Starting phenix.real_space_refine on Fri Aug 22 13:48:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eog_19854/08_2025/9eog_19854.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eog_19854/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9eog_19854/08_2025/9eog_19854.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eog_19854/08_2025/9eog_19854.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9eog_19854/08_2025/9eog_19854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eog_19854/08_2025/9eog_19854.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: B, C, D, E, F Time building chain proxies: 0.80, per 1000 atoms: 0.23 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: 0.29 Conformation dependent library (CDL) restraints added in 137.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.14 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: 0.45 Time building geometry restraints manager: 0.41 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.360 Find NCS groups from input model: 0.030 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:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.240 ------------------------------------------------------------------------------- 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= 0.633 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.001 ARG E 379 TYR 0.049 0.017 TYR C 310 PHE 0.049 0.009 PHE C 346 HIS 0.012 0.004 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00894 ( 3576) covalent geometry : angle 1.62832 ( 4782) hydrogen bonds : bond 0.14504 ( 58) hydrogen bonds : angle 8.35773 ( 174) *********************** 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 : 0.182 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: 0.7250 (tmtt) 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: 0.8138 time to fit residues: 116.0530 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 : 0.144 ------------------------------------------------------------------------------- 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 24 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 GLN C 374 HIS D 307 GLN D 336 GLN D 351 GLN 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.150065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.129961 restraints weight = 4087.304| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.57 r_work: 0.3896 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3784 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3576 Z= 0.132 Angle : 0.617 5.399 4782 Z= 0.313 Chirality : 0.052 0.148 534 Planarity : 0.004 0.029 612 Dihedral : 6.125 34.765 484 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.74 % Allowed : 17.16 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.02 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 379 TYR 0.005 0.001 TYR A 310 PHE 0.018 0.002 PHE A 346 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 3576) covalent geometry : angle 0.61738 ( 4782) hydrogen bonds : bond 0.02651 ( 58) hydrogen bonds : angle 5.92821 ( 174) *********************** 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 122 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.139 Fit side-chains REVERT: A 317 LYS cc_start: 0.8077 (ptpp) cc_final: 0.7693 (ptmt) REVERT: A 321 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.7965 (mtpt) REVERT: A 340 LYS cc_start: 0.8451 (ttmm) cc_final: 0.7843 (mttp) REVERT: A 348 ASP cc_start: 0.7422 (t0) cc_final: 0.7207 (m-30) REVERT: B 317 LYS cc_start: 0.8469 (ptpp) cc_final: 0.8025 (ptmt) REVERT: B 331 LYS cc_start: 0.8613 (mttp) cc_final: 0.8234 (mtpt) REVERT: B 358 ASP cc_start: 0.8511 (p0) cc_final: 0.8009 (p0) REVERT: C 317 LYS cc_start: 0.8312 (ptpp) cc_final: 0.7866 (ptmt) REVERT: C 331 LYS cc_start: 0.8709 (mttp) cc_final: 0.8276 (mtpm) REVERT: C 348 ASP cc_start: 0.7630 (t0) cc_final: 0.7418 (m-30) REVERT: C 358 ASP cc_start: 0.8040 (p0) cc_final: 0.7546 (p0) REVERT: D 311 LYS cc_start: 0.8432 (tmtt) cc_final: 0.7518 (pptt) REVERT: D 317 LYS cc_start: 0.8669 (ptpp) cc_final: 0.8117 (ptmm) REVERT: D 331 LYS cc_start: 0.8683 (mttp) cc_final: 0.8179 (mtpt) REVERT: D 340 LYS cc_start: 0.8628 (ttmm) cc_final: 0.8192 (mttm) REVERT: D 347 LYS cc_start: 0.8247 (ptmt) cc_final: 0.7649 (ptmt) REVERT: D 348 ASP cc_start: 0.7982 (t0) cc_final: 0.7691 (m-30) REVERT: D 349 ARG cc_start: 0.7565 (ptm160) cc_final: 0.7360 (ptm160) REVERT: D 358 ASP cc_start: 0.8383 (p0) cc_final: 0.8047 (p0) REVERT: D 375 LYS cc_start: 0.8537 (tttt) cc_final: 0.7954 (mttm) REVERT: E 311 LYS cc_start: 0.8098 (tmtt) cc_final: 0.7743 (ttmt) REVERT: E 317 LYS cc_start: 0.8142 (ptpp) cc_final: 0.7619 (ptmt) REVERT: E 331 LYS cc_start: 0.8747 (mttp) cc_final: 0.8244 (mtpt) REVERT: E 340 LYS cc_start: 0.8341 (ttmm) cc_final: 0.7953 (mttm) REVERT: E 348 ASP cc_start: 0.7546 (t0) cc_final: 0.7336 (m-30) REVERT: E 353 LYS cc_start: 0.8495 (mtpt) cc_final: 0.8183 (ttpp) REVERT: E 375 LYS cc_start: 0.8313 (tttt) cc_final: 0.7509 (mttp) REVERT: F 311 LYS cc_start: 0.8352 (tmtt) cc_final: 0.7550 (pptt) REVERT: F 317 LYS cc_start: 0.8601 (ptpt) cc_final: 0.8278 (ptmt) REVERT: F 331 LYS cc_start: 0.8735 (mttp) cc_final: 0.8437 (mtpt) REVERT: F 340 LYS cc_start: 0.8570 (mttt) cc_final: 0.8278 (mptm) outliers start: 7 outliers final: 1 residues processed: 120 average time/residue: 0.5931 time to fit residues: 73.0080 Evaluate side-chains 108 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 LYS 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 39 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 overall best weight: 3.1986 ------------------------------------------------------------------------------- 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** B 359 ASN C 330 HIS D 336 GLN D 368 ASN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.140563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.120808 restraints weight = 4280.756| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.55 r_work: 0.3771 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3662 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3576 Z= 0.238 Angle : 0.676 6.444 4782 Z= 0.336 Chirality : 0.055 0.145 534 Planarity : 0.004 0.028 612 Dihedral : 5.521 29.251 480 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.24 % Allowed : 22.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.46 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 349 TYR 0.017 0.004 TYR E 310 PHE 0.022 0.003 PHE E 346 HIS 0.003 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00543 ( 3576) covalent geometry : angle 0.67598 ( 4782) hydrogen bonds : bond 0.02888 ( 58) hydrogen bonds : angle 5.80435 ( 174) *********************** 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 124 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.147 Fit side-chains REVERT: A 311 LYS cc_start: 0.8207 (tmtt) cc_final: 0.7815 (ttpt) REVERT: A 317 LYS cc_start: 0.8207 (ptpp) cc_final: 0.7702 (ptmt) REVERT: A 331 LYS cc_start: 0.8631 (mttp) cc_final: 0.8225 (mtpm) REVERT: A 340 LYS cc_start: 0.8513 (ttmm) cc_final: 0.8010 (mttp) REVERT: A 348 ASP cc_start: 0.7623 (t0) cc_final: 0.7285 (m-30) REVERT: A 375 LYS cc_start: 0.8195 (tttt) cc_final: 0.7517 (mttm) REVERT: B 311 LYS cc_start: 0.8273 (tmtt) cc_final: 0.7716 (mmtt) REVERT: B 317 LYS cc_start: 0.8450 (ptpp) cc_final: 0.8025 (ptmt) REVERT: B 331 LYS cc_start: 0.8648 (mttp) cc_final: 0.8280 (mtpt) REVERT: B 358 ASP cc_start: 0.8685 (p0) cc_final: 0.8319 (p0) REVERT: C 311 LYS cc_start: 0.8395 (tmtt) cc_final: 0.7818 (mmtt) REVERT: C 317 LYS cc_start: 0.8284 (ptpp) cc_final: 0.7833 (ptmt) REVERT: C 331 LYS cc_start: 0.8770 (mttp) cc_final: 0.8278 (mtpt) REVERT: C 348 ASP cc_start: 0.7781 (t0) cc_final: 0.7537 (m-30) REVERT: C 358 ASP cc_start: 0.8240 (p0) cc_final: 0.7656 (p0) REVERT: C 375 LYS cc_start: 0.7980 (tttt) cc_final: 0.7269 (mttm) REVERT: D 311 LYS cc_start: 0.8534 (tmtt) cc_final: 0.7594 (pptt) REVERT: D 317 LYS cc_start: 0.8614 (ptpp) cc_final: 0.8074 (ptmt) REVERT: D 331 LYS cc_start: 0.8916 (mttp) cc_final: 0.8277 (mtpt) REVERT: D 340 LYS cc_start: 0.8892 (ttmm) cc_final: 0.8494 (mttp) REVERT: D 347 LYS cc_start: 0.8395 (ptmt) cc_final: 0.7719 (ptmt) REVERT: D 358 ASP cc_start: 0.8439 (p0) cc_final: 0.8208 (p0) REVERT: D 375 LYS cc_start: 0.8680 (tttt) cc_final: 0.7993 (mttm) REVERT: E 311 LYS cc_start: 0.8248 (tmtt) cc_final: 0.7847 (ttmt) REVERT: E 317 LYS cc_start: 0.8115 (ptpp) cc_final: 0.7659 (ptmt) REVERT: E 321 LYS cc_start: 0.8552 (ttmm) cc_final: 0.8060 (mtpt) REVERT: E 331 LYS cc_start: 0.8851 (mttp) cc_final: 0.8307 (mtpt) REVERT: E 348 ASP cc_start: 0.7642 (t0) cc_final: 0.7344 (m-30) REVERT: F 311 LYS cc_start: 0.8455 (tmtt) cc_final: 0.7530 (pptt) REVERT: F 317 LYS cc_start: 0.8623 (ptpt) cc_final: 0.8232 (ptmt) REVERT: F 331 LYS cc_start: 0.9000 (mttp) cc_final: 0.8690 (mtpt) REVERT: F 338 GLU cc_start: 0.8694 (tt0) cc_final: 0.8491 (tt0) REVERT: F 340 LYS cc_start: 0.8715 (mttt) cc_final: 0.8300 (mttp) outliers start: 9 outliers final: 5 residues processed: 119 average time/residue: 0.6917 time to fit residues: 84.1633 Evaluate side-chains 112 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.101 ------------------------------------------------------------------------------- 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 350 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 6 optimal weight: 0.4980 overall best weight: 3.8786 ------------------------------------------------------------------------------- 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 = 0.4156 r_free = 0.4156 target = 0.137820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.117429 restraints weight = 4254.312| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.58 r_work: 0.3757 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 3576 Z= 0.276 Angle : 0.696 7.798 4782 Z= 0.346 Chirality : 0.055 0.154 534 Planarity : 0.004 0.028 612 Dihedral : 5.390 29.153 476 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.23 % Allowed : 20.65 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.19 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 379 TYR 0.018 0.005 TYR A 310 PHE 0.023 0.003 PHE E 346 HIS 0.003 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00637 ( 3576) covalent geometry : angle 0.69567 ( 4782) hydrogen bonds : bond 0.02906 ( 58) hydrogen bonds : angle 5.86339 ( 174) *********************** 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 120 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.149 Fit side-chains REVERT: A 311 LYS cc_start: 0.8266 (tttt) cc_final: 0.7860 (ttpt) REVERT: A 317 LYS cc_start: 0.8180 (ptpp) cc_final: 0.7940 (ptmm) REVERT: A 331 LYS cc_start: 0.8658 (mttp) cc_final: 0.8243 (mtpm) REVERT: A 348 ASP cc_start: 0.7697 (t0) cc_final: 0.7352 (m-30) REVERT: A 375 LYS cc_start: 0.8185 (tttt) cc_final: 0.7479 (mttm) REVERT: B 311 LYS cc_start: 0.8277 (tttt) cc_final: 0.7727 (mmtt) REVERT: B 317 LYS cc_start: 0.8427 (ptpp) cc_final: 0.7989 (ptmt) REVERT: B 331 LYS cc_start: 0.8696 (mttp) cc_final: 0.8312 (mtpt) REVERT: B 347 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.7748 (ptmm) REVERT: B 358 ASP cc_start: 0.8757 (p0) cc_final: 0.8424 (p0) REVERT: C 311 LYS cc_start: 0.8375 (tttt) cc_final: 0.7824 (mmtt) REVERT: C 317 LYS cc_start: 0.8285 (ptpp) cc_final: 0.7836 (ptmt) REVERT: C 331 LYS cc_start: 0.8822 (mttp) cc_final: 0.8355 (mtpt) REVERT: C 347 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7775 (ptpp) REVERT: C 348 ASP cc_start: 0.7871 (t0) cc_final: 0.7661 (m-30) REVERT: C 358 ASP cc_start: 0.8294 (p0) cc_final: 0.7753 (p0) REVERT: D 311 LYS cc_start: 0.8582 (tttt) cc_final: 0.7602 (pptt) REVERT: D 317 LYS cc_start: 0.8608 (ptpp) cc_final: 0.8019 (ptmt) REVERT: D 331 LYS cc_start: 0.8866 (mttp) cc_final: 0.8274 (mtpt) REVERT: D 340 LYS cc_start: 0.8886 (ttmm) cc_final: 0.8507 (mttp) REVERT: D 347 LYS cc_start: 0.8388 (ptmt) cc_final: 0.7706 (ptmt) REVERT: D 358 ASP cc_start: 0.8493 (p0) cc_final: 0.8225 (p0) REVERT: D 375 LYS cc_start: 0.8636 (tttt) cc_final: 0.7991 (mttp) REVERT: E 311 LYS cc_start: 0.8305 (tttt) cc_final: 0.7919 (ttmt) REVERT: E 331 LYS cc_start: 0.8843 (mttp) cc_final: 0.8295 (mtpt) REVERT: E 348 ASP cc_start: 0.7713 (t0) cc_final: 0.7390 (m-30) REVERT: F 311 LYS cc_start: 0.8555 (tttt) cc_final: 0.7641 (pptt) REVERT: F 317 LYS cc_start: 0.8626 (ptpt) cc_final: 0.8274 (ptmt) REVERT: F 331 LYS cc_start: 0.9023 (mttp) cc_final: 0.8655 (mtpt) REVERT: F 340 LYS cc_start: 0.8721 (mttt) cc_final: 0.8344 (mttp) outliers start: 13 outliers final: 8 residues processed: 115 average time/residue: 0.7175 time to fit residues: 84.2164 Evaluate side-chains 114 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.4219 r_free = 0.4219 target = 0.143686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.123269 restraints weight = 4088.860| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.56 r_work: 0.3832 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3717 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3576 Z= 0.154 Angle : 0.621 8.132 4782 Z= 0.301 Chirality : 0.051 0.137 534 Planarity : 0.003 0.025 612 Dihedral : 4.959 32.842 476 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.74 % Allowed : 23.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 379 TYR 0.010 0.002 TYR A 310 PHE 0.014 0.002 PHE E 346 HIS 0.002 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 3576) covalent geometry : angle 0.62101 ( 4782) hydrogen bonds : bond 0.02448 ( 58) hydrogen bonds : angle 5.64226 ( 174) *********************** 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 98 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.177 Fit side-chains REVERT: A 317 LYS cc_start: 0.8160 (ptpp) cc_final: 0.7931 (ptmm) REVERT: A 331 LYS cc_start: 0.8595 (mttp) cc_final: 0.8242 (mtpm) REVERT: A 348 ASP cc_start: 0.7654 (t0) cc_final: 0.7356 (m-30) REVERT: B 311 LYS cc_start: 0.8263 (tttt) cc_final: 0.7686 (mmtm) REVERT: B 317 LYS cc_start: 0.8411 (ptpp) cc_final: 0.8004 (ptmt) REVERT: B 331 LYS cc_start: 0.8699 (mttp) cc_final: 0.8347 (mtpt) REVERT: B 343 LYS cc_start: 0.8135 (mtpp) cc_final: 0.7934 (ttmm) REVERT: B 358 ASP cc_start: 0.8669 (p0) cc_final: 0.8337 (p0) REVERT: C 317 LYS cc_start: 0.8301 (ptpp) cc_final: 0.7852 (ptmt) REVERT: C 331 LYS cc_start: 0.8776 (mttp) cc_final: 0.8369 (mtpt) REVERT: C 348 ASP cc_start: 0.7782 (t0) cc_final: 0.7563 (m-30) REVERT: C 356 SER cc_start: 0.8749 (p) cc_final: 0.8512 (m) REVERT: D 311 LYS cc_start: 0.8470 (tttt) cc_final: 0.7512 (pptt) REVERT: D 317 LYS cc_start: 0.8585 (ptpp) cc_final: 0.7984 (ptmt) REVERT: D 331 LYS cc_start: 0.8773 (mttp) cc_final: 0.8353 (mtpt) REVERT: D 340 LYS cc_start: 0.8780 (ttmm) cc_final: 0.8397 (mttp) REVERT: D 350 VAL cc_start: 0.8941 (OUTLIER) cc_final: 0.8738 (m) REVERT: D 358 ASP cc_start: 0.8348 (p0) cc_final: 0.8142 (p0) REVERT: D 375 LYS cc_start: 0.8546 (tttt) cc_final: 0.7961 (mttp) REVERT: E 311 LYS cc_start: 0.8204 (tttt) cc_final: 0.7854 (ttmt) REVERT: E 331 LYS cc_start: 0.8767 (mttp) cc_final: 0.8255 (mtpt) REVERT: E 358 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7535 (p0) REVERT: F 311 LYS cc_start: 0.8446 (tttt) cc_final: 0.7534 (pptt) REVERT: F 317 LYS cc_start: 0.8533 (ptpt) cc_final: 0.8021 (ptmt) REVERT: F 331 LYS cc_start: 0.8944 (mttp) cc_final: 0.8618 (mtpt) REVERT: F 340 LYS cc_start: 0.8677 (mttt) cc_final: 0.8322 (mttp) REVERT: F 370 LYS cc_start: 0.8675 (tttp) cc_final: 0.8430 (tttt) outliers start: 7 outliers final: 3 residues processed: 95 average time/residue: 0.7041 time to fit residues: 68.4271 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 : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 358 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.4212 r_free = 0.4212 target = 0.142827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.122289 restraints weight = 4133.966| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 2.57 r_work: 0.3792 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3576 Z= 0.173 Angle : 0.630 8.473 4782 Z= 0.303 Chirality : 0.051 0.138 534 Planarity : 0.003 0.024 612 Dihedral : 4.881 32.090 476 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.74 % Allowed : 23.88 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 379 TYR 0.012 0.003 TYR A 310 PHE 0.016 0.002 PHE E 346 HIS 0.002 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 3576) covalent geometry : angle 0.62960 ( 4782) hydrogen bonds : bond 0.02424 ( 58) hydrogen bonds : angle 5.56575 ( 174) *********************** 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 99 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.153 Fit side-chains REVERT: A 317 LYS cc_start: 0.8222 (ptpp) cc_final: 0.7982 (ptmm) REVERT: A 331 LYS cc_start: 0.8636 (mttp) cc_final: 0.8295 (mtpm) REVERT: A 348 ASP cc_start: 0.7653 (t0) cc_final: 0.7391 (m-30) REVERT: B 311 LYS cc_start: 0.8260 (tttt) cc_final: 0.7708 (mmtm) REVERT: B 317 LYS cc_start: 0.8428 (ptpp) cc_final: 0.8018 (ptmt) REVERT: B 331 LYS cc_start: 0.8727 (mttp) cc_final: 0.8359 (mtpt) REVERT: B 343 LYS cc_start: 0.8137 (mtpp) cc_final: 0.7935 (ttmm) REVERT: B 358 ASP cc_start: 0.8683 (p0) cc_final: 0.8339 (p0) REVERT: C 317 LYS cc_start: 0.8316 (ptpp) cc_final: 0.7851 (ptmt) REVERT: C 331 LYS cc_start: 0.8804 (mttp) cc_final: 0.8405 (mtpt) REVERT: C 348 ASP cc_start: 0.7763 (t0) cc_final: 0.7553 (m-30) REVERT: C 356 SER cc_start: 0.8820 (p) cc_final: 0.8591 (m) REVERT: C 375 LYS cc_start: 0.8168 (tttt) cc_final: 0.7530 (mttm) REVERT: D 311 LYS cc_start: 0.8475 (tttt) cc_final: 0.7533 (pptt) REVERT: D 317 LYS cc_start: 0.8562 (ptpp) cc_final: 0.7951 (ptmt) REVERT: D 331 LYS cc_start: 0.8880 (mttp) cc_final: 0.8366 (mtpt) REVERT: D 340 LYS cc_start: 0.8856 (ttmm) cc_final: 0.8470 (mttp) REVERT: D 358 ASP cc_start: 0.8357 (p0) cc_final: 0.8147 (p0) REVERT: D 375 LYS cc_start: 0.8549 (tttt) cc_final: 0.7971 (mttp) REVERT: E 311 LYS cc_start: 0.8236 (tttt) cc_final: 0.7902 (ttmt) REVERT: E 331 LYS cc_start: 0.8823 (mttp) cc_final: 0.8330 (mtpt) REVERT: F 311 LYS cc_start: 0.8485 (tttt) cc_final: 0.7608 (pptt) REVERT: F 317 LYS cc_start: 0.8541 (ptpt) cc_final: 0.8028 (ptmt) REVERT: F 331 LYS cc_start: 0.8964 (mttp) cc_final: 0.8666 (mtpt) REVERT: F 338 GLU cc_start: 0.8508 (tt0) cc_final: 0.8291 (tt0) REVERT: F 340 LYS cc_start: 0.8709 (mttt) cc_final: 0.8308 (mttp) REVERT: F 370 LYS cc_start: 0.8680 (tttp) cc_final: 0.8437 (tttt) outliers start: 7 outliers final: 4 residues processed: 96 average time/residue: 0.6832 time to fit residues: 67.1503 Evaluate side-chains 93 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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 350 VAL Chi-restraints excluded: chain D residue 369 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 20 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 = 0.4229 r_free = 0.4229 target = 0.143726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.123804 restraints weight = 4460.437| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.66 r_work: 0.3832 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3718 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3576 Z= 0.129 Angle : 0.602 8.648 4782 Z= 0.285 Chirality : 0.051 0.131 534 Planarity : 0.003 0.023 612 Dihedral : 4.659 34.735 476 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.49 % Allowed : 24.63 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.36), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.009 0.002 TYR A 310 PHE 0.012 0.001 PHE E 346 HIS 0.002 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 3576) covalent geometry : angle 0.60229 ( 4782) hydrogen bonds : bond 0.02164 ( 58) hydrogen bonds : angle 5.29659 ( 174) *********************** 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 98 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.189 Fit side-chains REVERT: A 317 LYS cc_start: 0.8281 (ptpp) cc_final: 0.8064 (ptmm) REVERT: A 331 LYS cc_start: 0.8650 (mttp) cc_final: 0.8359 (mtpm) REVERT: B 311 LYS cc_start: 0.8290 (tttt) cc_final: 0.7770 (mmtt) REVERT: B 317 LYS cc_start: 0.8451 (ptpp) cc_final: 0.8060 (ptmt) REVERT: B 331 LYS cc_start: 0.8749 (mttp) cc_final: 0.8432 (mtpt) REVERT: B 343 LYS cc_start: 0.8195 (mtpp) cc_final: 0.7467 (tmtt) REVERT: B 358 ASP cc_start: 0.8642 (p0) cc_final: 0.8297 (p0) REVERT: C 317 LYS cc_start: 0.8377 (ptpp) cc_final: 0.7931 (ptmt) REVERT: C 331 LYS cc_start: 0.8812 (mttp) cc_final: 0.8437 (mtpt) REVERT: C 356 SER cc_start: 0.8808 (p) cc_final: 0.8553 (m) REVERT: C 375 LYS cc_start: 0.8231 (tttt) cc_final: 0.7628 (mttm) REVERT: D 311 LYS cc_start: 0.8428 (tttt) cc_final: 0.7545 (pptt) REVERT: D 317 LYS cc_start: 0.8574 (ptpp) cc_final: 0.7981 (ptmt) REVERT: D 331 LYS cc_start: 0.8847 (mttp) cc_final: 0.8379 (mtpt) REVERT: D 340 LYS cc_start: 0.8778 (ttmm) cc_final: 0.8402 (mttp) REVERT: D 375 LYS cc_start: 0.8515 (tttt) cc_final: 0.8021 (mttp) REVERT: E 311 LYS cc_start: 0.8200 (tttt) cc_final: 0.7903 (ttmt) REVERT: E 331 LYS cc_start: 0.8818 (mttp) cc_final: 0.8395 (mtpt) REVERT: F 311 LYS cc_start: 0.8478 (tttt) cc_final: 0.7587 (pptt) REVERT: F 317 LYS cc_start: 0.8541 (ptpt) cc_final: 0.8243 (ptmt) REVERT: F 331 LYS cc_start: 0.8904 (mttp) cc_final: 0.8644 (mtpt) REVERT: F 338 GLU cc_start: 0.8483 (tt0) cc_final: 0.8275 (tt0) REVERT: F 340 LYS cc_start: 0.8684 (mttt) cc_final: 0.8284 (mttp) REVERT: F 370 LYS cc_start: 0.8689 (tttp) cc_final: 0.8474 (tttt) outliers start: 6 outliers final: 2 residues processed: 95 average time/residue: 0.6766 time to fit residues: 65.8757 Evaluate side-chains 93 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 325 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 35 optimal weight: 0.0770 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.9744 ------------------------------------------------------------------------------- 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 = 0.4232 r_free = 0.4232 target = 0.143881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.123364 restraints weight = 4180.379| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.57 r_work: 0.3809 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3695 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3929 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= 0.159 Angle : 0.632 8.963 4782 Z= 0.299 Chirality : 0.051 0.139 534 Planarity : 0.003 0.024 612 Dihedral : 4.737 33.319 476 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.24 % Allowed : 25.12 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.36), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.012 0.003 TYR A 310 PHE 0.015 0.002 PHE E 346 HIS 0.002 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 3576) covalent geometry : angle 0.63162 ( 4782) hydrogen bonds : bond 0.02320 ( 58) hydrogen bonds : angle 5.24984 ( 174) *********************** 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 98 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.149 Fit side-chains REVERT: A 317 LYS cc_start: 0.8221 (ptpp) cc_final: 0.7736 (ptmt) REVERT: A 331 LYS cc_start: 0.8615 (mttp) cc_final: 0.8286 (mtpm) REVERT: B 311 LYS cc_start: 0.8268 (tttt) cc_final: 0.7723 (mmtt) REVERT: B 317 LYS cc_start: 0.8432 (ptpp) cc_final: 0.8025 (ptmt) REVERT: B 331 LYS cc_start: 0.8724 (mttp) cc_final: 0.8361 (mtpt) REVERT: B 343 LYS cc_start: 0.8149 (mtpp) cc_final: 0.7408 (tmtt) REVERT: B 358 ASP cc_start: 0.8703 (p0) cc_final: 0.8364 (p0) REVERT: C 317 LYS cc_start: 0.8337 (ptpp) cc_final: 0.7878 (ptmt) REVERT: C 331 LYS cc_start: 0.8797 (mttp) cc_final: 0.8404 (mtpt) REVERT: C 356 SER cc_start: 0.8778 (p) cc_final: 0.8575 (m) REVERT: C 375 LYS cc_start: 0.8189 (tttt) cc_final: 0.7532 (mttm) REVERT: D 311 LYS cc_start: 0.8442 (tttt) cc_final: 0.7532 (pptt) REVERT: D 317 LYS cc_start: 0.8579 (ptpp) cc_final: 0.7973 (ptmt) REVERT: D 331 LYS cc_start: 0.8884 (mttp) cc_final: 0.8361 (mtpt) REVERT: D 340 LYS cc_start: 0.8883 (ttmm) cc_final: 0.8521 (mttp) REVERT: D 375 LYS cc_start: 0.8511 (tttt) cc_final: 0.7986 (mttp) REVERT: E 311 LYS cc_start: 0.8166 (tttt) cc_final: 0.7847 (ttmt) REVERT: E 331 LYS cc_start: 0.8847 (mttp) cc_final: 0.8383 (mtpt) REVERT: F 311 LYS cc_start: 0.8416 (tttt) cc_final: 0.7540 (pptt) REVERT: F 331 LYS cc_start: 0.8956 (mttp) cc_final: 0.8669 (mtpt) REVERT: F 338 GLU cc_start: 0.8537 (tt0) cc_final: 0.8332 (tt0) REVERT: F 340 LYS cc_start: 0.8702 (mttt) cc_final: 0.8295 (mttp) REVERT: F 370 LYS cc_start: 0.8658 (tttp) cc_final: 0.8429 (tttt) outliers start: 5 outliers final: 2 residues processed: 97 average time/residue: 0.6776 time to fit residues: 67.3028 Evaluate side-chains 93 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 325 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.4232 r_free = 0.4232 target = 0.143875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.123474 restraints weight = 4054.514| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 2.53 r_work: 0.3813 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3939 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= 0.160 Angle : 0.652 9.490 4782 Z= 0.302 Chirality : 0.051 0.139 534 Planarity : 0.003 0.035 612 Dihedral : 4.734 33.480 476 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.24 % Allowed : 25.62 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.36), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 379 TYR 0.012 0.003 TYR A 310 PHE 0.015 0.002 PHE E 346 HIS 0.002 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 3576) covalent geometry : angle 0.65201 ( 4782) hydrogen bonds : bond 0.02279 ( 58) hydrogen bonds : angle 5.20624 ( 174) *********************** 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 96 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.145 Fit side-chains REVERT: A 317 LYS cc_start: 0.8221 (ptpp) cc_final: 0.7745 (ptmt) REVERT: A 331 LYS cc_start: 0.8619 (mttp) cc_final: 0.8290 (mtpm) REVERT: B 311 LYS cc_start: 0.8248 (tttt) cc_final: 0.7699 (mmtt) REVERT: B 317 LYS cc_start: 0.8427 (ptpp) cc_final: 0.8014 (ptmt) REVERT: B 331 LYS cc_start: 0.8721 (mttp) cc_final: 0.8357 (mtpt) REVERT: B 343 LYS cc_start: 0.8143 (mtpp) cc_final: 0.7413 (tmtt) REVERT: B 358 ASP cc_start: 0.8691 (p0) cc_final: 0.8312 (p0) REVERT: C 317 LYS cc_start: 0.8351 (ptpp) cc_final: 0.7891 (ptmt) REVERT: C 331 LYS cc_start: 0.8802 (mttp) cc_final: 0.8403 (mtpt) REVERT: C 356 SER cc_start: 0.8759 (p) cc_final: 0.8544 (m) REVERT: C 375 LYS cc_start: 0.8188 (tttt) cc_final: 0.7529 (mttm) REVERT: D 311 LYS cc_start: 0.8448 (tttt) cc_final: 0.7543 (pptt) REVERT: D 317 LYS cc_start: 0.8582 (ptpp) cc_final: 0.7974 (ptmt) REVERT: D 331 LYS cc_start: 0.8876 (mttp) cc_final: 0.8354 (mtpt) REVERT: D 340 LYS cc_start: 0.8884 (ttmm) cc_final: 0.8523 (mttp) REVERT: D 375 LYS cc_start: 0.8516 (tttt) cc_final: 0.7984 (mttp) REVERT: E 311 LYS cc_start: 0.8162 (tttt) cc_final: 0.7842 (ttmt) REVERT: E 331 LYS cc_start: 0.8832 (mttp) cc_final: 0.8357 (mtpt) REVERT: F 311 LYS cc_start: 0.8409 (tttt) cc_final: 0.7538 (pptt) REVERT: F 331 LYS cc_start: 0.8957 (mttp) cc_final: 0.8669 (mtpt) REVERT: F 338 GLU cc_start: 0.8525 (tt0) cc_final: 0.8320 (tt0) REVERT: F 340 LYS cc_start: 0.8714 (mttt) cc_final: 0.8310 (mttp) REVERT: F 370 LYS cc_start: 0.8654 (tttp) cc_final: 0.8430 (tttt) outliers start: 5 outliers final: 2 residues processed: 95 average time/residue: 0.6798 time to fit residues: 66.0644 Evaluate side-chains 91 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS 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 26 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 0.0030 overall best weight: 1.9796 ------------------------------------------------------------------------------- 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 = 0.4237 r_free = 0.4237 target = 0.144213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.123728 restraints weight = 4154.729| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.57 r_work: 0.3813 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3700 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3987 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= 0.159 Angle : 0.655 9.611 4782 Z= 0.304 Chirality : 0.051 0.140 534 Planarity : 0.003 0.038 612 Dihedral : 4.750 33.479 476 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.00 % Allowed : 26.37 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.36), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 379 TYR 0.012 0.003 TYR A 310 PHE 0.015 0.002 PHE E 346 HIS 0.002 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 3576) covalent geometry : angle 0.65451 ( 4782) hydrogen bonds : bond 0.02251 ( 58) hydrogen bonds : angle 5.16466 ( 174) ********************** 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 95 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.154 Fit side-chains REVERT: A 317 LYS cc_start: 0.8262 (ptpp) cc_final: 0.7772 (ptmt) REVERT: A 331 LYS cc_start: 0.8621 (mttp) cc_final: 0.8288 (mtpm) REVERT: B 311 LYS cc_start: 0.8259 (tttt) cc_final: 0.7699 (mmtt) REVERT: B 317 LYS cc_start: 0.8430 (ptpp) cc_final: 0.8008 (ptmt) REVERT: B 331 LYS cc_start: 0.8720 (mttp) cc_final: 0.8352 (mtpt) REVERT: B 343 LYS cc_start: 0.8140 (mtpp) cc_final: 0.7408 (tmtt) REVERT: B 358 ASP cc_start: 0.8696 (p0) cc_final: 0.8318 (p0) REVERT: C 317 LYS cc_start: 0.8356 (ptpp) cc_final: 0.7891 (ptmt) REVERT: C 331 LYS cc_start: 0.8804 (mttp) cc_final: 0.8417 (mtpt) REVERT: C 356 SER cc_start: 0.8757 (p) cc_final: 0.8554 (m) REVERT: C 375 LYS cc_start: 0.8206 (tttt) cc_final: 0.7560 (mttm) REVERT: D 311 LYS cc_start: 0.8456 (tttt) cc_final: 0.7571 (pptt) REVERT: D 317 LYS cc_start: 0.8583 (ptpp) cc_final: 0.7972 (ptmt) REVERT: D 331 LYS cc_start: 0.8884 (mttp) cc_final: 0.8369 (mtpt) REVERT: D 340 LYS cc_start: 0.8883 (ttmm) cc_final: 0.8524 (mttp) REVERT: D 375 LYS cc_start: 0.8519 (tttt) cc_final: 0.7957 (mttp) REVERT: E 311 LYS cc_start: 0.8154 (tttt) cc_final: 0.7829 (ttmt) REVERT: E 331 LYS cc_start: 0.8843 (mttp) cc_final: 0.8370 (mtpt) REVERT: F 311 LYS cc_start: 0.8414 (tttt) cc_final: 0.7571 (pptt) REVERT: F 331 LYS cc_start: 0.8964 (mttp) cc_final: 0.8670 (mtpt) REVERT: F 340 LYS cc_start: 0.8701 (mttt) cc_final: 0.8295 (mttp) REVERT: F 370 LYS cc_start: 0.8652 (tttp) cc_final: 0.8432 (tttt) outliers start: 4 outliers final: 2 residues processed: 94 average time/residue: 0.6994 time to fit residues: 67.1672 Evaluate side-chains 91 residues out of total 402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS 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 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 41 optimal weight: 0.0470 chunk 3 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.3482 ------------------------------------------------------------------------------- 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 = 0.4273 r_free = 0.4273 target = 0.147200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.126764 restraints weight = 4085.397| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.56 r_work: 0.3848 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3576 Z= 0.125 Angle : 0.632 9.579 4782 Z= 0.291 Chirality : 0.050 0.136 534 Planarity : 0.003 0.041 612 Dihedral : 4.638 35.252 476 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.24 % Allowed : 26.62 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.36), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 379 TYR 0.009 0.002 TYR A 310 PHE 0.011 0.001 PHE E 346 HIS 0.002 0.001 HIS E 329 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 3576) covalent geometry : angle 0.63211 ( 4782) hydrogen bonds : bond 0.02080 ( 58) hydrogen bonds : angle 4.98896 ( 174) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1841.36 seconds wall clock time: 32 minutes 18.74 seconds (1938.74 seconds total)