Starting phenix.real_space_refine on Mon Mar 11 05:19:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9a_18273/03_2024/8q9a_18273.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9a_18273/03_2024/8q9a_18273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9a_18273/03_2024/8q9a_18273.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9a_18273/03_2024/8q9a_18273.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9a_18273/03_2024/8q9a_18273.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9a_18273/03_2024/8q9a_18273.pdb" } resolution = 3.04 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2193 2.51 5 N 648 2.21 5 O 660 1.98 5 H 3633 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 314": "OD1" <-> "OD2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 348": "OD1" <-> "OD2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 314": "OD1" <-> "OD2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 348": "OD1" <-> "OD2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "D PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 314": "OD1" <-> "OD2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 348": "OD1" <-> "OD2" Residue "F GLU 372": "OE1" <-> "OE2" Residue "F PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7140 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1186 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "B" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1194 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "C" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1186 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "D" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1194 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "E" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1186 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "F" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1194 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Time building chain proxies: 3.40, per 1000 atoms: 0.48 Number of scatterers: 7140 At special positions: 0 Unit cell: (117.832, 120.304, 37.904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 660 8.00 N 648 7.00 C 2193 6.00 H 3633 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 4.77 Conformation dependent library (CDL) restraints added in 682.8 milliseconds 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 798 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 19 sheets defined 0.0% alpha, 49.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.880A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 318 removed outlier: 6.229A pdb=" N LYS A 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 321 through 322 removed outlier: 6.590A pdb=" N LYS A 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 325 through 330 removed outlier: 6.867A pdb=" N GLY C 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASN A 327 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLY A 326 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASN E 327 " --> pdb=" O GLY A 326 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 337 through 342 removed outlier: 6.509A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N GLU E 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER A 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.441A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 350 through 354 removed outlier: 6.314A pdb=" N VAL A 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N LYS E 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N SER A 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.404A pdb=" N ASP A 358 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N THR C 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE A 360 " --> pdb=" O THR C 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 369 through 378 removed outlier: 6.430A pdb=" N LYS A 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N GLU C 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N HIS C 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR A 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N LEU C 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LYS A 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N PHE C 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR A 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.548A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.894A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 317 through 325 Processing sheet with id=AB5, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.557A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 337 through 342 removed outlier: 6.692A pdb=" N VAL B 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LYS F 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL B 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N GLU F 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER B 341 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.413A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 350 through 354 removed outlier: 6.430A pdb=" N GLN B 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ILE D 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS B 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL B 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LYS F 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER B 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 357 through 362 removed outlier: 6.869A pdb=" N LEU B 357 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ILE F 360 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN B 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N HIS F 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR B 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 368 through 378 removed outlier: 6.569A pdb=" N LYS B 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N GLU D 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE B 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N HIS D 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N THR B 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N LEU D 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS B 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N PHE D 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR B 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) 85 hydrogen bonds defined for protein. 255 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: 2.26 Time building geometry restraints manager: 5.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.09: 1121 1.09 - 1.27: 3094 1.27 - 1.45: 834 1.45 - 1.63: 2139 1.63 - 1.81: 6 Bond restraints: 7194 Sorted by residual: bond pdb=" NE2 GLN F 351 " pdb="HE21 GLN F 351 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N LYS B 331 " pdb=" H LYS B 331 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N VAL F 337 " pdb=" H VAL F 337 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N LEU B 344 " pdb=" H LEU B 344 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N TYR A 310 " pdb=" H TYR A 310 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 7189 not shown) Histogram of bond angle deviations from ideal: 96.06 - 102.70: 20 102.70 - 109.33: 4938 109.33 - 115.96: 4402 115.96 - 122.60: 3033 122.60 - 129.23: 708 Bond angle restraints: 13101 Sorted by residual: angle pdb=" CA HIS F 374 " pdb=" CB HIS F 374 " pdb=" CG HIS F 374 " ideal model delta sigma weight residual 113.80 122.36 -8.56 1.00e+00 1.00e+00 7.33e+01 angle pdb=" CA HIS D 374 " pdb=" CB HIS D 374 " pdb=" CG HIS D 374 " ideal model delta sigma weight residual 113.80 119.29 -5.49 1.00e+00 1.00e+00 3.02e+01 angle pdb=" CA ASP B 358 " pdb=" CB ASP B 358 " pdb=" CG ASP B 358 " ideal model delta sigma weight residual 112.60 117.97 -5.37 1.00e+00 1.00e+00 2.88e+01 angle pdb=" CA ASP C 358 " pdb=" CB ASP C 358 " pdb=" CG ASP C 358 " ideal model delta sigma weight residual 112.60 117.77 -5.17 1.00e+00 1.00e+00 2.67e+01 angle pdb=" CA ASP A 358 " pdb=" CB ASP A 358 " pdb=" CG ASP A 358 " ideal model delta sigma weight residual 112.60 117.69 -5.09 1.00e+00 1.00e+00 2.59e+01 ... (remaining 13096 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.55: 2906 14.55 - 29.11: 176 29.11 - 43.66: 94 43.66 - 58.22: 71 58.22 - 72.77: 65 Dihedral angle restraints: 3312 sinusoidal: 1896 harmonic: 1416 Sorted by residual: dihedral pdb=" CA GLY B 367 " pdb=" C GLY B 367 " pdb=" N ASN B 368 " pdb=" CA ASN B 368 " ideal model delta harmonic sigma weight residual 180.00 -152.92 -27.08 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA LEU E 357 " pdb=" C LEU E 357 " pdb=" N ASP E 358 " pdb=" CA ASP E 358 " ideal model delta harmonic sigma weight residual 180.00 153.50 26.50 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA LEU C 357 " pdb=" C LEU C 357 " pdb=" N ASP C 358 " pdb=" CA ASP C 358 " ideal model delta harmonic sigma weight residual 180.00 156.16 23.84 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 3309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 358 0.084 - 0.168: 138 0.168 - 0.252: 26 0.252 - 0.335: 6 0.335 - 0.419: 3 Chirality restraints: 531 Sorted by residual: chirality pdb=" CA LYS B 369 " pdb=" N LYS B 369 " pdb=" C LYS B 369 " pdb=" CB LYS B 369 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.40e+00 chirality pdb=" CA HIS F 374 " pdb=" N HIS F 374 " pdb=" C HIS F 374 " pdb=" CB HIS F 374 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CA LYS F 347 " pdb=" N LYS F 347 " pdb=" C LYS F 347 " pdb=" CB LYS F 347 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 528 not shown) Planarity restraints: 1047 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 349 " -0.118 9.50e-02 1.11e+02 8.69e-02 1.37e+02 pdb=" NE ARG D 349 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG D 349 " -0.040 2.00e-02 2.50e+03 pdb=" NH1 ARG D 349 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG D 349 " -0.059 2.00e-02 2.50e+03 pdb="HH11 ARG D 349 " 0.012 2.00e-02 2.50e+03 pdb="HH12 ARG D 349 " 0.093 2.00e-02 2.50e+03 pdb="HH21 ARG D 349 " 0.158 2.00e-02 2.50e+03 pdb="HH22 ARG D 349 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 359 " -0.073 2.00e-02 2.50e+03 6.96e-02 7.27e+01 pdb=" CG ASN A 359 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 359 " 0.048 2.00e-02 2.50e+03 pdb=" ND2 ASN A 359 " 0.069 2.00e-02 2.50e+03 pdb="HD21 ASN A 359 " 0.054 2.00e-02 2.50e+03 pdb="HD22 ASN A 359 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " 0.085 2.00e-02 2.50e+03 4.28e-02 5.49e+01 pdb=" CG TYR A 310 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " -0.046 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " 0.092 2.00e-02 2.50e+03 pdb=" HD1 TYR A 310 " 0.016 2.00e-02 2.50e+03 pdb=" HD2 TYR A 310 " -0.032 2.00e-02 2.50e+03 pdb=" HE1 TYR A 310 " -0.028 2.00e-02 2.50e+03 pdb=" HE2 TYR A 310 " 0.002 2.00e-02 2.50e+03 ... (remaining 1044 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 440 2.15 - 2.76: 11671 2.76 - 3.38: 18734 3.38 - 3.99: 24870 3.99 - 4.60: 35149 Nonbonded interactions: 90864 Sorted by model distance: nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.540 1.850 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.559 1.850 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.591 1.850 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.600 1.850 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.621 1.850 ... (remaining 90859 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 304 through 379) selection = (chain 'B' and resid 304 through 379) selection = (chain 'C' and resid 304 through 379) selection = (chain 'D' and resid 304 through 379) selection = (chain 'E' and resid 304 through 379) selection = (chain 'F' and resid 304 through 379) } 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: 3.070 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: 0.100 Extract box with map and model: 10.950 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 24.830 Find NCS groups from input model: 0.350 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 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 0.038 3561 Z= 0.721 Angle : 1.798 8.560 4761 Z= 1.201 Chirality : 0.092 0.419 531 Planarity : 0.010 0.049 609 Dihedral : 13.060 72.770 1365 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.75 % Allowed : 2.76 % Favored : 96.49 % Cbeta Deviations : 0.25 % 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 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.004 HIS B 374 PHE 0.045 0.016 PHE B 346 TYR 0.085 0.021 TYR A 310 ARG 0.005 0.001 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 136 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7789 (mttt) cc_final: 0.7151 (mttp) REVERT: A 338 GLU cc_start: 0.7652 (tt0) cc_final: 0.7371 (mt-10) REVERT: A 343 LYS cc_start: 0.8885 (mttt) cc_final: 0.8666 (mttm) REVERT: A 369 LYS cc_start: 0.7496 (mttt) cc_final: 0.6699 (mtpp) REVERT: B 307 GLN cc_start: 0.7551 (mt0) cc_final: 0.7196 (tt0) REVERT: B 331 LYS cc_start: 0.8268 (mttt) cc_final: 0.7904 (mtpp) REVERT: B 343 LYS cc_start: 0.8776 (mttt) cc_final: 0.8569 (mtpp) REVERT: B 347 LYS cc_start: 0.8447 (mttt) cc_final: 0.8204 (mttm) REVERT: B 375 LYS cc_start: 0.7763 (pttt) cc_final: 0.7545 (ptmt) REVERT: C 321 LYS cc_start: 0.8294 (mttt) cc_final: 0.7751 (mttm) REVERT: C 348 ASP cc_start: 0.7984 (t0) cc_final: 0.7186 (p0) REVERT: C 369 LYS cc_start: 0.8312 (mttt) cc_final: 0.7594 (mtpp) REVERT: D 311 LYS cc_start: 0.8280 (tttt) cc_final: 0.7868 (ttpt) REVERT: D 314 ASP cc_start: 0.8239 (t0) cc_final: 0.7922 (t0) REVERT: D 331 LYS cc_start: 0.8339 (mttt) cc_final: 0.7907 (mmmt) REVERT: D 375 LYS cc_start: 0.8321 (pttt) cc_final: 0.7793 (ptpp) REVERT: D 379 ARG cc_start: 0.6705 (mtt-85) cc_final: 0.6253 (mmt180) REVERT: E 321 LYS cc_start: 0.7870 (mttt) cc_final: 0.7353 (mttm) REVERT: E 338 GLU cc_start: 0.7476 (tt0) cc_final: 0.7105 (mt-10) REVERT: E 343 LYS cc_start: 0.9039 (mttt) cc_final: 0.8818 (mttm) REVERT: E 349 ARG cc_start: 0.6732 (mtm180) cc_final: 0.6005 (mmp-170) REVERT: E 353 LYS cc_start: 0.8327 (tttt) cc_final: 0.8081 (tttm) REVERT: E 356 SER cc_start: 0.7968 (p) cc_final: 0.7237 (t) REVERT: E 369 LYS cc_start: 0.7691 (mttt) cc_final: 0.6959 (mtpp) REVERT: F 331 LYS cc_start: 0.8456 (mttt) cc_final: 0.7446 (mmtt) REVERT: F 375 LYS cc_start: 0.7957 (pttt) cc_final: 0.7305 (ptpt) outliers start: 3 outliers final: 0 residues processed: 138 average time/residue: 0.6037 time to fit residues: 92.7289 Evaluate side-chains 97 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS C 362 HIS D 307 GLN D 327 ASN E 362 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3561 Z= 0.195 Angle : 0.548 5.035 4761 Z= 0.292 Chirality : 0.051 0.124 531 Planarity : 0.003 0.031 609 Dihedral : 5.740 19.171 474 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 2.01 % Allowed : 8.02 % Favored : 89.97 % 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: -1.43 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.08 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 374 PHE 0.014 0.001 PHE B 378 TYR 0.008 0.002 TYR D 310 ARG 0.002 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 106 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7695 (mttt) cc_final: 0.7058 (mttp) REVERT: A 369 LYS cc_start: 0.7658 (mttt) cc_final: 0.6930 (mtpp) REVERT: B 307 GLN cc_start: 0.7541 (mt0) cc_final: 0.7174 (tt0) REVERT: B 331 LYS cc_start: 0.8124 (mttt) cc_final: 0.7738 (mtpp) REVERT: B 343 LYS cc_start: 0.8763 (mttt) cc_final: 0.8497 (mtpp) REVERT: B 375 LYS cc_start: 0.7715 (pttt) cc_final: 0.7450 (ptmt) REVERT: C 317 LYS cc_start: 0.8398 (mtmt) cc_final: 0.7740 (ttmt) REVERT: C 321 LYS cc_start: 0.8251 (mttt) cc_final: 0.7733 (mttp) REVERT: C 340 LYS cc_start: 0.8417 (mttt) cc_final: 0.8210 (mttp) REVERT: C 369 LYS cc_start: 0.8307 (mttt) cc_final: 0.7635 (mtpp) REVERT: C 370 LYS cc_start: 0.8569 (ttmm) cc_final: 0.8365 (ttmm) REVERT: C 372 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7381 (mt-10) REVERT: D 307 GLN cc_start: 0.8245 (tt0) cc_final: 0.7644 (tm-30) REVERT: D 311 LYS cc_start: 0.8250 (tttt) cc_final: 0.7798 (ttpt) REVERT: D 314 ASP cc_start: 0.8331 (t0) cc_final: 0.7959 (t0) REVERT: D 331 LYS cc_start: 0.8260 (mttt) cc_final: 0.7779 (mmmt) REVERT: D 340 LYS cc_start: 0.8270 (mttt) cc_final: 0.8014 (mtpp) REVERT: D 375 LYS cc_start: 0.8267 (pttt) cc_final: 0.7726 (ptpp) REVERT: D 379 ARG cc_start: 0.6634 (mtt-85) cc_final: 0.6185 (mmp-170) REVERT: E 317 LYS cc_start: 0.7724 (mtmt) cc_final: 0.7079 (ptmt) REVERT: E 321 LYS cc_start: 0.7892 (mttt) cc_final: 0.7366 (mttm) REVERT: E 338 GLU cc_start: 0.7550 (tt0) cc_final: 0.7158 (mt-10) REVERT: E 343 LYS cc_start: 0.9134 (mttt) cc_final: 0.8841 (mttm) REVERT: E 347 LYS cc_start: 0.8796 (mttp) cc_final: 0.8522 (mtmm) REVERT: E 349 ARG cc_start: 0.6725 (mtm180) cc_final: 0.6002 (mmp-170) REVERT: E 369 LYS cc_start: 0.7710 (mttt) cc_final: 0.7155 (mtpp) REVERT: F 307 GLN cc_start: 0.7736 (mt0) cc_final: 0.7264 (tt0) REVERT: F 311 LYS cc_start: 0.8178 (tttt) cc_final: 0.7663 (ttpt) REVERT: F 331 LYS cc_start: 0.8417 (mttt) cc_final: 0.7453 (mmtt) REVERT: F 374 HIS cc_start: 0.7352 (OUTLIER) cc_final: 0.7127 (p90) outliers start: 8 outliers final: 7 residues processed: 114 average time/residue: 0.6354 time to fit residues: 80.4354 Evaluate side-chains 104 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 374 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 28 optimal weight: 0.0870 chunk 19 optimal weight: 5.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3561 Z= 0.147 Angle : 0.493 4.446 4761 Z= 0.258 Chirality : 0.051 0.132 531 Planarity : 0.003 0.037 609 Dihedral : 4.903 17.945 474 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.76 % Allowed : 10.28 % Favored : 86.97 % 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: -1.37 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 374 PHE 0.007 0.001 PHE B 346 TYR 0.008 0.002 TYR C 310 ARG 0.002 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7465 (mtpt) cc_final: 0.6959 (ttpt) REVERT: A 321 LYS cc_start: 0.7778 (mttt) cc_final: 0.7191 (mttm) REVERT: A 369 LYS cc_start: 0.7695 (mttt) cc_final: 0.7023 (mtpp) REVERT: B 307 GLN cc_start: 0.7710 (mt0) cc_final: 0.7259 (tt0) REVERT: B 331 LYS cc_start: 0.8100 (mttt) cc_final: 0.7721 (mtpp) REVERT: B 343 LYS cc_start: 0.8798 (mttt) cc_final: 0.8470 (mtpp) REVERT: B 353 LYS cc_start: 0.8091 (tttt) cc_final: 0.7754 (tttt) REVERT: B 375 LYS cc_start: 0.7738 (pttt) cc_final: 0.7286 (ptpp) REVERT: C 317 LYS cc_start: 0.8348 (mtmt) cc_final: 0.7849 (ttmt) REVERT: C 321 LYS cc_start: 0.8257 (mttt) cc_final: 0.7726 (mttp) REVERT: C 369 LYS cc_start: 0.8309 (mttt) cc_final: 0.7633 (mtpp) REVERT: C 372 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7607 (mt-10) REVERT: D 311 LYS cc_start: 0.8236 (tttt) cc_final: 0.7790 (ttpt) REVERT: D 314 ASP cc_start: 0.8441 (t0) cc_final: 0.8058 (t0) REVERT: D 331 LYS cc_start: 0.8272 (mttt) cc_final: 0.7774 (mmmt) REVERT: D 340 LYS cc_start: 0.8316 (mttt) cc_final: 0.8097 (mtpp) REVERT: D 374 HIS cc_start: 0.7405 (OUTLIER) cc_final: 0.6718 (p90) REVERT: D 375 LYS cc_start: 0.8334 (pttt) cc_final: 0.7674 (ptpp) REVERT: D 379 ARG cc_start: 0.6635 (mtt-85) cc_final: 0.6058 (mmp-170) REVERT: E 317 LYS cc_start: 0.7740 (mtmt) cc_final: 0.7087 (ptmt) REVERT: E 321 LYS cc_start: 0.8018 (mttt) cc_final: 0.7531 (mttm) REVERT: E 338 GLU cc_start: 0.7611 (tt0) cc_final: 0.7245 (mt-10) REVERT: E 347 LYS cc_start: 0.8792 (mttp) cc_final: 0.8557 (mtmm) REVERT: E 356 SER cc_start: 0.7649 (p) cc_final: 0.7132 (t) REVERT: E 369 LYS cc_start: 0.7728 (mttt) cc_final: 0.7084 (mtpp) REVERT: F 307 GLN cc_start: 0.7747 (mt0) cc_final: 0.7290 (tt0) REVERT: F 311 LYS cc_start: 0.8024 (tttt) cc_final: 0.7445 (ttpt) REVERT: F 331 LYS cc_start: 0.8458 (mttt) cc_final: 0.7485 (mmtt) REVERT: F 353 LYS cc_start: 0.8273 (tttt) cc_final: 0.8039 (tttt) REVERT: F 356 SER cc_start: 0.7278 (p) cc_final: 0.6557 (t) outliers start: 11 outliers final: 7 residues processed: 110 average time/residue: 0.6379 time to fit residues: 78.0081 Evaluate side-chains 103 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 40 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 0 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3561 Z= 0.107 Angle : 0.443 4.067 4761 Z= 0.228 Chirality : 0.051 0.132 531 Planarity : 0.003 0.040 609 Dihedral : 4.463 17.162 474 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 1.75 % Allowed : 11.28 % Favored : 86.97 % 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: -1.24 (0.34), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.94 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 374 PHE 0.004 0.001 PHE B 378 TYR 0.005 0.001 TYR B 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7538 (mtpt) cc_final: 0.6884 (ttpt) REVERT: A 321 LYS cc_start: 0.7770 (mttt) cc_final: 0.7182 (mttm) REVERT: A 369 LYS cc_start: 0.7703 (mttt) cc_final: 0.7080 (mtpp) REVERT: B 307 GLN cc_start: 0.7743 (mt0) cc_final: 0.7277 (tt0) REVERT: B 331 LYS cc_start: 0.8104 (mttt) cc_final: 0.7719 (mtpp) REVERT: B 375 LYS cc_start: 0.7751 (pttt) cc_final: 0.7540 (ptmm) REVERT: C 321 LYS cc_start: 0.8265 (mttt) cc_final: 0.7718 (mttp) REVERT: C 359 ASN cc_start: 0.8664 (t0) cc_final: 0.8145 (t0) REVERT: C 369 LYS cc_start: 0.8318 (mttt) cc_final: 0.7683 (mtpp) REVERT: C 372 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7474 (tt0) REVERT: D 311 LYS cc_start: 0.8202 (tttt) cc_final: 0.7783 (ttpt) REVERT: D 314 ASP cc_start: 0.8306 (t0) cc_final: 0.8083 (t0) REVERT: D 331 LYS cc_start: 0.8231 (mttt) cc_final: 0.7737 (mmmt) REVERT: D 340 LYS cc_start: 0.8389 (mttt) cc_final: 0.8118 (mtpp) REVERT: D 374 HIS cc_start: 0.6996 (OUTLIER) cc_final: 0.6765 (p90) REVERT: D 375 LYS cc_start: 0.8287 (pttt) cc_final: 0.7570 (ptpp) REVERT: D 379 ARG cc_start: 0.6483 (mtt-85) cc_final: 0.5972 (mmp-170) REVERT: E 317 LYS cc_start: 0.7776 (mtmt) cc_final: 0.7183 (ptmt) REVERT: E 321 LYS cc_start: 0.7939 (mttt) cc_final: 0.7464 (mttm) REVERT: E 338 GLU cc_start: 0.7637 (tt0) cc_final: 0.7291 (mt-10) REVERT: E 347 LYS cc_start: 0.8770 (mttp) cc_final: 0.8529 (mtmm) REVERT: E 356 SER cc_start: 0.7589 (p) cc_final: 0.7184 (t) REVERT: E 369 LYS cc_start: 0.7712 (mttt) cc_final: 0.7075 (mtpp) REVERT: F 307 GLN cc_start: 0.7738 (mt0) cc_final: 0.7155 (tm-30) REVERT: F 311 LYS cc_start: 0.7946 (tttt) cc_final: 0.7294 (mmtt) REVERT: F 331 LYS cc_start: 0.8462 (mttt) cc_final: 0.7480 (mmtt) REVERT: F 356 SER cc_start: 0.7245 (p) cc_final: 0.6576 (t) REVERT: F 362 HIS cc_start: 0.7831 (t-170) cc_final: 0.7619 (t-90) REVERT: F 375 LYS cc_start: 0.7788 (pttt) cc_final: 0.7201 (ptpt) outliers start: 7 outliers final: 3 residues processed: 104 average time/residue: 0.6110 time to fit residues: 70.7300 Evaluate side-chains 102 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3561 Z= 0.192 Angle : 0.474 4.090 4761 Z= 0.248 Chirality : 0.050 0.131 531 Planarity : 0.003 0.039 609 Dihedral : 4.609 17.115 474 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.26 % Allowed : 11.28 % Favored : 86.47 % 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: -1.20 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.91 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 374 PHE 0.007 0.001 PHE F 346 TYR 0.011 0.002 TYR D 310 ARG 0.002 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7837 (mttt) cc_final: 0.7232 (mttm) REVERT: A 369 LYS cc_start: 0.7700 (mttt) cc_final: 0.7089 (mtpp) REVERT: B 307 GLN cc_start: 0.7803 (mt0) cc_final: 0.7352 (tt0) REVERT: B 331 LYS cc_start: 0.8104 (mttt) cc_final: 0.7732 (mtpp) REVERT: B 353 LYS cc_start: 0.8080 (tttt) cc_final: 0.7784 (tttt) REVERT: C 317 LYS cc_start: 0.8338 (mtmt) cc_final: 0.7738 (ttmt) REVERT: C 321 LYS cc_start: 0.8296 (mttt) cc_final: 0.7737 (mttp) REVERT: C 369 LYS cc_start: 0.8297 (mttt) cc_final: 0.7665 (mtpp) REVERT: C 372 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7696 (mt-10) REVERT: D 311 LYS cc_start: 0.8219 (tttt) cc_final: 0.7773 (ttpt) REVERT: D 314 ASP cc_start: 0.8391 (t0) cc_final: 0.8065 (t0) REVERT: D 331 LYS cc_start: 0.8205 (mttt) cc_final: 0.7888 (mtpp) REVERT: D 340 LYS cc_start: 0.8405 (mttt) cc_final: 0.8111 (mtpp) REVERT: D 374 HIS cc_start: 0.7416 (OUTLIER) cc_final: 0.7147 (p90) REVERT: D 375 LYS cc_start: 0.8234 (pttt) cc_final: 0.7519 (ptpp) REVERT: D 379 ARG cc_start: 0.6681 (mtt-85) cc_final: 0.6246 (mmp-170) REVERT: E 311 LYS cc_start: 0.8523 (ttpt) cc_final: 0.7824 (ttmt) REVERT: E 317 LYS cc_start: 0.7834 (mtmt) cc_final: 0.7143 (ptmt) REVERT: E 321 LYS cc_start: 0.7930 (mttt) cc_final: 0.7446 (mttm) REVERT: E 347 LYS cc_start: 0.8887 (mttp) cc_final: 0.8621 (mtmm) REVERT: E 356 SER cc_start: 0.7562 (p) cc_final: 0.7139 (t) REVERT: E 369 LYS cc_start: 0.7729 (mttt) cc_final: 0.7106 (mtpp) REVERT: F 311 LYS cc_start: 0.7987 (tttt) cc_final: 0.7317 (mmtt) REVERT: F 331 LYS cc_start: 0.8452 (mttt) cc_final: 0.7463 (mmtt) REVERT: F 353 LYS cc_start: 0.8239 (tttt) cc_final: 0.7997 (tttt) REVERT: F 375 LYS cc_start: 0.7888 (pttt) cc_final: 0.7266 (ptpt) outliers start: 9 outliers final: 4 residues processed: 103 average time/residue: 0.6600 time to fit residues: 75.9375 Evaluate side-chains 100 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 8.9990 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3561 Z= 0.240 Angle : 0.494 4.209 4761 Z= 0.256 Chirality : 0.050 0.129 531 Planarity : 0.003 0.039 609 Dihedral : 4.767 17.700 474 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.76 % Allowed : 11.03 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.23 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.93 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 374 PHE 0.009 0.001 PHE B 378 TYR 0.009 0.002 TYR D 310 ARG 0.003 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7859 (mttt) cc_final: 0.7245 (mttp) REVERT: A 369 LYS cc_start: 0.7692 (mttt) cc_final: 0.7090 (mtpp) REVERT: B 307 GLN cc_start: 0.7815 (mt0) cc_final: 0.7368 (tt0) REVERT: B 331 LYS cc_start: 0.8133 (mttt) cc_final: 0.7797 (mtpp) REVERT: B 353 LYS cc_start: 0.8044 (tttt) cc_final: 0.7749 (tttt) REVERT: B 375 LYS cc_start: 0.8038 (ptmm) cc_final: 0.7626 (ptpp) REVERT: C 317 LYS cc_start: 0.8337 (mtmt) cc_final: 0.7843 (ttmt) REVERT: C 321 LYS cc_start: 0.8289 (mttt) cc_final: 0.7713 (mttp) REVERT: C 369 LYS cc_start: 0.8301 (mttt) cc_final: 0.7675 (mtpp) REVERT: D 311 LYS cc_start: 0.8236 (tttt) cc_final: 0.7788 (ttpt) REVERT: D 314 ASP cc_start: 0.8391 (t0) cc_final: 0.7969 (t0) REVERT: D 331 LYS cc_start: 0.8233 (mttt) cc_final: 0.7894 (mtpp) REVERT: D 340 LYS cc_start: 0.8402 (mttt) cc_final: 0.8095 (mtpp) REVERT: D 369 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7897 (ptmt) REVERT: D 374 HIS cc_start: 0.7564 (OUTLIER) cc_final: 0.7265 (p90) REVERT: D 375 LYS cc_start: 0.8195 (pttt) cc_final: 0.7531 (ptpp) REVERT: D 379 ARG cc_start: 0.6738 (mtt-85) cc_final: 0.6249 (mmp-170) REVERT: E 311 LYS cc_start: 0.8466 (ttpt) cc_final: 0.7785 (ttmt) REVERT: E 317 LYS cc_start: 0.7886 (mtmt) cc_final: 0.7115 (ptmt) REVERT: E 321 LYS cc_start: 0.7973 (mttt) cc_final: 0.7501 (mttm) REVERT: E 347 LYS cc_start: 0.8915 (mttp) cc_final: 0.8630 (mtmm) REVERT: E 356 SER cc_start: 0.7560 (p) cc_final: 0.7043 (t) REVERT: E 369 LYS cc_start: 0.7705 (mttt) cc_final: 0.7117 (mtpp) REVERT: F 311 LYS cc_start: 0.7987 (tttt) cc_final: 0.7171 (mmtt) REVERT: F 331 LYS cc_start: 0.8493 (mttt) cc_final: 0.7491 (mmtt) REVERT: F 353 LYS cc_start: 0.8310 (tttt) cc_final: 0.8049 (tttt) outliers start: 11 outliers final: 5 residues processed: 104 average time/residue: 0.6494 time to fit residues: 75.5478 Evaluate side-chains 101 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3561 Z= 0.272 Angle : 0.502 4.808 4761 Z= 0.262 Chirality : 0.050 0.128 531 Planarity : 0.003 0.042 609 Dihedral : 4.826 18.090 474 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.75 % Allowed : 13.03 % Favored : 85.21 % 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: -1.28 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.97 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 374 PHE 0.007 0.001 PHE F 346 TYR 0.011 0.002 TYR E 310 ARG 0.002 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7852 (mttt) cc_final: 0.7246 (mttp) REVERT: A 369 LYS cc_start: 0.7693 (mttt) cc_final: 0.7089 (mtpp) REVERT: B 307 GLN cc_start: 0.7815 (mt0) cc_final: 0.7339 (tt0) REVERT: B 331 LYS cc_start: 0.8166 (mttt) cc_final: 0.7831 (mtpp) REVERT: B 353 LYS cc_start: 0.8091 (tttt) cc_final: 0.7798 (tttt) REVERT: B 375 LYS cc_start: 0.8075 (ptmm) cc_final: 0.7498 (ptpp) REVERT: C 317 LYS cc_start: 0.8348 (mtmt) cc_final: 0.7809 (ttmt) REVERT: C 321 LYS cc_start: 0.8306 (mttt) cc_final: 0.7724 (mttp) REVERT: C 349 ARG cc_start: 0.7830 (mtm180) cc_final: 0.6157 (mtt-85) REVERT: C 369 LYS cc_start: 0.8303 (mttt) cc_final: 0.7664 (mtpp) REVERT: C 372 GLU cc_start: 0.8305 (tt0) cc_final: 0.8063 (tt0) REVERT: D 311 LYS cc_start: 0.8307 (tttt) cc_final: 0.7824 (ttpt) REVERT: D 314 ASP cc_start: 0.8433 (t0) cc_final: 0.8002 (t0) REVERT: D 331 LYS cc_start: 0.8215 (mttt) cc_final: 0.7938 (mtpp) REVERT: D 340 LYS cc_start: 0.8404 (mttt) cc_final: 0.8116 (mtpp) REVERT: D 374 HIS cc_start: 0.7594 (OUTLIER) cc_final: 0.7299 (p90) REVERT: D 375 LYS cc_start: 0.8210 (pttt) cc_final: 0.7511 (ptpp) REVERT: D 379 ARG cc_start: 0.6726 (mtt-85) cc_final: 0.6118 (mmt180) REVERT: E 311 LYS cc_start: 0.8524 (ttpt) cc_final: 0.7842 (ttmt) REVERT: E 317 LYS cc_start: 0.7828 (mtmt) cc_final: 0.6974 (ptmt) REVERT: E 321 LYS cc_start: 0.7955 (mttt) cc_final: 0.7484 (mttp) REVERT: E 347 LYS cc_start: 0.8918 (mttp) cc_final: 0.8625 (mtmm) REVERT: E 369 LYS cc_start: 0.7692 (mttt) cc_final: 0.7110 (mtpp) REVERT: F 311 LYS cc_start: 0.8048 (tttt) cc_final: 0.7298 (mmtt) REVERT: F 331 LYS cc_start: 0.8513 (mttt) cc_final: 0.8169 (mtpp) REVERT: F 353 LYS cc_start: 0.8311 (tttt) cc_final: 0.8038 (tttt) REVERT: F 375 LYS cc_start: 0.8009 (pttt) cc_final: 0.7327 (ptpt) outliers start: 7 outliers final: 5 residues processed: 97 average time/residue: 0.6576 time to fit residues: 70.8973 Evaluate side-chains 97 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3561 Z= 0.237 Angle : 0.492 5.033 4761 Z= 0.254 Chirality : 0.050 0.127 531 Planarity : 0.003 0.046 609 Dihedral : 4.750 18.238 474 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.01 % Allowed : 14.29 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.28 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.96 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 374 PHE 0.008 0.001 PHE B 378 TYR 0.009 0.002 TYR E 310 ARG 0.001 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7850 (mttt) cc_final: 0.7241 (mttp) REVERT: A 369 LYS cc_start: 0.7742 (mttt) cc_final: 0.7136 (mtpp) REVERT: B 307 GLN cc_start: 0.7795 (mt0) cc_final: 0.7340 (tt0) REVERT: B 331 LYS cc_start: 0.8166 (mttt) cc_final: 0.7824 (mtpp) REVERT: B 353 LYS cc_start: 0.8110 (tttt) cc_final: 0.7802 (tttt) REVERT: B 375 LYS cc_start: 0.8035 (ptmm) cc_final: 0.7619 (ptpp) REVERT: C 317 LYS cc_start: 0.8381 (mtmt) cc_final: 0.7735 (ttmt) REVERT: C 321 LYS cc_start: 0.8295 (mttt) cc_final: 0.7708 (mttp) REVERT: C 349 ARG cc_start: 0.7607 (mtm180) cc_final: 0.6178 (mtt-85) REVERT: C 369 LYS cc_start: 0.8287 (mttt) cc_final: 0.7666 (mtpp) REVERT: C 372 GLU cc_start: 0.8295 (tt0) cc_final: 0.8025 (tt0) REVERT: D 311 LYS cc_start: 0.8312 (tttt) cc_final: 0.7819 (ttpt) REVERT: D 314 ASP cc_start: 0.8444 (t0) cc_final: 0.8013 (t0) REVERT: D 331 LYS cc_start: 0.8196 (mttt) cc_final: 0.7923 (mtpp) REVERT: D 340 LYS cc_start: 0.8395 (mttt) cc_final: 0.8102 (mtpp) REVERT: D 374 HIS cc_start: 0.7541 (OUTLIER) cc_final: 0.7259 (p90) REVERT: D 375 LYS cc_start: 0.8213 (pttt) cc_final: 0.7518 (ptpp) REVERT: D 379 ARG cc_start: 0.6737 (mtt-85) cc_final: 0.6135 (mmt180) REVERT: E 311 LYS cc_start: 0.8459 (ttpt) cc_final: 0.7782 (ttmt) REVERT: E 317 LYS cc_start: 0.7851 (mtmt) cc_final: 0.6964 (ptmt) REVERT: E 321 LYS cc_start: 0.7932 (mttt) cc_final: 0.7480 (mttm) REVERT: E 347 LYS cc_start: 0.8917 (mttp) cc_final: 0.8633 (mtmm) REVERT: E 369 LYS cc_start: 0.7702 (mttt) cc_final: 0.7128 (mtpp) REVERT: F 311 LYS cc_start: 0.8063 (tttt) cc_final: 0.7304 (mmtt) REVERT: F 331 LYS cc_start: 0.8511 (mttt) cc_final: 0.8165 (mtpp) REVERT: F 353 LYS cc_start: 0.8282 (tttt) cc_final: 0.7996 (tttt) REVERT: F 375 LYS cc_start: 0.7968 (pttt) cc_final: 0.7315 (ptpt) outliers start: 8 outliers final: 5 residues processed: 100 average time/residue: 0.6454 time to fit residues: 71.6872 Evaluate side-chains 98 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 0.3980 chunk 41 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3561 Z= 0.264 Angle : 0.499 5.057 4761 Z= 0.259 Chirality : 0.050 0.127 531 Planarity : 0.004 0.047 609 Dihedral : 4.784 18.264 474 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.50 % Allowed : 15.29 % Favored : 83.21 % 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: -1.31 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.99 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 374 PHE 0.007 0.001 PHE B 378 TYR 0.010 0.002 TYR E 310 ARG 0.002 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7870 (mttt) cc_final: 0.7253 (mttp) REVERT: A 369 LYS cc_start: 0.7752 (mttt) cc_final: 0.7165 (mtpp) REVERT: B 307 GLN cc_start: 0.7791 (mt0) cc_final: 0.7309 (tt0) REVERT: B 331 LYS cc_start: 0.8165 (mttt) cc_final: 0.7815 (mtpp) REVERT: B 353 LYS cc_start: 0.8097 (tttt) cc_final: 0.7786 (tttt) REVERT: B 375 LYS cc_start: 0.7994 (ptmm) cc_final: 0.7587 (ptpp) REVERT: C 317 LYS cc_start: 0.8378 (mtmt) cc_final: 0.7856 (ttmt) REVERT: C 321 LYS cc_start: 0.8286 (mttt) cc_final: 0.7700 (mttp) REVERT: C 349 ARG cc_start: 0.7602 (mtm180) cc_final: 0.6150 (mtt-85) REVERT: C 369 LYS cc_start: 0.8286 (mttt) cc_final: 0.7674 (mtpp) REVERT: C 372 GLU cc_start: 0.8311 (tt0) cc_final: 0.8055 (tt0) REVERT: D 311 LYS cc_start: 0.8370 (tttt) cc_final: 0.7832 (ttpt) REVERT: D 314 ASP cc_start: 0.8463 (t0) cc_final: 0.8022 (t0) REVERT: D 331 LYS cc_start: 0.8183 (mttt) cc_final: 0.7918 (mtpp) REVERT: D 340 LYS cc_start: 0.8398 (mttt) cc_final: 0.8104 (mtpp) REVERT: D 374 HIS cc_start: 0.7553 (OUTLIER) cc_final: 0.7263 (p90) REVERT: D 375 LYS cc_start: 0.8221 (pttt) cc_final: 0.7516 (ptpp) REVERT: D 379 ARG cc_start: 0.6749 (mtt-85) cc_final: 0.6132 (mmt180) REVERT: E 311 LYS cc_start: 0.8482 (ttpt) cc_final: 0.7828 (ttmt) REVERT: E 317 LYS cc_start: 0.7852 (mtmt) cc_final: 0.6931 (ptmt) REVERT: E 321 LYS cc_start: 0.7913 (mttt) cc_final: 0.7475 (mttp) REVERT: E 347 LYS cc_start: 0.8923 (mttp) cc_final: 0.8626 (mtmm) REVERT: E 369 LYS cc_start: 0.7706 (mttt) cc_final: 0.7065 (mtpp) REVERT: F 311 LYS cc_start: 0.8082 (tttt) cc_final: 0.7397 (mmtt) REVERT: F 331 LYS cc_start: 0.8501 (mttt) cc_final: 0.8157 (mtpp) REVERT: F 353 LYS cc_start: 0.8277 (tttt) cc_final: 0.7977 (tttt) REVERT: F 375 LYS cc_start: 0.7971 (pttt) cc_final: 0.7760 (ptmt) outliers start: 6 outliers final: 5 residues processed: 95 average time/residue: 0.6479 time to fit residues: 68.7500 Evaluate side-chains 94 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.5349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3561 Z= 0.187 Angle : 0.470 5.015 4761 Z= 0.242 Chirality : 0.050 0.127 531 Planarity : 0.003 0.048 609 Dihedral : 4.591 18.409 474 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.50 % Allowed : 15.29 % Favored : 83.21 % 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: -1.30 (0.36), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.98 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 374 PHE 0.006 0.001 PHE B 378 TYR 0.006 0.001 TYR E 310 ARG 0.002 0.000 ARG A 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7865 (mttt) cc_final: 0.7250 (mttp) REVERT: A 369 LYS cc_start: 0.7767 (mttt) cc_final: 0.7174 (mtpp) REVERT: B 307 GLN cc_start: 0.7797 (mt0) cc_final: 0.7313 (tt0) REVERT: B 331 LYS cc_start: 0.8162 (mttt) cc_final: 0.7811 (mtpp) REVERT: B 353 LYS cc_start: 0.8089 (tttt) cc_final: 0.7782 (tttt) REVERT: B 375 LYS cc_start: 0.7989 (ptmm) cc_final: 0.7603 (ptpp) REVERT: C 317 LYS cc_start: 0.8370 (mtmt) cc_final: 0.7753 (ttmt) REVERT: C 321 LYS cc_start: 0.8239 (mttt) cc_final: 0.7637 (mttp) REVERT: C 349 ARG cc_start: 0.7584 (mtm180) cc_final: 0.6154 (mtt-85) REVERT: C 359 ASN cc_start: 0.8757 (t0) cc_final: 0.8135 (t0) REVERT: C 369 LYS cc_start: 0.8243 (mttt) cc_final: 0.7646 (mtpp) REVERT: C 372 GLU cc_start: 0.8238 (tt0) cc_final: 0.7986 (tt0) REVERT: D 311 LYS cc_start: 0.8346 (tttt) cc_final: 0.7827 (ttpt) REVERT: D 314 ASP cc_start: 0.8424 (t0) cc_final: 0.7998 (t0) REVERT: D 331 LYS cc_start: 0.8168 (mttt) cc_final: 0.7905 (mtpp) REVERT: D 340 LYS cc_start: 0.8401 (mttt) cc_final: 0.8101 (mtpp) REVERT: D 374 HIS cc_start: 0.7409 (OUTLIER) cc_final: 0.7153 (p90) REVERT: D 375 LYS cc_start: 0.8225 (pttt) cc_final: 0.7519 (ptpp) REVERT: D 379 ARG cc_start: 0.6725 (mtt-85) cc_final: 0.6096 (mmt180) REVERT: E 317 LYS cc_start: 0.7838 (mtmt) cc_final: 0.6944 (ptmt) REVERT: E 321 LYS cc_start: 0.7937 (mttt) cc_final: 0.7507 (mttm) REVERT: E 347 LYS cc_start: 0.8914 (mttp) cc_final: 0.8618 (mtmm) REVERT: E 369 LYS cc_start: 0.7695 (mttt) cc_final: 0.7037 (mtpp) REVERT: F 311 LYS cc_start: 0.8185 (tttt) cc_final: 0.7458 (tptt) REVERT: F 331 LYS cc_start: 0.8510 (mttt) cc_final: 0.8170 (mtpp) REVERT: F 353 LYS cc_start: 0.8291 (tttt) cc_final: 0.7999 (tttt) outliers start: 6 outliers final: 5 residues processed: 98 average time/residue: 0.6451 time to fit residues: 72.2690 Evaluate side-chains 99 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 327 ASN ** 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 = 0.4152 r_free = 0.4152 target = 0.148928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.132132 restraints weight = 12881.074| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 2.15 r_work: 0.3862 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3775 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.5413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3561 Z= 0.182 Angle : 0.477 5.155 4761 Z= 0.244 Chirality : 0.050 0.128 531 Planarity : 0.004 0.057 609 Dihedral : 4.493 18.249 474 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.01 % Allowed : 15.04 % Favored : 82.96 % 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: -1.30 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.98 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 374 PHE 0.006 0.001 PHE B 378 TYR 0.008 0.002 TYR E 310 ARG 0.002 0.000 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3128.06 seconds wall clock time: 55 minutes 40.99 seconds (3340.99 seconds total)