Starting phenix.real_space_refine on Mon Jan 13 18:35:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eog_19854/01_2025/9eog_19854.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eog_19854/01_2025/9eog_19854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eog_19854/01_2025/9eog_19854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eog_19854/01_2025/9eog_19854.map" model { file = "/net/cci-nas-00/data/ceres_data/9eog_19854/01_2025/9eog_19854.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eog_19854/01_2025/9eog_19854.cif" } resolution = 3.0 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= 0.002 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 2202 2.51 5 N 648 2.21 5 O 666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 3522 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 2.78, per 1000 atoms: 0.79 Number of scatterers: 3522 At special positions: 0 Unit cell: (74.984, 153.264, 37.904, 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 666 8.00 N 648 7.00 C 2202 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: 0.79 Conformation dependent library (CDL) restraints added in 418.5 milliseconds 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 804 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 59.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.494A pdb=" N GLN A 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N TYR E 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLN E 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N TYR F 310 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL E 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.775A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL E 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 319 removed outlier: 6.347A pdb=" N VAL A 318 " --> pdb=" O THR B 319 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 322 through 330 removed outlier: 8.880A pdb=" N CYS A 322 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU B 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 9.395A pdb=" N SER A 324 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 10.281A pdb=" N ASN B 327 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N GLY A 326 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N HIS B 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE A 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER E 324 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU A 325 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLY E 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASN A 327 " --> pdb=" O GLY E 326 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER F 324 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU E 325 " --> pdb=" O SER F 324 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLY F 326 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASN E 327 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 336 through 346 removed outlier: 6.859A pdb=" N VAL B 337 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLU A 338 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 339 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LYS A 340 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N SER B 341 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLU A 342 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 9.035A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 10.462A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N GLU E 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N SER A 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N LEU E 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LYS A 343 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N PHE E 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) removed outlier: 9.035A pdb=" N VAL E 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 10.462A pdb=" N LYS F 340 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N VAL E 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N GLU F 342 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N SER E 341 " --> pdb=" O GLU F 342 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU F 344 " --> pdb=" O SER E 341 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LYS E 343 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N PHE F 346 " --> pdb=" O LYS E 343 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASP E 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 351 through 362 removed outlier: 8.868A pdb=" N GLN A 351 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 10.344A pdb=" N ILE B 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N LYS A 353 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N SER B 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY A 355 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ASP B 358 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU A 357 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N ILE B 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASN A 359 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N HIS B 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N THR A 361 " --> pdb=" O HIS B 362 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER A 352 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS E 353 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE A 354 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY E 355 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER E 352 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS F 353 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE E 354 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY F 355 " --> pdb=" O ILE E 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 369 through 379 removed outlier: 6.603A pdb=" N LYS A 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N GLU E 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE A 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N HIS E 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N THR A 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU E 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS A 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N PHE E 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N THR A 377 " --> pdb=" O PHE E 378 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS E 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N GLU F 372 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE E 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N HIS F 374 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N THR E 373 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU F 376 " --> pdb=" O THR E 373 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LYS E 375 " --> pdb=" O LEU F 376 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N PHE F 378 " --> pdb=" O LYS E 375 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N THR E 377 " --> pdb=" O PHE F 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.493A pdb=" N GLN C 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N TYR D 310 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL C 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.775A pdb=" N VAL C 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 317 through 319 Processing sheet with id=AB2, first strand: chain 'C' and resid 322 through 330 removed outlier: 6.808A pdb=" N SER D 324 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU C 325 " --> pdb=" O SER D 324 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLY D 326 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASN C 327 " --> pdb=" O GLY D 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 336 through 346 removed outlier: 9.035A pdb=" N VAL C 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 10.462A pdb=" N LYS D 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N VAL C 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N GLU D 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N SER C 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU D 344 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LYS C 343 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N PHE D 346 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASP C 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 351 through 362 removed outlier: 6.867A pdb=" N SER C 352 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS D 353 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE C 354 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY D 355 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 369 through 379 removed outlier: 6.603A pdb=" N LYS C 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N GLU D 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE C 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N HIS D 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N THR C 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU D 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS C 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N PHE D 378 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N THR C 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 58 hydrogen bonds defined for protein. 174 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: 0.79 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 843 1.33 - 1.45: 816 1.45 - 1.57: 1911 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3576 Sorted by residual: bond pdb=" CG HIS D 330 " pdb=" CD2 HIS D 330 " ideal model delta sigma weight residual 1.354 1.307 0.047 1.10e-02 8.26e+03 1.80e+01 bond pdb=" CG HIS E 330 " pdb=" CD2 HIS E 330 " ideal model delta sigma weight residual 1.354 1.308 0.046 1.10e-02 8.26e+03 1.78e+01 bond pdb=" CG HIS A 330 " pdb=" CD2 HIS A 330 " ideal model delta sigma weight residual 1.354 1.308 0.046 1.10e-02 8.26e+03 1.77e+01 bond pdb=" CG HIS C 362 " pdb=" CD2 HIS C 362 " ideal model delta sigma weight residual 1.354 1.308 0.046 1.10e-02 8.26e+03 1.77e+01 bond pdb=" CG HIS C 330 " pdb=" CD2 HIS C 330 " ideal model delta sigma weight residual 1.354 1.308 0.046 1.10e-02 8.26e+03 1.76e+01 ... (remaining 3571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 3834 1.74 - 3.48: 678 3.48 - 5.21: 228 5.21 - 6.95: 36 6.95 - 8.69: 6 Bond angle restraints: 4782 Sorted by residual: angle pdb=" C ARG B 349 " pdb=" CA ARG B 349 " pdb=" CB ARG B 349 " ideal model delta sigma weight residual 111.63 120.32 -8.69 1.36e+00 5.41e-01 4.08e+01 angle pdb=" C ARG C 349 " pdb=" CA ARG C 349 " pdb=" CB ARG C 349 " ideal model delta sigma weight residual 111.63 120.31 -8.68 1.36e+00 5.41e-01 4.07e+01 angle pdb=" C ARG A 349 " pdb=" CA ARG A 349 " pdb=" CB ARG A 349 " ideal model delta sigma weight residual 111.63 120.30 -8.67 1.36e+00 5.41e-01 4.07e+01 angle pdb=" C ARG E 349 " pdb=" CA ARG E 349 " pdb=" CB ARG E 349 " ideal model delta sigma weight residual 111.63 120.29 -8.66 1.36e+00 5.41e-01 4.05e+01 angle pdb=" C ARG F 349 " pdb=" CA ARG F 349 " pdb=" CB ARG F 349 " ideal model delta sigma weight residual 111.63 120.28 -8.65 1.36e+00 5.41e-01 4.05e+01 ... (remaining 4777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.95: 1664 9.95 - 19.91: 358 19.91 - 29.86: 102 29.86 - 39.81: 30 39.81 - 49.76: 24 Dihedral angle restraints: 2178 sinusoidal: 912 harmonic: 1266 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 -149.79 -30.21 0 5.00e+00 4.00e-02 3.65e+01 dihedral pdb=" CA VAL E 318 " pdb=" C VAL E 318 " pdb=" N THR E 319 " pdb=" CA THR E 319 " ideal model delta harmonic sigma weight residual 180.00 -149.80 -30.20 0 5.00e+00 4.00e-02 3.65e+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 -149.81 -30.19 0 5.00e+00 4.00e-02 3.65e+01 ... (remaining 2175 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.080: 251 0.080 - 0.158: 241 0.158 - 0.236: 36 0.236 - 0.314: 0 0.314 - 0.391: 6 Chirality restraints: 534 Sorted by residual: chirality pdb=" CA ARG E 349 " pdb=" N ARG E 349 " pdb=" C ARG E 349 " pdb=" CB ARG E 349 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" CA ARG B 349 " pdb=" N ARG B 349 " pdb=" C ARG B 349 " pdb=" CB ARG B 349 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" CA ARG A 349 " pdb=" N ARG A 349 " pdb=" C ARG A 349 " pdb=" CB ARG A 349 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.79e+00 ... (remaining 531 not shown) Planarity restraints: 612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 366 " -0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C GLY B 366 " 0.063 2.00e-02 2.50e+03 pdb=" O GLY B 366 " -0.024 2.00e-02 2.50e+03 pdb=" N GLY B 367 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 366 " -0.017 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C GLY E 366 " 0.063 2.00e-02 2.50e+03 pdb=" O GLY E 366 " -0.024 2.00e-02 2.50e+03 pdb=" N GLY E 367 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 366 " 0.017 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C GLY C 366 " -0.063 2.00e-02 2.50e+03 pdb=" O GLY C 366 " 0.024 2.00e-02 2.50e+03 pdb=" N GLY C 367 " 0.021 2.00e-02 2.50e+03 ... (remaining 609 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.94: 1428 2.94 - 3.43: 3246 3.43 - 3.92: 5599 3.92 - 4.41: 5642 4.41 - 4.90: 11553 Nonbonded interactions: 27468 Sorted by model distance: nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.445 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.445 3.040 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.445 3.040 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.445 3.040 nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.445 3.040 ... (remaining 27463 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: 3.460 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: 0.050 Process input model: 12.930 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 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 0.047 3576 Z= 0.594 Angle : 1.628 8.689 4782 Z= 1.047 Chirality : 0.104 0.391 534 Planarity : 0.011 0.039 612 Dihedral : 12.855 49.764 1374 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.48 % Allowed : 4.48 % Favored : 91.04 % Cbeta Deviations : 1.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.37 % 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: -4.10 (0.27), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.21), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.004 HIS E 330 PHE 0.049 0.009 PHE C 346 TYR 0.049 0.017 TYR C 310 ARG 0.004 0.001 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.448 Fit side-chains REVERT: A 311 LYS cc_start: 0.8486 (tmtt) cc_final: 0.8059 (ttpt) REVERT: A 317 LYS cc_start: 0.8468 (ptpp) cc_final: 0.8197 (pttt) REVERT: A 321 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8522 (tppp) REVERT: A 331 LYS cc_start: 0.8749 (mttp) cc_final: 0.8450 (mtpm) REVERT: A 342 GLU cc_start: 0.8452 (tt0) cc_final: 0.8212 (mm-30) REVERT: A 375 LYS cc_start: 0.8509 (tttt) cc_final: 0.7763 (mptm) REVERT: B 311 LYS cc_start: 0.8545 (tmtt) cc_final: 0.7985 (mmtt) REVERT: B 316 SER cc_start: 0.9441 (p) cc_final: 0.9163 (p) REVERT: B 317 LYS cc_start: 0.8512 (ptpp) cc_final: 0.8218 (ptpt) REVERT: B 331 LYS cc_start: 0.8732 (mttp) cc_final: 0.7249 (tmtt) REVERT: B 349 ARG cc_start: 0.7988 (ptp-170) cc_final: 0.7733 (ptm160) REVERT: B 375 LYS cc_start: 0.8417 (tttt) cc_final: 0.7672 (mptm) REVERT: C 311 LYS cc_start: 0.8620 (tmtt) cc_final: 0.8030 (mmtt) REVERT: C 317 LYS cc_start: 0.8541 (ptpp) cc_final: 0.8203 (ptmt) REVERT: C 331 LYS cc_start: 0.8796 (mttp) cc_final: 0.8470 (mtpm) REVERT: C 375 LYS cc_start: 0.8454 (tttt) cc_final: 0.7748 (mptm) REVERT: D 311 LYS cc_start: 0.8741 (tmtt) cc_final: 0.7754 (pptt) REVERT: D 317 LYS cc_start: 0.8831 (ptpp) cc_final: 0.8384 (ptmt) REVERT: D 331 LYS cc_start: 0.8844 (mttp) cc_final: 0.8523 (mtpt) REVERT: D 375 LYS cc_start: 0.8954 (tttt) cc_final: 0.8356 (mttm) REVERT: E 311 LYS cc_start: 0.8526 (tmtt) cc_final: 0.8144 (ttmt) REVERT: E 317 LYS cc_start: 0.8512 (ptpp) cc_final: 0.8149 (ptmt) REVERT: E 321 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8341 (mtpt) REVERT: E 331 LYS cc_start: 0.8964 (mttp) cc_final: 0.8575 (mtpt) REVERT: E 342 GLU cc_start: 0.8582 (tt0) cc_final: 0.8130 (mm-30) REVERT: E 375 LYS cc_start: 0.8655 (tttt) cc_final: 0.7951 (mttm) REVERT: F 311 LYS cc_start: 0.8705 (tmtt) cc_final: 0.7759 (pptt) REVERT: F 331 LYS cc_start: 0.8888 (mttp) cc_final: 0.8627 (mtpt) REVERT: F 375 LYS cc_start: 0.8865 (tttt) cc_final: 0.8486 (mtpm) outliers start: 18 outliers final: 1 residues processed: 140 average time/residue: 1.6055 time to fit residues: 229.3046 Evaluate side-chains 131 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 128 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 321 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN A 351 GLN A 374 HIS B 307 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN B 374 HIS C 307 GLN C 330 HIS C 351 GLN C 374 HIS D 307 GLN D 336 GLN D 351 GLN D 368 ASN D 374 HIS E 307 GLN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS F 307 GLN F 368 ASN F 374 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.144888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.124875 restraints weight = 4156.542| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.59 r_work: 0.3820 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3576 Z= 0.284 Angle : 0.664 5.523 4782 Z= 0.339 Chirality : 0.054 0.160 534 Planarity : 0.004 0.027 612 Dihedral : 6.216 30.899 484 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.74 % Allowed : 16.92 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 374 PHE 0.021 0.003 PHE A 346 TYR 0.012 0.003 TYR A 310 ARG 0.002 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.455 Fit side-chains REVERT: A 317 LYS cc_start: 0.8111 (ptpp) cc_final: 0.7880 (ptmm) REVERT: A 348 ASP cc_start: 0.7492 (t0) cc_final: 0.7149 (m-30) REVERT: B 311 LYS cc_start: 0.8284 (tmtt) cc_final: 0.7735 (mmtt) REVERT: B 317 LYS cc_start: 0.8443 (ptpp) cc_final: 0.7995 (ptmt) REVERT: B 331 LYS cc_start: 0.8632 (mttp) cc_final: 0.8232 (mtpt) REVERT: B 358 ASP cc_start: 0.8633 (p0) cc_final: 0.8075 (p0) REVERT: C 317 LYS cc_start: 0.8257 (ptpp) cc_final: 0.7814 (ptmt) REVERT: C 331 LYS cc_start: 0.8746 (mttp) cc_final: 0.8324 (mtpm) REVERT: C 348 ASP cc_start: 0.7702 (t0) cc_final: 0.7452 (m-30) REVERT: C 358 ASP cc_start: 0.8177 (p0) cc_final: 0.7724 (p0) REVERT: D 311 LYS cc_start: 0.8533 (tmtt) cc_final: 0.7571 (pptt) REVERT: D 317 LYS cc_start: 0.8666 (ptpp) cc_final: 0.8128 (ptmt) REVERT: D 331 LYS cc_start: 0.8838 (mttp) cc_final: 0.8158 (mtpt) REVERT: D 340 LYS cc_start: 0.8794 (ttmm) cc_final: 0.8344 (mttm) REVERT: D 347 LYS cc_start: 0.8331 (ptmt) cc_final: 0.7739 (ptmt) REVERT: D 348 ASP cc_start: 0.8066 (t0) cc_final: 0.7801 (m-30) REVERT: D 358 ASP cc_start: 0.8508 (p0) cc_final: 0.8164 (p0) REVERT: D 375 LYS cc_start: 0.8610 (tttt) cc_final: 0.7969 (mttm) REVERT: E 311 LYS cc_start: 0.8217 (tmtt) cc_final: 0.7833 (ttmt) REVERT: E 317 LYS cc_start: 0.8126 (ptpp) cc_final: 0.7589 (ptmt) REVERT: E 331 LYS cc_start: 0.8836 (mttp) cc_final: 0.8282 (mtpt) REVERT: E 340 LYS cc_start: 0.8368 (ttmm) cc_final: 0.7968 (mttm) REVERT: E 348 ASP cc_start: 0.7590 (t0) cc_final: 0.7357 (m-30) REVERT: E 358 ASP cc_start: 0.8072 (p0) cc_final: 0.7681 (p0) REVERT: E 375 LYS cc_start: 0.8376 (tttt) cc_final: 0.7571 (mttp) REVERT: F 311 LYS cc_start: 0.8437 (tmtt) cc_final: 0.7588 (pptt) REVERT: F 317 LYS cc_start: 0.8611 (ptpt) cc_final: 0.8289 (ptmt) REVERT: F 331 LYS cc_start: 0.8910 (mttp) cc_final: 0.8550 (mtpt) REVERT: F 340 LYS cc_start: 0.8653 (mttt) cc_final: 0.8352 (mttm) REVERT: F 348 ASP cc_start: 0.8093 (t0) cc_final: 0.7889 (m-30) REVERT: F 358 ASP cc_start: 0.8333 (p0) cc_final: 0.8100 (p0) outliers start: 11 outliers final: 1 residues processed: 120 average time/residue: 1.3124 time to fit residues: 161.6984 Evaluate side-chains 108 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 325 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.145102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.125493 restraints weight = 4104.491| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.52 r_work: 0.3842 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3576 Z= 0.226 Angle : 0.600 6.223 4782 Z= 0.296 Chirality : 0.052 0.139 534 Planarity : 0.004 0.025 612 Dihedral : 5.122 32.044 476 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.24 % Allowed : 21.14 % Favored : 77.61 % 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: -2.32 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 362 PHE 0.016 0.002 PHE E 346 TYR 0.011 0.003 TYR A 310 ARG 0.001 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.436 Fit side-chains REVERT: A 317 LYS cc_start: 0.8148 (ptpp) cc_final: 0.7917 (ptmm) REVERT: A 331 LYS cc_start: 0.8586 (mttp) cc_final: 0.8207 (mtpm) REVERT: A 340 LYS cc_start: 0.8527 (ttmm) cc_final: 0.7991 (mttm) REVERT: A 348 ASP cc_start: 0.7528 (t0) cc_final: 0.7260 (m-30) REVERT: B 311 LYS cc_start: 0.8247 (tmtt) cc_final: 0.7666 (mmtt) REVERT: B 317 LYS cc_start: 0.8480 (ptpp) cc_final: 0.8055 (ptmt) REVERT: B 331 LYS cc_start: 0.8654 (mttp) cc_final: 0.8355 (mtmt) REVERT: B 358 ASP cc_start: 0.8650 (p0) cc_final: 0.8263 (p0) REVERT: C 317 LYS cc_start: 0.8227 (ptpp) cc_final: 0.7778 (ptmt) REVERT: C 331 LYS cc_start: 0.8729 (mttp) cc_final: 0.8265 (mtpt) REVERT: C 348 ASP cc_start: 0.7653 (t0) cc_final: 0.7443 (m-30) REVERT: C 358 ASP cc_start: 0.8163 (p0) cc_final: 0.7545 (p0) REVERT: D 311 LYS cc_start: 0.8445 (tmtt) cc_final: 0.7552 (pptt) REVERT: D 317 LYS cc_start: 0.8621 (ptpp) cc_final: 0.8038 (ptmm) REVERT: D 331 LYS cc_start: 0.8743 (mttp) cc_final: 0.8222 (mtpt) REVERT: D 340 LYS cc_start: 0.8713 (ttmm) cc_final: 0.8319 (mttp) REVERT: D 347 LYS cc_start: 0.8282 (ptmt) cc_final: 0.7692 (ptmt) REVERT: D 358 ASP cc_start: 0.8326 (p0) cc_final: 0.8069 (p0) REVERT: D 370 LYS cc_start: 0.8507 (tttp) cc_final: 0.8302 (tttt) REVERT: D 375 LYS cc_start: 0.8663 (tttt) cc_final: 0.7985 (mttm) REVERT: E 311 LYS cc_start: 0.8134 (tmtt) cc_final: 0.7777 (ttmt) REVERT: E 317 LYS cc_start: 0.8102 (ptpp) cc_final: 0.7644 (ptmt) REVERT: E 321 LYS cc_start: 0.8528 (ttmm) cc_final: 0.8047 (ttmt) REVERT: E 331 LYS cc_start: 0.8781 (mttp) cc_final: 0.8277 (mtpt) REVERT: E 348 ASP cc_start: 0.7501 (t0) cc_final: 0.7290 (m-30) REVERT: E 375 LYS cc_start: 0.8317 (tttt) cc_final: 0.7469 (mttp) REVERT: F 311 LYS cc_start: 0.8376 (tmtt) cc_final: 0.7463 (pptt) REVERT: F 331 LYS cc_start: 0.8908 (mttp) cc_final: 0.8626 (mtpt) REVERT: F 340 LYS cc_start: 0.8632 (mttt) cc_final: 0.8208 (mttp) outliers start: 5 outliers final: 3 residues processed: 104 average time/residue: 1.3835 time to fit residues: 147.4254 Evaluate side-chains 101 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 369 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 30 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.143275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.123090 restraints weight = 4313.102| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.60 r_work: 0.3824 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3710 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3576 Z= 0.235 Angle : 0.599 6.852 4782 Z= 0.293 Chirality : 0.051 0.135 534 Planarity : 0.004 0.026 612 Dihedral : 4.947 32.341 476 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.49 % Allowed : 20.90 % Favored : 77.61 % 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: -1.97 (0.34), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.015 0.002 PHE E 346 TYR 0.011 0.003 TYR A 310 ARG 0.001 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.406 Fit side-chains REVERT: A 317 LYS cc_start: 0.8284 (ptpp) cc_final: 0.7998 (ptmm) REVERT: A 331 LYS cc_start: 0.8660 (mttp) cc_final: 0.8346 (mtpm) REVERT: A 348 ASP cc_start: 0.7557 (t0) cc_final: 0.7311 (m-30) REVERT: B 311 LYS cc_start: 0.8255 (tttt) cc_final: 0.7717 (mmtt) REVERT: B 317 LYS cc_start: 0.8522 (ptpp) cc_final: 0.8128 (ptmt) REVERT: B 331 LYS cc_start: 0.8737 (mttp) cc_final: 0.8455 (mtpt) REVERT: B 343 LYS cc_start: 0.8180 (mtpp) cc_final: 0.7972 (ttmm) REVERT: B 358 ASP cc_start: 0.8628 (p0) cc_final: 0.8236 (p0) REVERT: C 317 LYS cc_start: 0.8328 (ptpp) cc_final: 0.7867 (ptmt) REVERT: C 331 LYS cc_start: 0.8790 (mttp) cc_final: 0.8401 (mtpt) REVERT: D 311 LYS cc_start: 0.8462 (tttt) cc_final: 0.7565 (pptt) REVERT: D 317 LYS cc_start: 0.8655 (ptpp) cc_final: 0.8099 (ptmm) REVERT: D 331 LYS cc_start: 0.8782 (mttp) cc_final: 0.8400 (mtpt) REVERT: D 340 LYS cc_start: 0.8747 (ttmm) cc_final: 0.8374 (mttp) REVERT: D 375 LYS cc_start: 0.8612 (tttt) cc_final: 0.7995 (mttp) REVERT: E 311 LYS cc_start: 0.8181 (tttt) cc_final: 0.7870 (ttmt) REVERT: E 317 LYS cc_start: 0.8250 (ptpp) cc_final: 0.7790 (ptmt) REVERT: E 321 LYS cc_start: 0.8532 (ttmm) cc_final: 0.8096 (ttmt) REVERT: E 331 LYS cc_start: 0.8846 (mttp) cc_final: 0.8414 (mtpt) REVERT: E 340 LYS cc_start: 0.8457 (ttmm) cc_final: 0.7961 (mttp) REVERT: F 311 LYS cc_start: 0.8385 (tttt) cc_final: 0.7507 (pptt) REVERT: F 331 LYS cc_start: 0.8909 (mttp) cc_final: 0.8679 (mtpt) REVERT: F 340 LYS cc_start: 0.8645 (mttt) cc_final: 0.8374 (mttm) REVERT: F 358 ASP cc_start: 0.8257 (p0) cc_final: 0.7905 (m-30) outliers start: 6 outliers final: 3 residues processed: 98 average time/residue: 1.4175 time to fit residues: 142.2850 Evaluate side-chains 90 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 369 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 15 optimal weight: 0.2980 chunk 22 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.143131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.122552 restraints weight = 4133.463| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.58 r_work: 0.3785 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3671 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3576 Z= 0.284 Angle : 0.616 7.543 4782 Z= 0.302 Chirality : 0.052 0.140 534 Planarity : 0.004 0.032 612 Dihedral : 4.930 31.668 476 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.74 % Allowed : 21.39 % Favored : 76.87 % 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: -1.87 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.017 0.002 PHE E 346 TYR 0.013 0.003 TYR A 310 ARG 0.001 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.399 Fit side-chains REVERT: A 311 LYS cc_start: 0.8245 (tttt) cc_final: 0.7875 (ttpt) REVERT: A 317 LYS cc_start: 0.8238 (ptpp) cc_final: 0.7746 (ptmt) REVERT: A 331 LYS cc_start: 0.8653 (mttp) cc_final: 0.8320 (mtpm) REVERT: A 375 LYS cc_start: 0.8206 (tttt) cc_final: 0.7498 (mttm) REVERT: B 311 LYS cc_start: 0.8267 (tttt) cc_final: 0.7738 (mmtt) REVERT: B 317 LYS cc_start: 0.8446 (ptpp) cc_final: 0.8039 (ptmt) REVERT: B 331 LYS cc_start: 0.8664 (mttp) cc_final: 0.8342 (mtpt) REVERT: B 343 LYS cc_start: 0.8155 (mtpp) cc_final: 0.7953 (ttmm) REVERT: B 358 ASP cc_start: 0.8680 (p0) cc_final: 0.8330 (p0) REVERT: C 317 LYS cc_start: 0.8329 (ptpp) cc_final: 0.7890 (ptmt) REVERT: C 331 LYS cc_start: 0.8834 (mttp) cc_final: 0.8440 (mtpt) REVERT: C 356 SER cc_start: 0.8796 (p) cc_final: 0.8557 (m) REVERT: D 311 LYS cc_start: 0.8490 (tttt) cc_final: 0.7559 (pptt) REVERT: D 317 LYS cc_start: 0.8593 (ptpp) cc_final: 0.7984 (ptmt) REVERT: D 331 LYS cc_start: 0.8895 (mttp) cc_final: 0.8415 (mtpt) REVERT: D 340 LYS cc_start: 0.8804 (ttmm) cc_final: 0.8433 (mttp) REVERT: D 349 ARG cc_start: 0.7606 (ptm160) cc_final: 0.5144 (ppt170) REVERT: D 375 LYS cc_start: 0.8565 (tttt) cc_final: 0.7982 (mttp) REVERT: E 311 LYS cc_start: 0.8213 (tttt) cc_final: 0.7871 (ttmt) REVERT: E 331 LYS cc_start: 0.8837 (mttp) cc_final: 0.8357 (mtpt) REVERT: F 311 LYS cc_start: 0.8450 (tttt) cc_final: 0.7561 (pptt) REVERT: F 331 LYS cc_start: 0.8968 (mttp) cc_final: 0.8678 (mtpt) REVERT: F 340 LYS cc_start: 0.8694 (mttt) cc_final: 0.8345 (mttp) REVERT: F 358 ASP cc_start: 0.8247 (p0) cc_final: 0.7852 (m-30) outliers start: 7 outliers final: 5 residues processed: 97 average time/residue: 1.4350 time to fit residues: 142.5109 Evaluate side-chains 93 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 1 optimal weight: 0.0470 chunk 7 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.141687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.120908 restraints weight = 4190.512| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.58 r_work: 0.3767 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 3576 Z= 0.321 Angle : 0.642 8.503 4782 Z= 0.312 Chirality : 0.052 0.146 534 Planarity : 0.004 0.035 612 Dihedral : 4.963 31.521 476 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.74 % Allowed : 22.39 % Favored : 75.87 % 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 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.019 0.002 PHE E 346 TYR 0.015 0.004 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) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.416 Fit side-chains REVERT: A 311 LYS cc_start: 0.8216 (tttt) cc_final: 0.7835 (ttpt) REVERT: A 317 LYS cc_start: 0.8259 (ptpp) cc_final: 0.8037 (ptmm) REVERT: A 331 LYS cc_start: 0.8699 (mttp) cc_final: 0.8134 (mtpt) REVERT: A 375 LYS cc_start: 0.8207 (tttt) cc_final: 0.7508 (mttm) REVERT: B 311 LYS cc_start: 0.8275 (tttt) cc_final: 0.7751 (mmtt) REVERT: B 317 LYS cc_start: 0.8437 (ptpp) cc_final: 0.8017 (ptmt) REVERT: B 331 LYS cc_start: 0.8737 (mttp) cc_final: 0.8360 (mtpt) REVERT: B 358 ASP cc_start: 0.8695 (p0) cc_final: 0.8311 (p0) REVERT: C 311 LYS cc_start: 0.8340 (tttt) cc_final: 0.7800 (mmtt) REVERT: C 317 LYS cc_start: 0.8361 (ptpp) cc_final: 0.7915 (ptmt) REVERT: C 331 LYS cc_start: 0.8828 (mttp) cc_final: 0.8410 (mtpt) REVERT: C 356 SER cc_start: 0.8792 (p) cc_final: 0.8554 (m) REVERT: C 375 LYS cc_start: 0.8074 (tttt) cc_final: 0.7353 (mttm) REVERT: D 311 LYS cc_start: 0.8496 (tttt) cc_final: 0.7566 (pptt) REVERT: D 317 LYS cc_start: 0.8576 (ptpp) cc_final: 0.7992 (ptmt) REVERT: D 331 LYS cc_start: 0.8904 (mttp) cc_final: 0.8389 (mtpt) REVERT: D 340 LYS cc_start: 0.8882 (ttmm) cc_final: 0.8507 (mttp) REVERT: D 349 ARG cc_start: 0.7588 (ptm160) cc_final: 0.5162 (ppt170) REVERT: D 375 LYS cc_start: 0.8563 (tttt) cc_final: 0.7966 (mttp) REVERT: E 311 LYS cc_start: 0.8245 (tttt) cc_final: 0.7898 (ttmt) REVERT: E 331 LYS cc_start: 0.8866 (mttp) cc_final: 0.8358 (mtpt) REVERT: F 311 LYS cc_start: 0.8441 (tttt) cc_final: 0.7563 (pptt) REVERT: F 331 LYS cc_start: 0.9004 (mttp) cc_final: 0.8675 (mtpt) REVERT: F 340 LYS cc_start: 0.8708 (mttt) cc_final: 0.8317 (mttp) REVERT: F 370 LYS cc_start: 0.8709 (tttp) cc_final: 0.8464 (tttt) outliers start: 7 outliers final: 5 residues processed: 96 average time/residue: 1.4949 time to fit residues: 146.8550 Evaluate side-chains 94 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.140795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.121095 restraints weight = 4202.445| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.45 r_work: 0.3789 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 3576 Z= 0.395 Angle : 0.689 8.825 4782 Z= 0.333 Chirality : 0.053 0.155 534 Planarity : 0.004 0.036 612 Dihedral : 5.102 30.151 476 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.99 % Allowed : 22.39 % Favored : 75.62 % 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: -1.89 (0.34), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.023 0.003 PHE E 346 TYR 0.018 0.005 TYR E 310 ARG 0.001 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.438 Fit side-chains REVERT: A 311 LYS cc_start: 0.8232 (tttt) cc_final: 0.7819 (ttpt) REVERT: A 317 LYS cc_start: 0.8276 (ptpp) cc_final: 0.8052 (ptmm) REVERT: A 331 LYS cc_start: 0.8697 (mttp) cc_final: 0.8136 (mtpt) REVERT: A 375 LYS cc_start: 0.8246 (tttt) cc_final: 0.7594 (mttm) REVERT: B 311 LYS cc_start: 0.8311 (tttt) cc_final: 0.7782 (mmtt) REVERT: B 317 LYS cc_start: 0.8512 (ptpp) cc_final: 0.8082 (ptmt) REVERT: B 331 LYS cc_start: 0.8711 (mttp) cc_final: 0.8344 (mtpt) REVERT: B 348 ASP cc_start: 0.8313 (m-30) cc_final: 0.8106 (m-30) REVERT: B 358 ASP cc_start: 0.8703 (p0) cc_final: 0.8289 (p0) REVERT: C 311 LYS cc_start: 0.8332 (tttt) cc_final: 0.7822 (mmtm) REVERT: C 317 LYS cc_start: 0.8381 (ptpp) cc_final: 0.7912 (ptmt) REVERT: C 331 LYS cc_start: 0.8782 (mttp) cc_final: 0.8342 (mtpt) REVERT: C 356 SER cc_start: 0.8835 (p) cc_final: 0.8592 (m) REVERT: C 375 LYS cc_start: 0.8095 (tttt) cc_final: 0.7346 (mttm) REVERT: D 311 LYS cc_start: 0.8519 (tttt) cc_final: 0.7607 (pptt) REVERT: D 317 LYS cc_start: 0.8625 (ptpp) cc_final: 0.8104 (ptmt) REVERT: D 331 LYS cc_start: 0.8892 (mttp) cc_final: 0.8373 (mtpt) REVERT: D 340 LYS cc_start: 0.8861 (ttmm) cc_final: 0.8502 (mttp) REVERT: D 349 ARG cc_start: 0.7585 (ptm160) cc_final: 0.5121 (ppt170) REVERT: D 375 LYS cc_start: 0.8605 (tttt) cc_final: 0.8010 (mttp) REVERT: D 379 ARG cc_start: 0.8260 (mpt-90) cc_final: 0.6425 (pmt170) REVERT: E 311 LYS cc_start: 0.8279 (tttt) cc_final: 0.7903 (ttmt) REVERT: E 331 LYS cc_start: 0.8845 (mttp) cc_final: 0.8338 (mtpt) REVERT: F 311 LYS cc_start: 0.8513 (tttt) cc_final: 0.7623 (pptt) REVERT: F 331 LYS cc_start: 0.9015 (mttp) cc_final: 0.8686 (mtpt) REVERT: F 340 LYS cc_start: 0.8718 (mttt) cc_final: 0.8327 (mttp) REVERT: F 358 ASP cc_start: 0.8285 (p0) cc_final: 0.7768 (m-30) outliers start: 8 outliers final: 6 residues processed: 104 average time/residue: 1.5515 time to fit residues: 164.9160 Evaluate side-chains 103 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.143455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.123745 restraints weight = 4201.554| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.47 r_work: 0.3820 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3709 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 3576 Z= 0.302 Angle : 0.663 9.289 4782 Z= 0.315 Chirality : 0.052 0.148 534 Planarity : 0.003 0.037 612 Dihedral : 4.949 31.655 476 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.99 % Allowed : 23.13 % Favored : 74.88 % 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 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 362 PHE 0.017 0.002 PHE E 346 TYR 0.014 0.003 TYR A 310 ARG 0.001 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.409 Fit side-chains REVERT: A 311 LYS cc_start: 0.8205 (tttt) cc_final: 0.7814 (ttpt) REVERT: A 317 LYS cc_start: 0.8270 (ptpp) cc_final: 0.8042 (ptmm) REVERT: A 331 LYS cc_start: 0.8669 (mttp) cc_final: 0.8122 (mtpt) REVERT: A 375 LYS cc_start: 0.8239 (tttt) cc_final: 0.7587 (mttm) REVERT: B 311 LYS cc_start: 0.8285 (tttt) cc_final: 0.7753 (mmtt) REVERT: B 317 LYS cc_start: 0.8497 (ptpp) cc_final: 0.8083 (ptmt) REVERT: B 331 LYS cc_start: 0.8710 (mttp) cc_final: 0.8345 (mtpt) REVERT: B 358 ASP cc_start: 0.8648 (p0) cc_final: 0.8231 (p0) REVERT: C 311 LYS cc_start: 0.8312 (tttt) cc_final: 0.7805 (mmtt) REVERT: C 317 LYS cc_start: 0.8391 (ptpp) cc_final: 0.7916 (ptmt) REVERT: C 331 LYS cc_start: 0.8779 (mttp) cc_final: 0.8369 (mtpt) REVERT: C 356 SER cc_start: 0.8792 (p) cc_final: 0.8547 (m) REVERT: C 375 LYS cc_start: 0.8072 (tttt) cc_final: 0.7374 (mttm) REVERT: D 311 LYS cc_start: 0.8477 (tttt) cc_final: 0.7563 (pptt) REVERT: D 317 LYS cc_start: 0.8616 (ptpp) cc_final: 0.8083 (ptmt) REVERT: D 331 LYS cc_start: 0.8871 (mttp) cc_final: 0.8354 (mtpt) REVERT: D 340 LYS cc_start: 0.8888 (ttmm) cc_final: 0.8524 (mttp) REVERT: D 349 ARG cc_start: 0.7607 (ptm160) cc_final: 0.5151 (ppt170) REVERT: D 375 LYS cc_start: 0.8584 (tttt) cc_final: 0.8017 (mttp) REVERT: D 379 ARG cc_start: 0.8259 (mpt-90) cc_final: 0.6439 (pmt170) REVERT: E 311 LYS cc_start: 0.8289 (tttt) cc_final: 0.7914 (ttmt) REVERT: E 331 LYS cc_start: 0.8825 (mttp) cc_final: 0.8321 (mtpt) REVERT: F 311 LYS cc_start: 0.8484 (tttt) cc_final: 0.7578 (pptt) REVERT: F 331 LYS cc_start: 0.9006 (mttp) cc_final: 0.8670 (mtpt) REVERT: F 340 LYS cc_start: 0.8697 (mttt) cc_final: 0.8308 (mttp) REVERT: F 358 ASP cc_start: 0.8240 (p0) cc_final: 0.7779 (m-30) REVERT: F 370 LYS cc_start: 0.8698 (tttp) cc_final: 0.8454 (tttt) outliers start: 8 outliers final: 6 residues processed: 97 average time/residue: 1.5359 time to fit residues: 152.3565 Evaluate side-chains 98 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 28 optimal weight: 0.0670 chunk 30 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.153192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.133675 restraints weight = 3977.940| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 2.46 r_work: 0.3957 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3845 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3576 Z= 0.148 Angle : 0.612 9.414 4782 Z= 0.282 Chirality : 0.050 0.126 534 Planarity : 0.003 0.036 612 Dihedral : 4.554 37.556 476 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.24 % Allowed : 24.13 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.007 0.001 PHE E 346 TYR 0.006 0.001 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) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.391 Fit side-chains REVERT: A 317 LYS cc_start: 0.8226 (ptpp) cc_final: 0.7950 (ptmm) REVERT: A 331 LYS cc_start: 0.8576 (mttp) cc_final: 0.8085 (mtpt) REVERT: A 375 LYS cc_start: 0.8232 (tttt) cc_final: 0.7612 (mttm) REVERT: B 317 LYS cc_start: 0.8532 (ptpp) cc_final: 0.8132 (ptmt) REVERT: B 331 LYS cc_start: 0.8687 (mttp) cc_final: 0.8401 (mtpt) REVERT: B 358 ASP cc_start: 0.8504 (p0) cc_final: 0.8135 (p0) REVERT: C 317 LYS cc_start: 0.8404 (ptpp) cc_final: 0.7953 (ptmt) REVERT: C 331 LYS cc_start: 0.8727 (mttp) cc_final: 0.8289 (mtpt) REVERT: C 356 SER cc_start: 0.8817 (p) cc_final: 0.8566 (m) REVERT: C 375 LYS cc_start: 0.8088 (tttt) cc_final: 0.7441 (mttm) REVERT: D 311 LYS cc_start: 0.8369 (tttt) cc_final: 0.7503 (pptt) REVERT: D 317 LYS cc_start: 0.8555 (ptpp) cc_final: 0.7950 (ptmt) REVERT: D 331 LYS cc_start: 0.8717 (mttp) cc_final: 0.8250 (mtpt) REVERT: D 340 LYS cc_start: 0.8740 (ttmm) cc_final: 0.8316 (mttm) REVERT: D 349 ARG cc_start: 0.7667 (ptm160) cc_final: 0.5231 (ppt170) REVERT: D 375 LYS cc_start: 0.8584 (tttt) cc_final: 0.8033 (mttp) REVERT: E 311 LYS cc_start: 0.8113 (tttt) cc_final: 0.7832 (ttmt) REVERT: E 331 LYS cc_start: 0.8769 (mttp) cc_final: 0.8356 (mtpt) REVERT: E 356 SER cc_start: 0.8760 (m) cc_final: 0.8417 (t) REVERT: F 311 LYS cc_start: 0.8421 (tttt) cc_final: 0.7553 (pptt) REVERT: F 331 LYS cc_start: 0.8798 (mttp) cc_final: 0.8518 (mtpt) REVERT: F 340 LYS cc_start: 0.8603 (mttt) cc_final: 0.8299 (mttp) REVERT: F 370 LYS cc_start: 0.8672 (tttp) cc_final: 0.8462 (tttt) outliers start: 5 outliers final: 1 residues processed: 100 average time/residue: 1.3883 time to fit residues: 142.3338 Evaluate side-chains 91 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 34 optimal weight: 0.0870 chunk 38 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 overall best weight: 2.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.143317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.123611 restraints weight = 4202.532| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 2.46 r_work: 0.3831 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3719 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3576 Z= 0.309 Angle : 0.696 9.524 4782 Z= 0.324 Chirality : 0.052 0.144 534 Planarity : 0.004 0.043 612 Dihedral : 4.810 32.512 476 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.75 % Allowed : 26.37 % Favored : 72.89 % 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 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.018 0.002 PHE E 346 TYR 0.015 0.004 TYR F 310 ARG 0.001 0.000 ARG C 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 0.404 Fit side-chains REVERT: A 317 LYS cc_start: 0.8268 (ptpp) cc_final: 0.7808 (ptmt) REVERT: A 331 LYS cc_start: 0.8631 (mttp) cc_final: 0.8069 (mtpt) REVERT: B 311 LYS cc_start: 0.8273 (tttt) cc_final: 0.7733 (mmtt) REVERT: B 317 LYS cc_start: 0.8505 (ptpp) cc_final: 0.8092 (ptmt) REVERT: B 331 LYS cc_start: 0.8642 (mttp) cc_final: 0.8301 (mtpt) REVERT: B 358 ASP cc_start: 0.8660 (p0) cc_final: 0.8288 (p0) REVERT: C 311 LYS cc_start: 0.8323 (tttt) cc_final: 0.7842 (mmtt) REVERT: C 317 LYS cc_start: 0.8350 (ptpp) cc_final: 0.7903 (ptmt) REVERT: C 331 LYS cc_start: 0.8797 (mttp) cc_final: 0.8304 (mtpt) REVERT: C 375 LYS cc_start: 0.8055 (tttt) cc_final: 0.7365 (mttm) REVERT: D 311 LYS cc_start: 0.8461 (tttt) cc_final: 0.7581 (pptt) REVERT: D 317 LYS cc_start: 0.8613 (ptpp) cc_final: 0.8083 (ptmt) REVERT: D 331 LYS cc_start: 0.8879 (mttp) cc_final: 0.8364 (mtpt) REVERT: D 340 LYS cc_start: 0.8891 (ttmm) cc_final: 0.8537 (mttp) REVERT: D 349 ARG cc_start: 0.7610 (ptm160) cc_final: 0.5144 (ppt170) REVERT: D 375 LYS cc_start: 0.8592 (tttt) cc_final: 0.7994 (mttp) REVERT: D 379 ARG cc_start: 0.8249 (mpt-90) cc_final: 0.6386 (pmt170) REVERT: E 311 LYS cc_start: 0.8184 (tttt) cc_final: 0.7864 (ttmt) REVERT: E 331 LYS cc_start: 0.8853 (mttp) cc_final: 0.8391 (mtpt) REVERT: F 311 LYS cc_start: 0.8438 (tttt) cc_final: 0.7537 (pptt) REVERT: F 331 LYS cc_start: 0.8971 (mttp) cc_final: 0.8696 (mtpt) REVERT: F 370 LYS cc_start: 0.8678 (tttp) cc_final: 0.8456 (tttt) outliers start: 3 outliers final: 2 residues processed: 97 average time/residue: 1.5004 time to fit residues: 148.9326 Evaluate side-chains 96 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 94 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.140929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.121103 restraints weight = 4214.104| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 2.46 r_work: 0.3796 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3683 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 3576 Z= 0.385 Angle : 0.729 9.598 4782 Z= 0.344 Chirality : 0.053 0.151 534 Planarity : 0.004 0.043 612 Dihedral : 5.034 31.266 476 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.00 % Allowed : 27.11 % Favored : 71.89 % 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: -1.89 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.021 0.003 PHE E 346 TYR 0.017 0.004 TYR F 310 ARG 0.001 0.000 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3611.01 seconds wall clock time: 64 minutes 36.38 seconds (3876.38 seconds total)