final: 0.8559 (p) REVERT: C 340 LYS cc_start: 0.8461 (mtpm) cc_final: 0.8015 (mtmt) REVERT: C 373 THR cc_start: 0.8491 (m) cc_final: 0.8108 (p) REVERT: C 375 LYS cc_start: 0.8300 (tttt) cc_final: 0.7977 (tttm) REVERT: D 311 LYS cc_start: 0.8488 (mtmt) cc_final: 0.7279 (pptt) REVERT: D 340 LYS cc_start: 0.8539 (mtpm) cc_final: 0.8201 (mttt) REVERT: D 373 THR cc_start: 0.8682 (m) cc_final: 0.8395 (p) REVERT: E 311 LYS cc_start: 0.8273 (mtmt) cc_final: 0.7888 (mmtt) REVERT: E 317 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8061 (ptpp) REVERT: E 331 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8735 (mtmm) REVERT: E 340 LYS cc_start: 0.8403 (mtpm) cc_final: 0.8043 (mttt) REVERT: E 349 ARG cc_start: 0.8767 (mtt180) cc_final: 0.7355 (mtp180) REVERT: E 375 LYS cc_start: 0.8203 (tttt) cc_final: 0.7785 (tttm) REVERT: F 311 LYS cc_start: 0.8134 (mtmt) cc_final: 0.7669 (mmtt) REVERT: F 331 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8894 (ttmt) REVERT: F 340 LYS cc_start: 0.8398 (mtpm) cc_final: 0.8013 (mttt) REVERT: F 347 LYS cc_start: 0.8824 (mptt) cc_final: 0.8605 (mptp) REVERT: F 349 ARG cc_start: 0.8767 (mtt180) cc_final: 0.7022 (tpt90) outliers start: 11 outliers final: 3 residues processed: 131 average time/residue: 1.4213 time to fit residues: 190.3128 Evaluate side-chains 132 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain E residue 317 LYS 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 25 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.154866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.112899 restraints weight = 3658.033| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.81 r_work: 0.3568 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3498 Z= 0.262 Angle : 0.571 4.529 4680 Z= 0.293 Chirality : 0.050 0.129 528 Planarity : 0.002 0.013 594 Dihedral : 4.914 15.284 462 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 : 3.28 % Allowed : 21.21 % Favored : 75.51 % 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 (0.34), 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 0.001 HIS B 329 PHE 0.008 0.001 PHE A 346 TYR 0.012 0.003 TYR A 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 136 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8410 (mtmt) REVERT: A 340 LYS cc_start: 0.8366 (mtpm) cc_final: 0.8029 (mttt) REVERT: A 375 LYS cc_start: 0.7957 (tttt) cc_final: 0.7711 (tptm) REVERT: B 311 LYS cc_start: 0.8414 (mtmt) cc_final: 0.7336 (pptt) REVERT: B 338 GLU cc_start: 0.8535 (tt0) cc_final: 0.8043 (tt0) REVERT: B 340 LYS cc_start: 0.8674 (mtpm) cc_final: 0.8245 (mtmt) REVERT: B 373 THR cc_start: 0.8783 (m) cc_final: 0.8529 (p) REVERT: B 375 LYS cc_start: 0.8326 (tttm) cc_final: 0.7874 (tppp) REVERT: C 340 LYS cc_start: 0.8395 (mtpm) cc_final: 0.7986 (mtmt) REVERT: C 373 THR cc_start: 0.8480 (m) cc_final: 0.8066 (p) REVERT: C 375 LYS cc_start: 0.8253 (tttt) cc_final: 0.7935 (tttm) REVERT: D 311 LYS cc_start: 0.8437 (mtmt) cc_final: 0.7292 (pptt) REVERT: D 340 LYS cc_start: 0.8501 (mtpm) cc_final: 0.8160 (mttt) REVERT: D 373 THR cc_start: 0.8624 (m) cc_final: 0.8372 (p) REVERT: E 311 LYS cc_start: 0.8214 (mtmt) cc_final: 0.7805 (mmtt) REVERT: E 317 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8128 (ptpp) REVERT: E 331 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8714 (mtmm) REVERT: E 340 LYS cc_start: 0.8375 (mtpm) cc_final: 0.8046 (mttt) REVERT: E 349 ARG cc_start: 0.8734 (mtt180) cc_final: 0.7301 (mmp-170) REVERT: E 375 LYS cc_start: 0.8174 (tttt) cc_final: 0.7764 (tttm) REVERT: F 311 LYS cc_start: 0.8094 (mtmt) cc_final: 0.7632 (mmtt) REVERT: F 340 LYS cc_start: 0.8378 (mtpm) cc_final: 0.8000 (mttt) REVERT: F 347 LYS cc_start: 0.8839 (mptt) cc_final: 0.8613 (mptp) REVERT: F 349 ARG cc_start: 0.8759 (mtt180) cc_final: 0.7025 (tpt90) outliers start: 13 outliers final: 2 residues processed: 128 average time/residue: 1.4140 time to fit residues: 185.1507 Evaluate side-chains 120 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain E residue 317 LYS 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 36 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.152266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.110240 restraints weight = 3651.732| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.82 r_work: 0.3531 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 3498 Z= 0.448 Angle : 0.678 6.284 4680 Z= 0.348 Chirality : 0.052 0.137 528 Planarity : 0.003 0.017 594 Dihedral : 5.195 16.538 462 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.78 % Allowed : 22.22 % 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: -1.77 (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 0.011 0.002 PHE A 346 TYR 0.015 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 129 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8616 (mtmt) REVERT: A 340 LYS cc_start: 0.8449 (mtpm) cc_final: 0.8008 (mttp) REVERT: A 373 THR cc_start: 0.8444 (m) cc_final: 0.7949 (p) REVERT: A 375 LYS cc_start: 0.7996 (tttt) cc_final: 0.7616 (tttm) REVERT: B 311 LYS cc_start: 0.8455 (mtmt) cc_final: 0.7405 (pptt) REVERT: B 340 LYS cc_start: 0.8666 (mtpm) cc_final: 0.8258 (mttt) REVERT: B 373 THR cc_start: 0.8789 (m) cc_final: 0.8532 (p) REVERT: C 340 LYS cc_start: 0.8447 (mtpm) cc_final: 0.8009 (mtmt) REVERT: C 373 THR cc_start: 0.8498 (m) cc_final: 0.8045 (p) REVERT: C 375 LYS cc_start: 0.8291 (tttt) cc_final: 0.7978 (tttm) REVERT: D 311 LYS cc_start: 0.8494 (mtmt) cc_final: 0.7322 (pptt) REVERT: D 314 ASP cc_start: 0.8520 (t0) cc_final: 0.8175 (t0) REVERT: D 340 LYS cc_start: 0.8539 (mtpm) cc_final: 0.8191 (mttt) REVERT: D 373 THR cc_start: 0.8675 (m) cc_final: 0.8398 (p) REVERT: E 311 LYS cc_start: 0.8279 (mtmt) cc_final: 0.7877 (mmtt) REVERT: E 317 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8105 (ptpp) REVERT: E 331 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8726 (mtmm) REVERT: E 340 LYS cc_start: 0.8380 (mtpm) cc_final: 0.8034 (mttt) REVERT: E 349 ARG cc_start: 0.8785 (mtt180) cc_final: 0.7358 (mtp180) REVERT: E 375 LYS cc_start: 0.8176 (tttt) cc_final: 0.7773 (tttm) REVERT: F 311 LYS cc_start: 0.8148 (mtmt) cc_final: 0.7676 (mmtt) REVERT: F 340 LYS cc_start: 0.8415 (mtpm) cc_final: 0.8021 (mttt) REVERT: F 347 LYS cc_start: 0.8848 (mptt) cc_final: 0.8641 (mptp) REVERT: F 349 ARG cc_start: 0.8767 (mtt180) cc_final: 0.7029 (tpt90) REVERT: F 375 LYS cc_start: 0.8060 (tttm) cc_final: 0.7658 (tttp) outliers start: 11 outliers final: 3 residues processed: 124 average time/residue: 1.3566 time to fit residues: 172.2708 Evaluate side-chains 124 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 317 LYS 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 16 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 0.0060 chunk 18 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 overall best weight: 1.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.155785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.113805 restraints weight = 3634.265| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.82 r_work: 0.3583 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 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= 0.201 Angle : 0.558 9.181 4680 Z= 0.279 Chirality : 0.050 0.174 528 Planarity : 0.002 0.014 594 Dihedral : 4.808 15.205 462 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.77 % Allowed : 23.23 % 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: -1.69 (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 0.008 0.001 PHE A 346 TYR 0.011 0.003 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 124 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8338 (mtpm) cc_final: 0.8053 (mttt) REVERT: A 375 LYS cc_start: 0.7926 (tttt) cc_final: 0.7677 (tptm) REVERT: B 311 LYS cc_start: 0.8420 (mtmt) cc_final: 0.7366 (pptt) REVERT: B 338 GLU cc_start: 0.8535 (tt0) cc_final: 0.8287 (tt0) REVERT: B 340 LYS cc_start: 0.8670 (mtpm) cc_final: 0.8242 (mtmt) REVERT: B 375 LYS cc_start: 0.8304 (tttm) cc_final: 0.7845 (tppp) REVERT: C 340 LYS cc_start: 0.8379 (mtpm) cc_final: 0.7972 (mtmt) REVERT: C 373 THR cc_start: 0.8488 (m) cc_final: 0.8074 (p) REVERT: C 375 LYS cc_start: 0.8220 (tttt) cc_final: 0.7918 (tttm) REVERT: D 311 LYS cc_start: 0.8437 (mtmt) cc_final: 0.7315 (pptt) REVERT: D 314 ASP cc_start: 0.8421 (t0) cc_final: 0.8112 (t0) REVERT: D 340 LYS cc_start: 0.8482 (mtpm) cc_final: 0.8136 (mttt) REVERT: D 373 THR cc_start: 0.8581 (m) cc_final: 0.8362 (p) REVERT: E 311 LYS cc_start: 0.8177 (mtmt) cc_final: 0.7821 (mmtt) REVERT: E 331 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8728 (mtmm) REVERT: E 340 LYS cc_start: 0.8343 (mtpm) cc_final: 0.8014 (mttp) REVERT: E 349 ARG cc_start: 0.8743 (mtt180) cc_final: 0.7307 (mmp-170) REVERT: E 375 LYS cc_start: 0.8146 (tttt) cc_final: 0.7752 (tttm) REVERT: F 311 LYS cc_start: 0.8083 (mtmt) cc_final: 0.7643 (mmtt) REVERT: F 340 LYS cc_start: 0.8370 (mtpm) cc_final: 0.7984 (mttt) REVERT: F 347 LYS cc_start: 0.8837 (mptt) cc_final: 0.8627 (mptp) outliers start: 7 outliers final: 3 residues processed: 121 average time/residue: 1.3648 time to fit residues: 169.0999 Evaluate side-chains 121 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 311 LYS 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 22 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- 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 = 0.4212 r_free = 0.4212 target = 0.157150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.115210 restraints weight = 3571.044| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.80 r_work: 0.3606 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.3260 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= 0.159 Angle : 0.528 9.756 4680 Z= 0.260 Chirality : 0.049 0.129 528 Planarity : 0.002 0.014 594 Dihedral : 4.551 14.272 462 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.52 % Allowed : 23.48 % 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: -1.60 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 329 PHE 0.008 0.001 PHE A 346 TYR 0.010 0.002 TYR B 310 ARG 0.001 0.000 ARG D 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 127 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 121 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8469 (mtmt) REVERT: A 340 LYS cc_start: 0.8336 (mtpm) cc_final: 0.8044 (mttt) REVERT: A 375 LYS cc_start: 0.7913 (tttt) cc_final: 0.7666 (tptm) REVERT: B 311 LYS cc_start: 0.8414 (mtmt) cc_final: 0.7381 (pptt) REVERT: B 338 GLU cc_start: 0.8526 (tt0) cc_final: 0.8130 (tt0) REVERT: B 340 LYS cc_start: 0.8630 (mtpm) cc_final: 0.8217 (mtmt) REVERT: B 375 LYS cc_start: 0.8272 (tttm) cc_final: 0.7824 (tppp) REVERT: C 340 LYS cc_start: 0.8350 (mtpm) cc_final: 0.7941 (mtmt) REVERT: C 373 THR cc_start: 0.8460 (m) cc_final: 0.8023 (p) REVERT: C 375 LYS cc_start: 0.8154 (tttt) cc_final: 0.7848 (tttm) REVERT: D 311 LYS cc_start: 0.8463 (mtmt) cc_final: 0.7339 (pptt) REVERT: D 314 ASP cc_start: 0.8366 (t0) cc_final: 0.8070 (t0) REVERT: D 340 LYS cc_start: 0.8470 (mtpm) cc_final: 0.8133 (mttt) REVERT: D 373 THR cc_start: 0.8600 (m) cc_final: 0.8378 (p) REVERT: E 311 LYS cc_start: 0.8192 (mtmt) cc_final: 0.7814 (mmtt) REVERT: E 331 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8734 (mtmm) REVERT: E 340 LYS cc_start: 0.8353 (mtpm) cc_final: 0.8011 (mttt) REVERT: E 349 ARG cc_start: 0.8737 (mtt180) cc_final: 0.7311 (mmp-170) REVERT: E 375 LYS cc_start: 0.8121 (tttt) cc_final: 0.7873 (tptm) REVERT: F 311 LYS cc_start: 0.8121 (mtmt) cc_final: 0.7651 (mmtt) REVERT: F 340 LYS cc_start: 0.8353 (mtpm) cc_final: 0.7961 (mttt) REVERT: F 347 LYS cc_start: 0.8815 (mptt) cc_final: 0.8586 (mptp) outliers start: 6 outliers final: 1 residues processed: 123 average time/residue: 1.4371 time to fit residues: 180.7269 Evaluate side-chains 118 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS 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 24 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 16 optimal weight: 0.0870 chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 overall best weight: 2.1764 ------------------------------------------------------------------------------- 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 = 0.4195 r_free = 0.4195 target = 0.155702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.113691 restraints weight = 3636.242| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 1.80 r_work: 0.3593 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.3221 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= 0.218 Angle : 0.562 9.699 4680 Z= 0.278 Chirality : 0.049 0.155 528 Planarity : 0.002 0.014 594 Dihedral : 4.653 15.319 462 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % 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: -1.62 (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 E 329 PHE 0.008 0.001 PHE A 346 TYR 0.010 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 120 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 116 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8434 (mtmt) REVERT: A 340 LYS cc_start: 0.8331 (mtpm) cc_final: 0.8047 (mttt) REVERT: A 375 LYS cc_start: 0.7927 (tttt) cc_final: 0.7669 (tptm) REVERT: B 311 LYS cc_start: 0.8422 (mtmt) cc_final: 0.7395 (pptt) REVERT: B 338 GLU cc_start: 0.8533 (tt0) cc_final: 0.8113 (tt0) REVERT: B 340 LYS cc_start: 0.8650 (mtpm) cc_final: 0.8228 (mtmt) REVERT: B 375 LYS cc_start: 0.8298 (tttm) cc_final: 0.7837 (tppp) REVERT: C 340 LYS cc_start: 0.8375 (mtpm) cc_final: 0.7957 (mttt) REVERT: C 373 THR cc_start: 0.8467 (m) cc_final: 0.8036 (p) REVERT: C 375 LYS cc_start: 0.8162 (tttt) cc_final: 0.7853 (tttm) REVERT: D 311 LYS cc_start: 0.8463 (mtmt) cc_final: 0.7391 (pptt) REVERT: D 340 LYS cc_start: 0.8488 (mtpm) cc_final: 0.8145 (mttt) REVERT: D 373 THR cc_start: 0.8599 (m) cc_final: 0.8353 (p) REVERT: E 311 LYS cc_start: 0.8207 (mtmt) cc_final: 0.7803 (mmtt) REVERT: E 331 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8718 (mtmm) REVERT: E 340 LYS cc_start: 0.8362 (mtpm) cc_final: 0.8009 (mttt) REVERT: E 349 ARG cc_start: 0.8727 (mtt180) cc_final: 0.7311 (mmp-170) REVERT: E 375 LYS cc_start: 0.8155 (tttt) cc_final: 0.7767 (tttm) REVERT: F 311 LYS cc_start: 0.8103 (mtmt) cc_final: 0.7660 (mmtt) REVERT: F 340 LYS cc_start: 0.8365 (mtpm) cc_final: 0.7982 (mttt) REVERT: F 347 LYS cc_start: 0.8837 (mptt) cc_final: 0.8607 (mptp) outliers start: 4 outliers final: 1 residues processed: 120 average time/residue: 1.3911 time to fit residues: 170.8138 Evaluate side-chains 118 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS 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 30 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 22 optimal weight: 0.0870 chunk 40 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- 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 = 0.4206 r_free = 0.4206 target = 0.156719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.114840 restraints weight = 3621.719| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 1.79 r_work: 0.3612 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.3299 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= 0.172 Angle : 0.535 9.626 4680 Z= 0.264 Chirality : 0.049 0.128 528 Planarity : 0.002 0.014 594 Dihedral : 4.525 14.655 462 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.76 % Allowed : 24.24 % 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: -1.59 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 329 PHE 0.007 0.001 PHE A 346 TYR 0.010 0.002 TYR B 310 ARG 0.001 0.000 ARG D 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4402.21 seconds wall clock time: 78 minutes 15.71 seconds (4695.71 seconds total)