Starting phenix.real_space_refine on Sat Aug 3 06:21:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9a_18273/08_2024/8q9a_18273.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9a_18273/08_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_18273/08_2024/8q9a_18273.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9a_18273/08_2024/8q9a_18273.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9a_18273/08_2024/8q9a_18273.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9a_18273/08_2024/8q9a_18273.cif" } 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-5409/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: 7.94, per 1000 atoms: 1.11 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: 5.16 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.77 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: 2.23 Time building geometry restraints manager: 5.42 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 2.450 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.559 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.591 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.600 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.621 2.450 ... (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 Time spend for trying shortcut: 0.00 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: 3.610 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 29.660 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.520 ------------------------------------------------------------------------------- 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 : 0.592 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: 0.6115 time to fit residues: 94.0264 Evaluate side-chains 97 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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: 1.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS A 368 ASN B 327 ASN C 362 HIS C 368 ASN D 307 GLN D 327 ASN E 362 HIS F 327 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3561 Z= 0.191 Angle : 0.563 5.093 4761 Z= 0.304 Chirality : 0.052 0.130 531 Planarity : 0.003 0.031 609 Dihedral : 5.760 18.995 474 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.26 % Allowed : 7.27 % Favored : 90.48 % 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: -1.50 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.13 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 374 PHE 0.013 0.001 PHE B 378 TYR 0.010 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 113 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 104 time to evaluate : 0.730 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 321 LYS cc_start: 0.7784 (mttt) cc_final: 0.7187 (mttm) REVERT: A 369 LYS cc_start: 0.7795 (mttt) cc_final: 0.7000 (mtpp) REVERT: B 307 GLN cc_start: 0.7653 (mt0) cc_final: 0.7278 (tt0) REVERT: B 331 LYS cc_start: 0.8248 (mttt) cc_final: 0.7860 (mtpp) REVERT: B 343 LYS cc_start: 0.8793 (mttt) cc_final: 0.8512 (mtpp) REVERT: B 375 LYS cc_start: 0.7722 (pttt) cc_final: 0.7459 (ptmt) REVERT: C 321 LYS cc_start: 0.8195 (mttt) cc_final: 0.7680 (mttp) REVERT: C 340 LYS cc_start: 0.8410 (mttt) cc_final: 0.8182 (mttp) REVERT: C 359 ASN cc_start: 0.8600 (t0) cc_final: 0.8047 (t0) REVERT: C 369 LYS cc_start: 0.8288 (mttt) cc_final: 0.7617 (mtpp) REVERT: C 372 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7501 (mt-10) REVERT: D 307 GLN cc_start: 0.8178 (tt0) cc_final: 0.7609 (tm-30) REVERT: D 311 LYS cc_start: 0.8302 (tttt) cc_final: 0.7819 (ttpt) REVERT: D 314 ASP cc_start: 0.8369 (t0) cc_final: 0.8102 (t0) REVERT: D 331 LYS cc_start: 0.8295 (mttt) cc_final: 0.7878 (mmmt) REVERT: D 340 LYS cc_start: 0.8328 (mttt) cc_final: 0.7982 (mtpp) REVERT: D 375 LYS cc_start: 0.8300 (pttt) cc_final: 0.7753 (ptpp) REVERT: D 379 ARG cc_start: 0.6521 (mtt-85) cc_final: 0.5823 (mmp-170) REVERT: E 317 LYS cc_start: 0.7814 (mtmt) cc_final: 0.7125 (ptmt) REVERT: E 321 LYS cc_start: 0.7993 (mttt) cc_final: 0.7448 (mttm) REVERT: E 338 GLU cc_start: 0.7712 (tt0) cc_final: 0.7213 (mt-10) REVERT: E 343 LYS cc_start: 0.9138 (mttt) cc_final: 0.8837 (mttm) REVERT: E 349 ARG cc_start: 0.6924 (mtm180) cc_final: 0.6038 (mmp-170) REVERT: E 356 SER cc_start: 0.7966 (p) cc_final: 0.7447 (t) REVERT: E 369 LYS cc_start: 0.7802 (mttt) cc_final: 0.7213 (mtpp) REVERT: F 307 GLN cc_start: 0.7760 (mt0) cc_final: 0.7300 (tt0) REVERT: F 311 LYS cc_start: 0.8182 (tttt) cc_final: 0.7316 (mmtm) REVERT: F 331 LYS cc_start: 0.8426 (mttt) cc_final: 0.7478 (mmtt) REVERT: F 356 SER cc_start: 0.7404 (p) cc_final: 0.6682 (t) outliers start: 9 outliers final: 7 residues processed: 113 average time/residue: 0.6149 time to fit residues: 78.8982 Evaluate side-chains 97 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 0.1980 chunk 19 optimal weight: 5.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- 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: 0.7812 moved from start: 0.4322 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= 0.183 Angle : 0.518 5.026 4761 Z= 0.275 Chirality : 0.052 0.133 531 Planarity : 0.003 0.037 609 Dihedral : 5.061 17.871 474 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.26 % Allowed : 8.77 % Favored : 88.97 % 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 0.004 0.001 HIS B 374 PHE 0.009 0.001 PHE B 346 TYR 0.010 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 104 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 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: A 321 LYS cc_start: 0.7908 (mttt) cc_final: 0.7300 (mttm) REVERT: A 369 LYS cc_start: 0.7761 (mttt) cc_final: 0.7078 (mtpp) REVERT: B 307 GLN cc_start: 0.7727 (mt0) cc_final: 0.7382 (tt0) REVERT: B 331 LYS cc_start: 0.8223 (mttt) cc_final: 0.7838 (mtpp) REVERT: B 375 LYS cc_start: 0.7800 (pttt) cc_final: 0.7305 (ptpp) REVERT: C 321 LYS cc_start: 0.8202 (mttt) cc_final: 0.7661 (mttp) REVERT: C 340 LYS cc_start: 0.8509 (mttt) cc_final: 0.8261 (mttp) REVERT: C 359 ASN cc_start: 0.8647 (t0) cc_final: 0.8061 (t0) REVERT: C 369 LYS cc_start: 0.8240 (mttt) cc_final: 0.7625 (mtpp) REVERT: C 372 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7555 (mt-10) REVERT: D 311 LYS cc_start: 0.8334 (tttt) cc_final: 0.7823 (ttpt) REVERT: D 314 ASP cc_start: 0.8530 (t0) cc_final: 0.8194 (t0) REVERT: D 331 LYS cc_start: 0.8345 (mttt) cc_final: 0.7873 (mmmt) REVERT: D 340 LYS cc_start: 0.8320 (mttt) cc_final: 0.7970 (mtpp) REVERT: D 375 LYS cc_start: 0.8309 (pttt) cc_final: 0.7664 (ptpp) REVERT: D 379 ARG cc_start: 0.6419 (mtt-85) cc_final: 0.5734 (mmp-170) REVERT: E 317 LYS cc_start: 0.7910 (mtmt) cc_final: 0.7203 (ptmt) REVERT: E 321 LYS cc_start: 0.8081 (mttt) cc_final: 0.7580 (mttm) REVERT: E 343 LYS cc_start: 0.9180 (mttt) cc_final: 0.8974 (mttm) REVERT: E 356 SER cc_start: 0.7826 (p) cc_final: 0.7381 (t) REVERT: E 369 LYS cc_start: 0.7794 (mttt) cc_final: 0.7137 (mtpp) REVERT: F 307 GLN cc_start: 0.7788 (mt0) cc_final: 0.7369 (tt0) REVERT: F 311 LYS cc_start: 0.8073 (tttt) cc_final: 0.7261 (mmtm) REVERT: F 331 LYS cc_start: 0.8444 (mttt) cc_final: 0.7480 (mmtt) REVERT: F 356 SER cc_start: 0.7364 (p) cc_final: 0.6621 (t) outliers start: 9 outliers final: 6 residues processed: 104 average time/residue: 0.6671 time to fit residues: 77.2088 Evaluate side-chains 94 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 25 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN D 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 3561 Z= 0.402 Angle : 0.590 5.264 4761 Z= 0.316 Chirality : 0.052 0.133 531 Planarity : 0.004 0.038 609 Dihedral : 5.506 17.711 474 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.51 % Allowed : 9.77 % Favored : 87.72 % 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 (0.34), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 374 PHE 0.011 0.002 PHE F 346 TYR 0.017 0.004 TYR D 310 ARG 0.003 0.000 ARG D 379 *********************** 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 95 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7873 (mttt) cc_final: 0.7235 (mttp) REVERT: A 369 LYS cc_start: 0.7703 (mttt) cc_final: 0.7028 (mtpp) REVERT: B 307 GLN cc_start: 0.7807 (mt0) cc_final: 0.7388 (tt0) REVERT: B 331 LYS cc_start: 0.8208 (mttt) cc_final: 0.7880 (mtpp) REVERT: B 353 LYS cc_start: 0.8152 (tttt) cc_final: 0.7851 (tttt) REVERT: B 375 LYS cc_start: 0.7758 (pttt) cc_final: 0.7319 (ptpp) REVERT: C 321 LYS cc_start: 0.8241 (mttt) cc_final: 0.7659 (mttp) REVERT: C 340 LYS cc_start: 0.8515 (mttt) cc_final: 0.8296 (mttp) REVERT: C 369 LYS cc_start: 0.8276 (mttt) cc_final: 0.7666 (mtpp) REVERT: C 372 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7670 (mt-10) REVERT: D 311 LYS cc_start: 0.8389 (tttt) cc_final: 0.7839 (ttpt) REVERT: D 331 LYS cc_start: 0.8298 (mttt) cc_final: 0.7998 (mtpp) REVERT: D 340 LYS cc_start: 0.8368 (mttt) cc_final: 0.8024 (mtpp) REVERT: D 375 LYS cc_start: 0.8263 (pttt) cc_final: 0.7586 (ptpp) REVERT: D 379 ARG cc_start: 0.6638 (mtt-85) cc_final: 0.6048 (mmt180) REVERT: E 321 LYS cc_start: 0.8002 (mttt) cc_final: 0.7528 (mttm) REVERT: E 343 LYS cc_start: 0.9175 (mttt) cc_final: 0.8895 (mttm) REVERT: E 356 SER cc_start: 0.7747 (p) cc_final: 0.7163 (t) REVERT: E 369 LYS cc_start: 0.7722 (mttt) cc_final: 0.7051 (mtpp) REVERT: F 311 LYS cc_start: 0.8063 (tttt) cc_final: 0.7217 (mmtm) REVERT: F 331 LYS cc_start: 0.8552 (mttt) cc_final: 0.7577 (mmtt) REVERT: F 353 LYS cc_start: 0.8263 (tttt) cc_final: 0.8006 (tttt) REVERT: F 375 LYS cc_start: 0.7920 (pttt) cc_final: 0.7249 (ptpt) outliers start: 10 outliers final: 6 residues processed: 93 average time/residue: 0.6475 time to fit residues: 67.2223 Evaluate side-chains 89 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 341 SER Chi-restraints excluded: chain D residue 369 LYS 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: 2.9990 chunk 16 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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: 0.7855 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3561 Z= 0.245 Angle : 0.511 4.657 4761 Z= 0.266 Chirality : 0.051 0.129 531 Planarity : 0.003 0.041 609 Dihedral : 5.122 17.604 474 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.50 % Allowed : 11.78 % Favored : 86.72 % 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: -1.52 (0.34), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 374 PHE 0.006 0.001 PHE B 378 TYR 0.008 0.002 TYR C 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 94 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 0.555 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: 0.7942 (mttt) cc_final: 0.7321 (mttp) REVERT: A 369 LYS cc_start: 0.7702 (mttt) cc_final: 0.7108 (mtpp) REVERT: B 307 GLN cc_start: 0.7842 (mt0) cc_final: 0.7373 (tt0) REVERT: B 331 LYS cc_start: 0.8206 (mttt) cc_final: 0.7875 (mtpp) REVERT: B 375 LYS cc_start: 0.7823 (pttt) cc_final: 0.7606 (ptmm) REVERT: C 321 LYS cc_start: 0.8194 (mttt) cc_final: 0.7597 (mttp) REVERT: C 340 LYS cc_start: 0.8554 (mttt) cc_final: 0.8329 (mttp) REVERT: C 369 LYS cc_start: 0.8267 (mttt) cc_final: 0.7659 (mtpp) REVERT: C 372 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7658 (mt-10) REVERT: D 311 LYS cc_start: 0.8380 (tttt) cc_final: 0.7828 (ttpt) REVERT: D 331 LYS cc_start: 0.8302 (mttt) cc_final: 0.7999 (mtpp) REVERT: D 340 LYS cc_start: 0.8351 (mttt) cc_final: 0.7992 (mtpp) REVERT: D 375 LYS cc_start: 0.8287 (pttt) cc_final: 0.7564 (ptpp) REVERT: D 379 ARG cc_start: 0.6537 (mtt-85) cc_final: 0.6066 (mmp-170) REVERT: E 317 LYS cc_start: 0.7875 (mtmt) cc_final: 0.6851 (ptmt) REVERT: E 321 LYS cc_start: 0.8043 (mttt) cc_final: 0.7566 (mttp) REVERT: E 343 LYS cc_start: 0.9169 (mttt) cc_final: 0.8908 (mttm) REVERT: E 356 SER cc_start: 0.7805 (p) cc_final: 0.7308 (t) REVERT: E 369 LYS cc_start: 0.7738 (mttt) cc_final: 0.7121 (mtpp) REVERT: F 311 LYS cc_start: 0.7996 (tttt) cc_final: 0.7242 (mmtt) REVERT: F 331 LYS cc_start: 0.8562 (mttt) cc_final: 0.7578 (mmtt) REVERT: F 353 LYS cc_start: 0.8342 (tttt) cc_final: 0.8087 (tttt) outliers start: 6 outliers final: 5 residues processed: 92 average time/residue: 0.6527 time to fit residues: 67.0178 Evaluate side-chains 91 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain D residue 319 THR 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: 4.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.5071 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= 0.191 Angle : 0.486 4.718 4761 Z= 0.252 Chirality : 0.051 0.130 531 Planarity : 0.003 0.041 609 Dihedral : 4.845 17.554 474 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.26 % Allowed : 11.78 % Favored : 85.96 % 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: -1.50 (0.34), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.13 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 374 PHE 0.005 0.001 PHE F 346 TYR 0.008 0.002 TYR C 310 ARG 0.001 0.000 ARG D 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 96 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 0.610 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: A 321 LYS cc_start: 0.7894 (mttt) cc_final: 0.7284 (mttp) REVERT: A 353 LYS cc_start: 0.8344 (ttpp) cc_final: 0.7948 (tttm) REVERT: A 369 LYS cc_start: 0.7796 (mttt) cc_final: 0.7188 (mtpp) REVERT: B 307 GLN cc_start: 0.7833 (mt0) cc_final: 0.7398 (tt0) REVERT: B 331 LYS cc_start: 0.8221 (mttt) cc_final: 0.7886 (mtpp) REVERT: B 375 LYS cc_start: 0.7801 (pttt) cc_final: 0.7585 (ptmm) REVERT: C 321 LYS cc_start: 0.8201 (mttt) cc_final: 0.7607 (mttp) REVERT: C 340 LYS cc_start: 0.8530 (mttt) cc_final: 0.8309 (mttp) REVERT: C 349 ARG cc_start: 0.7756 (mtm180) cc_final: 0.6108 (mtt-85) REVERT: C 359 ASN cc_start: 0.8878 (t0) cc_final: 0.8265 (t0) REVERT: C 369 LYS cc_start: 0.8263 (mttt) cc_final: 0.7649 (mtpp) REVERT: C 372 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7666 (mt-10) REVERT: D 311 LYS cc_start: 0.8349 (tttt) cc_final: 0.7807 (ttpt) REVERT: D 331 LYS cc_start: 0.8323 (mttt) cc_final: 0.8038 (mtpp) REVERT: D 340 LYS cc_start: 0.8356 (mttt) cc_final: 0.7996 (mtpp) REVERT: D 375 LYS cc_start: 0.8250 (pttt) cc_final: 0.7513 (ptpp) REVERT: D 379 ARG cc_start: 0.6490 (mtt-85) cc_final: 0.5993 (mmp-170) REVERT: E 317 LYS cc_start: 0.7868 (mtmt) cc_final: 0.6883 (ptmt) REVERT: E 321 LYS cc_start: 0.8003 (mttt) cc_final: 0.7526 (mttm) REVERT: E 343 LYS cc_start: 0.9152 (mttt) cc_final: 0.8909 (mttm) REVERT: E 356 SER cc_start: 0.7918 (p) cc_final: 0.7455 (t) REVERT: E 369 LYS cc_start: 0.7758 (mttt) cc_final: 0.7154 (mtpp) REVERT: F 311 LYS cc_start: 0.8019 (tttt) cc_final: 0.7235 (mmtt) REVERT: F 331 LYS cc_start: 0.8565 (mttt) cc_final: 0.7579 (mmtt) REVERT: F 356 SER cc_start: 0.7328 (p) cc_final: 0.6610 (t) REVERT: F 375 LYS cc_start: 0.7916 (ptmt) cc_final: 0.7302 (ptpp) outliers start: 9 outliers final: 6 residues processed: 92 average time/residue: 0.6797 time to fit residues: 69.9265 Evaluate side-chains 92 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 342 GLU 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: 8.9990 chunk 25 optimal weight: 0.0170 chunk 24 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.9424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3561 Z= 0.195 Angle : 0.481 4.807 4761 Z= 0.248 Chirality : 0.051 0.131 531 Planarity : 0.003 0.043 609 Dihedral : 4.735 17.627 474 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.26 % Allowed : 12.28 % Favored : 85.46 % 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 (0.34), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 374 PHE 0.005 0.001 PHE F 346 TYR 0.010 0.002 TYR C 310 ARG 0.002 0.000 ARG E 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 101 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.633 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: A 321 LYS cc_start: 0.7910 (mttt) cc_final: 0.7304 (mttp) REVERT: A 353 LYS cc_start: 0.8365 (ttpp) cc_final: 0.7969 (tttm) REVERT: A 369 LYS cc_start: 0.7781 (mttt) cc_final: 0.7187 (mtpp) REVERT: B 307 GLN cc_start: 0.7866 (mt0) cc_final: 0.7408 (tt0) REVERT: B 331 LYS cc_start: 0.8222 (mttt) cc_final: 0.7893 (mtpp) REVERT: B 375 LYS cc_start: 0.7769 (pttt) cc_final: 0.7301 (ptpp) REVERT: C 321 LYS cc_start: 0.8204 (mttt) cc_final: 0.7601 (mttp) REVERT: C 340 LYS cc_start: 0.8539 (mttt) cc_final: 0.8313 (mttp) REVERT: C 349 ARG cc_start: 0.7484 (mtm180) cc_final: 0.6047 (mtt-85) REVERT: C 359 ASN cc_start: 0.8843 (t0) cc_final: 0.8255 (t0) REVERT: C 369 LYS cc_start: 0.8264 (mttt) cc_final: 0.7648 (mtpp) REVERT: C 372 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7644 (mt-10) REVERT: D 311 LYS cc_start: 0.8342 (tttt) cc_final: 0.7768 (ttpt) REVERT: D 331 LYS cc_start: 0.8278 (mttt) cc_final: 0.7951 (mtpp) REVERT: D 340 LYS cc_start: 0.8339 (mttt) cc_final: 0.7968 (mtpp) REVERT: D 375 LYS cc_start: 0.8293 (pttt) cc_final: 0.7568 (ptpp) REVERT: D 379 ARG cc_start: 0.6469 (mtt-85) cc_final: 0.5992 (mmp-170) REVERT: E 317 LYS cc_start: 0.7871 (mtmt) cc_final: 0.6889 (ptmt) REVERT: E 321 LYS cc_start: 0.8023 (mttt) cc_final: 0.7561 (mttm) REVERT: E 343 LYS cc_start: 0.9177 (mttt) cc_final: 0.8915 (mttm) REVERT: E 356 SER cc_start: 0.7919 (p) cc_final: 0.7498 (t) REVERT: E 369 LYS cc_start: 0.7728 (mttt) cc_final: 0.7156 (mtpp) REVERT: F 311 LYS cc_start: 0.7982 (tttt) cc_final: 0.7166 (mmtt) REVERT: F 331 LYS cc_start: 0.8581 (mttt) cc_final: 0.7586 (mmtt) REVERT: F 356 SER cc_start: 0.7374 (p) cc_final: 0.6753 (t) REVERT: F 375 LYS cc_start: 0.7954 (ptmt) cc_final: 0.7308 (ptpp) outliers start: 9 outliers final: 7 residues processed: 99 average time/residue: 0.6401 time to fit residues: 70.6412 Evaluate side-chains 99 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 369 LYS 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: 4.9990 chunk 31 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 0.1980 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3561 Z= 0.235 Angle : 0.496 5.019 4761 Z= 0.258 Chirality : 0.051 0.130 531 Planarity : 0.003 0.042 609 Dihedral : 4.799 17.735 474 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.75 % Allowed : 12.78 % Favored : 85.46 % 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: -1.61 (0.34), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 374 PHE 0.005 0.001 PHE F 346 TYR 0.010 0.002 TYR C 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 97 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 0.579 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: 0.7914 (mttt) cc_final: 0.7309 (mttp) REVERT: A 353 LYS cc_start: 0.8373 (ttpp) cc_final: 0.7979 (tttm) REVERT: A 369 LYS cc_start: 0.7788 (mttt) cc_final: 0.7190 (mtpp) REVERT: B 307 GLN cc_start: 0.7866 (mt0) cc_final: 0.7390 (tt0) REVERT: B 311 LYS cc_start: 0.7817 (tttt) cc_final: 0.7545 (mttt) REVERT: B 331 LYS cc_start: 0.8218 (mttt) cc_final: 0.7885 (mtpp) REVERT: B 375 LYS cc_start: 0.7743 (pttt) cc_final: 0.7278 (ptpp) REVERT: C 321 LYS cc_start: 0.8212 (mttt) cc_final: 0.7602 (mttp) REVERT: C 340 LYS cc_start: 0.8545 (mttt) cc_final: 0.8315 (mttp) REVERT: C 349 ARG cc_start: 0.7501 (mtm180) cc_final: 0.6057 (mtt-85) REVERT: C 369 LYS cc_start: 0.8252 (mttt) cc_final: 0.7636 (mtpp) REVERT: C 372 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7660 (mt-10) REVERT: D 311 LYS cc_start: 0.8356 (tttt) cc_final: 0.7777 (ttpt) REVERT: D 331 LYS cc_start: 0.8281 (mttt) cc_final: 0.7936 (mtpp) REVERT: D 375 LYS cc_start: 0.8350 (pttt) cc_final: 0.7615 (ptpp) REVERT: D 379 ARG cc_start: 0.6524 (mtt-85) cc_final: 0.6023 (mmp-170) REVERT: E 321 LYS cc_start: 0.7981 (mttt) cc_final: 0.7544 (mttm) REVERT: E 343 LYS cc_start: 0.9171 (mttt) cc_final: 0.8898 (mttm) REVERT: E 356 SER cc_start: 0.7847 (p) cc_final: 0.7383 (t) REVERT: E 369 LYS cc_start: 0.7724 (mttt) cc_final: 0.7150 (mtpp) REVERT: F 311 LYS cc_start: 0.8050 (tttt) cc_final: 0.7127 (mmtm) REVERT: F 331 LYS cc_start: 0.8595 (mttt) cc_final: 0.7587 (mmtt) REVERT: F 356 SER cc_start: 0.7372 (p) cc_final: 0.6759 (t) REVERT: F 375 LYS cc_start: 0.7967 (ptmt) cc_final: 0.7381 (ptpp) outliers start: 7 outliers final: 6 residues processed: 95 average time/residue: 0.6625 time to fit residues: 70.4091 Evaluate side-chains 96 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain D residue 319 THR 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: 4.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3561 Z= 0.345 Angle : 0.544 5.038 4761 Z= 0.286 Chirality : 0.051 0.129 531 Planarity : 0.004 0.042 609 Dihedral : 5.099 18.022 474 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.01 % Allowed : 12.78 % 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: -1.69 (0.34), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 374 PHE 0.007 0.001 PHE F 346 TYR 0.013 0.003 TYR C 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 93 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7914 (mttt) cc_final: 0.7313 (mttp) REVERT: A 353 LYS cc_start: 0.8392 (ttpp) cc_final: 0.7989 (tttm) REVERT: A 369 LYS cc_start: 0.7795 (mttt) cc_final: 0.7179 (mtpp) REVERT: B 307 GLN cc_start: 0.7841 (mt0) cc_final: 0.7356 (tt0) REVERT: B 311 LYS cc_start: 0.7784 (tttt) cc_final: 0.7539 (mttt) REVERT: B 331 LYS cc_start: 0.8240 (mttt) cc_final: 0.7908 (mtpp) REVERT: B 353 LYS cc_start: 0.8156 (tttt) cc_final: 0.7844 (tttt) REVERT: B 375 LYS cc_start: 0.7716 (pttt) cc_final: 0.7239 (ptpp) REVERT: C 321 LYS cc_start: 0.8219 (mttt) cc_final: 0.7621 (mttp) REVERT: C 340 LYS cc_start: 0.8541 (mttt) cc_final: 0.8338 (mttp) REVERT: C 349 ARG cc_start: 0.7520 (mtm180) cc_final: 0.6065 (mtt-85) REVERT: C 369 LYS cc_start: 0.8255 (mttt) cc_final: 0.7623 (mtpp) REVERT: C 372 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7752 (mt-10) REVERT: D 311 LYS cc_start: 0.8351 (tttt) cc_final: 0.7796 (ttpt) REVERT: D 331 LYS cc_start: 0.8263 (mttt) cc_final: 0.7899 (mtpp) REVERT: D 375 LYS cc_start: 0.8330 (pttt) cc_final: 0.7588 (ptpp) REVERT: D 379 ARG cc_start: 0.6679 (mtt-85) cc_final: 0.6019 (mmt180) REVERT: E 321 LYS cc_start: 0.7972 (mttt) cc_final: 0.7527 (mttm) REVERT: E 343 LYS cc_start: 0.9146 (mttt) cc_final: 0.8867 (mttm) REVERT: E 356 SER cc_start: 0.7782 (p) cc_final: 0.7209 (t) REVERT: E 369 LYS cc_start: 0.7718 (mttt) cc_final: 0.7132 (mtpp) REVERT: F 311 LYS cc_start: 0.8088 (tttt) cc_final: 0.7163 (mmtm) REVERT: F 331 LYS cc_start: 0.8577 (mttt) cc_final: 0.8243 (mtpp) REVERT: F 353 LYS cc_start: 0.8297 (tttt) cc_final: 0.7995 (tttt) REVERT: F 375 LYS cc_start: 0.7989 (ptmt) cc_final: 0.7400 (ptpp) outliers start: 8 outliers final: 5 residues processed: 91 average time/residue: 0.6128 time to fit residues: 62.7413 Evaluate side-chains 92 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 26 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3561 Z= 0.157 Angle : 0.472 4.739 4761 Z= 0.243 Chirality : 0.051 0.128 531 Planarity : 0.004 0.046 609 Dihedral : 4.661 17.649 474 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.25 % Allowed : 14.29 % Favored : 84.46 % 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: -1.64 (0.34), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 374 PHE 0.004 0.001 PHE B 378 TYR 0.006 0.001 TYR C 310 ARG 0.001 0.000 ARG F 379 ********************** 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 95 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.654 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: 0.7916 (mttt) cc_final: 0.7298 (mttp) REVERT: A 353 LYS cc_start: 0.8380 (ttpp) cc_final: 0.7978 (tttm) REVERT: A 369 LYS cc_start: 0.7822 (mttt) cc_final: 0.7224 (mtpp) REVERT: B 307 GLN cc_start: 0.7845 (mt0) cc_final: 0.7375 (tt0) REVERT: B 311 LYS cc_start: 0.7720 (tttt) cc_final: 0.7387 (mttt) REVERT: B 331 LYS cc_start: 0.8242 (mttt) cc_final: 0.7909 (mtpp) REVERT: B 375 LYS cc_start: 0.7762 (pttt) cc_final: 0.7317 (ptpp) REVERT: C 321 LYS cc_start: 0.8180 (mttt) cc_final: 0.7546 (mttp) REVERT: C 340 LYS cc_start: 0.8545 (mttt) cc_final: 0.8311 (mttp) REVERT: C 349 ARG cc_start: 0.7493 (mtm180) cc_final: 0.6050 (mtt-85) REVERT: C 359 ASN cc_start: 0.8821 (t0) cc_final: 0.8215 (t0) REVERT: C 369 LYS cc_start: 0.8245 (mttt) cc_final: 0.7656 (mtpp) REVERT: C 372 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7673 (mt-10) REVERT: D 311 LYS cc_start: 0.8329 (tttt) cc_final: 0.7721 (ttpt) REVERT: D 331 LYS cc_start: 0.8295 (mttt) cc_final: 0.7957 (mtpp) REVERT: D 340 LYS cc_start: 0.8335 (mttt) cc_final: 0.7933 (mtpp) REVERT: D 375 LYS cc_start: 0.8361 (pttt) cc_final: 0.7633 (ptpp) REVERT: D 379 ARG cc_start: 0.6498 (mtt-85) cc_final: 0.6018 (mmp-170) REVERT: E 321 LYS cc_start: 0.7979 (mttt) cc_final: 0.7524 (mttm) REVERT: E 343 LYS cc_start: 0.9146 (mttt) cc_final: 0.8791 (mttm) REVERT: E 356 SER cc_start: 0.7877 (p) cc_final: 0.7434 (t) REVERT: E 369 LYS cc_start: 0.7744 (mttt) cc_final: 0.7162 (mtpp) REVERT: F 311 LYS cc_start: 0.8065 (tttt) cc_final: 0.7030 (mmtm) REVERT: F 331 LYS cc_start: 0.8615 (mttt) cc_final: 0.7615 (mmtt) REVERT: F 356 SER cc_start: 0.7413 (p) cc_final: 0.6819 (t) REVERT: F 375 LYS cc_start: 0.7952 (ptmt) cc_final: 0.7368 (ptpp) outliers start: 5 outliers final: 5 residues processed: 94 average time/residue: 0.6792 time to fit residues: 71.3055 Evaluate side-chains 94 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.147783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.130601 restraints weight = 13370.106| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.25 r_work: 0.3887 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3796 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.5401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3561 Z= 0.183 Angle : 0.482 5.833 4761 Z= 0.247 Chirality : 0.050 0.128 531 Planarity : 0.004 0.047 609 Dihedral : 4.622 17.727 474 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.25 % Allowed : 14.29 % Favored : 84.46 % 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: -1.62 (0.34), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 374 PHE 0.004 0.001 PHE F 346 TYR 0.008 0.002 TYR C 310 ARG 0.001 0.000 ARG D 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3158.55 seconds wall clock time: 55 minutes 54.29 seconds (3354.29 seconds total)