Starting phenix.real_space_refine on Fri Aug 22 15:39:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q7m_18224/08_2025/8q7m_18224.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q7m_18224/08_2025/8q7m_18224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8q7m_18224/08_2025/8q7m_18224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q7m_18224/08_2025/8q7m_18224.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8q7m_18224/08_2025/8q7m_18224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q7m_18224/08_2025/8q7m_18224.map" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 9 5.16 5 C 3210 2.51 5 N 939 2.21 5 O 951 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5109 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 568 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "B" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 568 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "C" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 568 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "D" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "E" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "F" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "G" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "H" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "I" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Time building chain proxies: 1.42, per 1000 atoms: 0.28 Number of scatterers: 5109 At special positions: 0 Unit cell: (161.504, 161.504, 50.264, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 9 16.00 O 951 8.00 N 939 7.00 C 3210 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.27 Conformation dependent library (CDL) restraints added in 227.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1170 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 28 sheets defined 0.0% alpha, 52.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 307 through 310 Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.878A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 325 removed outlier: 6.471A pdb=" N LYS A 317 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N SER B 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR A 319 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N CYS B 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS A 321 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N SER B 324 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLY A 323 " --> pdb=" O SER B 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 328 through 330 Processing sheet with id=AA5, first strand: chain 'B' and resid 336 through 339 Processing sheet with id=AA6, first strand: chain 'B' and resid 342 through 346 removed outlier: 7.031A pdb=" N LYS A 343 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N PHE B 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASP A 345 " --> pdb=" O PHE B 346 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LYS C 343 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 350 through 354 removed outlier: 6.447A pdb=" N GLN A 351 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE B 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LYS A 353 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 357 through 362 removed outlier: 6.609A pdb=" N LEU A 357 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ILE C 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASN A 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N HIS C 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 368 through 373 removed outlier: 6.539A pdb=" N LYS A 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N GLU B 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE A 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 376 through 378 removed outlier: 6.557A pdb=" N THR A 377 " --> pdb=" O PHE B 378 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU A 376 " --> pdb=" O THR C 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 307 through 310 Processing sheet with id=AB3, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.824A pdb=" N VAL D 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 317 through 325 Processing sheet with id=AB5, first strand: chain 'E' and resid 328 through 330 removed outlier: 6.487A pdb=" N ILE D 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 336 through 340 removed outlier: 6.351A pdb=" N GLN D 336 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N VAL F 339 " --> pdb=" O GLN D 336 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU D 338 " --> pdb=" O VAL F 339 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 343 through 346 removed outlier: 6.431A pdb=" N LYS D 343 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N PHE F 346 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ASP D 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 351 through 354 removed outlier: 6.461A pdb=" N GLN D 351 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ILE F 354 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LYS D 353 " --> pdb=" O ILE F 354 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 357 through 362 removed outlier: 6.696A pdb=" N LEU D 357 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ILE E 360 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASN D 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N HIS E 362 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N THR D 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 368 through 377 removed outlier: 6.550A pdb=" N LYS D 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N GLU F 372 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE D 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N HIS F 374 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N THR D 373 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU F 376 " --> pdb=" O THR D 373 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS D 375 " --> pdb=" O LEU F 376 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 306 through 310 removed outlier: 6.547A pdb=" N GLN G 307 " --> pdb=" O ILE I 308 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N TYR I 310 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL G 309 " --> pdb=" O TYR I 310 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 313 through 314 removed outlier: 6.826A pdb=" N VAL G 313 " --> pdb=" O ASP I 314 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 317 through 322 removed outlier: 6.386A pdb=" N VAL H 318 " --> pdb=" O THR I 319 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N LYS I 321 " --> pdb=" O VAL H 318 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER H 320 " --> pdb=" O LYS I 321 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 325 through 330 removed outlier: 7.010A pdb=" N GLY I 326 " --> pdb=" O LEU G 325 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN G 327 " --> pdb=" O GLY I 326 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLY H 326 " --> pdb=" O ASN I 327 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N HIS I 329 " --> pdb=" O GLY H 326 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE H 328 " --> pdb=" O HIS I 329 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 336 through 340 removed outlier: 6.590A pdb=" N GLN G 336 " --> pdb=" O VAL I 337 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N VAL I 339 " --> pdb=" O GLN G 336 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLU G 338 " --> pdb=" O VAL I 339 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 343 through 348 removed outlier: 6.861A pdb=" N LEU G 344 " --> pdb=" O LYS I 343 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASP I 345 " --> pdb=" O LEU G 344 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N PHE G 346 " --> pdb=" O ASP I 345 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LYS I 347 " --> pdb=" O PHE G 346 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU H 344 " --> pdb=" O ASP I 345 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N LYS I 347 " --> pdb=" O LEU H 344 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N PHE H 346 " --> pdb=" O LYS I 347 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 351 through 354 removed outlier: 6.685A pdb=" N GLN G 351 " --> pdb=" O SER I 352 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N ILE I 354 " --> pdb=" O GLN G 351 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LYS G 353 " --> pdb=" O ILE I 354 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 357 through 362 Processing sheet with id=AD1, first strand: chain 'G' and resid 369 through 378 removed outlier: 6.509A pdb=" N LYS G 369 " --> pdb=" O LYS I 370 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N GLU I 372 " --> pdb=" O LYS G 369 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE G 371 " --> pdb=" O GLU I 372 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N HIS I 374 " --> pdb=" O ILE G 371 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR G 373 " --> pdb=" O HIS I 374 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N LEU I 376 " --> pdb=" O THR G 373 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LYS G 375 " --> pdb=" O LEU I 376 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N PHE I 378 " --> pdb=" O LYS G 375 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N THR G 377 " --> pdb=" O PHE I 378 " (cutoff:3.500A) 131 hydrogen bonds defined for protein. 393 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.49 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1374 1.33 - 1.45: 692 1.45 - 1.57: 3115 1.57 - 1.69: 0 1.69 - 1.81: 9 Bond restraints: 5190 Sorted by residual: bond pdb=" CZ ARG I 349 " pdb=" NH2 ARG I 349 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 7.89e+00 bond pdb=" CZ ARG G 349 " pdb=" NH2 ARG G 349 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.76e+00 bond pdb=" CZ ARG H 349 " pdb=" NH2 ARG H 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.24e+00 bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.12e+00 bond pdb=" CZ ARG C 379 " pdb=" NH2 ARG C 379 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.05e+00 ... (remaining 5185 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 5384 2.30 - 4.60: 1367 4.60 - 6.90: 185 6.90 - 9.20: 7 9.20 - 11.50: 2 Bond angle restraints: 6945 Sorted by residual: angle pdb=" CA ASP B 358 " pdb=" CB ASP B 358 " pdb=" CG ASP B 358 " ideal model delta sigma weight residual 112.60 119.33 -6.73 1.00e+00 1.00e+00 4.54e+01 angle pdb=" CA PHE D 346 " pdb=" CB PHE D 346 " pdb=" CG PHE D 346 " ideal model delta sigma weight residual 113.80 120.52 -6.72 1.00e+00 1.00e+00 4.51e+01 angle pdb=" C LYS F 370 " pdb=" CA LYS F 370 " pdb=" CB LYS F 370 " ideal model delta sigma weight residual 109.65 121.15 -11.50 1.75e+00 3.27e-01 4.32e+01 angle pdb=" N LYS E 347 " pdb=" CA LYS E 347 " pdb=" C LYS E 347 " ideal model delta sigma weight residual 113.19 122.72 -9.53 1.58e+00 4.01e-01 3.64e+01 angle pdb=" CA PHE E 346 " pdb=" CB PHE E 346 " pdb=" CG PHE E 346 " ideal model delta sigma weight residual 113.80 119.53 -5.73 1.00e+00 1.00e+00 3.28e+01 ... (remaining 6940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 2973 16.98 - 33.95: 143 33.95 - 50.93: 27 50.93 - 67.91: 8 67.91 - 84.88: 8 Dihedral angle restraints: 3159 sinusoidal: 1320 harmonic: 1839 Sorted by residual: dihedral pdb=" C LYS F 370 " pdb=" N LYS F 370 " pdb=" CA LYS F 370 " pdb=" CB LYS F 370 " ideal model delta harmonic sigma weight residual -122.60 -139.39 16.79 0 2.50e+00 1.60e-01 4.51e+01 dihedral pdb=" CA GLY D 334 " pdb=" C GLY D 334 " pdb=" N GLY D 335 " pdb=" CA GLY D 335 " ideal model delta harmonic sigma weight residual 180.00 -151.00 -29.00 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" N LYS F 370 " pdb=" C LYS F 370 " pdb=" CA LYS F 370 " pdb=" CB LYS F 370 " ideal model delta harmonic sigma weight residual 122.80 136.21 -13.41 0 2.50e+00 1.60e-01 2.88e+01 ... (remaining 3156 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 599 0.111 - 0.221: 154 0.221 - 0.332: 18 0.332 - 0.442: 11 0.442 - 0.553: 1 Chirality restraints: 783 Sorted by residual: chirality pdb=" CA LYS F 370 " pdb=" N LYS F 370 " pdb=" C LYS F 370 " pdb=" CB LYS F 370 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.63e+00 chirality pdb=" CA LYS E 347 " pdb=" N LYS E 347 " pdb=" C LYS E 347 " pdb=" CB LYS E 347 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" CA LYS D 347 " pdb=" N LYS D 347 " pdb=" C LYS D 347 " pdb=" CB LYS D 347 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.62e+00 ... (remaining 780 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 310 " 0.080 2.00e-02 2.50e+03 4.50e-02 4.05e+01 pdb=" CG TYR I 310 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR I 310 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR I 310 " -0.040 2.00e-02 2.50e+03 pdb=" CE1 TYR I 310 " -0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR I 310 " -0.023 2.00e-02 2.50e+03 pdb=" CZ TYR I 310 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR I 310 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 310 " 0.079 2.00e-02 2.50e+03 4.44e-02 3.95e+01 pdb=" CG TYR G 310 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR G 310 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR G 310 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR G 310 " -0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR G 310 " -0.022 2.00e-02 2.50e+03 pdb=" CZ TYR G 310 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR G 310 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 378 " 0.060 2.00e-02 2.50e+03 3.71e-02 2.41e+01 pdb=" CG PHE H 378 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE H 378 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE H 378 " -0.030 2.00e-02 2.50e+03 pdb=" CE1 PHE H 378 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE H 378 " 0.016 2.00e-02 2.50e+03 pdb=" CZ PHE H 378 " 0.026 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 2245 2.97 - 3.45: 4035 3.45 - 3.94: 8195 3.94 - 4.42: 7979 4.42 - 4.90: 15876 Nonbonded interactions: 38330 Sorted by model distance: nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.490 3.040 nonbonded pdb=" OD1 ASP G 314 " pdb=" OG SER G 316 " model vdw 2.510 3.040 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.510 3.040 nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.518 3.040 nonbonded pdb=" OD1 ASP I 314 " pdb=" OG SER I 316 " model vdw 2.528 3.040 ... (remaining 38325 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' and resid 306 through 378) selection = (chain 'B' and resid 306 through 378) selection = (chain 'C' and resid 306 through 378) selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = (chain 'G' and resid 306 through 378) selection = (chain 'H' and resid 306 through 378) selection = (chain 'I' and resid 306 through 378) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.890 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: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.690 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 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 0.047 5190 Z= 0.691 Angle : 1.958 11.497 6945 Z= 1.286 Chirality : 0.105 0.553 783 Planarity : 0.009 0.052 882 Dihedral : 11.701 84.883 1989 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 0.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.17 % Allowed : 3.08 % Favored : 96.75 % Cbeta Deviations : 0.68 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.26), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.20), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 349 TYR 0.080 0.019 TYR I 310 PHE 0.060 0.014 PHE H 378 HIS 0.021 0.004 HIS H 330 Details of bonding type rmsd covalent geometry : bond 0.01099 ( 5190) covalent geometry : angle 1.95764 ( 6945) hydrogen bonds : bond 0.10783 ( 131) hydrogen bonds : angle 7.79999 ( 393) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8826 (ttmt) cc_final: 0.8376 (tmtt) REVERT: A 317 LYS cc_start: 0.7605 (pttt) cc_final: 0.7309 (ptpp) REVERT: A 340 LYS cc_start: 0.8392 (tttt) cc_final: 0.7939 (ttmm) REVERT: A 351 GLN cc_start: 0.7835 (mt0) cc_final: 0.6647 (mp10) REVERT: A 369 LYS cc_start: 0.6831 (mttt) cc_final: 0.6540 (mtpp) REVERT: A 373 THR cc_start: 0.8088 (m) cc_final: 0.7469 (p) REVERT: B 317 LYS cc_start: 0.8038 (pttt) cc_final: 0.7691 (ptpp) REVERT: B 340 LYS cc_start: 0.8492 (tttt) cc_final: 0.8183 (ttmm) REVERT: B 348 ASP cc_start: 0.8213 (t0) cc_final: 0.7459 (p0) REVERT: C 311 LYS cc_start: 0.8731 (ttmt) cc_final: 0.8392 (mttm) REVERT: C 317 LYS cc_start: 0.7892 (pttt) cc_final: 0.7592 (ptpp) REVERT: C 349 ARG cc_start: 0.7549 (mtm180) cc_final: 0.6645 (mtt-85) REVERT: C 351 GLN cc_start: 0.7773 (mt0) cc_final: 0.7386 (mt0) REVERT: C 369 LYS cc_start: 0.7251 (mttt) cc_final: 0.6977 (ttmt) REVERT: C 373 THR cc_start: 0.7944 (m) cc_final: 0.7209 (p) REVERT: C 379 ARG cc_start: 0.6470 (tpp80) cc_final: 0.6238 (ttp-170) REVERT: D 311 LYS cc_start: 0.8444 (pttt) cc_final: 0.7822 (ptmm) REVERT: D 360 ILE cc_start: 0.8031 (tt) cc_final: 0.7735 (mt) REVERT: E 311 LYS cc_start: 0.8458 (pttt) cc_final: 0.7905 (ptmm) REVERT: E 317 LYS cc_start: 0.7466 (pttt) cc_final: 0.7114 (ptpt) REVERT: F 311 LYS cc_start: 0.8424 (ttmt) cc_final: 0.7840 (tttm) REVERT: F 372 GLU cc_start: 0.7279 (pt0) cc_final: 0.6987 (pt0) REVERT: G 378 PHE cc_start: 0.7351 (t80) cc_final: 0.7001 (t80) outliers start: 1 outliers final: 0 residues processed: 222 average time/residue: 0.1165 time to fit residues: 29.9741 Evaluate side-chains 159 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN C 327 ASN D 330 HIS D 362 HIS E 327 ASN E 330 HIS E 362 HIS F 327 ASN F 330 HIS G 368 ASN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 359 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.159108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.124414 restraints weight = 6497.115| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 1.94 r_work: 0.3849 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3758 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5190 Z= 0.173 Angle : 0.737 7.744 6945 Z= 0.370 Chirality : 0.054 0.160 783 Planarity : 0.003 0.023 882 Dihedral : 6.289 19.922 684 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.56 % Allowed : 10.43 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.26), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.13 (0.20), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 349 TYR 0.019 0.003 TYR H 310 PHE 0.015 0.002 PHE A 378 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 5190) covalent geometry : angle 0.73740 ( 6945) hydrogen bonds : bond 0.02566 ( 131) hydrogen bonds : angle 5.91653 ( 393) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8167 (pttt) cc_final: 0.7944 (ptpp) REVERT: A 340 LYS cc_start: 0.9002 (tttt) cc_final: 0.8789 (mttp) REVERT: A 373 THR cc_start: 0.8388 (m) cc_final: 0.8128 (p) REVERT: B 347 LYS cc_start: 0.9255 (mttm) cc_final: 0.8962 (mttt) REVERT: B 348 ASP cc_start: 0.8706 (t0) cc_final: 0.7996 (p0) REVERT: C 317 LYS cc_start: 0.8204 (pttt) cc_final: 0.7993 (ptpp) REVERT: C 349 ARG cc_start: 0.8334 (mtm180) cc_final: 0.8034 (mtp85) REVERT: C 351 GLN cc_start: 0.8353 (mt0) cc_final: 0.8092 (mt0) REVERT: C 369 LYS cc_start: 0.7810 (mttt) cc_final: 0.7556 (ttmt) REVERT: C 379 ARG cc_start: 0.7138 (tpp80) cc_final: 0.5906 (ttp-170) REVERT: D 311 LYS cc_start: 0.8652 (pttt) cc_final: 0.8172 (ptmt) REVERT: E 311 LYS cc_start: 0.8533 (pttt) cc_final: 0.8096 (ptmm) REVERT: E 360 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8242 (mt) REVERT: F 311 LYS cc_start: 0.8540 (ttmt) cc_final: 0.8034 (tttm) REVERT: F 317 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8263 (ptpp) REVERT: F 349 ARG cc_start: 0.8396 (ttm110) cc_final: 0.7855 (mtp85) REVERT: F 370 LYS cc_start: 0.5212 (OUTLIER) cc_final: 0.4142 (pttt) REVERT: G 369 LYS cc_start: 0.7625 (mttp) cc_final: 0.7155 (mttt) REVERT: G 374 HIS cc_start: 0.7636 (m-70) cc_final: 0.5649 (p-80) REVERT: H 310 TYR cc_start: 0.8057 (t80) cc_final: 0.7697 (t80) REVERT: H 374 HIS cc_start: 0.8050 (m-70) cc_final: 0.7578 (m-70) REVERT: I 374 HIS cc_start: 0.8189 (m90) cc_final: 0.7918 (m-70) outliers start: 15 outliers final: 10 residues processed: 166 average time/residue: 0.1164 time to fit residues: 22.4000 Evaluate side-chains 146 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 375 LYS Chi-restraints excluded: chain G residue 368 ASN Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain I residue 352 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 36 optimal weight: 0.6980 chunk 47 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 23 optimal weight: 0.0770 chunk 54 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 overall best weight: 1.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN B 327 ASN G 368 ASN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 ASN ** H 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 359 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.159963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.125392 restraints weight = 6480.923| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 1.97 r_work: 0.3862 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3769 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5190 Z= 0.121 Angle : 0.630 6.939 6945 Z= 0.312 Chirality : 0.050 0.138 783 Planarity : 0.002 0.018 882 Dihedral : 5.573 16.682 684 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.39 % Allowed : 10.60 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.27), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.20), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 349 TYR 0.016 0.002 TYR H 310 PHE 0.013 0.002 PHE A 378 HIS 0.003 0.001 HIS I 330 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 5190) covalent geometry : angle 0.63007 ( 6945) hydrogen bonds : bond 0.02074 ( 131) hydrogen bonds : angle 5.32536 ( 393) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8312 (pttt) cc_final: 0.7952 (ptpp) REVERT: A 373 THR cc_start: 0.8374 (m) cc_final: 0.8149 (p) REVERT: B 348 ASP cc_start: 0.8714 (t0) cc_final: 0.8027 (p0) REVERT: C 349 ARG cc_start: 0.8380 (mtm180) cc_final: 0.8032 (mtp85) REVERT: C 369 LYS cc_start: 0.7881 (mttt) cc_final: 0.7622 (ttmt) REVERT: D 311 LYS cc_start: 0.8610 (pttt) cc_final: 0.8156 (ptmt) REVERT: E 311 LYS cc_start: 0.8456 (pttt) cc_final: 0.8020 (ptmm) REVERT: F 311 LYS cc_start: 0.8474 (ttmt) cc_final: 0.8047 (tttp) REVERT: F 349 ARG cc_start: 0.8417 (ttm110) cc_final: 0.7984 (mtp85) REVERT: G 311 LYS cc_start: 0.5039 (mmmt) cc_final: 0.4779 (mmmt) REVERT: G 321 LYS cc_start: 0.8220 (mttm) cc_final: 0.7726 (mmmt) REVERT: G 369 LYS cc_start: 0.7797 (mttp) cc_final: 0.7426 (mptt) REVERT: G 374 HIS cc_start: 0.7641 (m-70) cc_final: 0.5591 (p-80) REVERT: H 310 TYR cc_start: 0.7999 (t80) cc_final: 0.7773 (t80) REVERT: H 374 HIS cc_start: 0.8123 (m-70) cc_final: 0.7803 (m-70) REVERT: I 359 ASN cc_start: 0.7604 (m-40) cc_final: 0.7345 (m110) REVERT: I 369 LYS cc_start: 0.7484 (mttp) cc_final: 0.7181 (mptt) REVERT: I 374 HIS cc_start: 0.8207 (m90) cc_final: 0.7900 (m-70) outliers start: 14 outliers final: 10 residues processed: 137 average time/residue: 0.0990 time to fit residues: 16.0579 Evaluate side-chains 136 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 375 LYS Chi-restraints excluded: chain H residue 305 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 4 optimal weight: 6.9990 chunk 61 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 30 optimal weight: 0.0370 chunk 47 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 53 optimal weight: 0.0060 overall best weight: 1.9478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 359 ASN H 368 ASN ** H 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.157132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.122513 restraints weight = 6491.478| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 1.94 r_work: 0.3846 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3755 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5190 Z= 0.120 Angle : 0.601 7.159 6945 Z= 0.291 Chirality : 0.050 0.131 783 Planarity : 0.002 0.020 882 Dihedral : 5.153 14.178 684 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.39 % Allowed : 12.48 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.28), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.21), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 349 TYR 0.016 0.002 TYR A 310 PHE 0.010 0.001 PHE A 378 HIS 0.002 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 5190) covalent geometry : angle 0.60140 ( 6945) hydrogen bonds : bond 0.01830 ( 131) hydrogen bonds : angle 4.88227 ( 393) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8246 (pttt) cc_final: 0.7905 (ptpp) REVERT: A 373 THR cc_start: 0.8349 (m) cc_final: 0.8115 (p) REVERT: B 340 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8658 (mttp) REVERT: B 348 ASP cc_start: 0.8677 (t0) cc_final: 0.8056 (p0) REVERT: C 311 LYS cc_start: 0.8845 (mtmt) cc_final: 0.8044 (mmmt) REVERT: C 349 ARG cc_start: 0.8356 (mtm180) cc_final: 0.8060 (mtp85) REVERT: C 369 LYS cc_start: 0.7950 (mttt) cc_final: 0.7650 (ttmt) REVERT: D 311 LYS cc_start: 0.8616 (pttt) cc_final: 0.8176 (ptmt) REVERT: E 311 LYS cc_start: 0.8446 (pttt) cc_final: 0.8119 (ptmt) REVERT: E 360 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8445 (mt) REVERT: F 311 LYS cc_start: 0.8456 (ttmt) cc_final: 0.8051 (tttm) REVERT: F 342 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7817 (tm-30) REVERT: F 349 ARG cc_start: 0.8430 (ttm110) cc_final: 0.8020 (mtp85) REVERT: F 370 LYS cc_start: 0.4879 (OUTLIER) cc_final: 0.3672 (mptt) REVERT: F 372 GLU cc_start: 0.8141 (pt0) cc_final: 0.7905 (pt0) REVERT: G 311 LYS cc_start: 0.5380 (mmmt) cc_final: 0.5150 (mmmt) REVERT: G 321 LYS cc_start: 0.8228 (mttm) cc_final: 0.7751 (mmmt) REVERT: G 336 GLN cc_start: 0.7585 (tt0) cc_final: 0.7175 (mt0) REVERT: G 369 LYS cc_start: 0.7660 (mttp) cc_final: 0.7228 (mptt) REVERT: G 374 HIS cc_start: 0.7592 (m-70) cc_final: 0.5607 (p-80) REVERT: H 310 TYR cc_start: 0.8076 (t80) cc_final: 0.7757 (t80) REVERT: H 325 LEU cc_start: 0.8426 (mt) cc_final: 0.8157 (mp) REVERT: H 374 HIS cc_start: 0.8118 (m-70) cc_final: 0.7758 (m-70) REVERT: I 369 LYS cc_start: 0.7473 (mttp) cc_final: 0.7143 (mptt) REVERT: I 374 HIS cc_start: 0.8226 (m90) cc_final: 0.7819 (m-70) outliers start: 14 outliers final: 10 residues processed: 137 average time/residue: 0.1096 time to fit residues: 17.6747 Evaluate side-chains 138 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 375 LYS Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain H residue 328 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 17 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 51 optimal weight: 0.0270 chunk 49 optimal weight: 0.1980 chunk 34 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 overall best weight: 4.0444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 359 ASN H 368 ASN ** H 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.151627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.117454 restraints weight = 6668.679| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.95 r_work: 0.3773 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3682 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5190 Z= 0.202 Angle : 0.653 7.201 6945 Z= 0.326 Chirality : 0.052 0.153 783 Planarity : 0.003 0.021 882 Dihedral : 5.353 17.219 684 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.91 % Allowed : 12.82 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.28), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.18 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 349 TYR 0.015 0.003 TYR A 310 PHE 0.008 0.002 PHE F 378 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 5190) covalent geometry : angle 0.65307 ( 6945) hydrogen bonds : bond 0.02075 ( 131) hydrogen bonds : angle 4.83853 ( 393) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8365 (pttt) cc_final: 0.8051 (ptpp) REVERT: A 373 THR cc_start: 0.8368 (m) cc_final: 0.8104 (p) REVERT: B 347 LYS cc_start: 0.9277 (mttm) cc_final: 0.9018 (mttt) REVERT: B 348 ASP cc_start: 0.8758 (t0) cc_final: 0.8108 (p0) REVERT: C 311 LYS cc_start: 0.8947 (mtmt) cc_final: 0.8174 (mmmt) REVERT: C 349 ARG cc_start: 0.8384 (mtm180) cc_final: 0.8122 (mtp85) REVERT: C 369 LYS cc_start: 0.8078 (mttt) cc_final: 0.7744 (ttmt) REVERT: D 311 LYS cc_start: 0.8653 (pttt) cc_final: 0.8282 (ptmt) REVERT: E 311 LYS cc_start: 0.8595 (pttt) cc_final: 0.8305 (ptmt) REVERT: E 360 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8427 (mt) REVERT: F 311 LYS cc_start: 0.8492 (ttmt) cc_final: 0.8107 (tttm) REVERT: F 342 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8030 (tm-30) REVERT: F 349 ARG cc_start: 0.8497 (ttm110) cc_final: 0.8077 (mtp85) REVERT: F 370 LYS cc_start: 0.4935 (OUTLIER) cc_final: 0.4059 (mmmt) REVERT: G 336 GLN cc_start: 0.7705 (tt0) cc_final: 0.7330 (mt0) REVERT: G 374 HIS cc_start: 0.7552 (m-70) cc_final: 0.5612 (p90) REVERT: H 310 TYR cc_start: 0.8091 (t80) cc_final: 0.7809 (t80) REVERT: H 325 LEU cc_start: 0.8469 (mt) cc_final: 0.8234 (mp) REVERT: H 374 HIS cc_start: 0.7978 (m-70) cc_final: 0.7595 (m90) REVERT: I 374 HIS cc_start: 0.8348 (m90) cc_final: 0.7781 (m-70) outliers start: 17 outliers final: 11 residues processed: 142 average time/residue: 0.1169 time to fit residues: 19.5163 Evaluate side-chains 139 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 375 LYS Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain H residue 328 ILE Chi-restraints excluded: chain H residue 341 SER Chi-restraints excluded: chain I residue 306 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 8 optimal weight: 4.9990 chunk 59 optimal weight: 20.0000 chunk 28 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.152488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.118495 restraints weight = 6672.712| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.96 r_work: 0.3791 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3699 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5190 Z= 0.173 Angle : 0.620 7.861 6945 Z= 0.308 Chirality : 0.051 0.143 783 Planarity : 0.003 0.030 882 Dihedral : 5.174 15.915 684 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.39 % Allowed : 14.19 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.29), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 349 TYR 0.019 0.003 TYR A 310 PHE 0.006 0.001 PHE A 346 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 5190) covalent geometry : angle 0.61996 ( 6945) hydrogen bonds : bond 0.01944 ( 131) hydrogen bonds : angle 4.69064 ( 393) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8365 (pttt) cc_final: 0.8011 (ptpp) REVERT: A 373 THR cc_start: 0.8347 (m) cc_final: 0.8059 (p) REVERT: B 311 LYS cc_start: 0.8861 (mtmt) cc_final: 0.8589 (mttm) REVERT: B 348 ASP cc_start: 0.8765 (t0) cc_final: 0.8086 (p0) REVERT: B 349 ARG cc_start: 0.8697 (mtp85) cc_final: 0.8462 (mtp85) REVERT: C 311 LYS cc_start: 0.8968 (mtmt) cc_final: 0.8227 (mmmt) REVERT: C 349 ARG cc_start: 0.8375 (mtm180) cc_final: 0.8095 (mtp85) REVERT: C 369 LYS cc_start: 0.8017 (mttt) cc_final: 0.7688 (ttmt) REVERT: D 311 LYS cc_start: 0.8637 (pttt) cc_final: 0.8248 (ptmt) REVERT: E 311 LYS cc_start: 0.8602 (pttt) cc_final: 0.8201 (ptmm) REVERT: E 360 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8509 (mt) REVERT: F 311 LYS cc_start: 0.8525 (ttmt) cc_final: 0.8097 (tttm) REVERT: F 342 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7992 (tm-30) REVERT: F 349 ARG cc_start: 0.8468 (ttm110) cc_final: 0.8028 (mtp85) REVERT: F 370 LYS cc_start: 0.4791 (OUTLIER) cc_final: 0.3935 (tppt) REVERT: F 372 GLU cc_start: 0.8271 (pt0) cc_final: 0.8005 (pt0) REVERT: G 321 LYS cc_start: 0.8175 (mttm) cc_final: 0.7756 (mmmt) REVERT: G 336 GLN cc_start: 0.7715 (tt0) cc_final: 0.7292 (mt0) REVERT: G 369 LYS cc_start: 0.7820 (mttp) cc_final: 0.7318 (mttt) REVERT: G 374 HIS cc_start: 0.7609 (m-70) cc_final: 0.5686 (p90) REVERT: H 310 TYR cc_start: 0.8032 (t80) cc_final: 0.7773 (t80) REVERT: H 374 HIS cc_start: 0.7914 (m-70) cc_final: 0.7641 (m90) REVERT: I 336 GLN cc_start: 0.7853 (tt0) cc_final: 0.7481 (mt0) REVERT: I 374 HIS cc_start: 0.8350 (m90) cc_final: 0.7909 (m90) outliers start: 14 outliers final: 10 residues processed: 141 average time/residue: 0.1209 time to fit residues: 19.9145 Evaluate side-chains 135 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 375 LYS Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain H residue 328 ILE Chi-restraints excluded: chain H residue 341 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 3 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 57 optimal weight: 30.0000 chunk 29 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 9 optimal weight: 0.0980 chunk 39 optimal weight: 0.3980 chunk 13 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.154095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.120269 restraints weight = 6607.201| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 1.96 r_work: 0.3817 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 5190 Z= 0.136 Angle : 0.624 8.134 6945 Z= 0.303 Chirality : 0.050 0.136 783 Planarity : 0.003 0.036 882 Dihedral : 4.992 15.406 684 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.39 % Allowed : 14.36 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.29), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 349 TYR 0.017 0.002 TYR A 310 PHE 0.005 0.001 PHE A 346 HIS 0.002 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 5190) covalent geometry : angle 0.62403 ( 6945) hydrogen bonds : bond 0.01785 ( 131) hydrogen bonds : angle 4.53527 ( 393) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8336 (pttt) cc_final: 0.7987 (ptpp) REVERT: A 373 THR cc_start: 0.8346 (m) cc_final: 0.8056 (p) REVERT: B 311 LYS cc_start: 0.8861 (mtmt) cc_final: 0.8588 (mttm) REVERT: B 340 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8691 (mttp) REVERT: B 348 ASP cc_start: 0.8739 (t0) cc_final: 0.8095 (p0) REVERT: B 368 ASN cc_start: 0.8409 (t0) cc_final: 0.8170 (m110) REVERT: C 311 LYS cc_start: 0.8887 (mtmt) cc_final: 0.8077 (mmmt) REVERT: C 349 ARG cc_start: 0.8383 (mtm180) cc_final: 0.8094 (mtp85) REVERT: C 369 LYS cc_start: 0.8020 (mttt) cc_final: 0.7676 (ttmt) REVERT: D 311 LYS cc_start: 0.8612 (pttt) cc_final: 0.8237 (ptmt) REVERT: E 311 LYS cc_start: 0.8591 (pttt) cc_final: 0.8197 (ptmm) REVERT: E 360 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8529 (mt) REVERT: F 311 LYS cc_start: 0.8501 (ttmt) cc_final: 0.8083 (tttm) REVERT: F 342 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7994 (tm-30) REVERT: F 349 ARG cc_start: 0.8479 (ttm110) cc_final: 0.8033 (mtp85) REVERT: F 370 LYS cc_start: 0.4742 (OUTLIER) cc_final: 0.3905 (tppt) REVERT: F 372 GLU cc_start: 0.8254 (pt0) cc_final: 0.7915 (pt0) REVERT: G 336 GLN cc_start: 0.7763 (tt0) cc_final: 0.7344 (mt0) REVERT: G 374 HIS cc_start: 0.7616 (m-70) cc_final: 0.5715 (p90) REVERT: H 310 TYR cc_start: 0.7995 (t80) cc_final: 0.7741 (t80) REVERT: H 311 LYS cc_start: 0.8753 (ttmt) cc_final: 0.8468 (ttpt) REVERT: H 374 HIS cc_start: 0.7942 (m-70) cc_final: 0.7648 (m90) REVERT: I 336 GLN cc_start: 0.7910 (tt0) cc_final: 0.7528 (mt0) REVERT: I 374 HIS cc_start: 0.8411 (m90) cc_final: 0.7987 (m90) outliers start: 14 outliers final: 10 residues processed: 134 average time/residue: 0.1069 time to fit residues: 16.9489 Evaluate side-chains 134 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 375 LYS Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain H residue 328 ILE Chi-restraints excluded: chain H residue 341 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 55 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 41 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.154004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.120238 restraints weight = 6436.088| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 1.85 r_work: 0.3786 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3696 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5190 Z= 0.193 Angle : 0.654 7.788 6945 Z= 0.323 Chirality : 0.052 0.150 783 Planarity : 0.003 0.041 882 Dihedral : 5.134 15.880 684 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.22 % Allowed : 14.70 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.29), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 349 TYR 0.015 0.003 TYR A 310 PHE 0.007 0.001 PHE A 346 HIS 0.002 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 5190) covalent geometry : angle 0.65414 ( 6945) hydrogen bonds : bond 0.02048 ( 131) hydrogen bonds : angle 4.55443 ( 393) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8383 (pttt) cc_final: 0.7996 (ptpp) REVERT: A 373 THR cc_start: 0.8341 (m) cc_final: 0.8052 (p) REVERT: B 311 LYS cc_start: 0.8855 (mtmt) cc_final: 0.8609 (mttm) REVERT: B 340 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8823 (mtpt) REVERT: B 348 ASP cc_start: 0.8730 (t0) cc_final: 0.8118 (p0) REVERT: C 311 LYS cc_start: 0.8890 (mtmt) cc_final: 0.8288 (mmtm) REVERT: C 349 ARG cc_start: 0.8373 (mtm180) cc_final: 0.8131 (mtp85) REVERT: C 369 LYS cc_start: 0.8026 (mttt) cc_final: 0.7715 (ttmt) REVERT: D 311 LYS cc_start: 0.8691 (pttt) cc_final: 0.8164 (ptmm) REVERT: E 311 LYS cc_start: 0.8612 (pttt) cc_final: 0.8236 (ptmm) REVERT: E 360 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8529 (mt) REVERT: F 311 LYS cc_start: 0.8501 (ttmt) cc_final: 0.8058 (tttm) REVERT: F 342 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8044 (tm-30) REVERT: F 349 ARG cc_start: 0.8504 (ttm110) cc_final: 0.8061 (mtp85) REVERT: F 370 LYS cc_start: 0.4707 (OUTLIER) cc_final: 0.3900 (tppt) REVERT: G 336 GLN cc_start: 0.7845 (tt0) cc_final: 0.7402 (mt0) REVERT: H 310 TYR cc_start: 0.8006 (t80) cc_final: 0.7729 (t80) REVERT: H 317 LYS cc_start: 0.7961 (ptmt) cc_final: 0.7665 (ptmm) REVERT: H 374 HIS cc_start: 0.7971 (m-70) cc_final: 0.7670 (m90) REVERT: I 336 GLN cc_start: 0.7996 (tt0) cc_final: 0.7749 (tt0) outliers start: 13 outliers final: 10 residues processed: 129 average time/residue: 0.1098 time to fit residues: 16.8229 Evaluate side-chains 130 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 375 LYS Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain H residue 328 ILE Chi-restraints excluded: chain H residue 341 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 15 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.152339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.118835 restraints weight = 6413.137| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.84 r_work: 0.3772 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3682 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.4798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5190 Z= 0.209 Angle : 0.676 9.141 6945 Z= 0.332 Chirality : 0.052 0.149 783 Planarity : 0.004 0.049 882 Dihedral : 5.199 16.248 684 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.39 % Allowed : 15.56 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.29), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 349 TYR 0.017 0.003 TYR A 310 PHE 0.007 0.001 PHE A 346 HIS 0.002 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 5190) covalent geometry : angle 0.67613 ( 6945) hydrogen bonds : bond 0.02073 ( 131) hydrogen bonds : angle 4.57440 ( 393) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8393 (pttt) cc_final: 0.7987 (ptpp) REVERT: A 373 THR cc_start: 0.8350 (m) cc_final: 0.8065 (p) REVERT: B 311 LYS cc_start: 0.8851 (mtmt) cc_final: 0.8608 (mttm) REVERT: B 348 ASP cc_start: 0.8712 (t0) cc_final: 0.8125 (p0) REVERT: C 311 LYS cc_start: 0.8857 (mtmt) cc_final: 0.8250 (mmtm) REVERT: C 349 ARG cc_start: 0.8412 (mtm180) cc_final: 0.8174 (mtp85) REVERT: C 369 LYS cc_start: 0.8091 (mttt) cc_final: 0.7789 (ttmt) REVERT: D 311 LYS cc_start: 0.8697 (pttt) cc_final: 0.8238 (ptmm) REVERT: E 360 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8562 (mt) REVERT: F 311 LYS cc_start: 0.8489 (ttmt) cc_final: 0.8058 (tttm) REVERT: F 314 ASP cc_start: 0.7852 (t0) cc_final: 0.7579 (t0) REVERT: F 340 LYS cc_start: 0.8804 (tttt) cc_final: 0.8548 (tttp) REVERT: F 342 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8077 (tm-30) REVERT: F 349 ARG cc_start: 0.8505 (ttm110) cc_final: 0.8055 (mtp85) REVERT: F 370 LYS cc_start: 0.4851 (OUTLIER) cc_final: 0.3986 (tppt) REVERT: F 372 GLU cc_start: 0.8293 (pt0) cc_final: 0.8064 (pt0) REVERT: H 317 LYS cc_start: 0.8044 (ptmt) cc_final: 0.7755 (ptmm) outliers start: 14 outliers final: 10 residues processed: 129 average time/residue: 0.1162 time to fit residues: 17.6200 Evaluate side-chains 131 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 375 LYS Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain H residue 341 SER Chi-restraints excluded: chain H residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 61 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 374 HIS I 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.155237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.121561 restraints weight = 6372.774| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 1.84 r_work: 0.3815 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5190 Z= 0.136 Angle : 0.635 7.705 6945 Z= 0.307 Chirality : 0.050 0.153 783 Planarity : 0.003 0.054 882 Dihedral : 4.988 15.217 684 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.05 % Allowed : 15.73 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.96 (0.29), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 349 TYR 0.025 0.003 TYR H 310 PHE 0.005 0.001 PHE B 378 HIS 0.003 0.001 HIS H 374 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 5190) covalent geometry : angle 0.63464 ( 6945) hydrogen bonds : bond 0.01951 ( 131) hydrogen bonds : angle 4.46132 ( 393) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8326 (pttt) cc_final: 0.7896 (ptpp) REVERT: A 373 THR cc_start: 0.8340 (m) cc_final: 0.8067 (p) REVERT: B 311 LYS cc_start: 0.8873 (mtmt) cc_final: 0.8605 (mttm) REVERT: B 348 ASP cc_start: 0.8737 (t0) cc_final: 0.8096 (p0) REVERT: C 311 LYS cc_start: 0.8734 (mtmt) cc_final: 0.8007 (mmmt) REVERT: C 349 ARG cc_start: 0.8382 (mtm180) cc_final: 0.8144 (mtp85) REVERT: C 369 LYS cc_start: 0.8045 (mttt) cc_final: 0.7724 (ttmt) REVERT: D 311 LYS cc_start: 0.8651 (pttt) cc_final: 0.8186 (ptmm) REVERT: E 360 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8538 (mt) REVERT: F 311 LYS cc_start: 0.8463 (ttmt) cc_final: 0.8018 (tttm) REVERT: F 314 ASP cc_start: 0.7765 (t0) cc_final: 0.7427 (t0) REVERT: F 342 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7997 (tm-30) REVERT: F 349 ARG cc_start: 0.8485 (ttm110) cc_final: 0.8027 (mtp85) REVERT: F 370 LYS cc_start: 0.4597 (OUTLIER) cc_final: 0.3845 (tppt) REVERT: G 321 LYS cc_start: 0.8094 (mttm) cc_final: 0.7828 (mmmt) REVERT: G 369 LYS cc_start: 0.7849 (mttp) cc_final: 0.7349 (mttt) REVERT: I 336 GLN cc_start: 0.8123 (tt0) cc_final: 0.7865 (tt0) outliers start: 12 outliers final: 10 residues processed: 121 average time/residue: 0.0990 time to fit residues: 14.3588 Evaluate side-chains 122 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 375 LYS Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain H residue 328 ILE Chi-restraints excluded: chain H residue 341 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 28 optimal weight: 0.0040 chunk 19 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 50 optimal weight: 0.3980 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 336 GLN H 374 HIS I 374 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.160592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.126533 restraints weight = 6350.331| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 1.88 r_work: 0.3923 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3832 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 5190 Z= 0.090 Angle : 0.588 7.637 6945 Z= 0.281 Chirality : 0.049 0.153 783 Planarity : 0.003 0.051 882 Dihedral : 4.610 14.388 684 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.20 % Allowed : 17.09 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.98 (0.29), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 349 TYR 0.016 0.002 TYR H 310 PHE 0.006 0.001 PHE B 378 HIS 0.003 0.000 HIS H 374 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 5190) covalent geometry : angle 0.58819 ( 6945) hydrogen bonds : bond 0.01702 ( 131) hydrogen bonds : angle 4.18549 ( 393) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1628.48 seconds wall clock time: 28 minutes 34.18 seconds (1714.18 seconds total)