Starting phenix.real_space_refine on Sun Jun 8 13:18:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qkv_14054/06_2025/7qkv_14054.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qkv_14054/06_2025/7qkv_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7qkv_14054/06_2025/7qkv_14054.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qkv_14054/06_2025/7qkv_14054.map" model { file = "/net/cci-nas-00/data/ceres_data/7qkv_14054/06_2025/7qkv_14054.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qkv_14054/06_2025/7qkv_14054.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.53, per 1000 atoms: 0.58 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: 2.14 Conformation dependent library (CDL) restraints added in 770.5 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: 0.99 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: 3.42 Time building geometry restraints manager: 2.68 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: 0.01 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: 4.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.150 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.530 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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:3.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.380 ------------------------------------------------------------------------------- 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 : 0.73 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (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 HIS 0.018 0.006 HIS G 330 PHE 0.032 0.013 PHE I 346 TYR 0.290 0.091 TYR E 310 ARG 0.004 0.001 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.11634 ( 70) hydrogen bonds : angle 7.62890 ( 210) covalent geometry : bond 0.01106 ( 4770) covalent geometry : angle 1.91586 ( 6381) *********************** 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 : 0.807 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: 0.7309 (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 346 PHE cc_start: 0.8364 (m-80) cc_final: 0.8059 (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 343 LYS cc_start: 0.8191 (mttt) cc_final: 0.7456 (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: 0.8105 (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: 0.7840 (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: 0.4273 time to fit residues: 93.4172 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 : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.4710 r_free = 0.4710 target = 0.197722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.176682 restraints weight = 17428.568| |-----------------------------------------------------------------------------| r_work (start): 0.4547 rms_B_bonded: 2.49 r_work: 0.4488 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.4418 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.4418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 4770 Z= 0.264 Angle : 0.730 6.607 6381 Z= 0.388 Chirality : 0.051 0.143 720 Planarity : 0.003 0.024 810 Dihedral : 7.879 28.829 630 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.67 % Allowed : 17.04 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.26), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.20), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 330 PHE 0.007 0.001 PHE E 346 TYR 0.033 0.007 TYR D 310 ARG 0.001 0.000 ARG I 349 Details of bonding type rmsd hydrogen bonds : bond 0.02910 ( 70) hydrogen bonds : angle 6.10716 ( 210) covalent geometry : bond 0.00600 ( 4770) covalent geometry : angle 0.73009 ( 6381) *********************** 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 117 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 327 ASN cc_start: 0.7164 (m-40) cc_final: 0.6935 (t0) REVERT: B 345 ASP cc_start: 0.6903 (m-30) cc_final: 0.6695 (m-30) REVERT: B 346 PHE cc_start: 0.8058 (m-80) cc_final: 0.7743 (m-80) REVERT: B 347 LYS cc_start: 0.8059 (mttt) cc_final: 0.7394 (tmtt) REVERT: B 376 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8475 (mt) REVERT: A 347 LYS cc_start: 0.8044 (mttt) cc_final: 0.7231 (tmtt) REVERT: A 358 ASP cc_start: 0.8056 (m-30) cc_final: 0.7804 (t0) REVERT: C 347 LYS cc_start: 0.8168 (mttt) cc_final: 0.7350 (tmtt) REVERT: C 358 ASP cc_start: 0.7861 (m-30) cc_final: 0.7621 (t0) REVERT: C 376 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8311 (mt) REVERT: D 311 LYS cc_start: 0.8358 (mtmt) cc_final: 0.8067 (mmtm) REVERT: D 343 LYS cc_start: 0.8360 (mttt) cc_final: 0.7305 (mmpt) REVERT: D 347 LYS cc_start: 0.7965 (mttt) cc_final: 0.7674 (tmtt) REVERT: E 311 LYS cc_start: 0.8430 (mtmt) cc_final: 0.7829 (mmtm) REVERT: E 343 LYS cc_start: 0.8516 (mttt) cc_final: 0.7521 (mmpt) REVERT: E 347 LYS cc_start: 0.7948 (mttt) cc_final: 0.7613 (tmtt) REVERT: F 311 LYS cc_start: 0.8667 (ttmt) cc_final: 0.7959 (mmtm) REVERT: F 347 LYS cc_start: 0.8080 (mttt) cc_final: 0.7564 (tmtt) REVERT: F 351 GLN cc_start: 0.8112 (mp10) cc_final: 0.7484 (tt0) REVERT: G 347 LYS cc_start: 0.8278 (mttt) cc_final: 0.7578 (pttp) REVERT: G 358 ASP cc_start: 0.7843 (m-30) cc_final: 0.7607 (t0) REVERT: H 345 ASP cc_start: 0.6415 (m-30) cc_final: 0.6206 (m-30) REVERT: H 347 LYS cc_start: 0.8154 (mttt) cc_final: 0.7502 (pttp) REVERT: H 358 ASP cc_start: 0.8116 (m-30) cc_final: 0.7738 (t0) REVERT: I 347 LYS cc_start: 0.8063 (mttt) cc_final: 0.7407 (pttp) REVERT: I 358 ASP cc_start: 0.7830 (m-30) cc_final: 0.7460 (t0) outliers start: 9 outliers final: 7 residues processed: 115 average time/residue: 0.4705 time to fit residues: 66.6236 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 : 0.926 ------------------------------------------------------------------------------- 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 33 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 22 optimal weight: 0.2980 chunk 25 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- 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 = 0.4755 r_free = 0.4755 target = 0.201071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.179505 restraints weight = 17351.966| |-----------------------------------------------------------------------------| r_work (start): 0.4590 rms_B_bonded: 2.57 r_work: 0.4520 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.4434 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.4434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4770 Z= 0.155 Angle : 0.586 4.589 6381 Z= 0.311 Chirality : 0.050 0.141 720 Planarity : 0.003 0.022 810 Dihedral : 6.620 23.099 630 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.04 % Allowed : 17.22 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.25), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.19), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 330 PHE 0.007 0.001 PHE D 346 TYR 0.014 0.003 TYR D 310 ARG 0.002 0.000 ARG G 349 Details of bonding type rmsd hydrogen bonds : bond 0.02125 ( 70) hydrogen bonds : angle 5.48954 ( 210) covalent geometry : bond 0.00339 ( 4770) covalent geometry : angle 0.58640 ( 6381) *********************** 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 118 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 345 ASP cc_start: 0.6660 (m-30) cc_final: 0.6175 (m-30) REVERT: B 346 PHE cc_start: 0.8074 (m-80) cc_final: 0.7795 (m-80) REVERT: B 347 LYS cc_start: 0.7977 (mttt) cc_final: 0.7239 (tmtt) REVERT: A 347 LYS cc_start: 0.8013 (mttt) cc_final: 0.7210 (tmtt) REVERT: A 358 ASP cc_start: 0.8101 (m-30) cc_final: 0.7703 (t0) REVERT: C 327 ASN cc_start: 0.7381 (m-40) cc_final: 0.6666 (t0) REVERT: C 347 LYS cc_start: 0.8154 (mttt) cc_final: 0.7289 (tmtt) REVERT: C 358 ASP cc_start: 0.8035 (m-30) cc_final: 0.7631 (t0) REVERT: D 343 LYS cc_start: 0.8177 (mttt) cc_final: 0.7192 (mmpt) REVERT: D 347 LYS cc_start: 0.7865 (mttt) cc_final: 0.7587 (tmtt) REVERT: E 342 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7292 (mm-30) REVERT: E 343 LYS cc_start: 0.8484 (mttt) cc_final: 0.7453 (mmpt) REVERT: E 347 LYS cc_start: 0.7988 (mttt) cc_final: 0.7632 (tmtt) REVERT: F 311 LYS cc_start: 0.8623 (ttmt) cc_final: 0.7910 (mmtm) REVERT: F 347 LYS cc_start: 0.8186 (mttt) cc_final: 0.7662 (tmtt) REVERT: F 351 GLN cc_start: 0.8097 (mp10) cc_final: 0.7477 (tt0) REVERT: G 347 LYS cc_start: 0.8307 (mttt) cc_final: 0.7555 (pttp) REVERT: H 347 LYS cc_start: 0.8200 (mttt) cc_final: 0.7433 (pttp) REVERT: H 358 ASP cc_start: 0.8117 (m-30) cc_final: 0.7678 (t0) REVERT: I 347 LYS cc_start: 0.8024 (mttt) cc_final: 0.7390 (pttp) REVERT: I 358 ASP cc_start: 0.8013 (m-30) cc_final: 0.7583 (t0) outliers start: 11 outliers final: 6 residues processed: 111 average time/residue: 0.4285 time to fit residues: 58.2564 Evaluate side-chains 100 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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 45 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 overall best weight: 3.5786 ------------------------------------------------------------------------------- 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 = 0.4741 r_free = 0.4741 target = 0.199989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.178505 restraints weight = 17249.370| |-----------------------------------------------------------------------------| r_work (start): 0.4576 rms_B_bonded: 2.55 r_work: 0.4515 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.4440 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.4440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4770 Z= 0.180 Angle : 0.579 4.895 6381 Z= 0.305 Chirality : 0.050 0.141 720 Planarity : 0.003 0.027 810 Dihedral : 6.223 19.447 630 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.48 % Allowed : 18.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.26), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.19), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 329 PHE 0.005 0.001 PHE D 346 TYR 0.015 0.003 TYR D 310 ARG 0.001 0.000 ARG H 349 Details of bonding type rmsd hydrogen bonds : bond 0.01914 ( 70) hydrogen bonds : angle 5.19551 ( 210) covalent geometry : bond 0.00402 ( 4770) covalent geometry : angle 0.57916 ( 6381) *********************** 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 101 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 346 PHE cc_start: 0.8080 (m-80) cc_final: 0.7789 (m-80) REVERT: B 347 LYS cc_start: 0.7998 (mttt) cc_final: 0.7198 (tmtt) REVERT: A 347 LYS cc_start: 0.7976 (mttt) cc_final: 0.7205 (tmtt) REVERT: A 358 ASP cc_start: 0.8107 (m-30) cc_final: 0.7722 (t0) REVERT: C 347 LYS cc_start: 0.8127 (mttt) cc_final: 0.7185 (tmtt) REVERT: C 358 ASP cc_start: 0.8076 (m-30) cc_final: 0.7653 (t0) REVERT: D 311 LYS cc_start: 0.8548 (pttt) cc_final: 0.8138 (mmtm) REVERT: D 343 LYS cc_start: 0.8253 (mttt) cc_final: 0.7233 (mmpt) REVERT: D 347 LYS cc_start: 0.7836 (mttt) cc_final: 0.7574 (tmtt) REVERT: E 311 LYS cc_start: 0.8713 (ttmt) cc_final: 0.7980 (mmtm) REVERT: E 327 ASN cc_start: 0.7459 (m-40) cc_final: 0.7041 (t0) REVERT: E 342 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7281 (mm-30) REVERT: E 343 LYS cc_start: 0.8486 (mttt) cc_final: 0.7435 (mmpt) REVERT: E 347 LYS cc_start: 0.8015 (mttt) cc_final: 0.7628 (tmtt) REVERT: F 311 LYS cc_start: 0.8601 (ttmt) cc_final: 0.7938 (mmtm) REVERT: F 327 ASN cc_start: 0.7565 (m-40) cc_final: 0.7305 (t0) REVERT: F 347 LYS cc_start: 0.8182 (mttt) cc_final: 0.7590 (tmtt) REVERT: F 351 GLN cc_start: 0.8106 (mp10) cc_final: 0.7459 (tt0) REVERT: G 347 LYS cc_start: 0.8250 (mttt) cc_final: 0.7435 (pttp) REVERT: H 311 LYS cc_start: 0.8739 (ttmt) cc_final: 0.8022 (ttpt) REVERT: H 347 LYS cc_start: 0.8174 (mttt) cc_final: 0.7465 (pttp) REVERT: H 358 ASP cc_start: 0.8143 (m-30) cc_final: 0.7697 (t0) REVERT: I 347 LYS cc_start: 0.7989 (mttt) cc_final: 0.7337 (pttp) REVERT: I 358 ASP cc_start: 0.8002 (m-30) cc_final: 0.7605 (t0) outliers start: 8 outliers final: 7 residues processed: 98 average time/residue: 0.4678 time to fit residues: 55.3394 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 : 0.850 ------------------------------------------------------------------------------- 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 356 SER Chi-restraints excluded: chain E residue 376 LEU 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 5 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 49 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 = 0.4806 r_free = 0.4806 target = 0.195959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.172740 restraints weight = 17110.320| |-----------------------------------------------------------------------------| r_work (start): 0.4626 rms_B_bonded: 2.79 r_work: 0.4530 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.4530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.5262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4770 Z= 0.144 Angle : 0.547 4.409 6381 Z= 0.287 Chirality : 0.049 0.142 720 Planarity : 0.004 0.034 810 Dihedral : 5.824 18.041 630 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.59 % Allowed : 17.41 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.26), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.20), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.004 0.001 PHE D 346 TYR 0.012 0.003 TYR F 310 ARG 0.001 0.000 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.01697 ( 70) hydrogen bonds : angle 4.87354 ( 210) covalent geometry : bond 0.00322 ( 4770) covalent geometry : angle 0.54713 ( 6381) *********************** 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 108 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 346 PHE cc_start: 0.8134 (m-80) cc_final: 0.7875 (m-80) REVERT: B 347 LYS cc_start: 0.7936 (mttt) cc_final: 0.7144 (tmtt) REVERT: A 327 ASN cc_start: 0.7679 (t0) cc_final: 0.7358 (t0) REVERT: A 347 LYS cc_start: 0.7911 (mttt) cc_final: 0.7094 (tmtt) REVERT: A 358 ASP cc_start: 0.8124 (m-30) cc_final: 0.7607 (t0) REVERT: C 347 LYS cc_start: 0.8059 (mttt) cc_final: 0.7156 (tmtt) REVERT: C 358 ASP cc_start: 0.8128 (m-30) cc_final: 0.7561 (t0) REVERT: D 311 LYS cc_start: 0.8560 (pttt) cc_final: 0.8072 (mmtm) REVERT: D 343 LYS cc_start: 0.8260 (mttt) cc_final: 0.7244 (mmpt) REVERT: D 347 LYS cc_start: 0.7905 (mttt) cc_final: 0.7574 (tmtt) REVERT: D 358 ASP cc_start: 0.8138 (t0) cc_final: 0.7918 (t0) REVERT: E 311 LYS cc_start: 0.8648 (ttmt) cc_final: 0.7955 (mmtm) REVERT: E 327 ASN cc_start: 0.7406 (m-40) cc_final: 0.6992 (t0) REVERT: E 342 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7155 (mm-30) REVERT: E 343 LYS cc_start: 0.8538 (mttt) cc_final: 0.7408 (mmpt) REVERT: E 347 LYS cc_start: 0.8002 (mttt) cc_final: 0.7612 (tmtt) REVERT: F 311 LYS cc_start: 0.8546 (ttmt) cc_final: 0.7898 (mmtm) REVERT: F 327 ASN cc_start: 0.7464 (m-40) cc_final: 0.7223 (t0) REVERT: F 347 LYS cc_start: 0.8168 (mttt) cc_final: 0.7550 (tmtt) REVERT: F 351 GLN cc_start: 0.7930 (mp10) cc_final: 0.7214 (tt0) REVERT: G 347 LYS cc_start: 0.8304 (mttt) cc_final: 0.7418 (pttm) REVERT: H 311 LYS cc_start: 0.8641 (ttmt) cc_final: 0.7919 (ttpt) REVERT: H 347 LYS cc_start: 0.8221 (mttt) cc_final: 0.7411 (pttp) REVERT: H 358 ASP cc_start: 0.8081 (m-30) cc_final: 0.7550 (t0) REVERT: H 376 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8140 (mt) REVERT: I 347 LYS cc_start: 0.7978 (mttt) cc_final: 0.7254 (pttp) REVERT: I 358 ASP cc_start: 0.7973 (m-30) cc_final: 0.7495 (t0) outliers start: 14 outliers final: 10 residues processed: 105 average time/residue: 0.4218 time to fit residues: 54.4952 Evaluate side-chains 99 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 356 SER 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 Chi-restraints excluded: chain H residue 376 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 7 optimal weight: 0.1980 chunk 15 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 36 optimal weight: 0.0070 chunk 53 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 overall best weight: 2.6404 ------------------------------------------------------------------------------- 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 = 0.4800 r_free = 0.4800 target = 0.195882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.172684 restraints weight = 17150.953| |-----------------------------------------------------------------------------| r_work (start): 0.4622 rms_B_bonded: 2.81 r_work: 0.4545 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.4455 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.4455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4770 Z= 0.139 Angle : 0.527 4.445 6381 Z= 0.277 Chirality : 0.049 0.139 720 Planarity : 0.004 0.040 810 Dihedral : 5.572 17.720 630 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.15 % Allowed : 18.15 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.26), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.20), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 330 PHE 0.004 0.001 PHE D 346 TYR 0.012 0.003 TYR F 310 ARG 0.002 0.000 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.01571 ( 70) hydrogen bonds : angle 4.70546 ( 210) covalent geometry : bond 0.00312 ( 4770) covalent geometry : angle 0.52696 ( 6381) *********************** 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 115 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 346 PHE cc_start: 0.8166 (m-80) cc_final: 0.7909 (m-80) REVERT: B 347 LYS cc_start: 0.7991 (mttt) cc_final: 0.7257 (tmtt) REVERT: B 358 ASP cc_start: 0.8229 (t0) cc_final: 0.8009 (t0) REVERT: A 347 LYS cc_start: 0.8038 (mttt) cc_final: 0.7299 (tmtt) REVERT: A 358 ASP cc_start: 0.8263 (m-30) cc_final: 0.7645 (t0) REVERT: C 347 LYS cc_start: 0.7983 (mttt) cc_final: 0.7155 (tmtt) REVERT: C 358 ASP cc_start: 0.8150 (m-30) cc_final: 0.7554 (t0) REVERT: D 311 LYS cc_start: 0.8633 (pttt) cc_final: 0.8108 (mmtm) REVERT: D 343 LYS cc_start: 0.8290 (mttt) cc_final: 0.7305 (mmpt) REVERT: D 347 LYS cc_start: 0.7898 (mttt) cc_final: 0.7556 (tmtt) REVERT: D 351 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7168 (mt0) REVERT: D 358 ASP cc_start: 0.8229 (t0) cc_final: 0.7966 (t0) REVERT: E 311 LYS cc_start: 0.8736 (ttmt) cc_final: 0.7994 (mmtm) REVERT: E 327 ASN cc_start: 0.7397 (m-40) cc_final: 0.6961 (t0) REVERT: E 331 LYS cc_start: 0.6212 (mmtt) cc_final: 0.6007 (mmpt) REVERT: E 343 LYS cc_start: 0.8544 (mttt) cc_final: 0.7387 (mmpt) REVERT: E 347 LYS cc_start: 0.8050 (mttt) cc_final: 0.7622 (tmtt) REVERT: F 311 LYS cc_start: 0.8626 (ttmt) cc_final: 0.7906 (mmtm) REVERT: F 327 ASN cc_start: 0.7441 (m-40) cc_final: 0.7186 (t0) REVERT: F 347 LYS cc_start: 0.8157 (mttt) cc_final: 0.7503 (tmtt) REVERT: F 351 GLN cc_start: 0.7890 (mp10) cc_final: 0.7206 (tt0) REVERT: G 347 LYS cc_start: 0.8294 (mttt) cc_final: 0.7481 (pttm) REVERT: H 311 LYS cc_start: 0.8688 (ttmt) cc_final: 0.7938 (ttpt) REVERT: H 347 LYS cc_start: 0.8165 (mttt) cc_final: 0.7432 (pttp) REVERT: H 358 ASP cc_start: 0.8148 (m-30) cc_final: 0.7566 (t0) REVERT: H 376 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8176 (mt) REVERT: I 347 LYS cc_start: 0.8041 (mttt) cc_final: 0.7251 (pttp) REVERT: I 358 ASP cc_start: 0.8076 (m-30) cc_final: 0.7549 (t0) REVERT: I 376 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8160 (mt) outliers start: 17 outliers final: 11 residues processed: 108 average time/residue: 0.4331 time to fit residues: 57.1265 Evaluate side-chains 105 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 351 GLN 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 Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain H residue 376 LEU Chi-restraints excluded: chain I residue 376 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 41 optimal weight: 0.0980 chunk 49 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 53 optimal weight: 0.0970 chunk 40 optimal weight: 5.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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 = 0.4828 r_free = 0.4828 target = 0.199189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.175565 restraints weight = 17097.235| |-----------------------------------------------------------------------------| r_work (start): 0.4661 rms_B_bonded: 2.86 r_work: 0.4583 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.4583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.5594 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= 0.108 Angle : 0.500 4.077 6381 Z= 0.261 Chirality : 0.049 0.137 720 Planarity : 0.004 0.049 810 Dihedral : 5.227 16.527 630 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.59 % Allowed : 19.07 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (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 HIS 0.003 0.001 HIS B 330 PHE 0.003 0.001 PHE D 346 TYR 0.010 0.002 TYR F 310 ARG 0.001 0.000 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.01401 ( 70) hydrogen bonds : angle 4.47999 ( 210) covalent geometry : bond 0.00247 ( 4770) covalent geometry : angle 0.50040 ( 6381) *********************** 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 109 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 346 PHE cc_start: 0.8174 (m-80) cc_final: 0.7961 (m-80) REVERT: B 347 LYS cc_start: 0.7974 (mttt) cc_final: 0.7283 (tmtt) REVERT: A 347 LYS cc_start: 0.8049 (mttt) cc_final: 0.7358 (tmtt) REVERT: A 358 ASP cc_start: 0.8088 (m-30) cc_final: 0.7568 (t0) REVERT: C 347 LYS cc_start: 0.7981 (mttt) cc_final: 0.7183 (tmtt) REVERT: D 311 LYS cc_start: 0.8571 (pttt) cc_final: 0.8054 (mmtm) REVERT: D 343 LYS cc_start: 0.8287 (mttt) cc_final: 0.7340 (mmpt) REVERT: D 347 LYS cc_start: 0.7885 (mttt) cc_final: 0.7582 (tmtt) REVERT: E 311 LYS cc_start: 0.8643 (ttmt) cc_final: 0.7902 (mmtm) REVERT: E 327 ASN cc_start: 0.7359 (m-40) cc_final: 0.7039 (t0) REVERT: E 343 LYS cc_start: 0.8500 (mttt) cc_final: 0.7399 (mmpt) REVERT: E 347 LYS cc_start: 0.7987 (mttt) cc_final: 0.7612 (tmtt) REVERT: F 311 LYS cc_start: 0.8541 (ttmt) cc_final: 0.7839 (mmtm) REVERT: F 347 LYS cc_start: 0.8121 (mttt) cc_final: 0.7517 (tmtt) REVERT: F 351 GLN cc_start: 0.7777 (mp10) cc_final: 0.7120 (tt0) REVERT: G 347 LYS cc_start: 0.8315 (mttt) cc_final: 0.7523 (pttm) REVERT: H 311 LYS cc_start: 0.8626 (ttmt) cc_final: 0.7895 (ttpt) REVERT: H 347 LYS cc_start: 0.8184 (mttt) cc_final: 0.7463 (pttp) REVERT: H 358 ASP cc_start: 0.8027 (m-30) cc_final: 0.7487 (t0) REVERT: H 376 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8193 (mt) REVERT: I 347 LYS cc_start: 0.8058 (mttt) cc_final: 0.7336 (pttp) REVERT: I 358 ASP cc_start: 0.8013 (m-30) cc_final: 0.7638 (t0) REVERT: I 376 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8163 (mt) outliers start: 14 outliers final: 11 residues processed: 104 average time/residue: 0.4291 time to fit residues: 54.5443 Evaluate side-chains 102 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 356 SER 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 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 Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain H residue 376 LEU Chi-restraints excluded: chain I residue 376 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 44 optimal weight: 0.0270 chunk 23 optimal weight: 3.9990 chunk 41 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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 = 0.4880 r_free = 0.4880 target = 0.205669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.181703 restraints weight = 16883.820| |-----------------------------------------------------------------------------| r_work (start): 0.4708 rms_B_bonded: 2.89 r_work: 0.4631 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.4631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.5784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4770 Z= 0.079 Angle : 0.474 3.685 6381 Z= 0.249 Chirality : 0.049 0.135 720 Planarity : 0.004 0.056 810 Dihedral : 4.791 14.563 630 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.85 % Allowed : 19.07 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.27), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.21), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.002 0.001 PHE A 346 TYR 0.004 0.001 TYR B 310 ARG 0.001 0.000 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.01511 ( 70) hydrogen bonds : angle 4.12175 ( 210) covalent geometry : bond 0.00193 ( 4770) covalent geometry : angle 0.47399 ( 6381) *********************** 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 116 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 346 PHE cc_start: 0.8206 (m-80) cc_final: 0.8006 (m-80) REVERT: B 347 LYS cc_start: 0.7922 (mttt) cc_final: 0.7237 (tmtt) REVERT: A 347 LYS cc_start: 0.8027 (mttt) cc_final: 0.7344 (tmtt) REVERT: A 358 ASP cc_start: 0.8208 (m-30) cc_final: 0.7709 (t0) REVERT: A 375 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8083 (mtpt) REVERT: C 347 LYS cc_start: 0.7997 (mttt) cc_final: 0.7214 (tmtt) REVERT: D 311 LYS cc_start: 0.8549 (pttt) cc_final: 0.7958 (mmtm) REVERT: D 343 LYS cc_start: 0.8270 (mttt) cc_final: 0.7316 (mmpt) REVERT: D 347 LYS cc_start: 0.7883 (mttt) cc_final: 0.7567 (tmtt) REVERT: E 311 LYS cc_start: 0.8606 (ttmt) cc_final: 0.7925 (mmtm) REVERT: E 327 ASN cc_start: 0.7296 (m-40) cc_final: 0.7024 (t0) REVERT: E 343 LYS cc_start: 0.8359 (mttt) cc_final: 0.7286 (mmpt) REVERT: E 347 LYS cc_start: 0.7970 (mttt) cc_final: 0.7604 (tmtt) REVERT: F 347 LYS cc_start: 0.8075 (mttt) cc_final: 0.7500 (tmtt) REVERT: G 347 LYS cc_start: 0.8320 (mttt) cc_final: 0.7528 (pttm) REVERT: H 311 LYS cc_start: 0.8597 (ttmt) cc_final: 0.7850 (ttpt) REVERT: H 347 LYS cc_start: 0.8185 (mttt) cc_final: 0.7477 (pttp) REVERT: H 358 ASP cc_start: 0.8068 (m-30) cc_final: 0.7568 (t0) REVERT: H 376 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8103 (mt) REVERT: I 347 LYS cc_start: 0.8003 (mttt) cc_final: 0.7321 (pttp) REVERT: I 358 ASP cc_start: 0.8003 (m-30) cc_final: 0.7619 (t0) REVERT: I 376 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8115 (mt) outliers start: 10 outliers final: 6 residues processed: 112 average time/residue: 0.4850 time to fit residues: 65.9497 Evaluate side-chains 107 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 376 LEU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain H residue 376 LEU Chi-restraints excluded: chain I residue 376 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 36 optimal weight: 0.4980 chunk 2 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.4841 r_free = 0.4841 target = 0.201988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.178353 restraints weight = 16859.518| |-----------------------------------------------------------------------------| r_work (start): 0.4673 rms_B_bonded: 2.85 r_work: 0.4592 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.4592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.5866 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= 0.103 Angle : 0.487 4.064 6381 Z= 0.257 Chirality : 0.049 0.146 720 Planarity : 0.004 0.055 810 Dihedral : 4.842 14.930 630 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.22 % Allowed : 18.89 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.002 0.000 HIS C 330 PHE 0.002 0.001 PHE D 346 TYR 0.011 0.002 TYR F 310 ARG 0.002 0.000 ARG H 349 Details of bonding type rmsd hydrogen bonds : bond 0.01449 ( 70) hydrogen bonds : angle 4.18186 ( 210) covalent geometry : bond 0.00237 ( 4770) covalent geometry : angle 0.48711 ( 6381) *********************** 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 113 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 346 PHE cc_start: 0.8191 (m-80) cc_final: 0.7955 (m-80) REVERT: B 347 LYS cc_start: 0.7947 (mttt) cc_final: 0.7252 (tmtt) REVERT: A 347 LYS cc_start: 0.8013 (mttt) cc_final: 0.7324 (tmtt) REVERT: A 358 ASP cc_start: 0.8298 (m-30) cc_final: 0.7673 (t0) REVERT: A 375 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8109 (mtpt) REVERT: C 347 LYS cc_start: 0.8006 (mttt) cc_final: 0.7238 (tmtt) REVERT: D 311 LYS cc_start: 0.8581 (pttt) cc_final: 0.7965 (mmtm) REVERT: D 343 LYS cc_start: 0.8291 (mttt) cc_final: 0.7337 (mmpt) REVERT: D 347 LYS cc_start: 0.7906 (mttt) cc_final: 0.7583 (tmtt) REVERT: E 311 LYS cc_start: 0.8609 (ttmt) cc_final: 0.7889 (mmtm) REVERT: E 327 ASN cc_start: 0.7243 (m-40) cc_final: 0.7001 (t0) REVERT: E 343 LYS cc_start: 0.8447 (mttt) cc_final: 0.7309 (mmpt) REVERT: E 347 LYS cc_start: 0.7967 (mttt) cc_final: 0.7594 (tmtt) REVERT: F 342 GLU cc_start: 0.7379 (mt-10) cc_final: 0.6870 (mt-10) REVERT: F 347 LYS cc_start: 0.8081 (mttt) cc_final: 0.7493 (tmtt) REVERT: G 347 LYS cc_start: 0.8340 (mttt) cc_final: 0.7553 (pttm) REVERT: H 311 LYS cc_start: 0.8643 (ttmt) cc_final: 0.7912 (ttpt) REVERT: H 347 LYS cc_start: 0.8202 (mttt) cc_final: 0.7464 (pttp) REVERT: H 358 ASP cc_start: 0.8106 (m-30) cc_final: 0.7503 (t0) REVERT: H 376 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8145 (mt) REVERT: I 347 LYS cc_start: 0.8014 (mttt) cc_final: 0.7329 (pttp) REVERT: I 358 ASP cc_start: 0.8093 (m-30) cc_final: 0.7683 (t0) REVERT: I 376 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8154 (mt) outliers start: 12 outliers final: 6 residues processed: 108 average time/residue: 0.4628 time to fit residues: 60.9390 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 : 1.087 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain H residue 376 LEU Chi-restraints excluded: chain I residue 376 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 42 optimal weight: 0.3980 chunk 36 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.4865 r_free = 0.4865 target = 0.203661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.179729 restraints weight = 16826.566| |-----------------------------------------------------------------------------| r_work (start): 0.4691 rms_B_bonded: 2.89 r_work: 0.4613 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.4613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.5951 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= 0.089 Angle : 0.480 3.979 6381 Z= 0.252 Chirality : 0.049 0.142 720 Planarity : 0.004 0.055 810 Dihedral : 4.714 14.615 630 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.85 % Allowed : 19.44 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.28), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.21), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 330 PHE 0.002 0.001 PHE H 346 TYR 0.008 0.001 TYR D 310 ARG 0.001 0.000 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.01332 ( 70) hydrogen bonds : angle 4.08519 ( 210) covalent geometry : bond 0.00212 ( 4770) covalent geometry : angle 0.47991 ( 6381) ********************** 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 111 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 346 PHE cc_start: 0.8171 (m-80) cc_final: 0.7939 (m-80) REVERT: B 347 LYS cc_start: 0.7936 (mttt) cc_final: 0.7257 (tmtt) REVERT: A 347 LYS cc_start: 0.8003 (mttt) cc_final: 0.7327 (tmtt) REVERT: A 358 ASP cc_start: 0.8264 (m-30) cc_final: 0.7678 (t0) REVERT: A 375 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8090 (mtpt) REVERT: C 347 LYS cc_start: 0.7990 (mttt) cc_final: 0.7220 (tmtt) REVERT: D 311 LYS cc_start: 0.8554 (pttt) cc_final: 0.7946 (mmtm) REVERT: D 343 LYS cc_start: 0.8284 (mttt) cc_final: 0.7329 (mmpt) REVERT: D 347 LYS cc_start: 0.7889 (mttt) cc_final: 0.7592 (tmtt) REVERT: D 351 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.7046 (mt0) REVERT: D 358 ASP cc_start: 0.8161 (t0) cc_final: 0.7928 (t0) REVERT: E 311 LYS cc_start: 0.8584 (ttmt) cc_final: 0.7940 (mmtm) REVERT: E 327 ASN cc_start: 0.7292 (m-40) cc_final: 0.7040 (t0) REVERT: E 343 LYS cc_start: 0.8383 (mttt) cc_final: 0.7282 (mmpt) REVERT: E 347 LYS cc_start: 0.7967 (mttt) cc_final: 0.7598 (tmtt) REVERT: F 342 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6842 (mt-10) REVERT: F 347 LYS cc_start: 0.8086 (mttt) cc_final: 0.7495 (tmtt) REVERT: G 347 LYS cc_start: 0.8328 (mttt) cc_final: 0.7579 (pttm) REVERT: H 311 LYS cc_start: 0.8659 (ttmt) cc_final: 0.7905 (ttpt) REVERT: H 347 LYS cc_start: 0.8169 (mttt) cc_final: 0.7452 (pttp) REVERT: H 358 ASP cc_start: 0.8066 (m-30) cc_final: 0.7459 (t0) REVERT: H 376 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8140 (mt) REVERT: I 347 LYS cc_start: 0.8044 (mttt) cc_final: 0.7328 (pttp) REVERT: I 358 ASP cc_start: 0.8062 (m-30) cc_final: 0.7660 (t0) REVERT: I 376 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8160 (mt) outliers start: 10 outliers final: 5 residues processed: 107 average time/residue: 0.4733 time to fit residues: 61.1195 Evaluate side-chains 106 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 351 GLN Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain H residue 376 LEU Chi-restraints excluded: chain I residue 376 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4892 r_free = 0.4892 target = 0.206731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.182679 restraints weight = 16710.996| |-----------------------------------------------------------------------------| r_work (start): 0.4719 rms_B_bonded: 2.90 r_work: 0.4637 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.6029 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= 0.081 Angle : 0.477 3.906 6381 Z= 0.251 Chirality : 0.049 0.142 720 Planarity : 0.004 0.055 810 Dihedral : 4.547 13.810 630 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.67 % Allowed : 19.81 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.28), residues: 603 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.21), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 362 PHE 0.002 0.001 PHE D 346 TYR 0.006 0.001 TYR B 310 ARG 0.002 0.000 ARG H 349 Details of bonding type rmsd hydrogen bonds : bond 0.01308 ( 70) hydrogen bonds : angle 3.96778 ( 210) covalent geometry : bond 0.00195 ( 4770) covalent geometry : angle 0.47669 ( 6381) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5475.60 seconds wall clock time: 95 minutes 14.86 seconds (5714.86 seconds total)