Starting phenix.real_space_refine on Thu Mar 6 06:09:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q7m_18224/03_2025/8q7m_18224.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q7m_18224/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8q7m_18224/03_2025/8q7m_18224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q7m_18224/03_2025/8q7m_18224.map" model { file = "/net/cci-nas-00/data/ceres_data/8q7m_18224/03_2025/8q7m_18224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q7m_18224/03_2025/8q7m_18224.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.69, per 1000 atoms: 1.11 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: 1.39 Conformation dependent library (CDL) restraints added in 729.7 milliseconds 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: 1.12 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: 1.58 Time building geometry restraints manager: 1.74 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: 0.02 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: 4.640 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: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 20.610 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.370 ------------------------------------------------------------------------------- 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= 0.760 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (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 HIS 0.021 0.004 HIS H 330 PHE 0.060 0.014 PHE H 378 TYR 0.080 0.019 TYR I 310 ARG 0.008 0.001 ARG E 349 *********************** 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 : 0.916 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: 0.7308 (ptpp) REVERT: A 340 LYS cc_start: 0.8392 (tttt) cc_final: 0.7937 (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: 0.6541 (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: 0.7692 (ptpp) REVERT: B 340 LYS cc_start: 0.8492 (tttt) cc_final: 0.8182 (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: 0.7593 (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: 0.6976 (ttmt) REVERT: C 373 THR cc_start: 0.7944 (m) cc_final: 0.7208 (p) REVERT: C 379 ARG cc_start: 0.6470 (tpp80) cc_final: 0.6239 (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: 0.7737 (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: 0.7115 (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: 0.6999 (t80) outliers start: 1 outliers final: 0 residues processed: 222 average time/residue: 0.3223 time to fit residues: 82.8081 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 : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 C 327 ASN D 330 HIS D 362 HIS E 327 ASN 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 = 0.4316 r_free = 0.4316 target = 0.162183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.127484 restraints weight = 6410.721| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 1.94 r_work: 0.3886 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3794 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5190 Z= 0.216 Angle : 0.720 8.034 6945 Z= 0.357 Chirality : 0.053 0.150 783 Planarity : 0.003 0.023 882 Dihedral : 6.206 19.706 684 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.88 % Allowed : 10.43 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.26), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.20), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.014 0.002 PHE A 378 TYR 0.018 0.003 TYR H 310 ARG 0.005 0.000 ARG F 349 *********************** 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 164 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.9004 (tttt) cc_final: 0.8799 (mttp) REVERT: A 373 THR cc_start: 0.8372 (m) cc_final: 0.8125 (p) REVERT: B 317 LYS cc_start: 0.8237 (pttt) cc_final: 0.8035 (ptpp) REVERT: B 347 LYS cc_start: 0.9219 (mttm) cc_final: 0.8898 (mttt) REVERT: B 348 ASP cc_start: 0.8722 (t0) cc_final: 0.7886 (p0) REVERT: C 349 ARG cc_start: 0.8339 (mtm180) cc_final: 0.8044 (mtp85) REVERT: C 369 LYS cc_start: 0.7807 (mttt) cc_final: 0.7565 (ttmt) REVERT: C 379 ARG cc_start: 0.7084 (tpp80) cc_final: 0.5858 (ttp-170) REVERT: D 311 LYS cc_start: 0.8615 (pttt) cc_final: 0.8102 (ptmm) REVERT: D 349 ARG cc_start: 0.8333 (ttm110) cc_final: 0.7830 (mtp85) REVERT: E 311 LYS cc_start: 0.8447 (pttt) cc_final: 0.8024 (ptmm) REVERT: E 360 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8203 (mt) REVERT: F 311 LYS cc_start: 0.8489 (ttmt) cc_final: 0.7997 (tttm) REVERT: F 317 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8118 (ptpp) REVERT: F 349 ARG cc_start: 0.8377 (ttm110) cc_final: 0.7844 (mtp85) REVERT: G 374 HIS cc_start: 0.7609 (m-70) cc_final: 0.5604 (p-80) REVERT: H 310 TYR cc_start: 0.8079 (t80) cc_final: 0.7552 (t80) REVERT: H 374 HIS cc_start: 0.8084 (m-70) cc_final: 0.7584 (m-70) REVERT: I 317 LYS cc_start: 0.8063 (pttt) cc_final: 0.7597 (ptmt) REVERT: I 374 HIS cc_start: 0.8177 (m90) cc_final: 0.7952 (m-70) outliers start: 11 outliers final: 9 residues processed: 158 average time/residue: 0.2945 time to fit residues: 54.2274 Evaluate side-chains 141 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 375 LYS Chi-restraints excluded: chain G residue 368 ASN Chi-restraints excluded: chain H residue 305 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 51 optimal weight: 0.0770 chunk 14 optimal weight: 7.9990 chunk 52 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 overall best weight: 6.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.151867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.117868 restraints weight = 6559.593| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 1.91 r_work: 0.3760 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 5190 Z= 0.476 Angle : 0.761 7.025 6945 Z= 0.391 Chirality : 0.056 0.162 783 Planarity : 0.003 0.026 882 Dihedral : 6.058 17.400 684 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.91 % Allowed : 11.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.27), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.18 (0.21), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS A 374 PHE 0.012 0.002 PHE H 378 TYR 0.015 0.003 TYR G 310 ARG 0.002 0.000 ARG B 349 *********************** 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 147 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.9022 (tttt) cc_final: 0.8816 (mttp) REVERT: A 373 THR cc_start: 0.8362 (m) cc_final: 0.8085 (p) REVERT: B 317 LYS cc_start: 0.8424 (pttt) cc_final: 0.8211 (ptpp) REVERT: B 348 ASP cc_start: 0.8755 (t0) cc_final: 0.8006 (p0) REVERT: C 311 LYS cc_start: 0.8980 (pttt) cc_final: 0.8479 (mmtt) REVERT: C 349 ARG cc_start: 0.8349 (mtm180) cc_final: 0.8068 (mtp85) REVERT: C 351 GLN cc_start: 0.8353 (mt0) cc_final: 0.8047 (mt0) REVERT: C 372 GLU cc_start: 0.8155 (pt0) cc_final: 0.7854 (pt0) REVERT: C 379 ARG cc_start: 0.7275 (tpp80) cc_final: 0.7050 (mtm110) REVERT: D 311 LYS cc_start: 0.8682 (pttt) cc_final: 0.8225 (ptmt) REVERT: D 349 ARG cc_start: 0.8373 (ttm110) cc_final: 0.7872 (mtp85) REVERT: E 311 LYS cc_start: 0.8628 (pttt) cc_final: 0.8167 (ptmm) REVERT: F 311 LYS cc_start: 0.8541 (ttmt) cc_final: 0.8085 (tttm) REVERT: F 342 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7928 (tm-30) REVERT: F 349 ARG cc_start: 0.8485 (ttm110) cc_final: 0.8005 (mtp85) REVERT: F 370 LYS cc_start: 0.5433 (OUTLIER) cc_final: 0.4000 (mptt) REVERT: G 311 LYS cc_start: 0.5100 (mmmt) cc_final: 0.4784 (mmmt) REVERT: G 321 LYS cc_start: 0.8186 (mttm) cc_final: 0.7850 (mmmt) REVERT: G 374 HIS cc_start: 0.7572 (m-70) cc_final: 0.5589 (p90) REVERT: H 310 TYR cc_start: 0.8082 (t80) cc_final: 0.7775 (t80) REVERT: H 317 LYS cc_start: 0.7918 (ptmt) cc_final: 0.7578 (ptmm) REVERT: H 325 LEU cc_start: 0.8420 (mt) cc_final: 0.8160 (mp) REVERT: H 374 HIS cc_start: 0.8107 (m-70) cc_final: 0.7731 (m-70) REVERT: I 374 HIS cc_start: 0.8289 (m90) cc_final: 0.7785 (m-70) outliers start: 17 outliers final: 11 residues processed: 141 average time/residue: 0.2909 time to fit residues: 48.7221 Evaluate side-chains 133 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 319 THR Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 371 ILE 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 I residue 306 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 52 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 49 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.154452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.120095 restraints weight = 6569.108| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 1.95 r_work: 0.3786 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3692 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3972 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= 0.288 Angle : 0.647 6.561 6945 Z= 0.323 Chirality : 0.051 0.137 783 Planarity : 0.003 0.020 882 Dihedral : 5.583 16.445 684 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.74 % Allowed : 14.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.28), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.21), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 330 PHE 0.007 0.001 PHE A 378 TYR 0.014 0.003 TYR G 310 ARG 0.003 0.000 ARG B 349 *********************** 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 143 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.9003 (tttt) cc_final: 0.8800 (mttp) REVERT: A 373 THR cc_start: 0.8353 (m) cc_final: 0.8116 (p) REVERT: B 348 ASP cc_start: 0.8745 (t0) cc_final: 0.8023 (p0) REVERT: C 311 LYS cc_start: 0.9005 (pttt) cc_final: 0.8380 (mmtt) REVERT: C 349 ARG cc_start: 0.8358 (mtm180) cc_final: 0.8061 (mtp85) REVERT: C 351 GLN cc_start: 0.8283 (mt0) cc_final: 0.8005 (mt0) REVERT: C 379 ARG cc_start: 0.7291 (tpp80) cc_final: 0.7040 (mtm110) REVERT: D 311 LYS cc_start: 0.8657 (pttt) cc_final: 0.8254 (ptmt) REVERT: D 349 ARG cc_start: 0.8325 (ttm110) cc_final: 0.7851 (mtp85) REVERT: E 311 LYS cc_start: 0.8558 (pttt) cc_final: 0.8258 (ptmt) REVERT: E 360 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8447 (mt) REVERT: F 311 LYS cc_start: 0.8501 (ttmt) cc_final: 0.8050 (tttm) REVERT: F 342 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8001 (tm-30) REVERT: F 349 ARG cc_start: 0.8461 (ttm110) cc_final: 0.7989 (mtp85) REVERT: F 370 LYS cc_start: 0.5008 (OUTLIER) cc_final: 0.4053 (tppt) REVERT: G 311 LYS cc_start: 0.5189 (mmmt) cc_final: 0.4906 (mmmt) REVERT: G 321 LYS cc_start: 0.8174 (mttm) cc_final: 0.7842 (mmmt) REVERT: G 374 HIS cc_start: 0.7599 (m-70) cc_final: 0.5671 (p90) REVERT: H 310 TYR cc_start: 0.8097 (t80) cc_final: 0.7678 (t80) REVERT: H 325 LEU cc_start: 0.8462 (mt) cc_final: 0.8207 (mp) REVERT: H 374 HIS cc_start: 0.8089 (m-70) cc_final: 0.7646 (m-70) REVERT: I 374 HIS cc_start: 0.8279 (m90) cc_final: 0.7775 (m-70) outliers start: 16 outliers final: 13 residues processed: 137 average time/residue: 0.4040 time to fit residues: 66.0575 Evaluate side-chains 134 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 371 ILE Chi-restraints excluded: chain F residue 375 LYS Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain H residue 306 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 12 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 43 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 42 optimal weight: 9.9990 chunk 49 optimal weight: 0.0570 chunk 22 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 overall best weight: 4.4106 ------------------------------------------------------------------------------- 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 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 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 = 0.4208 r_free = 0.4208 target = 0.152492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.118632 restraints weight = 6483.504| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 1.94 r_work: 0.3764 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5190 Z= 0.344 Angle : 0.657 6.522 6945 Z= 0.330 Chirality : 0.052 0.147 783 Planarity : 0.003 0.024 882 Dihedral : 5.466 15.506 684 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.08 % Allowed : 15.04 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.28), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.21), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 374 PHE 0.007 0.002 PHE H 378 TYR 0.013 0.003 TYR A 310 ARG 0.003 0.000 ARG B 349 *********************** 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 139 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8921 (mtmt) cc_final: 0.8325 (mtmt) REVERT: A 373 THR cc_start: 0.8374 (m) cc_final: 0.8076 (p) REVERT: B 311 LYS cc_start: 0.8999 (ttpt) cc_final: 0.8518 (mttt) REVERT: B 348 ASP cc_start: 0.8744 (t0) cc_final: 0.8058 (p0) REVERT: B 349 ARG cc_start: 0.8616 (mtp85) cc_final: 0.8385 (mtp85) REVERT: B 373 THR cc_start: 0.8398 (m) cc_final: 0.7996 (p) REVERT: C 311 LYS cc_start: 0.9023 (pttt) cc_final: 0.8164 (mmmt) REVERT: C 349 ARG cc_start: 0.8357 (mtm180) cc_final: 0.8074 (mtp85) REVERT: C 369 LYS cc_start: 0.7986 (mttt) cc_final: 0.7652 (ttmt) REVERT: C 379 ARG cc_start: 0.7365 (tpp80) cc_final: 0.7021 (mtm110) REVERT: D 311 LYS cc_start: 0.8687 (pttt) cc_final: 0.8332 (ptmt) REVERT: D 349 ARG cc_start: 0.8321 (ttm110) cc_final: 0.7846 (mtp85) REVERT: E 360 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8423 (mt) REVERT: F 311 LYS cc_start: 0.8439 (ttmt) cc_final: 0.8028 (tttm) REVERT: F 342 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8010 (tm-30) REVERT: F 349 ARG cc_start: 0.8504 (ttm110) cc_final: 0.8027 (mtp85) REVERT: F 370 LYS cc_start: 0.5039 (OUTLIER) cc_final: 0.4343 (mmmt) REVERT: G 321 LYS cc_start: 0.8160 (mttm) cc_final: 0.7859 (mmmt) REVERT: G 374 HIS cc_start: 0.7564 (m-70) cc_final: 0.5669 (p90) REVERT: H 310 TYR cc_start: 0.8100 (t80) cc_final: 0.7839 (t80) REVERT: H 349 ARG cc_start: 0.5984 (mtm180) cc_final: 0.5772 (ptt90) REVERT: H 374 HIS cc_start: 0.7942 (m-70) cc_final: 0.7592 (m90) REVERT: I 310 TYR cc_start: 0.8324 (t80) cc_final: 0.7643 (t80) REVERT: I 336 GLN cc_start: 0.7968 (tt0) cc_final: 0.7756 (tt0) REVERT: I 374 HIS cc_start: 0.8386 (m90) cc_final: 0.7686 (m-70) outliers start: 18 outliers final: 13 residues processed: 132 average time/residue: 0.2981 time to fit residues: 46.3712 Evaluate side-chains 132 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 371 ILE Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 328 ILE Chi-restraints excluded: chain H residue 341 SER Chi-restraints excluded: chain H residue 356 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 29 optimal weight: 4.9990 chunk 55 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 327 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.154646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.120540 restraints weight = 6344.346| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 1.92 r_work: 0.3791 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5190 Z= 0.279 Angle : 0.634 8.077 6945 Z= 0.309 Chirality : 0.051 0.134 783 Planarity : 0.003 0.028 882 Dihedral : 5.273 16.625 684 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.56 % Allowed : 15.90 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.29), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 374 PHE 0.008 0.001 PHE A 378 TYR 0.013 0.002 TYR A 310 ARG 0.002 0.000 ARG B 349 *********************** 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 134 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 373 THR cc_start: 0.8359 (m) cc_final: 0.8076 (p) REVERT: B 348 ASP cc_start: 0.8728 (t0) cc_final: 0.8099 (p0) REVERT: B 373 THR cc_start: 0.8375 (m) cc_final: 0.7978 (p) REVERT: C 311 LYS cc_start: 0.8950 (pttt) cc_final: 0.8040 (mmmt) REVERT: C 349 ARG cc_start: 0.8385 (mtm180) cc_final: 0.8125 (mtp85) REVERT: C 369 LYS cc_start: 0.7982 (mttt) cc_final: 0.7693 (ttmt) REVERT: C 379 ARG cc_start: 0.7363 (tpp80) cc_final: 0.7067 (mtm110) REVERT: D 311 LYS cc_start: 0.8682 (pttt) cc_final: 0.8191 (ptmm) REVERT: D 349 ARG cc_start: 0.8328 (ttm110) cc_final: 0.7864 (mtp85) REVERT: E 360 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8482 (mt) REVERT: F 342 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8031 (tm-30) REVERT: F 349 ARG cc_start: 0.8502 (ttm110) cc_final: 0.8021 (mtp85) REVERT: F 370 LYS cc_start: 0.4936 (OUTLIER) cc_final: 0.4301 (mmmt) REVERT: G 321 LYS cc_start: 0.8175 (mttm) cc_final: 0.7916 (mmmt) REVERT: G 374 HIS cc_start: 0.7569 (m-70) cc_final: 0.5545 (p90) REVERT: H 310 TYR cc_start: 0.8006 (t80) cc_final: 0.7504 (t80) REVERT: H 311 LYS cc_start: 0.8746 (ttmt) cc_final: 0.8497 (ttpt) REVERT: H 374 HIS cc_start: 0.8058 (m-70) cc_final: 0.7613 (m-70) REVERT: I 336 GLN cc_start: 0.7964 (tt0) cc_final: 0.7764 (tt0) REVERT: I 374 HIS cc_start: 0.8394 (m90) cc_final: 0.8004 (m90) outliers start: 15 outliers final: 10 residues processed: 128 average time/residue: 0.2546 time to fit residues: 38.5582 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 : 0.566 ------------------------------------------------------------------------------- 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 H residue 328 ILE Chi-restraints excluded: chain H residue 341 SER Chi-restraints excluded: chain H residue 356 SER Chi-restraints excluded: chain I residue 306 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 39 optimal weight: 0.6980 chunk 13 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 43 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.152021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.118596 restraints weight = 6390.291| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 1.90 r_work: 0.3760 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3671 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5190 Z= 0.373 Angle : 0.669 7.732 6945 Z= 0.334 Chirality : 0.052 0.147 783 Planarity : 0.003 0.034 882 Dihedral : 5.361 16.581 684 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.56 % Allowed : 15.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (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 HIS 0.003 0.001 HIS B 374 PHE 0.015 0.002 PHE B 378 TYR 0.018 0.003 TYR A 310 ARG 0.004 0.001 ARG A 349 *********************** 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 135 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.684 Fit side-chains REVERT: A 373 THR cc_start: 0.8398 (m) cc_final: 0.8085 (p) REVERT: B 347 LYS cc_start: 0.9280 (mttm) cc_final: 0.9029 (mttt) REVERT: B 348 ASP cc_start: 0.8739 (t0) cc_final: 0.8077 (p0) REVERT: B 373 THR cc_start: 0.8400 (m) cc_final: 0.7989 (p) REVERT: C 311 LYS cc_start: 0.8984 (pttt) cc_final: 0.8105 (mmmt) REVERT: C 349 ARG cc_start: 0.8384 (mtm180) cc_final: 0.8118 (mtp85) REVERT: C 369 LYS cc_start: 0.7988 (mttt) cc_final: 0.7678 (ttmt) REVERT: C 372 GLU cc_start: 0.8120 (pt0) cc_final: 0.7798 (pt0) REVERT: C 379 ARG cc_start: 0.7382 (tpp80) cc_final: 0.7019 (mtm110) REVERT: D 311 LYS cc_start: 0.8661 (pttt) cc_final: 0.8162 (ptmm) REVERT: D 349 ARG cc_start: 0.8329 (ttm110) cc_final: 0.7850 (mtp85) REVERT: E 360 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8468 (mt) REVERT: F 342 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8085 (tm-30) REVERT: F 349 ARG cc_start: 0.8532 (ttm110) cc_final: 0.8037 (mtp85) REVERT: F 370 LYS cc_start: 0.4959 (OUTLIER) cc_final: 0.4025 (tppt) REVERT: G 321 LYS cc_start: 0.8136 (mttm) cc_final: 0.7878 (mmmt) REVERT: G 374 HIS cc_start: 0.7584 (m-70) cc_final: 0.5580 (p90) REVERT: H 310 TYR cc_start: 0.8021 (t80) cc_final: 0.7710 (t80) REVERT: H 317 LYS cc_start: 0.7861 (ptmt) cc_final: 0.7538 (ptmm) REVERT: H 374 HIS cc_start: 0.8019 (m-70) cc_final: 0.7690 (m90) REVERT: I 374 HIS cc_start: 0.8414 (m90) cc_final: 0.7953 (m90) outliers start: 15 outliers final: 13 residues processed: 130 average time/residue: 0.3621 time to fit residues: 55.1617 Evaluate side-chains 128 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 371 ILE Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 328 ILE Chi-restraints excluded: chain H residue 341 SER Chi-restraints excluded: chain H residue 356 SER Chi-restraints excluded: chain I residue 306 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 61 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 chunk 20 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- 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 = 0.4240 r_free = 0.4240 target = 0.154252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.120714 restraints weight = 6344.698| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 1.90 r_work: 0.3794 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3702 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5190 Z= 0.260 Angle : 0.628 7.993 6945 Z= 0.309 Chirality : 0.050 0.133 783 Planarity : 0.003 0.043 882 Dihedral : 5.160 15.905 684 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.56 % Allowed : 15.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.29), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 374 PHE 0.011 0.001 PHE B 378 TYR 0.017 0.002 TYR A 310 ARG 0.006 0.001 ARG H 349 *********************** 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 129 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 373 THR cc_start: 0.8359 (m) cc_final: 0.8074 (p) REVERT: B 311 LYS cc_start: 0.8858 (mtmt) cc_final: 0.8606 (mttm) REVERT: B 348 ASP cc_start: 0.8714 (t0) cc_final: 0.8089 (p0) REVERT: B 373 THR cc_start: 0.8351 (m) cc_final: 0.7952 (p) REVERT: C 311 LYS cc_start: 0.8932 (pttt) cc_final: 0.8014 (mmmt) REVERT: C 349 ARG cc_start: 0.8386 (mtm180) cc_final: 0.8088 (mtp85) REVERT: C 369 LYS cc_start: 0.8013 (mttt) cc_final: 0.7701 (ttmt) REVERT: C 379 ARG cc_start: 0.7380 (tpp80) cc_final: 0.7053 (mtm110) REVERT: D 311 LYS cc_start: 0.8646 (pttt) cc_final: 0.8173 (ptmm) REVERT: D 349 ARG cc_start: 0.8333 (ttm110) cc_final: 0.7864 (mtp85) REVERT: E 360 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8491 (mt) REVERT: F 342 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8033 (tm-30) REVERT: F 349 ARG cc_start: 0.8517 (ttm110) cc_final: 0.8025 (mtp85) REVERT: F 370 LYS cc_start: 0.4899 (OUTLIER) cc_final: 0.3927 (tppt) REVERT: G 321 LYS cc_start: 0.8119 (mttm) cc_final: 0.7855 (mmmt) REVERT: G 374 HIS cc_start: 0.7571 (m-70) cc_final: 0.5559 (p90) REVERT: H 317 LYS cc_start: 0.7888 (ptmt) cc_final: 0.7567 (ptmm) REVERT: H 374 HIS cc_start: 0.8060 (m-70) cc_final: 0.7729 (m90) REVERT: I 374 HIS cc_start: 0.8426 (m90) cc_final: 0.7981 (m90) outliers start: 15 outliers final: 12 residues processed: 124 average time/residue: 0.3178 time to fit residues: 47.3559 Evaluate side-chains 126 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 371 ILE Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 328 ILE Chi-restraints excluded: chain H residue 341 SER Chi-restraints excluded: chain H residue 356 SER Chi-restraints excluded: chain I residue 306 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 48 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 57 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 374 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 = 0.4216 r_free = 0.4216 target = 0.151909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.118511 restraints weight = 6318.242| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 1.89 r_work: 0.3768 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5190 Z= 0.360 Angle : 0.674 8.121 6945 Z= 0.336 Chirality : 0.052 0.146 783 Planarity : 0.003 0.047 882 Dihedral : 5.306 16.534 684 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.56 % Allowed : 15.90 % Favored : 81.54 % 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: -2.10 (0.29), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 330 PHE 0.010 0.002 PHE B 378 TYR 0.020 0.003 TYR A 310 ARG 0.004 0.000 ARG H 349 *********************** 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 129 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: A 373 THR cc_start: 0.8359 (m) cc_final: 0.8083 (p) REVERT: B 311 LYS cc_start: 0.8917 (mtmt) cc_final: 0.8616 (mttm) REVERT: B 348 ASP cc_start: 0.8745 (t0) cc_final: 0.8107 (p0) REVERT: C 311 LYS cc_start: 0.8805 (pttt) cc_final: 0.7963 (mmtm) REVERT: C 349 ARG cc_start: 0.8376 (mtm180) cc_final: 0.8100 (mtp85) REVERT: C 369 LYS cc_start: 0.8025 (mttt) cc_final: 0.7700 (ttmt) REVERT: C 379 ARG cc_start: 0.7403 (tpp80) cc_final: 0.7074 (mtm110) REVERT: D 349 ARG cc_start: 0.8355 (ttm110) cc_final: 0.7880 (mtp85) REVERT: E 360 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8476 (mt) REVERT: F 342 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8086 (tm-30) REVERT: F 349 ARG cc_start: 0.8533 (ttm110) cc_final: 0.8033 (mtp85) REVERT: F 370 LYS cc_start: 0.4867 (OUTLIER) cc_final: 0.4041 (tppt) REVERT: G 321 LYS cc_start: 0.8057 (mttm) cc_final: 0.7832 (mmmt) REVERT: G 374 HIS cc_start: 0.7620 (m-70) cc_final: 0.5640 (p90) REVERT: H 310 TYR cc_start: 0.7948 (t80) cc_final: 0.7620 (t80) REVERT: H 317 LYS cc_start: 0.7875 (ptmt) cc_final: 0.7559 (ptmm) REVERT: H 374 HIS cc_start: 0.7998 (m-70) cc_final: 0.7740 (m90) REVERT: I 374 HIS cc_start: 0.8496 (m90) cc_final: 0.8004 (m90) outliers start: 15 outliers final: 12 residues processed: 125 average time/residue: 0.2462 time to fit residues: 36.8065 Evaluate side-chains 123 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 D residue 344 LEU Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain H residue 319 THR Chi-restraints excluded: chain H residue 328 ILE Chi-restraints excluded: chain H residue 341 SER Chi-restraints excluded: chain H residue 356 SER Chi-restraints excluded: chain I residue 306 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 51 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 61 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 327 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.155881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.122193 restraints weight = 6303.670| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 1.92 r_work: 0.3820 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3729 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5190 Z= 0.219 Angle : 0.614 8.059 6945 Z= 0.299 Chirality : 0.050 0.131 783 Planarity : 0.003 0.049 882 Dihedral : 5.008 15.456 684 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.22 % Allowed : 16.24 % Favored : 81.54 % 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: -2.10 (0.29), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 362 PHE 0.006 0.001 PHE B 378 TYR 0.013 0.002 TYR A 310 ARG 0.005 0.000 ARG H 349 ********************** 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 128 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 373 THR cc_start: 0.8343 (m) cc_final: 0.8065 (p) REVERT: B 311 LYS cc_start: 0.8922 (mtmt) cc_final: 0.8604 (mttm) REVERT: B 318 VAL cc_start: 0.9166 (t) cc_final: 0.8877 (t) REVERT: B 348 ASP cc_start: 0.8707 (t0) cc_final: 0.8084 (p0) REVERT: B 373 THR cc_start: 0.8358 (m) cc_final: 0.7958 (p) REVERT: C 311 LYS cc_start: 0.8621 (pttt) cc_final: 0.7791 (mmmt) REVERT: C 349 ARG cc_start: 0.8398 (mtm180) cc_final: 0.8125 (mtp85) REVERT: C 369 LYS cc_start: 0.7994 (mttt) cc_final: 0.7691 (ttmt) REVERT: C 379 ARG cc_start: 0.7381 (tpp80) cc_final: 0.7065 (mtm110) REVERT: D 311 LYS cc_start: 0.8650 (pttt) cc_final: 0.8223 (ptmm) REVERT: D 349 ARG cc_start: 0.8354 (ttm110) cc_final: 0.7881 (mtp85) REVERT: E 360 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8519 (mt) REVERT: F 342 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8018 (tm-30) REVERT: F 349 ARG cc_start: 0.8521 (ttm110) cc_final: 0.8018 (mtp85) REVERT: F 370 LYS cc_start: 0.4801 (OUTLIER) cc_final: 0.3864 (tppt) REVERT: G 374 HIS cc_start: 0.7573 (m-70) cc_final: 0.5538 (p90) REVERT: H 374 HIS cc_start: 0.7967 (m-70) cc_final: 0.7702 (m90) REVERT: I 359 ASN cc_start: 0.7864 (m-40) cc_final: 0.7573 (m-40) REVERT: I 374 HIS cc_start: 0.8457 (m90) cc_final: 0.8009 (m90) outliers start: 13 outliers final: 9 residues processed: 124 average time/residue: 0.2367 time to fit residues: 35.4739 Evaluate side-chains 125 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 319 THR Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 319 THR 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 52 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 58 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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 = 0.4224 r_free = 0.4224 target = 0.152460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.118966 restraints weight = 6416.783| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.91 r_work: 0.3778 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5190 Z= 0.349 Angle : 0.663 8.146 6945 Z= 0.330 Chirality : 0.052 0.143 783 Planarity : 0.003 0.049 882 Dihedral : 5.229 16.152 684 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.22 % Allowed : 15.90 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.29), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 374 PHE 0.008 0.002 PHE A 346 TYR 0.015 0.003 TYR A 310 ARG 0.005 0.000 ARG H 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4080.27 seconds wall clock time: 73 minutes 50.85 seconds (4430.85 seconds total)