Starting phenix.real_space_refine on Wed Mar 4 00:38:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qkv_14054/03_2026/7qkv_14054.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qkv_14054/03_2026/7qkv_14054.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7qkv_14054/03_2026/7qkv_14054.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qkv_14054/03_2026/7qkv_14054.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qkv_14054/03_2026/7qkv_14054.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qkv_14054/03_2026/7qkv_14054.map" } resolution = 3.23 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: 5 Type Number sf(0) Gaussians S 9 5.16 5 C 2934 2.51 5 N 864 2.21 5 O 891 1.98 5 H 4887 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9585 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "A" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "C" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "D" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "E" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "F" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "G" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "H" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "I" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Time building chain proxies: 1.75, per 1000 atoms: 0.18 Number of scatterers: 9585 At special positions: 0 Unit cell: (128.544, 131.84, 33.784, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 O 891 8.00 N 864 7.00 C 2934 6.00 H 4887 1.00 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: 0.88 Conformation dependent library (CDL) restraints added in 191.9 milliseconds 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1080 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 24 sheets defined 0.0% alpha, 40.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.960A pdb=" N VAL B 313 " --> pdb=" O ASP G 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 317 through 318 removed outlier: 6.348A pdb=" N LYS B 317 " --> pdb=" O VAL G 318 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 324 through 330 removed outlier: 9.642A pdb=" N SER B 324 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 10.493A pdb=" N ASN D 327 " --> pdb=" O SER B 324 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLY B 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N HIS D 329 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU B 325 " --> pdb=" O SER G 324 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY G 326 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN B 327 " --> pdb=" O GLY G 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 337 through 342 removed outlier: 6.553A pdb=" N VAL B 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N LYS D 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL B 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N GLU D 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N SER B 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.391A pdb=" N ASP B 345 " --> pdb=" O PHE G 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 350 through 357 removed outlier: 6.468A pdb=" N GLN B 351 " --> pdb=" O SER G 352 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE G 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS B 353 " --> pdb=" O ILE G 354 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N SER G 356 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLY B 355 " --> pdb=" O SER G 356 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.381A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 369 through 374 removed outlier: 6.448A pdb=" N LYS B 369 " --> pdb=" O LYS G 370 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N GLU G 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE B 371 " --> pdb=" O GLU G 372 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N HIS G 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR B 373 " --> pdb=" O HIS G 374 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.914A pdb=" N VAL A 313 " --> pdb=" O ASP H 314 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 317 through 318 removed outlier: 6.355A pdb=" N LYS A 317 " --> pdb=" O VAL H 318 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 324 through 330 removed outlier: 9.663A pdb=" N SER A 324 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 10.501A pdb=" N ASN E 327 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLY A 326 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N HIS E 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE A 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU A 325 " --> pdb=" O SER H 324 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLY H 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASN A 327 " --> pdb=" O GLY H 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 337 through 342 removed outlier: 6.532A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N GLU E 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER A 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 345 through 346 removed outlier: 6.493A pdb=" N ASP A 345 " --> pdb=" O PHE H 346 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 350 through 357 removed outlier: 6.277A pdb=" N VAL A 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N LYS E 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N SER A 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N GLY E 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE A 354 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU E 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N SER A 356 " --> pdb=" O LEU E 357 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 360 through 362 removed outlier: 6.353A pdb=" N THR A 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 369 through 374 removed outlier: 6.321A pdb=" N LYS A 370 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N THR E 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLU A 372 " --> pdb=" O THR E 373 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LYS A 369 " --> pdb=" O LYS H 370 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N GLU H 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE A 371 " --> pdb=" O GLU H 372 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N HIS H 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N THR A 373 " --> pdb=" O HIS H 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 313 through 314 removed outlier: 6.953A pdb=" N VAL C 313 " --> pdb=" O ASP I 314 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 317 through 318 removed outlier: 6.425A pdb=" N LYS C 317 " --> pdb=" O VAL I 318 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 324 through 330 removed outlier: 9.636A pdb=" N SER C 324 " --> pdb=" O LEU F 325 " (cutoff:3.500A) removed outlier: 10.480A pdb=" N ASN F 327 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLY C 326 " --> pdb=" O ASN F 327 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N HIS F 329 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE C 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU C 325 " --> pdb=" O SER I 324 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLY I 326 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN C 327 " --> pdb=" O GLY I 326 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 337 through 342 removed outlier: 6.574A pdb=" N VAL C 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N LYS F 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL C 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N GLU F 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N SER C 341 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 345 through 346 removed outlier: 6.557A pdb=" N ASP C 345 " --> pdb=" O PHE I 346 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 350 through 357 removed outlier: 6.275A pdb=" N VAL C 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N LYS F 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N SER C 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N GLY F 355 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE C 354 " --> pdb=" O GLY F 355 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU F 357 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N SER C 356 " --> pdb=" O LEU F 357 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 360 through 362 removed outlier: 6.395A pdb=" N THR C 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 369 through 374 removed outlier: 6.483A pdb=" N LYS C 369 " --> pdb=" O LYS I 370 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N GLU I 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE C 371 " --> pdb=" O GLU I 372 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N HIS I 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR C 373 " --> pdb=" O HIS I 374 " (cutoff:3.500A) 70 hydrogen bonds defined for protein. 210 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: 1.83 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.93 - 1.11: 4878 1.11 - 1.28: 792 1.28 - 1.45: 1147 1.45 - 1.63: 2831 1.63 - 1.80: 9 Bond restraints: 9657 Sorted by residual: bond pdb=" N GLN A 336 " pdb=" H GLN A 336 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N ASN D 359 " pdb=" H ASN D 359 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N GLY H 367 " pdb=" H GLY H 367 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NE2 GLN B 336 " pdb="HE21 GLN B 336 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N LYS D 331 " pdb=" H LYS D 331 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 9652 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 14545 2.47 - 4.94: 2366 4.94 - 7.40: 657 7.40 - 9.87: 54 9.87 - 12.34: 9 Bond angle restraints: 17631 Sorted by residual: angle pdb=" N GLY A 326 " pdb=" CA GLY A 326 " pdb=" C GLY A 326 " ideal model delta sigma weight residual 110.42 118.54 -8.12 1.49e+00 4.50e-01 2.97e+01 angle pdb=" C LYS A 375 " pdb=" N LEU A 376 " pdb=" CA LEU A 376 " ideal model delta sigma weight residual 122.36 130.55 -8.19 1.60e+00 3.91e-01 2.62e+01 angle pdb=" C ASP B 348 " pdb=" N ARG B 349 " pdb=" CA ARG B 349 " ideal model delta sigma weight residual 121.31 128.60 -7.29 1.49e+00 4.50e-01 2.39e+01 angle pdb=" N GLY C 326 " pdb=" CA GLY C 326 " pdb=" C GLY C 326 " ideal model delta sigma weight residual 110.55 118.57 -8.02 1.64e+00 3.72e-01 2.39e+01 angle pdb=" C ASP F 348 " pdb=" N ARG F 349 " pdb=" CA ARG F 349 " ideal model delta sigma weight residual 121.31 128.52 -7.21 1.49e+00 4.50e-01 2.34e+01 ... (remaining 17626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.16: 3682 13.16 - 26.31: 423 26.31 - 39.47: 145 39.47 - 52.62: 62 52.62 - 65.78: 134 Dihedral angle restraints: 4446 sinusoidal: 2556 harmonic: 1890 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 -152.57 -27.43 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA LYS H 375 " pdb=" C LYS H 375 " pdb=" N LEU H 376 " pdb=" CA LEU H 376 " ideal model delta harmonic sigma weight residual 180.00 152.92 27.08 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA VAL G 350 " pdb=" C VAL G 350 " pdb=" N GLN G 351 " pdb=" CA GLN G 351 " ideal model delta harmonic sigma weight residual 180.00 153.06 26.94 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 4443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 364 0.065 - 0.130: 244 0.130 - 0.194: 90 0.194 - 0.259: 16 0.259 - 0.323: 6 Chirality restraints: 720 Sorted by residual: chirality pdb=" CA LYS F 311 " pdb=" N LYS F 311 " pdb=" C LYS F 311 " pdb=" CB LYS F 311 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA LYS E 311 " pdb=" N LYS E 311 " pdb=" C LYS E 311 " pdb=" CB LYS E 311 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA ASN F 327 " pdb=" N ASN F 327 " pdb=" C ASN F 327 " pdb=" CB ASN F 327 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 717 not shown) Planarity restraints: 1395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " -0.336 2.00e-02 2.50e+03 1.44e-01 6.26e+02 pdb=" CG TYR E 310 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " 0.103 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " 0.101 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " 0.091 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " 0.063 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " -0.289 2.00e-02 2.50e+03 pdb=" HD1 TYR E 310 " 0.058 2.00e-02 2.50e+03 pdb=" HD2 TYR E 310 " 0.113 2.00e-02 2.50e+03 pdb=" HE1 TYR E 310 " 0.056 2.00e-02 2.50e+03 pdb=" HE2 TYR E 310 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 310 " -0.224 2.00e-02 2.50e+03 1.01e-01 3.05e+02 pdb=" CG TYR H 310 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR H 310 " 0.069 2.00e-02 2.50e+03 pdb=" CD2 TYR H 310 " 0.077 2.00e-02 2.50e+03 pdb=" CE1 TYR H 310 " 0.075 2.00e-02 2.50e+03 pdb=" CE2 TYR H 310 " 0.053 2.00e-02 2.50e+03 pdb=" CZ TYR H 310 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR H 310 " -0.215 2.00e-02 2.50e+03 pdb=" HD1 TYR H 310 " 0.010 2.00e-02 2.50e+03 pdb=" HD2 TYR H 310 " 0.057 2.00e-02 2.50e+03 pdb=" HE1 TYR H 310 " 0.045 2.00e-02 2.50e+03 pdb=" HE2 TYR H 310 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " 0.226 2.00e-02 2.50e+03 9.95e-02 2.97e+02 pdb=" CG TYR F 310 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " -0.074 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " -0.084 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " -0.073 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " -0.055 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " 0.204 2.00e-02 2.50e+03 pdb=" HD1 TYR F 310 " -0.004 2.00e-02 2.50e+03 pdb=" HD2 TYR F 310 " -0.040 2.00e-02 2.50e+03 pdb=" HE1 TYR F 310 " -0.027 2.00e-02 2.50e+03 pdb=" HE2 TYR F 310 " -0.007 2.00e-02 2.50e+03 ... (remaining 1392 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 702 2.17 - 2.77: 16377 2.77 - 3.38: 25469 3.38 - 3.99: 33649 3.99 - 4.60: 47837 Nonbonded interactions: 124034 Sorted by model distance: nonbonded pdb=" OD1 ASP I 314 " pdb=" HG SER I 316 " model vdw 1.556 2.450 nonbonded pdb=" OD1 ASP H 314 " pdb=" HG SER H 316 " model vdw 1.559 2.450 nonbonded pdb=" OD1 ASP G 314 " pdb=" HG SER G 316 " model vdw 1.563 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.610 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.618 2.450 ... (remaining 124029 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 5.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.370 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 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 : 0.011 0.033 4770 Z= 0.700 Angle : 1.916 8.186 6381 Z= 1.248 Chirality : 0.094 0.323 720 Planarity : 0.015 0.166 810 Dihedral : 12.281 56.991 1836 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 0.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % 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 are not related in a simple way. whole: -2.11 (0.28), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.22), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 349 TYR 0.290 0.091 TYR E 310 PHE 0.032 0.013 PHE I 346 HIS 0.018 0.006 HIS G 330 Details of bonding type rmsd covalent geometry : bond 0.01106 ( 4770) covalent geometry : angle 1.91586 ( 6381) hydrogen bonds : bond 0.11634 ( 70) hydrogen bonds : angle 7.62890 ( 210) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 346 PHE cc_start: 0.8125 (m-80) cc_final: 0.7866 (m-80) REVERT: B 347 LYS cc_start: 0.7885 (mttt) cc_final: 0.7276 (tmtt) REVERT: B 358 ASP cc_start: 0.8448 (m-30) cc_final: 0.8055 (t0) REVERT: A 327 ASN cc_start: 0.7512 (m-40) cc_final: 0.7308 (m-40) REVERT: A 343 LYS cc_start: 0.8500 (mttt) cc_final: 0.7686 (mttm) REVERT: A 347 LYS cc_start: 0.7999 (mttt) cc_final: 0.7434 (tptp) REVERT: A 358 ASP cc_start: 0.8546 (m-30) cc_final: 0.8066 (t0) REVERT: C 342 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7171 (mm-30) REVERT: C 346 PHE cc_start: 0.8364 (m-80) cc_final: 0.8058 (m-80) REVERT: C 358 ASP cc_start: 0.8441 (m-30) cc_final: 0.8057 (t0) REVERT: D 311 LYS cc_start: 0.7191 (mtmt) cc_final: 0.6616 (mmtm) REVERT: D 347 LYS cc_start: 0.7807 (mttt) cc_final: 0.7558 (tmtt) REVERT: E 311 LYS cc_start: 0.7213 (mtmt) cc_final: 0.6420 (mmtm) REVERT: E 347 LYS cc_start: 0.7878 (mttt) cc_final: 0.7520 (tmtt) REVERT: F 342 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7208 (mt-10) REVERT: F 343 LYS cc_start: 0.8191 (mttt) cc_final: 0.7457 (mmpt) REVERT: F 347 LYS cc_start: 0.7980 (mttt) cc_final: 0.7577 (tmtt) REVERT: F 351 GLN cc_start: 0.7827 (mp10) cc_final: 0.7423 (tt0) REVERT: G 345 ASP cc_start: 0.6807 (m-30) cc_final: 0.6475 (m-30) REVERT: G 347 LYS cc_start: 0.8104 (mttt) cc_final: 0.7523 (pttp) REVERT: G 358 ASP cc_start: 0.8475 (m-30) cc_final: 0.8106 (t0) REVERT: H 343 LYS cc_start: 0.8536 (mttt) cc_final: 0.8127 (mttm) REVERT: H 347 LYS cc_start: 0.7854 (mttt) cc_final: 0.7345 (pttp) REVERT: H 358 ASP cc_start: 0.8445 (m-30) cc_final: 0.8003 (t0) REVERT: I 343 LYS cc_start: 0.8423 (mttt) cc_final: 0.7844 (mttm) REVERT: I 347 LYS cc_start: 0.7730 (mttt) cc_final: 0.7290 (pttp) REVERT: I 358 ASP cc_start: 0.8454 (m-30) cc_final: 0.8043 (t0) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1950 time to fit residues: 41.9575 Evaluate side-chains 109 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS A 362 HIS C 362 HIS D 362 HIS E 362 HIS F 362 HIS G 362 HIS H 362 HIS I 362 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.200542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.179462 restraints weight = 17382.461| |-----------------------------------------------------------------------------| r_work (start): 0.4571 rms_B_bonded: 2.49 r_work: 0.4509 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.4436 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.4436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 4770 Z= 0.244 Angle : 0.701 6.591 6381 Z= 0.370 Chirality : 0.052 0.140 720 Planarity : 0.003 0.023 810 Dihedral : 7.770 28.463 630 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.67 % Allowed : 16.48 % Favored : 81.85 % 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 are not related in a simple way. whole: -2.46 (0.26), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.20), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 349 TYR 0.029 0.006 TYR D 310 PHE 0.009 0.001 PHE E 346 HIS 0.005 0.002 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00571 ( 4770) covalent geometry : angle 0.70059 ( 6381) hydrogen bonds : bond 0.02608 ( 70) hydrogen bonds : angle 5.99039 ( 210) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 346 PHE cc_start: 0.8050 (m-80) cc_final: 0.7739 (m-80) REVERT: B 347 LYS cc_start: 0.8046 (mttt) cc_final: 0.7356 (tmtt) REVERT: B 376 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8469 (mt) REVERT: A 347 LYS cc_start: 0.8066 (mttt) cc_final: 0.7210 (tmtt) REVERT: A 358 ASP cc_start: 0.8029 (m-30) cc_final: 0.7789 (t0) REVERT: C 327 ASN cc_start: 0.7406 (m-40) cc_final: 0.6964 (t0) REVERT: C 342 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7315 (mt-10) REVERT: C 347 LYS cc_start: 0.8161 (mttt) cc_final: 0.7347 (tmtt) REVERT: C 358 ASP cc_start: 0.7851 (m-30) cc_final: 0.7578 (t0) REVERT: C 376 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8279 (mt) REVERT: D 311 LYS cc_start: 0.8333 (mtmt) cc_final: 0.8054 (mmtm) REVERT: D 343 LYS cc_start: 0.8338 (mttt) cc_final: 0.7271 (mmpt) REVERT: D 347 LYS cc_start: 0.7997 (mttt) cc_final: 0.7716 (tmtt) REVERT: E 311 LYS cc_start: 0.8378 (mtmt) cc_final: 0.7766 (mmtm) REVERT: E 343 LYS cc_start: 0.8495 (mttt) cc_final: 0.7479 (mmpt) REVERT: E 347 LYS cc_start: 0.7983 (mttt) cc_final: 0.7676 (tmtt) REVERT: F 311 LYS cc_start: 0.8651 (ttmt) cc_final: 0.7986 (mmtm) REVERT: F 342 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7382 (mt-10) REVERT: F 347 LYS cc_start: 0.8084 (mttt) cc_final: 0.7562 (tmtt) REVERT: F 351 GLN cc_start: 0.8024 (mp10) cc_final: 0.7452 (tt0) REVERT: G 345 ASP cc_start: 0.6347 (m-30) cc_final: 0.6129 (m-30) REVERT: G 347 LYS cc_start: 0.8286 (mttt) cc_final: 0.7573 (pttp) REVERT: G 358 ASP cc_start: 0.7817 (m-30) cc_final: 0.7596 (t0) REVERT: H 347 LYS cc_start: 0.8170 (mttt) cc_final: 0.7496 (pttp) REVERT: H 358 ASP cc_start: 0.8106 (m-30) cc_final: 0.7714 (t0) REVERT: I 347 LYS cc_start: 0.8099 (mttt) cc_final: 0.7405 (pttp) REVERT: I 358 ASP cc_start: 0.7802 (m-30) cc_final: 0.7428 (t0) outliers start: 9 outliers final: 7 residues processed: 116 average time/residue: 0.1953 time to fit residues: 27.5741 Evaluate side-chains 103 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain I residue 356 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 19 optimal weight: 7.9990 chunk 24 optimal weight: 0.3980 chunk 15 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 9 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 368 ASN H 368 ASN I 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.205596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.183670 restraints weight = 17158.384| |-----------------------------------------------------------------------------| r_work (start): 0.4626 rms_B_bonded: 2.59 r_work: 0.4564 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.4488 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.4488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4770 Z= 0.122 Angle : 0.557 4.016 6381 Z= 0.294 Chirality : 0.050 0.138 720 Planarity : 0.003 0.025 810 Dihedral : 6.303 21.168 630 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.04 % Allowed : 18.33 % Favored : 79.63 % 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 are not related in a simple way. whole: -2.68 (0.25), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.19), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 349 TYR 0.012 0.002 TYR D 310 PHE 0.007 0.001 PHE D 346 HIS 0.003 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 4770) covalent geometry : angle 0.55700 ( 6381) hydrogen bonds : bond 0.01948 ( 70) hydrogen bonds : angle 5.27172 ( 210) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 346 PHE cc_start: 0.8095 (m-80) cc_final: 0.7824 (m-80) REVERT: B 347 LYS cc_start: 0.7963 (mttt) cc_final: 0.7244 (tmtt) REVERT: A 347 LYS cc_start: 0.8027 (mttt) cc_final: 0.7194 (tmtt) REVERT: A 358 ASP cc_start: 0.8081 (m-30) cc_final: 0.7647 (t0) REVERT: C 327 ASN cc_start: 0.7276 (m-40) cc_final: 0.6956 (t0) REVERT: C 342 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7358 (mt-10) REVERT: C 347 LYS cc_start: 0.8131 (mttt) cc_final: 0.7306 (tmtt) REVERT: C 358 ASP cc_start: 0.7973 (m-30) cc_final: 0.7576 (t0) REVERT: D 343 LYS cc_start: 0.8141 (mttt) cc_final: 0.7126 (mmpt) REVERT: D 347 LYS cc_start: 0.7876 (mttt) cc_final: 0.7587 (tmtt) REVERT: E 327 ASN cc_start: 0.7393 (m-40) cc_final: 0.7120 (t0) REVERT: E 342 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7282 (mm-30) REVERT: E 343 LYS cc_start: 0.8203 (mttt) cc_final: 0.7322 (mmpt) REVERT: E 347 LYS cc_start: 0.8010 (mttt) cc_final: 0.7647 (tmtt) REVERT: F 311 LYS cc_start: 0.8583 (ttmt) cc_final: 0.7875 (mmtm) REVERT: F 342 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7418 (mt-10) REVERT: F 347 LYS cc_start: 0.8172 (mttt) cc_final: 0.7645 (tmtt) REVERT: F 351 GLN cc_start: 0.8023 (mp10) cc_final: 0.7496 (tt0) REVERT: F 363 VAL cc_start: 0.8998 (t) cc_final: 0.8798 (m) REVERT: G 347 LYS cc_start: 0.8308 (mttt) cc_final: 0.7559 (pttp) REVERT: H 347 LYS cc_start: 0.8231 (mttt) cc_final: 0.7482 (pttp) REVERT: H 358 ASP cc_start: 0.8091 (m-30) cc_final: 0.7635 (t0) REVERT: I 347 LYS cc_start: 0.8023 (mttt) cc_final: 0.7384 (pttp) REVERT: I 358 ASP cc_start: 0.7999 (m-30) cc_final: 0.7578 (t0) outliers start: 11 outliers final: 6 residues processed: 113 average time/residue: 0.1928 time to fit residues: 26.7343 Evaluate side-chains 103 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 376 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 26 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 41 optimal weight: 0.2980 chunk 47 optimal weight: 5.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.209077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.187255 restraints weight = 17143.573| |-----------------------------------------------------------------------------| r_work (start): 0.4655 rms_B_bonded: 2.59 r_work: 0.4590 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.4508 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.4508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4770 Z= 0.107 Angle : 0.527 4.147 6381 Z= 0.275 Chirality : 0.049 0.139 720 Planarity : 0.003 0.034 810 Dihedral : 5.733 17.210 630 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.11 % Allowed : 18.52 % Favored : 80.37 % 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 are not related in a simple way. whole: -2.67 (0.25), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.19), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 349 TYR 0.009 0.002 TYR D 310 PHE 0.004 0.001 PHE D 346 HIS 0.002 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 4770) covalent geometry : angle 0.52690 ( 6381) hydrogen bonds : bond 0.01615 ( 70) hydrogen bonds : angle 4.76168 ( 210) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 327 ASN cc_start: 0.8131 (t0) cc_final: 0.7921 (t0) REVERT: B 346 PHE cc_start: 0.8102 (m-80) cc_final: 0.7857 (m-80) REVERT: B 347 LYS cc_start: 0.8017 (mttt) cc_final: 0.7208 (tmtt) REVERT: A 327 ASN cc_start: 0.7710 (t0) cc_final: 0.7431 (t0) REVERT: A 331 LYS cc_start: 0.8470 (tttt) cc_final: 0.8228 (mtpt) REVERT: A 347 LYS cc_start: 0.7990 (mttt) cc_final: 0.7246 (tmtt) REVERT: A 358 ASP cc_start: 0.8070 (m-30) cc_final: 0.7618 (t0) REVERT: C 342 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7382 (mt-10) REVERT: C 347 LYS cc_start: 0.8156 (mttt) cc_final: 0.7292 (tmtt) REVERT: C 358 ASP cc_start: 0.7957 (m-30) cc_final: 0.7550 (t0) REVERT: D 311 LYS cc_start: 0.8492 (pttt) cc_final: 0.8003 (mmtm) REVERT: D 327 ASN cc_start: 0.8194 (t0) cc_final: 0.7921 (t0) REVERT: D 342 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7009 (mm-30) REVERT: D 343 LYS cc_start: 0.8147 (mttt) cc_final: 0.7213 (mmmt) REVERT: D 347 LYS cc_start: 0.7847 (mttt) cc_final: 0.7574 (tmtt) REVERT: E 311 LYS cc_start: 0.8594 (ttmt) cc_final: 0.7898 (mmtm) REVERT: E 327 ASN cc_start: 0.7468 (m-40) cc_final: 0.7177 (t0) REVERT: E 342 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7237 (mm-30) REVERT: E 343 LYS cc_start: 0.8250 (mttt) cc_final: 0.7299 (mmpt) REVERT: E 347 LYS cc_start: 0.7962 (mttt) cc_final: 0.7584 (tmtt) REVERT: F 311 LYS cc_start: 0.8490 (ttmt) cc_final: 0.7819 (mmtm) REVERT: F 347 LYS cc_start: 0.8126 (mttt) cc_final: 0.7561 (tmtt) REVERT: F 351 GLN cc_start: 0.7948 (mp10) cc_final: 0.7457 (tt0) REVERT: F 363 VAL cc_start: 0.9030 (t) cc_final: 0.8826 (m) REVERT: G 347 LYS cc_start: 0.8321 (mttt) cc_final: 0.7608 (pttp) REVERT: H 347 LYS cc_start: 0.8236 (mttt) cc_final: 0.7552 (pttp) REVERT: H 358 ASP cc_start: 0.8044 (m-30) cc_final: 0.7540 (t0) REVERT: I 347 LYS cc_start: 0.8031 (mttt) cc_final: 0.7376 (pttp) REVERT: I 358 ASP cc_start: 0.8019 (m-30) cc_final: 0.7582 (t0) outliers start: 6 outliers final: 6 residues processed: 105 average time/residue: 0.2139 time to fit residues: 27.2973 Evaluate side-chains 98 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 356 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.196904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.175521 restraints weight = 17550.549| |-----------------------------------------------------------------------------| r_work (start): 0.4550 rms_B_bonded: 2.59 r_work: 0.4480 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4395 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.4395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.5216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4770 Z= 0.241 Angle : 0.607 5.096 6381 Z= 0.324 Chirality : 0.050 0.150 720 Planarity : 0.004 0.035 810 Dihedral : 6.179 19.580 630 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.67 % Allowed : 18.89 % Favored : 79.44 % 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 are not related in a simple way. whole: -2.83 (0.26), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.19), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 349 TYR 0.023 0.005 TYR F 310 PHE 0.005 0.001 PHE D 346 HIS 0.004 0.001 HIS D 329 Details of bonding type rmsd covalent geometry : bond 0.00537 ( 4770) covalent geometry : angle 0.60714 ( 6381) hydrogen bonds : bond 0.01939 ( 70) hydrogen bonds : angle 5.14447 ( 210) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 345 ASP cc_start: 0.6740 (m-30) cc_final: 0.6349 (m-30) REVERT: B 346 PHE cc_start: 0.8122 (m-80) cc_final: 0.7825 (m-80) REVERT: B 347 LYS cc_start: 0.7958 (mttt) cc_final: 0.7280 (tmtt) REVERT: A 347 LYS cc_start: 0.7976 (mttt) cc_final: 0.7187 (tmtt) REVERT: A 358 ASP cc_start: 0.8150 (m-30) cc_final: 0.7729 (t0) REVERT: C 342 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7154 (mt-10) REVERT: C 347 LYS cc_start: 0.8092 (mttt) cc_final: 0.7162 (tmtt) REVERT: C 358 ASP cc_start: 0.8143 (m-30) cc_final: 0.7666 (t0) REVERT: D 311 LYS cc_start: 0.8671 (pttt) cc_final: 0.8224 (mmtm) REVERT: D 343 LYS cc_start: 0.8482 (mttt) cc_final: 0.7353 (mmpt) REVERT: D 347 LYS cc_start: 0.7890 (mttt) cc_final: 0.7506 (tmtt) REVERT: E 311 LYS cc_start: 0.8788 (ttmt) cc_final: 0.7980 (mmtm) REVERT: E 327 ASN cc_start: 0.7691 (m-40) cc_final: 0.7176 (t0) REVERT: E 343 LYS cc_start: 0.8566 (mttt) cc_final: 0.7497 (mmpt) REVERT: E 347 LYS cc_start: 0.8033 (mttt) cc_final: 0.7595 (tmtt) REVERT: F 311 LYS cc_start: 0.8665 (ttmt) cc_final: 0.8019 (mmtm) REVERT: F 347 LYS cc_start: 0.8169 (mttt) cc_final: 0.7479 (tmtt) REVERT: F 351 GLN cc_start: 0.8083 (mp10) cc_final: 0.7396 (tt0) REVERT: G 347 LYS cc_start: 0.8303 (mttt) cc_final: 0.7515 (pttm) REVERT: H 325 LEU cc_start: 0.8660 (tt) cc_final: 0.8456 (tp) REVERT: H 347 LYS cc_start: 0.8242 (mttt) cc_final: 0.7492 (pttp) REVERT: H 358 ASP cc_start: 0.8198 (m-30) cc_final: 0.7711 (t0) REVERT: I 347 LYS cc_start: 0.8011 (mttt) cc_final: 0.7321 (pttp) REVERT: I 358 ASP cc_start: 0.8031 (m-30) cc_final: 0.7641 (t0) outliers start: 9 outliers final: 7 residues processed: 102 average time/residue: 0.1902 time to fit residues: 23.8215 Evaluate side-chains 95 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 356 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.204068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.182579 restraints weight = 17099.712| |-----------------------------------------------------------------------------| r_work (start): 0.4610 rms_B_bonded: 2.60 r_work: 0.4552 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4477 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.4477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4770 Z= 0.130 Angle : 0.533 4.451 6381 Z= 0.279 Chirality : 0.049 0.145 720 Planarity : 0.004 0.041 810 Dihedral : 5.624 17.949 630 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.22 % Allowed : 17.22 % Favored : 80.56 % 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 are not related in a simple way. whole: -2.84 (0.26), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.20), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 349 TYR 0.011 0.002 TYR D 310 PHE 0.003 0.001 PHE D 346 HIS 0.002 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 4770) covalent geometry : angle 0.53312 ( 6381) hydrogen bonds : bond 0.01595 ( 70) hydrogen bonds : angle 4.79040 ( 210) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 346 PHE cc_start: 0.8175 (m-80) cc_final: 0.7918 (m-80) REVERT: B 347 LYS cc_start: 0.7938 (mttt) cc_final: 0.7279 (tmtt) REVERT: A 347 LYS cc_start: 0.7987 (mttt) cc_final: 0.7178 (tmtt) REVERT: A 358 ASP cc_start: 0.8099 (m-30) cc_final: 0.7688 (t0) REVERT: C 342 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7241 (mt-10) REVERT: C 347 LYS cc_start: 0.8025 (mttt) cc_final: 0.7215 (tmtt) REVERT: C 358 ASP cc_start: 0.8059 (m-30) cc_final: 0.7609 (t0) REVERT: D 311 LYS cc_start: 0.8623 (pttt) cc_final: 0.8200 (mmtm) REVERT: D 343 LYS cc_start: 0.8362 (mttt) cc_final: 0.7309 (mmpt) REVERT: D 347 LYS cc_start: 0.7823 (mttt) cc_final: 0.7507 (tmtt) REVERT: E 311 LYS cc_start: 0.8703 (ttmt) cc_final: 0.7989 (mmtm) REVERT: E 327 ASN cc_start: 0.7487 (m-40) cc_final: 0.7130 (t0) REVERT: E 343 LYS cc_start: 0.8538 (mttt) cc_final: 0.7418 (mmpt) REVERT: E 347 LYS cc_start: 0.8017 (mttt) cc_final: 0.7638 (tmtt) REVERT: F 311 LYS cc_start: 0.8608 (ttmt) cc_final: 0.8013 (mmtm) REVERT: F 347 LYS cc_start: 0.8108 (mttt) cc_final: 0.7571 (tmtt) REVERT: F 351 GLN cc_start: 0.8044 (mp10) cc_final: 0.7448 (tt0) REVERT: G 347 LYS cc_start: 0.8277 (mttt) cc_final: 0.7557 (pttm) REVERT: G 376 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8263 (mt) REVERT: H 311 LYS cc_start: 0.8676 (ttmt) cc_final: 0.7984 (ttpt) REVERT: H 347 LYS cc_start: 0.8248 (mttt) cc_final: 0.7518 (pttm) REVERT: H 358 ASP cc_start: 0.8123 (m-30) cc_final: 0.7614 (t0) REVERT: H 376 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8209 (mt) REVERT: I 347 LYS cc_start: 0.8017 (mttt) cc_final: 0.7334 (pttp) REVERT: I 358 ASP cc_start: 0.7986 (m-30) cc_final: 0.7555 (t0) outliers start: 12 outliers final: 10 residues processed: 103 average time/residue: 0.1833 time to fit residues: 23.2105 Evaluate side-chains 99 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain G residue 376 LEU Chi-restraints excluded: chain H residue 376 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 46 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.204614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.182699 restraints weight = 17065.177| |-----------------------------------------------------------------------------| r_work (start): 0.4612 rms_B_bonded: 2.66 r_work: 0.4554 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.4478 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.4478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.5530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4770 Z= 0.122 Angle : 0.512 4.236 6381 Z= 0.270 Chirality : 0.049 0.148 720 Planarity : 0.004 0.047 810 Dihedral : 5.376 16.949 630 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.15 % Allowed : 16.48 % Favored : 80.37 % 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 are not related in a simple way. whole: -2.77 (0.26), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.20), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 349 TYR 0.011 0.002 TYR D 310 PHE 0.003 0.001 PHE D 346 HIS 0.002 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 4770) covalent geometry : angle 0.51234 ( 6381) hydrogen bonds : bond 0.01616 ( 70) hydrogen bonds : angle 4.57260 ( 210) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 346 PHE cc_start: 0.8188 (m-80) cc_final: 0.7940 (m-80) REVERT: B 347 LYS cc_start: 0.7976 (mttt) cc_final: 0.7289 (tmtt) REVERT: A 347 LYS cc_start: 0.8110 (mttt) cc_final: 0.7458 (tmtt) REVERT: A 358 ASP cc_start: 0.8086 (m-30) cc_final: 0.7641 (t0) REVERT: C 342 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7211 (mt-10) REVERT: C 347 LYS cc_start: 0.8010 (mttt) cc_final: 0.7199 (tmtt) REVERT: D 311 LYS cc_start: 0.8665 (pttt) cc_final: 0.8113 (mmtm) REVERT: D 343 LYS cc_start: 0.8237 (mttt) cc_final: 0.7227 (mmpt) REVERT: D 347 LYS cc_start: 0.7832 (mttt) cc_final: 0.7497 (tmtt) REVERT: D 351 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7315 (mt0) REVERT: E 311 LYS cc_start: 0.8720 (ttmt) cc_final: 0.8040 (mmtm) REVERT: E 327 ASN cc_start: 0.7517 (m-40) cc_final: 0.7134 (t0) REVERT: E 331 LYS cc_start: 0.6251 (mmtt) cc_final: 0.6041 (mmpt) REVERT: E 343 LYS cc_start: 0.8535 (mttt) cc_final: 0.7405 (mmpt) REVERT: E 347 LYS cc_start: 0.8038 (mttt) cc_final: 0.7610 (tmtt) REVERT: F 311 LYS cc_start: 0.8609 (ttmt) cc_final: 0.8010 (mmtm) REVERT: F 347 LYS cc_start: 0.8104 (mttt) cc_final: 0.7570 (tmtt) REVERT: F 351 GLN cc_start: 0.8009 (mp10) cc_final: 0.7404 (tt0) REVERT: G 347 LYS cc_start: 0.8321 (mttt) cc_final: 0.7575 (pttm) REVERT: G 376 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8268 (mt) REVERT: H 311 LYS cc_start: 0.8716 (ttmt) cc_final: 0.7991 (ttpt) REVERT: H 347 LYS cc_start: 0.8192 (mttt) cc_final: 0.7554 (pttm) REVERT: H 358 ASP cc_start: 0.8107 (m-30) cc_final: 0.7570 (t0) REVERT: H 376 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8206 (mt) REVERT: I 347 LYS cc_start: 0.8045 (mttt) cc_final: 0.7346 (pttp) REVERT: I 358 ASP cc_start: 0.8014 (m-30) cc_final: 0.7704 (t0) outliers start: 17 outliers final: 10 residues processed: 105 average time/residue: 0.2133 time to fit residues: 27.0017 Evaluate side-chains 99 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain G residue 376 LEU Chi-restraints excluded: chain H residue 376 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 30 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 31 optimal weight: 0.2980 chunk 5 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 0.0050 chunk 40 optimal weight: 7.9990 chunk 11 optimal weight: 0.0370 chunk 50 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 overall best weight: 2.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.203344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.181159 restraints weight = 16904.565| |-----------------------------------------------------------------------------| r_work (start): 0.4602 rms_B_bonded: 2.68 r_work: 0.4541 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.4463 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.4463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.5623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4770 Z= 0.134 Angle : 0.513 4.293 6381 Z= 0.271 Chirality : 0.049 0.145 720 Planarity : 0.004 0.049 810 Dihedral : 5.304 16.795 630 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.59 % Allowed : 17.59 % Favored : 79.81 % 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 are not related in a simple way. whole: -2.81 (0.26), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.20), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 349 TYR 0.012 0.003 TYR D 310 PHE 0.003 0.001 PHE D 346 HIS 0.003 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 4770) covalent geometry : angle 0.51278 ( 6381) hydrogen bonds : bond 0.01639 ( 70) hydrogen bonds : angle 4.56051 ( 210) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 346 PHE cc_start: 0.8182 (m-80) cc_final: 0.7926 (m-80) REVERT: B 347 LYS cc_start: 0.7962 (mttt) cc_final: 0.7273 (tmtt) REVERT: A 347 LYS cc_start: 0.8104 (mttt) cc_final: 0.7454 (tmtt) REVERT: A 358 ASP cc_start: 0.8195 (m-30) cc_final: 0.7749 (t0) REVERT: C 342 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7198 (mt-10) REVERT: C 347 LYS cc_start: 0.7984 (mttt) cc_final: 0.7210 (tmtt) REVERT: D 311 LYS cc_start: 0.8665 (pttt) cc_final: 0.8109 (mmtm) REVERT: D 343 LYS cc_start: 0.8259 (mttt) cc_final: 0.7313 (mmpt) REVERT: D 347 LYS cc_start: 0.7866 (mttt) cc_final: 0.7539 (tmtt) REVERT: D 351 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7347 (mt0) REVERT: E 311 LYS cc_start: 0.8734 (ttmt) cc_final: 0.8002 (mmtm) REVERT: E 327 ASN cc_start: 0.7544 (m-40) cc_final: 0.7161 (t0) REVERT: E 343 LYS cc_start: 0.8544 (mttt) cc_final: 0.7406 (mmpt) REVERT: E 347 LYS cc_start: 0.8038 (mttt) cc_final: 0.7598 (tmtt) REVERT: F 311 LYS cc_start: 0.8635 (ttmt) cc_final: 0.8009 (mmtm) REVERT: F 347 LYS cc_start: 0.8087 (mttt) cc_final: 0.7520 (tmtt) REVERT: F 351 GLN cc_start: 0.7993 (mp10) cc_final: 0.7441 (tt0) REVERT: G 347 LYS cc_start: 0.8325 (mttt) cc_final: 0.7569 (pttm) REVERT: G 376 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8307 (mt) REVERT: H 311 LYS cc_start: 0.8731 (ttmt) cc_final: 0.8011 (ttpt) REVERT: H 347 LYS cc_start: 0.8191 (mttt) cc_final: 0.7567 (pttm) REVERT: H 358 ASP cc_start: 0.8132 (m-30) cc_final: 0.7598 (t0) REVERT: H 376 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8254 (mt) REVERT: I 347 LYS cc_start: 0.8044 (mttt) cc_final: 0.7335 (pttp) REVERT: I 358 ASP cc_start: 0.8029 (m-30) cc_final: 0.7712 (t0) outliers start: 14 outliers final: 9 residues processed: 100 average time/residue: 0.2101 time to fit residues: 25.3541 Evaluate side-chains 98 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain G residue 376 LEU Chi-restraints excluded: chain H residue 376 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 52 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 44 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.208879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.186976 restraints weight = 16954.856| |-----------------------------------------------------------------------------| r_work (start): 0.4641 rms_B_bonded: 2.67 r_work: 0.4582 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.4503 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.4503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.5739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4770 Z= 0.092 Angle : 0.486 3.834 6381 Z= 0.256 Chirality : 0.049 0.139 720 Planarity : 0.004 0.055 810 Dihedral : 4.950 15.617 630 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.22 % Allowed : 17.59 % Favored : 80.19 % 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 are not related in a simple way. whole: -2.72 (0.27), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.21), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 349 TYR 0.007 0.001 TYR G 310 PHE 0.002 0.001 PHE F 346 HIS 0.002 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 4770) covalent geometry : angle 0.48635 ( 6381) hydrogen bonds : bond 0.01449 ( 70) hydrogen bonds : angle 4.31538 ( 210) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 346 PHE cc_start: 0.8192 (m-80) cc_final: 0.7963 (m-80) REVERT: B 347 LYS cc_start: 0.7961 (mttt) cc_final: 0.7267 (tmtt) REVERT: A 347 LYS cc_start: 0.8078 (mttt) cc_final: 0.7439 (tmtt) REVERT: A 358 ASP cc_start: 0.8230 (m-30) cc_final: 0.7717 (t0) REVERT: C 342 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7181 (mt-10) REVERT: C 347 LYS cc_start: 0.8006 (mttt) cc_final: 0.7207 (tmtt) REVERT: D 311 LYS cc_start: 0.8624 (pttt) cc_final: 0.8066 (mmtm) REVERT: D 343 LYS cc_start: 0.8229 (mttt) cc_final: 0.7286 (mmpt) REVERT: D 347 LYS cc_start: 0.7884 (mttt) cc_final: 0.7478 (tmtt) REVERT: E 311 LYS cc_start: 0.8706 (ttmt) cc_final: 0.8009 (mmtm) REVERT: E 327 ASN cc_start: 0.7432 (m-40) cc_final: 0.7114 (t0) REVERT: E 343 LYS cc_start: 0.8484 (mttt) cc_final: 0.7336 (mmpt) REVERT: E 347 LYS cc_start: 0.8075 (mttt) cc_final: 0.7624 (tmtt) REVERT: F 311 LYS cc_start: 0.8593 (ttmt) cc_final: 0.7880 (mmtm) REVERT: F 347 LYS cc_start: 0.8116 (mttt) cc_final: 0.7514 (tmtt) REVERT: G 347 LYS cc_start: 0.8325 (mttt) cc_final: 0.7597 (pttm) REVERT: G 376 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8267 (mt) REVERT: H 311 LYS cc_start: 0.8708 (ttmt) cc_final: 0.7982 (ttpt) REVERT: H 347 LYS cc_start: 0.8208 (mttt) cc_final: 0.7601 (pttm) REVERT: H 358 ASP cc_start: 0.8104 (m-30) cc_final: 0.7538 (t0) REVERT: H 376 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8248 (mt) REVERT: I 347 LYS cc_start: 0.8064 (mttt) cc_final: 0.7333 (pttp) REVERT: I 358 ASP cc_start: 0.8006 (m-30) cc_final: 0.7684 (t0) outliers start: 12 outliers final: 9 residues processed: 106 average time/residue: 0.2129 time to fit residues: 27.1302 Evaluate side-chains 105 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain G residue 376 LEU Chi-restraints excluded: chain H residue 376 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.210191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.188122 restraints weight = 16821.667| |-----------------------------------------------------------------------------| r_work (start): 0.4656 rms_B_bonded: 2.71 r_work: 0.4595 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.4514 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.4514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.5834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4770 Z= 0.089 Angle : 0.473 3.733 6381 Z= 0.251 Chirality : 0.049 0.140 720 Planarity : 0.005 0.059 810 Dihedral : 4.747 14.948 630 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.85 % Allowed : 17.78 % Favored : 80.37 % 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 are not related in a simple way. whole: -2.60 (0.28), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.21), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 349 TYR 0.008 0.001 TYR D 310 PHE 0.002 0.001 PHE F 346 HIS 0.002 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 4770) covalent geometry : angle 0.47257 ( 6381) hydrogen bonds : bond 0.01367 ( 70) hydrogen bonds : angle 4.19481 ( 210) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1206 Ramachandran restraints generated. 603 Oldfield, 0 Emsley, 603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 346 PHE cc_start: 0.8191 (m-80) cc_final: 0.7952 (m-80) REVERT: B 347 LYS cc_start: 0.7958 (mttt) cc_final: 0.7257 (tmtt) REVERT: A 347 LYS cc_start: 0.8075 (mttt) cc_final: 0.7441 (tmtt) REVERT: A 358 ASP cc_start: 0.8110 (m-30) cc_final: 0.7637 (t0) REVERT: A 375 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8226 (mtpt) REVERT: C 342 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7255 (mt-10) REVERT: C 347 LYS cc_start: 0.8006 (mttt) cc_final: 0.7207 (tmtt) REVERT: D 311 LYS cc_start: 0.8624 (pttt) cc_final: 0.8003 (mmtm) REVERT: D 343 LYS cc_start: 0.8258 (mttt) cc_final: 0.7306 (mmpt) REVERT: D 347 LYS cc_start: 0.7873 (mttt) cc_final: 0.7482 (tmtt) REVERT: E 311 LYS cc_start: 0.8684 (ttmt) cc_final: 0.7997 (mmtm) REVERT: E 327 ASN cc_start: 0.7384 (m-40) cc_final: 0.7117 (t0) REVERT: E 343 LYS cc_start: 0.8435 (mttt) cc_final: 0.7271 (mmpt) REVERT: E 347 LYS cc_start: 0.8023 (mttt) cc_final: 0.7577 (tmtt) REVERT: F 347 LYS cc_start: 0.8116 (mttt) cc_final: 0.7515 (tmtt) REVERT: G 347 LYS cc_start: 0.8332 (mttt) cc_final: 0.7586 (pttm) REVERT: G 376 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8292 (mt) REVERT: H 311 LYS cc_start: 0.8727 (ttmt) cc_final: 0.7985 (ttpt) REVERT: H 347 LYS cc_start: 0.8192 (mttt) cc_final: 0.7639 (pttm) REVERT: H 358 ASP cc_start: 0.8168 (m-30) cc_final: 0.7588 (t0) REVERT: H 376 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8203 (mt) REVERT: I 347 LYS cc_start: 0.8086 (mttt) cc_final: 0.7326 (pttp) REVERT: I 358 ASP cc_start: 0.7995 (m-30) cc_final: 0.7658 (t0) outliers start: 10 outliers final: 7 residues processed: 106 average time/residue: 0.2110 time to fit residues: 26.9144 Evaluate side-chains 108 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain G residue 376 LEU Chi-restraints excluded: chain H residue 376 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 30 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 11 optimal weight: 0.3980 chunk 17 optimal weight: 5.9990 chunk 45 optimal weight: 0.3980 chunk 21 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.210564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.188505 restraints weight = 16983.655| |-----------------------------------------------------------------------------| r_work (start): 0.4664 rms_B_bonded: 2.69 r_work: 0.4604 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.4522 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.4522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.5908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4770 Z= 0.090 Angle : 0.471 3.731 6381 Z= 0.249 Chirality : 0.049 0.137 720 Planarity : 0.005 0.062 810 Dihedral : 4.665 14.336 630 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.85 % Allowed : 17.78 % Favored : 80.37 % 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 are not related in a simple way. whole: -2.57 (0.28), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.21), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 349 TYR 0.009 0.001 TYR F 310 PHE 0.002 0.001 PHE B 346 HIS 0.002 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 4770) covalent geometry : angle 0.47082 ( 6381) hydrogen bonds : bond 0.01397 ( 70) hydrogen bonds : angle 4.12623 ( 210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2777.48 seconds wall clock time: 47 minutes 56.09 seconds (2876.09 seconds total)