Starting phenix.real_space_refine on Wed Mar 5 20:09:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ern_19927/03_2025/9ern_19927.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ern_19927/03_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_19927/03_2025/9ern_19927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ern_19927/03_2025/9ern_19927.map" model { file = "/net/cci-nas-00/data/ceres_data/9ern_19927/03_2025/9ern_19927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ern_19927/03_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 2.49, per 1000 atoms: 0.72 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: 0.67 Conformation dependent library (CDL) restraints added in 421.7 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: 0.42 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: 0.70 Time building geometry restraints manager: 0.81 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: 4.460 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.870 Find NCS groups from input model: 0.060 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:11.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.360 ------------------------------------------------------------------------------- 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 : 0.427 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: 1.4230 time to fit residues: 206.3834 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 : 0.436 ------------------------------------------------------------------------------- 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: 0.0020 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 351 GLN F 362 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.161692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.120027 restraints weight = 3530.472| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.79 r_work: 0.3644 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3498 Z= 0.147 Angle : 0.534 3.996 4680 Z= 0.282 Chirality : 0.049 0.138 528 Planarity : 0.004 0.034 594 Dihedral : 4.954 15.188 462 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.26 % Allowed : 15.66 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 0.009 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 145 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 140 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8404 (mtpm) cc_final: 0.8099 (mttt) REVERT: A 375 LYS cc_start: 0.8036 (tttt) cc_final: 0.7678 (tttm) REVERT: B 311 LYS cc_start: 0.8441 (mtmt) cc_final: 0.6783 (pptt) REVERT: B 338 GLU cc_start: 0.8557 (tt0) cc_final: 0.8325 (tt0) REVERT: B 340 LYS cc_start: 0.8626 (mtpm) cc_final: 0.8251 (mttt) REVERT: B 347 LYS cc_start: 0.8872 (mptt) cc_final: 0.8639 (mptp) REVERT: C 340 LYS cc_start: 0.8430 (mtpm) cc_final: 0.8029 (mttt) REVERT: C 345 ASP cc_start: 0.8400 (m-30) cc_final: 0.8042 (t0) REVERT: C 375 LYS cc_start: 0.8228 (tttt) cc_final: 0.7874 (tttm) REVERT: D 311 LYS cc_start: 0.8365 (mtmt) cc_final: 0.6766 (pptt) REVERT: D 317 LYS cc_start: 0.8525 (pttt) cc_final: 0.8273 (ptpt) REVERT: D 321 LYS cc_start: 0.8563 (ttpt) cc_final: 0.8317 (mtmm) REVERT: D 340 LYS cc_start: 0.8596 (mtpm) cc_final: 0.8258 (mttt) REVERT: D 375 LYS cc_start: 0.8688 (tttt) cc_final: 0.8487 (tttt) REVERT: E 311 LYS cc_start: 0.7969 (mtmt) cc_final: 0.7528 (mmtt) REVERT: E 340 LYS cc_start: 0.8410 (mtpm) cc_final: 0.8051 (mttt) REVERT: E 349 ARG cc_start: 0.8724 (mtt180) cc_final: 0.7283 (mmp-170) REVERT: F 311 LYS cc_start: 0.7905 (mtmt) cc_final: 0.7443 (mmtt) REVERT: F 340 LYS cc_start: 0.8417 (mtpm) cc_final: 0.7957 (mttt) REVERT: F 347 LYS cc_start: 0.8762 (mptt) cc_final: 0.8512 (mptp) REVERT: F 349 ARG cc_start: 0.8721 (mtt180) cc_final: 0.7106 (mmp-170) REVERT: F 373 THR cc_start: 0.8405 (m) cc_final: 0.7904 (p) REVERT: F 375 LYS cc_start: 0.8073 (tttt) cc_final: 0.7738 (tttt) outliers start: 5 outliers final: 1 residues processed: 142 average time/residue: 1.3922 time to fit residues: 202.1127 Evaluate side-chains 123 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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: 9.9990 chunk 34 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 0.0470 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS E 330 HIS E 351 GLN F 330 HIS F 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.157113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.114965 restraints weight = 3521.411| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.81 r_work: 0.3586 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3498 Z= 0.237 Angle : 0.564 3.900 4680 Z= 0.293 Chirality : 0.050 0.133 528 Planarity : 0.003 0.027 594 Dihedral : 4.817 15.259 462 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.42 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: -1.93 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.25), 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 0.014 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 138 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8408 (mtpm) cc_final: 0.8086 (mttt) REVERT: A 375 LYS cc_start: 0.7993 (tttt) cc_final: 0.7543 (tttm) REVERT: B 311 LYS cc_start: 0.8423 (mtmt) cc_final: 0.7089 (pptt) REVERT: B 317 LYS cc_start: 0.8643 (ptpt) cc_final: 0.8423 (ptpt) REVERT: B 338 GLU cc_start: 0.8574 (tt0) cc_final: 0.8281 (tt0) REVERT: B 340 LYS cc_start: 0.8639 (mtpm) cc_final: 0.8240 (mttt) REVERT: B 375 LYS cc_start: 0.8333 (tttm) cc_final: 0.7801 (tppp) REVERT: C 340 LYS cc_start: 0.8418 (mtpm) cc_final: 0.8004 (mttt) REVERT: C 345 ASP cc_start: 0.8440 (m-30) cc_final: 0.8014 (t0) REVERT: C 373 THR cc_start: 0.8451 (m) cc_final: 0.8018 (p) REVERT: C 375 LYS cc_start: 0.8291 (tttt) cc_final: 0.7938 (tttm) REVERT: D 311 LYS cc_start: 0.8385 (mtmt) cc_final: 0.7051 (pptt) REVERT: D 317 LYS cc_start: 0.8559 (pttt) cc_final: 0.8298 (ptpt) REVERT: D 340 LYS cc_start: 0.8535 (mtpm) cc_final: 0.8204 (mttt) REVERT: E 311 LYS cc_start: 0.8113 (mtmt) cc_final: 0.7696 (mmtt) REVERT: E 340 LYS cc_start: 0.8434 (mtpm) cc_final: 0.8056 (mttt) REVERT: E 349 ARG cc_start: 0.8728 (mtt180) cc_final: 0.7249 (mmp-170) REVERT: F 311 LYS cc_start: 0.8050 (mtmt) cc_final: 0.7582 (mmtt) REVERT: F 331 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8794 (ttmt) REVERT: F 340 LYS cc_start: 0.8400 (mtpm) cc_final: 0.7953 (mttt) REVERT: F 347 LYS cc_start: 0.8778 (mptt) cc_final: 0.8507 (mptp) REVERT: F 373 THR cc_start: 0.8458 (m) cc_final: 0.8074 (p) REVERT: F 375 LYS cc_start: 0.8085 (tttt) cc_final: 0.7629 (tttt) outliers start: 9 outliers final: 2 residues processed: 134 average time/residue: 1.4168 time to fit residues: 194.0728 Evaluate side-chains 124 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 121 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 26 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.156134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.113863 restraints weight = 3578.206| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.83 r_work: 0.3586 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3498 Z= 0.265 Angle : 0.579 6.022 4680 Z= 0.296 Chirality : 0.050 0.130 528 Planarity : 0.003 0.022 594 Dihedral : 4.842 15.801 462 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.27 % Allowed : 21.21 % Favored : 76.52 % 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: -1.86 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.008 0.002 PHE A 346 TYR 0.012 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 129 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8394 (mtpm) cc_final: 0.8024 (mttt) REVERT: A 375 LYS cc_start: 0.7984 (tttt) cc_final: 0.7527 (tttm) REVERT: B 311 LYS cc_start: 0.8425 (mtmt) cc_final: 0.7184 (pptt) REVERT: B 338 GLU cc_start: 0.8529 (tt0) cc_final: 0.8287 (tt0) REVERT: B 340 LYS cc_start: 0.8657 (mtpm) cc_final: 0.8227 (mttt) REVERT: B 375 LYS cc_start: 0.8327 (tttm) cc_final: 0.7825 (tppp) REVERT: C 340 LYS cc_start: 0.8399 (mtpm) cc_final: 0.7976 (mttt) REVERT: C 373 THR cc_start: 0.8468 (m) cc_final: 0.8049 (p) REVERT: C 375 LYS cc_start: 0.8251 (tttt) cc_final: 0.7920 (tttm) REVERT: D 311 LYS cc_start: 0.8381 (mtmt) cc_final: 0.7135 (pptt) REVERT: D 340 LYS cc_start: 0.8520 (mtpm) cc_final: 0.8171 (mttt) REVERT: D 375 LYS cc_start: 0.8653 (tttt) cc_final: 0.8331 (tttm) REVERT: E 311 LYS cc_start: 0.8118 (mtmt) cc_final: 0.7722 (mmtt) REVERT: E 340 LYS cc_start: 0.8398 (mtpm) cc_final: 0.8022 (mttt) REVERT: E 349 ARG cc_start: 0.8740 (mtt180) cc_final: 0.7218 (mmp-170) REVERT: E 375 LYS cc_start: 0.8167 (tttt) cc_final: 0.7757 (tttm) REVERT: F 311 LYS cc_start: 0.7999 (mtmt) cc_final: 0.7555 (mmtt) REVERT: F 340 LYS cc_start: 0.8394 (mtpm) cc_final: 0.7959 (mttt) REVERT: F 347 LYS cc_start: 0.8770 (mptt) cc_final: 0.8505 (mptp) REVERT: F 349 ARG cc_start: 0.8717 (mtt180) cc_final: 0.6925 (tpt90) REVERT: F 373 THR cc_start: 0.8469 (m) cc_final: 0.8086 (p) REVERT: F 375 LYS cc_start: 0.8049 (tttt) cc_final: 0.7829 (tttm) outliers start: 9 outliers final: 2 residues processed: 125 average time/residue: 1.3852 time to fit residues: 177.0518 Evaluate side-chains 122 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 120 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 41 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN B 362 HIS F 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.151661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.109674 restraints weight = 3619.461| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.81 r_work: 0.3520 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 3498 Z= 0.507 Angle : 0.728 9.797 4680 Z= 0.372 Chirality : 0.054 0.141 528 Planarity : 0.003 0.016 594 Dihedral : 5.230 16.887 462 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.02 % Allowed : 22.47 % 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: -1.85 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 329 PHE 0.012 0.002 PHE A 346 TYR 0.015 0.005 TYR C 310 ARG 0.003 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8538 (mtmt) REVERT: A 340 LYS cc_start: 0.8474 (mtpm) cc_final: 0.8031 (mttp) REVERT: A 373 THR cc_start: 0.8471 (m) cc_final: 0.7938 (p) REVERT: A 375 LYS cc_start: 0.8033 (tttt) cc_final: 0.7652 (tttm) REVERT: B 311 LYS cc_start: 0.8448 (mtmt) cc_final: 0.7326 (pptt) REVERT: B 340 LYS cc_start: 0.8702 (mtpm) cc_final: 0.8264 (mttt) REVERT: B 373 THR cc_start: 0.8817 (m) cc_final: 0.8553 (p) REVERT: C 340 LYS cc_start: 0.8463 (mtpm) cc_final: 0.8017 (mtmt) REVERT: C 373 THR cc_start: 0.8515 (m) cc_final: 0.8082 (p) REVERT: C 375 LYS cc_start: 0.8304 (tttt) cc_final: 0.7973 (tttm) REVERT: D 311 LYS cc_start: 0.8479 (mtmt) cc_final: 0.7260 (pptt) REVERT: D 340 LYS cc_start: 0.8549 (mtpm) cc_final: 0.8220 (mttt) REVERT: E 311 LYS cc_start: 0.8298 (mtmt) cc_final: 0.7909 (mmtt) REVERT: E 331 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8669 (mtmm) REVERT: E 340 LYS cc_start: 0.8399 (mtpm) cc_final: 0.8043 (mttt) REVERT: E 348 ASP cc_start: 0.8434 (t0) cc_final: 0.8234 (t0) REVERT: E 349 ARG cc_start: 0.8761 (mtt180) cc_final: 0.7299 (mtp180) REVERT: E 375 LYS cc_start: 0.8195 (tttt) cc_final: 0.7787 (tttm) REVERT: F 311 LYS cc_start: 0.8153 (mtmt) cc_final: 0.7661 (mmtt) REVERT: F 340 LYS cc_start: 0.8397 (mtpm) cc_final: 0.8017 (mttt) REVERT: F 347 LYS cc_start: 0.8838 (mptt) cc_final: 0.8618 (mptp) REVERT: F 349 ARG cc_start: 0.8733 (mtt180) cc_final: 0.7028 (tpt90) REVERT: F 375 LYS cc_start: 0.8080 (tttt) cc_final: 0.7849 (tttt) outliers start: 8 outliers final: 1 residues processed: 131 average time/residue: 1.3585 time to fit residues: 182.0531 Evaluate side-chains 128 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 125 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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=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: 5.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 15 optimal weight: 9.9990 chunk 40 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 = 0.4189 r_free = 0.4189 target = 0.155370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.113386 restraints weight = 3658.476| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.81 r_work: 0.3576 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.3027 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= 0.233 Angle : 0.580 9.864 4680 Z= 0.288 Chirality : 0.050 0.149 528 Planarity : 0.002 0.014 594 Dihedral : 4.842 15.577 462 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.53 % Allowed : 22.47 % 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 0.008 0.001 PHE A 346 TYR 0.011 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 130 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8350 (mtpm) cc_final: 0.8067 (mttt) REVERT: A 375 LYS cc_start: 0.7952 (tttt) cc_final: 0.7703 (tptm) REVERT: B 311 LYS cc_start: 0.8424 (mtmt) cc_final: 0.7338 (pptt) REVERT: B 338 GLU cc_start: 0.8522 (tt0) cc_final: 0.8272 (tt0) REVERT: B 340 LYS cc_start: 0.8660 (mtpm) cc_final: 0.8246 (mtmt) REVERT: B 375 LYS cc_start: 0.8308 (tttm) cc_final: 0.7859 (tppp) REVERT: C 340 LYS cc_start: 0.8397 (mtpm) cc_final: 0.7993 (mtmt) REVERT: C 373 THR cc_start: 0.8480 (m) cc_final: 0.8099 (p) REVERT: C 375 LYS cc_start: 0.8255 (tttt) cc_final: 0.7931 (tttm) REVERT: D 311 LYS cc_start: 0.8393 (mtmt) cc_final: 0.7250 (pptt) REVERT: D 340 LYS cc_start: 0.8494 (mtpm) cc_final: 0.8155 (mttt) REVERT: E 311 LYS cc_start: 0.8206 (mtmt) cc_final: 0.7813 (mmtt) REVERT: E 340 LYS cc_start: 0.8372 (mtpm) cc_final: 0.8052 (mttt) REVERT: E 349 ARG cc_start: 0.8725 (mtt180) cc_final: 0.7283 (mmp-170) REVERT: E 375 LYS cc_start: 0.8143 (tttt) cc_final: 0.7738 (tttm) REVERT: F 311 LYS cc_start: 0.8041 (mtmt) cc_final: 0.7611 (mmtt) REVERT: F 340 LYS cc_start: 0.8382 (mtpm) cc_final: 0.8004 (mttt) REVERT: F 347 LYS cc_start: 0.8818 (mptt) cc_final: 0.8590 (mptp) REVERT: F 349 ARG cc_start: 0.8754 (mtt180) cc_final: 0.7026 (tpt90) REVERT: F 375 LYS cc_start: 0.8088 (tttt) cc_final: 0.7850 (tttm) outliers start: 10 outliers final: 2 residues processed: 123 average time/residue: 1.4147 time to fit residues: 177.8588 Evaluate side-chains 121 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 119 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 311 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.4158 r_free = 0.4158 target = 0.152588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.110550 restraints weight = 3643.026| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.81 r_work: 0.3542 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 3498 Z= 0.418 Angle : 0.683 10.051 4680 Z= 0.344 Chirality : 0.052 0.170 528 Planarity : 0.003 0.016 594 Dihedral : 5.095 16.073 462 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.02 % Allowed : 22.22 % 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: -1.79 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (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 0.014 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 130 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8548 (mtmt) REVERT: A 340 LYS cc_start: 0.8440 (mtpm) cc_final: 0.8005 (mttp) REVERT: A 375 LYS cc_start: 0.8004 (tttt) cc_final: 0.7582 (tttm) REVERT: B 311 LYS cc_start: 0.8473 (mtmt) cc_final: 0.7366 (pptt) REVERT: B 340 LYS cc_start: 0.8687 (mtpm) cc_final: 0.8254 (mttt) REVERT: B 373 THR cc_start: 0.8782 (m) cc_final: 0.8522 (p) REVERT: C 340 LYS cc_start: 0.8444 (mtpm) cc_final: 0.8005 (mtmt) REVERT: C 373 THR cc_start: 0.8517 (m) cc_final: 0.8148 (p) REVERT: C 375 LYS cc_start: 0.8270 (tttt) cc_final: 0.7958 (tttm) REVERT: D 311 LYS cc_start: 0.8481 (mtmt) cc_final: 0.7293 (pptt) REVERT: D 340 LYS cc_start: 0.8537 (mtpm) cc_final: 0.8201 (mttt) REVERT: E 311 LYS cc_start: 0.8268 (mtmt) cc_final: 0.7898 (mmtt) REVERT: E 331 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8681 (mtmm) REVERT: E 340 LYS cc_start: 0.8366 (mtpm) cc_final: 0.8035 (mttt) REVERT: E 349 ARG cc_start: 0.8773 (mtt180) cc_final: 0.7353 (mtp180) REVERT: E 375 LYS cc_start: 0.8189 (tttt) cc_final: 0.7785 (tttm) REVERT: F 311 LYS cc_start: 0.8126 (mtmt) cc_final: 0.7652 (mmtt) REVERT: F 340 LYS cc_start: 0.8410 (mtpm) cc_final: 0.8014 (mttt) REVERT: F 347 LYS cc_start: 0.8850 (mptt) cc_final: 0.8637 (mptp) REVERT: F 349 ARG cc_start: 0.8767 (mtt180) cc_final: 0.7033 (tpt90) outliers start: 8 outliers final: 2 residues processed: 126 average time/residue: 1.4044 time to fit residues: 180.9280 Evaluate side-chains 126 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 122 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 331 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- 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 = 0.4178 r_free = 0.4178 target = 0.154273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.112332 restraints weight = 3635.486| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 1.79 r_work: 0.3572 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.3043 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= 0.291 Angle : 0.608 9.806 4680 Z= 0.305 Chirality : 0.051 0.151 528 Planarity : 0.002 0.014 594 Dihedral : 4.945 15.722 462 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 : 2.27 % Allowed : 22.22 % 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: -1.72 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS E 329 PHE 0.009 0.002 PHE A 346 TYR 0.012 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 128 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8502 (mtmt) REVERT: A 340 LYS cc_start: 0.8367 (mtpm) cc_final: 0.8034 (mttt) REVERT: A 375 LYS cc_start: 0.7957 (tttt) cc_final: 0.7553 (tttm) REVERT: B 311 LYS cc_start: 0.8435 (mtmt) cc_final: 0.7368 (pptt) REVERT: B 340 LYS cc_start: 0.8679 (mtpm) cc_final: 0.8242 (mttt) REVERT: B 375 LYS cc_start: 0.8307 (tttm) cc_final: 0.7866 (tppp) REVERT: C 340 LYS cc_start: 0.8403 (mtpm) cc_final: 0.7980 (mtmt) REVERT: C 373 THR cc_start: 0.8481 (m) cc_final: 0.8109 (p) REVERT: C 375 LYS cc_start: 0.8249 (tttt) cc_final: 0.7944 (tttm) REVERT: D 311 LYS cc_start: 0.8452 (mtmt) cc_final: 0.7302 (pptt) REVERT: D 340 LYS cc_start: 0.8502 (mtpm) cc_final: 0.8155 (mttt) REVERT: E 311 LYS cc_start: 0.8236 (mtmt) cc_final: 0.7843 (mmtt) REVERT: E 331 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8730 (mtmm) REVERT: E 340 LYS cc_start: 0.8358 (mtpm) cc_final: 0.8035 (mttt) REVERT: E 349 ARG cc_start: 0.8730 (mtt180) cc_final: 0.7311 (mmp-170) REVERT: E 375 LYS cc_start: 0.8141 (tttt) cc_final: 0.7760 (tttm) REVERT: F 311 LYS cc_start: 0.8104 (mtmt) cc_final: 0.7636 (mmtt) REVERT: F 340 LYS cc_start: 0.8374 (mtpm) cc_final: 0.7995 (mttt) REVERT: F 347 LYS cc_start: 0.8852 (mptt) cc_final: 0.8635 (mptp) REVERT: F 349 ARG cc_start: 0.8757 (mtt180) cc_final: 0.7040 (tpt90) outliers start: 9 outliers final: 4 residues processed: 125 average time/residue: 1.3778 time to fit residues: 176.1893 Evaluate side-chains 125 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE 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 331 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 13 optimal weight: 0.0770 chunk 3 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- 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 = 0.153551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.111609 restraints weight = 3576.113| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.80 r_work: 0.3550 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3498 Z= 0.321 Angle : 0.632 10.454 4680 Z= 0.315 Chirality : 0.051 0.202 528 Planarity : 0.003 0.015 594 Dihedral : 4.987 15.806 462 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.77 % Allowed : 22.73 % 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: -1.71 (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 0.001 0.001 HIS B 329 PHE 0.010 0.002 PHE A 346 TYR 0.012 0.003 TYR A 310 ARG 0.001 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 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: 0.9044 (OUTLIER) cc_final: 0.8613 (mtmt) REVERT: A 340 LYS cc_start: 0.8373 (mtpm) cc_final: 0.8041 (mttt) REVERT: A 375 LYS cc_start: 0.7962 (tttt) cc_final: 0.7545 (tttm) REVERT: B 311 LYS cc_start: 0.8430 (mtmt) cc_final: 0.7377 (pptt) REVERT: B 340 LYS cc_start: 0.8671 (mtpm) cc_final: 0.8234 (mttt) REVERT: B 373 THR cc_start: 0.8780 (m) cc_final: 0.8519 (p) REVERT: B 375 LYS cc_start: 0.8313 (tttm) cc_final: 0.7870 (tppp) REVERT: C 340 LYS cc_start: 0.8421 (mtpm) cc_final: 0.7992 (mtmt) REVERT: C 373 THR cc_start: 0.8482 (m) cc_final: 0.8111 (p) REVERT: C 375 LYS cc_start: 0.8254 (tttt) cc_final: 0.7939 (tttm) REVERT: D 311 LYS cc_start: 0.8460 (mtmt) cc_final: 0.7319 (pptt) REVERT: D 340 LYS cc_start: 0.8509 (mtpm) cc_final: 0.8168 (mttt) REVERT: E 311 LYS cc_start: 0.8231 (mtmt) cc_final: 0.7839 (mmtt) REVERT: E 340 LYS cc_start: 0.8361 (mtpm) cc_final: 0.8038 (mttt) REVERT: E 349 ARG cc_start: 0.8755 (mtt180) cc_final: 0.7337 (mmp-170) REVERT: E 375 LYS cc_start: 0.8143 (tttt) cc_final: 0.7757 (tttm) REVERT: F 311 LYS cc_start: 0.8121 (mtmt) cc_final: 0.7645 (mmtt) REVERT: F 340 LYS cc_start: 0.8372 (mtpm) cc_final: 0.7991 (mttt) REVERT: F 347 LYS cc_start: 0.8850 (mptt) cc_final: 0.8639 (mptp) REVERT: F 349 ARG cc_start: 0.8769 (mtt180) cc_final: 0.7035 (tpt90) outliers start: 7 outliers final: 3 residues processed: 122 average time/residue: 1.3923 time to fit residues: 173.6989 Evaluate side-chains 122 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4225 r_free = 0.4225 target = 0.158100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.116166 restraints weight = 3607.980| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 1.81 r_work: 0.3632 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3498 Z= 0.138 Angle : 0.517 9.325 4680 Z= 0.256 Chirality : 0.049 0.134 528 Planarity : 0.002 0.013 594 Dihedral : 4.516 14.298 462 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.26 % Allowed : 22.98 % 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: -1.59 (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 0.006 0.001 PHE A 346 TYR 0.009 0.002 TYR B 310 ARG 0.001 0.000 ARG D 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 129 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 124 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8330 (mtpm) cc_final: 0.8038 (mttt) REVERT: A 347 LYS cc_start: 0.8843 (mptp) cc_final: 0.8627 (mptt) REVERT: A 375 LYS cc_start: 0.7908 (tttt) cc_final: 0.7493 (tttm) REVERT: B 311 LYS cc_start: 0.8427 (mtmt) cc_final: 0.7369 (pptt) REVERT: B 317 LYS cc_start: 0.8629 (ptpt) cc_final: 0.8328 (ptpt) REVERT: B 338 GLU cc_start: 0.8521 (tt0) cc_final: 0.8303 (tt0) REVERT: B 340 LYS cc_start: 0.8594 (mtpm) cc_final: 0.8191 (mtmt) REVERT: B 375 LYS cc_start: 0.8270 (tttm) cc_final: 0.7843 (tppp) REVERT: C 340 LYS cc_start: 0.8337 (mtpm) cc_final: 0.7937 (mtmt) REVERT: C 373 THR cc_start: 0.8468 (m) cc_final: 0.8065 (p) REVERT: C 375 LYS cc_start: 0.8168 (tttt) cc_final: 0.7850 (tttm) REVERT: D 311 LYS cc_start: 0.8439 (mtmt) cc_final: 0.7305 (pptt) REVERT: D 314 ASP cc_start: 0.8323 (t0) cc_final: 0.8015 (t0) REVERT: D 340 LYS cc_start: 0.8461 (mtpm) cc_final: 0.8096 (mttt) REVERT: D 375 LYS cc_start: 0.8616 (tttt) cc_final: 0.8294 (tttm) REVERT: E 311 LYS cc_start: 0.8141 (mtmt) cc_final: 0.7783 (mmtt) REVERT: E 340 LYS cc_start: 0.8346 (mtpm) cc_final: 0.8016 (mttt) REVERT: E 349 ARG cc_start: 0.8715 (mtt180) cc_final: 0.7319 (mmp-170) REVERT: E 375 LYS cc_start: 0.8137 (tttt) cc_final: 0.7890 (tptm) REVERT: F 311 LYS cc_start: 0.8108 (mtmt) cc_final: 0.7643 (mmtt) REVERT: F 340 LYS cc_start: 0.8366 (mtpm) cc_final: 0.7977 (mttt) REVERT: F 347 LYS cc_start: 0.8817 (mptt) cc_final: 0.8594 (mptp) REVERT: F 375 LYS cc_start: 0.8041 (tttt) cc_final: 0.7608 (tttp) outliers start: 5 outliers final: 2 residues processed: 126 average time/residue: 1.3730 time to fit residues: 176.9406 Evaluate side-chains 122 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 120 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 311 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 = 0.4202 r_free = 0.4202 target = 0.156311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.114038 restraints weight = 3609.438| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 1.82 r_work: 0.3593 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.3225 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= 0.185 Angle : 0.554 9.557 4680 Z= 0.269 Chirality : 0.049 0.128 528 Planarity : 0.002 0.014 594 Dihedral : 4.559 14.539 462 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.01 % Allowed : 24.49 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.18 (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 0.009 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: 4497.79 seconds wall clock time: 77 minutes 18.18 seconds (4638.18 seconds total)