Starting phenix.real_space_refine on Wed Feb 12 04:27:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q9a_18273/02_2025/8q9a_18273.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q9a_18273/02_2025/8q9a_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/cci-nas-00/data/ceres_data/8q9a_18273/02_2025/8q9a_18273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q9a_18273/02_2025/8q9a_18273.map" model { file = "/net/cci-nas-00/data/ceres_data/8q9a_18273/02_2025/8q9a_18273.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q9a_18273/02_2025/8q9a_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. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.25, per 1000 atoms: 0.74 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 709.7 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: 0.78 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: 2.45 Time building geometry restraints manager: 2.07 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: 0.00 - 2.59: 11168 2.59 - 5.17: 1494 5.17 - 7.76: 419 7.76 - 10.35: 14 10.35 - 12.94: 6 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: 2.380 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: 0.120 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.330 Find NCS groups from input model: 0.240 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.470 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 3 poor density : 136 time to evaluate : 0.613 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: 0.6315 time to fit residues: 96.6945 Evaluate side-chains 97 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.147182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.129199 restraints weight = 13281.266| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 2.25 r_work: 0.3969 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3883 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 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 to be fit. rotamer outliers: 9 poor density : 104 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: A 321 LYS cc_start: 0.8573 (mttt) cc_final: 0.8150 (mttm) REVERT: A 369 LYS cc_start: 0.8561 (mttt) cc_final: 0.8052 (mtpp) REVERT: B 307 GLN cc_start: 0.7994 (mt0) cc_final: 0.7531 (tt0) REVERT: B 331 LYS cc_start: 0.8402 (mttt) cc_final: 0.7999 (mtpp) REVERT: B 343 LYS cc_start: 0.9068 (mttt) cc_final: 0.8821 (mtpp) REVERT: C 321 LYS cc_start: 0.8570 (mttt) cc_final: 0.8180 (mttp) REVERT: C 369 LYS cc_start: 0.8668 (mttt) cc_final: 0.8293 (mtpp) REVERT: C 372 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7810 (mt-10) REVERT: D 307 GLN cc_start: 0.8315 (tt0) cc_final: 0.7774 (tm-30) REVERT: D 311 LYS cc_start: 0.8640 (tttt) cc_final: 0.8256 (ttpt) REVERT: D 331 LYS cc_start: 0.8469 (mttt) cc_final: 0.8018 (mmmt) REVERT: D 340 LYS cc_start: 0.8585 (mttt) cc_final: 0.8285 (mtpp) REVERT: D 375 LYS cc_start: 0.8566 (pttt) cc_final: 0.8160 (ptpp) REVERT: D 379 ARG cc_start: 0.7121 (mtt-85) cc_final: 0.5899 (mmp-170) REVERT: E 317 LYS cc_start: 0.8231 (mtmt) cc_final: 0.7697 (ptmt) REVERT: E 321 LYS cc_start: 0.8693 (mttt) cc_final: 0.8310 (mttm) REVERT: E 338 GLU cc_start: 0.8226 (tt0) cc_final: 0.7805 (mt-10) REVERT: E 343 LYS cc_start: 0.9136 (mttt) cc_final: 0.8858 (mttm) REVERT: E 349 ARG cc_start: 0.7180 (mtm180) cc_final: 0.6213 (mmp-170) REVERT: E 356 SER cc_start: 0.8327 (p) cc_final: 0.8005 (t) REVERT: E 369 LYS cc_start: 0.8514 (mttt) cc_final: 0.8158 (mtpp) REVERT: F 307 GLN cc_start: 0.8056 (mt0) cc_final: 0.7515 (tt0) REVERT: F 311 LYS cc_start: 0.8550 (tttt) cc_final: 0.7800 (mmtm) REVERT: F 331 LYS cc_start: 0.8511 (mttt) cc_final: 0.7552 (mmtt) REVERT: F 356 SER cc_start: 0.7513 (p) cc_final: 0.6817 (t) outliers start: 9 outliers final: 7 residues processed: 113 average time/residue: 0.6150 time to fit residues: 77.3892 Evaluate side-chains 94 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 34 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.142876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.124411 restraints weight = 13610.794| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.39 r_work: 0.3940 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3852 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3561 Z= 0.194 Angle : 0.526 4.956 4761 Z= 0.280 Chirality : 0.052 0.133 531 Planarity : 0.003 0.036 609 Dihedral : 5.114 17.882 474 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.01 % Allowed : 9.27 % Favored : 88.72 % 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: -1.43 (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 0.009 0.001 PHE B 346 TYR 0.010 0.002 TYR D 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 102 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.604 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: 0.8658 (mttt) cc_final: 0.8227 (mttm) REVERT: A 369 LYS cc_start: 0.8535 (mttt) cc_final: 0.8095 (mtpp) REVERT: B 307 GLN cc_start: 0.8095 (mt0) cc_final: 0.7665 (tt0) REVERT: B 331 LYS cc_start: 0.8337 (mttt) cc_final: 0.7929 (mtpp) REVERT: B 375 LYS cc_start: 0.8394 (ptmt) cc_final: 0.7885 (ptpp) REVERT: C 321 LYS cc_start: 0.8607 (mttt) cc_final: 0.8192 (mttp) REVERT: C 369 LYS cc_start: 0.8683 (mttt) cc_final: 0.8322 (mtpp) REVERT: C 372 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7877 (mt-10) REVERT: D 311 LYS cc_start: 0.8664 (tttt) cc_final: 0.8270 (ttpt) REVERT: D 331 LYS cc_start: 0.8510 (mttt) cc_final: 0.7997 (mmmt) REVERT: D 340 LYS cc_start: 0.8607 (mttt) cc_final: 0.8306 (mtpp) REVERT: D 375 LYS cc_start: 0.8565 (pttt) cc_final: 0.8071 (ptpp) REVERT: D 379 ARG cc_start: 0.7050 (mtt-85) cc_final: 0.5829 (mmp-170) REVERT: E 317 LYS cc_start: 0.8289 (mtmt) cc_final: 0.7721 (ptmt) REVERT: E 321 LYS cc_start: 0.8788 (mttt) cc_final: 0.8422 (mttm) REVERT: E 356 SER cc_start: 0.8079 (p) cc_final: 0.7822 (t) REVERT: E 369 LYS cc_start: 0.8564 (mttt) cc_final: 0.8135 (mtpp) REVERT: F 311 LYS cc_start: 0.8472 (tttt) cc_final: 0.7754 (mmtm) REVERT: F 331 LYS cc_start: 0.8527 (mttt) cc_final: 0.7551 (mmtt) REVERT: F 356 SER cc_start: 0.7426 (p) cc_final: 0.6675 (t) outliers start: 8 outliers final: 5 residues processed: 102 average time/residue: 0.7021 time to fit residues: 79.2043 Evaluate side-chains 92 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 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 28 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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 = 0.4222 r_free = 0.4222 target = 0.154622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.137630 restraints weight = 12899.519| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.16 r_work: 0.3926 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3835 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3561 Z= 0.192 Angle : 0.488 4.139 4761 Z= 0.257 Chirality : 0.051 0.131 531 Planarity : 0.003 0.041 609 Dihedral : 4.918 17.228 474 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.26 % Allowed : 9.77 % Favored : 87.97 % 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 (0.34), 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 0.002 0.001 HIS D 374 PHE 0.007 0.001 PHE F 346 TYR 0.010 0.002 TYR D 310 ARG 0.002 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 98 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.609 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: 0.8713 (mttt) cc_final: 0.8250 (mttp) REVERT: A 369 LYS cc_start: 0.8524 (mttt) cc_final: 0.8168 (mtpp) REVERT: B 307 GLN cc_start: 0.8157 (mt0) cc_final: 0.7611 (tt0) REVERT: B 331 LYS cc_start: 0.8428 (mttt) cc_final: 0.8009 (mtpp) REVERT: B 375 LYS cc_start: 0.8365 (ptmt) cc_final: 0.7808 (ptpp) REVERT: C 321 LYS cc_start: 0.8651 (mttt) cc_final: 0.8226 (mttp) REVERT: C 369 LYS cc_start: 0.8768 (mttt) cc_final: 0.8429 (mtpp) REVERT: D 311 LYS cc_start: 0.8702 (tttt) cc_final: 0.8321 (ttpt) REVERT: D 331 LYS cc_start: 0.8572 (mttt) cc_final: 0.8091 (mmmt) REVERT: D 340 LYS cc_start: 0.8618 (mttt) cc_final: 0.8298 (mtpp) REVERT: D 375 LYS cc_start: 0.8550 (pttt) cc_final: 0.8016 (ptpp) REVERT: D 379 ARG cc_start: 0.7074 (mtt-85) cc_final: 0.5941 (mmp-170) REVERT: E 317 LYS cc_start: 0.8386 (mtmt) cc_final: 0.7670 (ptmt) REVERT: E 321 LYS cc_start: 0.8815 (mttt) cc_final: 0.8480 (mttp) REVERT: E 369 LYS cc_start: 0.8570 (mttt) cc_final: 0.8196 (mtpp) REVERT: F 311 LYS cc_start: 0.8406 (tttt) cc_final: 0.7834 (mmtt) REVERT: F 331 LYS cc_start: 0.8575 (mttt) cc_final: 0.7611 (mmtt) REVERT: F 356 SER cc_start: 0.7533 (p) cc_final: 0.6855 (t) REVERT: F 375 LYS cc_start: 0.8278 (pttt) cc_final: 0.7799 (ptpt) outliers start: 9 outliers final: 5 residues processed: 96 average time/residue: 0.6618 time to fit residues: 70.5274 Evaluate side-chains 91 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 30 optimal weight: 0.0470 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.158172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.141093 restraints weight = 12691.722| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 2.16 r_work: 0.3961 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3868 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.5080 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= 0.132 Angle : 0.458 4.366 4761 Z= 0.237 Chirality : 0.051 0.130 531 Planarity : 0.003 0.041 609 Dihedral : 4.588 16.697 474 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.75 % Allowed : 10.78 % Favored : 87.47 % 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: -1.37 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.03 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 374 PHE 0.004 0.001 PHE B 346 TYR 0.007 0.001 TYR C 310 ARG 0.003 0.000 ARG B 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 96 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.714 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: 0.8747 (mttt) cc_final: 0.8292 (mttp) REVERT: A 369 LYS cc_start: 0.8541 (mttt) cc_final: 0.8213 (mtpp) REVERT: B 307 GLN cc_start: 0.8178 (mt0) cc_final: 0.7649 (tt0) REVERT: B 331 LYS cc_start: 0.8435 (mttt) cc_final: 0.8011 (mtpp) REVERT: B 375 LYS cc_start: 0.8382 (ptmt) cc_final: 0.7907 (ptpp) REVERT: C 321 LYS cc_start: 0.8638 (mttt) cc_final: 0.8199 (mttp) REVERT: C 369 LYS cc_start: 0.8755 (mttt) cc_final: 0.8437 (mtpp) REVERT: D 311 LYS cc_start: 0.8597 (tttt) cc_final: 0.8187 (ttpt) REVERT: D 331 LYS cc_start: 0.8541 (mttt) cc_final: 0.8074 (mmmt) REVERT: D 340 LYS cc_start: 0.8633 (mttt) cc_final: 0.8324 (mtpp) REVERT: D 375 LYS cc_start: 0.8567 (pttt) cc_final: 0.7970 (ptpp) REVERT: D 379 ARG cc_start: 0.7003 (mtt-85) cc_final: 0.5841 (mmp-170) REVERT: E 317 LYS cc_start: 0.8405 (mtmt) cc_final: 0.7785 (ptmt) REVERT: E 321 LYS cc_start: 0.8812 (mttt) cc_final: 0.8487 (mttm) REVERT: E 369 LYS cc_start: 0.8558 (mttt) cc_final: 0.8211 (mtpp) REVERT: F 311 LYS cc_start: 0.8369 (tttt) cc_final: 0.7783 (mmtt) REVERT: F 331 LYS cc_start: 0.8528 (mttt) cc_final: 0.7557 (mmtt) REVERT: F 356 SER cc_start: 0.7537 (p) cc_final: 0.6987 (t) outliers start: 7 outliers final: 5 residues processed: 92 average time/residue: 0.6596 time to fit residues: 67.4892 Evaluate side-chains 90 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 7 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.155571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.138703 restraints weight = 12877.023| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 2.16 r_work: 0.3937 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3845 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.5199 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= 0.172 Angle : 0.467 4.571 4761 Z= 0.241 Chirality : 0.051 0.130 531 Planarity : 0.003 0.040 609 Dihedral : 4.563 16.494 474 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.01 % Allowed : 11.03 % 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: -1.40 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.06 (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 0.007 0.002 TYR E 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 96 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.611 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: 0.8731 (mttt) cc_final: 0.8282 (mttp) REVERT: A 369 LYS cc_start: 0.8558 (mttt) cc_final: 0.8226 (mtpp) REVERT: B 307 GLN cc_start: 0.8214 (mt0) cc_final: 0.7658 (tt0) REVERT: B 331 LYS cc_start: 0.8425 (mttt) cc_final: 0.7998 (mtpp) REVERT: B 375 LYS cc_start: 0.8385 (ptmt) cc_final: 0.7885 (ptpp) REVERT: C 321 LYS cc_start: 0.8656 (mttt) cc_final: 0.8203 (mttp) REVERT: C 369 LYS cc_start: 0.8770 (mttt) cc_final: 0.8457 (mtpp) REVERT: D 311 LYS cc_start: 0.8595 (tttt) cc_final: 0.8216 (ttpt) REVERT: D 331 LYS cc_start: 0.8562 (mttt) cc_final: 0.8076 (mmmt) REVERT: D 340 LYS cc_start: 0.8649 (mttt) cc_final: 0.8312 (mtpp) REVERT: D 375 LYS cc_start: 0.8549 (pttt) cc_final: 0.7946 (ptpp) REVERT: D 379 ARG cc_start: 0.7015 (mtt-85) cc_final: 0.6062 (mmp-170) REVERT: E 317 LYS cc_start: 0.8457 (mtmt) cc_final: 0.7788 (ptmt) REVERT: E 321 LYS cc_start: 0.8827 (mttt) cc_final: 0.8517 (mttm) REVERT: E 369 LYS cc_start: 0.8553 (mttt) cc_final: 0.8211 (mtpp) REVERT: F 311 LYS cc_start: 0.8331 (tttt) cc_final: 0.7575 (mmtt) REVERT: F 331 LYS cc_start: 0.8601 (mttt) cc_final: 0.7630 (mmtt) REVERT: F 356 SER cc_start: 0.7515 (p) cc_final: 0.6966 (t) REVERT: F 375 LYS cc_start: 0.8301 (pttt) cc_final: 0.7808 (ptpp) outliers start: 8 outliers final: 4 residues processed: 93 average time/residue: 0.6768 time to fit residues: 69.9470 Evaluate side-chains 91 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 0.0570 chunk 40 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 11 optimal weight: 0.0980 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.8304 ------------------------------------------------------------------------------- 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 = 0.4219 r_free = 0.4219 target = 0.150590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.133407 restraints weight = 13352.525| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 2.27 r_work: 0.3928 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3836 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3561 Z= 0.181 Angle : 0.468 4.698 4761 Z= 0.241 Chirality : 0.051 0.130 531 Planarity : 0.003 0.040 609 Dihedral : 4.548 16.555 474 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.10 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: -1.43 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.08 (0.27), 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 0.008 0.002 TYR E 310 ARG 0.003 0.000 ARG B 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 97 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 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: A 321 LYS cc_start: 0.8765 (mttt) cc_final: 0.8332 (mttp) REVERT: A 353 LYS cc_start: 0.8911 (ttpp) cc_final: 0.8613 (tttm) REVERT: A 369 LYS cc_start: 0.8575 (mttt) cc_final: 0.8279 (mtpp) REVERT: B 307 GLN cc_start: 0.8214 (mt0) cc_final: 0.7704 (tt0) REVERT: B 331 LYS cc_start: 0.8476 (mttt) cc_final: 0.8130 (mtpp) REVERT: B 375 LYS cc_start: 0.8401 (ptmt) cc_final: 0.7931 (ptpp) REVERT: C 321 LYS cc_start: 0.8646 (mttt) cc_final: 0.8223 (mttp) REVERT: C 369 LYS cc_start: 0.8766 (mttt) cc_final: 0.8490 (mtpp) REVERT: D 311 LYS cc_start: 0.8586 (tttt) cc_final: 0.8222 (ttpt) REVERT: D 331 LYS cc_start: 0.8585 (mttt) cc_final: 0.8114 (mmmt) REVERT: D 340 LYS cc_start: 0.8652 (mttt) cc_final: 0.8318 (mtpp) REVERT: D 375 LYS cc_start: 0.8564 (pttt) cc_final: 0.7966 (ptpp) REVERT: D 379 ARG cc_start: 0.7028 (mtt-85) cc_final: 0.6104 (mmp-170) REVERT: E 305 SER cc_start: 0.8056 (m) cc_final: 0.7780 (p) REVERT: E 317 LYS cc_start: 0.8441 (mtmt) cc_final: 0.7769 (ptmt) REVERT: E 321 LYS cc_start: 0.8844 (mttt) cc_final: 0.8548 (mttp) REVERT: E 369 LYS cc_start: 0.8610 (mttt) cc_final: 0.8273 (mtpp) REVERT: F 311 LYS cc_start: 0.8390 (tttt) cc_final: 0.7640 (mmtt) REVERT: F 331 LYS cc_start: 0.8668 (mttt) cc_final: 0.7720 (mmtt) REVERT: F 356 SER cc_start: 0.7573 (p) cc_final: 0.7047 (t) REVERT: F 375 LYS cc_start: 0.8372 (pttt) cc_final: 0.7922 (ptpp) outliers start: 9 outliers final: 7 residues processed: 94 average time/residue: 0.6723 time to fit residues: 69.9598 Evaluate side-chains 95 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 F residue 319 THR Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 348 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 6.9990 chunk 9 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4245 r_free = 0.4245 target = 0.156625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.139624 restraints weight = 12835.805| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 2.16 r_work: 0.3951 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3858 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.5409 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= 0.138 Angle : 0.445 4.518 4761 Z= 0.228 Chirality : 0.051 0.129 531 Planarity : 0.003 0.042 609 Dihedral : 4.343 16.109 474 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.50 % Allowed : 12.28 % 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: -1.40 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.06 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS B 374 PHE 0.004 0.001 PHE B 378 TYR 0.006 0.001 TYR E 310 ARG 0.002 0.000 ARG B 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 to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.474 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: 0.8752 (mttt) cc_final: 0.8299 (mttp) REVERT: A 369 LYS cc_start: 0.8597 (mttt) cc_final: 0.8287 (mtpp) REVERT: B 307 GLN cc_start: 0.8191 (mt0) cc_final: 0.7608 (tt0) REVERT: B 331 LYS cc_start: 0.8438 (mttt) cc_final: 0.8076 (mtpp) REVERT: B 375 LYS cc_start: 0.8368 (ptmt) cc_final: 0.7858 (ptpp) REVERT: C 321 LYS cc_start: 0.8621 (mttt) cc_final: 0.8175 (mttp) REVERT: C 349 ARG cc_start: 0.7860 (mtm180) cc_final: 0.6210 (mtt-85) REVERT: C 369 LYS cc_start: 0.8710 (mttt) cc_final: 0.8425 (mtpp) REVERT: D 311 LYS cc_start: 0.8560 (tttt) cc_final: 0.8159 (ttpt) REVERT: D 331 LYS cc_start: 0.8543 (mttt) cc_final: 0.8057 (mmmt) REVERT: D 340 LYS cc_start: 0.8632 (mttt) cc_final: 0.8284 (mtpp) REVERT: D 375 LYS cc_start: 0.8550 (pttt) cc_final: 0.7890 (ptpp) REVERT: D 379 ARG cc_start: 0.6925 (mtt-85) cc_final: 0.5985 (mmp-170) REVERT: E 305 SER cc_start: 0.8057 (m) cc_final: 0.7775 (p) REVERT: E 317 LYS cc_start: 0.8409 (mtmt) cc_final: 0.7821 (ttpt) REVERT: E 321 LYS cc_start: 0.8819 (mttt) cc_final: 0.8515 (mttm) REVERT: E 369 LYS cc_start: 0.8608 (mttt) cc_final: 0.8251 (mtpp) REVERT: F 307 GLN cc_start: 0.8135 (mt0) cc_final: 0.7466 (tm-30) REVERT: F 311 LYS cc_start: 0.8288 (tttt) cc_final: 0.7552 (mmtt) REVERT: F 331 LYS cc_start: 0.8618 (mttt) cc_final: 0.7644 (mmtt) REVERT: F 356 SER cc_start: 0.7572 (p) cc_final: 0.7038 (t) REVERT: F 375 LYS cc_start: 0.8323 (pttt) cc_final: 0.7863 (ptpp) outliers start: 6 outliers final: 6 residues processed: 98 average time/residue: 0.6835 time to fit residues: 74.6185 Evaluate side-chains 101 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain F residue 348 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 0.0980 chunk 22 optimal weight: 0.9980 chunk 30 optimal weight: 0.0870 chunk 10 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- 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 = 0.4275 r_free = 0.4275 target = 0.155057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.138013 restraints weight = 13268.441| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 2.19 r_work: 0.3976 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3883 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3561 Z= 0.122 Angle : 0.435 4.460 4761 Z= 0.222 Chirality : 0.051 0.130 531 Planarity : 0.003 0.041 609 Dihedral : 4.149 15.715 474 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.75 % Allowed : 12.53 % Favored : 85.71 % 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: -1.39 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.05 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 374 PHE 0.003 0.001 PHE B 378 TYR 0.006 0.001 TYR C 310 ARG 0.002 0.000 ARG B 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 105 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.549 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: 0.8752 (mttt) cc_final: 0.8296 (mttp) REVERT: A 369 LYS cc_start: 0.8598 (mttt) cc_final: 0.8299 (mtpp) REVERT: B 307 GLN cc_start: 0.8188 (mt0) cc_final: 0.7617 (tt0) REVERT: B 331 LYS cc_start: 0.8455 (mttt) cc_final: 0.8014 (mtpp) REVERT: B 375 LYS cc_start: 0.8330 (ptmt) cc_final: 0.7842 (ptpp) REVERT: C 321 LYS cc_start: 0.8603 (mttt) cc_final: 0.8149 (mttp) REVERT: C 349 ARG cc_start: 0.7628 (mtm180) cc_final: 0.6227 (mtt-85) REVERT: C 369 LYS cc_start: 0.8672 (mttt) cc_final: 0.8420 (mtpp) REVERT: D 311 LYS cc_start: 0.8555 (tttt) cc_final: 0.8165 (ttpt) REVERT: D 331 LYS cc_start: 0.8520 (mttt) cc_final: 0.8042 (mmmt) REVERT: D 340 LYS cc_start: 0.8601 (mttt) cc_final: 0.8262 (mtpp) REVERT: D 375 LYS cc_start: 0.8532 (pttt) cc_final: 0.7874 (ptpp) REVERT: D 379 ARG cc_start: 0.6884 (mtt-85) cc_final: 0.5885 (mmp-170) REVERT: E 317 LYS cc_start: 0.8391 (mtmt) cc_final: 0.7766 (ptmt) REVERT: E 321 LYS cc_start: 0.8805 (mttt) cc_final: 0.8520 (mttm) REVERT: E 369 LYS cc_start: 0.8598 (mttt) cc_final: 0.8254 (mtpp) REVERT: F 307 GLN cc_start: 0.8132 (mt0) cc_final: 0.7464 (tm-30) REVERT: F 311 LYS cc_start: 0.8256 (tttt) cc_final: 0.7506 (mmtt) REVERT: F 331 LYS cc_start: 0.8614 (mttt) cc_final: 0.7626 (mmtt) REVERT: F 356 SER cc_start: 0.7424 (p) cc_final: 0.6940 (t) outliers start: 7 outliers final: 6 residues processed: 102 average time/residue: 0.6613 time to fit residues: 74.9547 Evaluate side-chains 102 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain F residue 348 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 2.9990 chunk 19 optimal weight: 0.0980 chunk 8 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.4262 r_free = 0.4262 target = 0.153984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.136937 restraints weight = 13447.963| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 2.20 r_work: 0.3960 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3865 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.5561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3561 Z= 0.145 Angle : 0.451 5.601 4761 Z= 0.230 Chirality : 0.050 0.129 531 Planarity : 0.004 0.041 609 Dihedral : 4.198 15.778 474 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.75 % Allowed : 12.53 % Favored : 85.71 % 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: -1.41 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 374 PHE 0.005 0.001 PHE B 378 TYR 0.007 0.001 TYR E 310 ARG 0.005 0.000 ARG B 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 105 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.688 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: 0.8746 (mttt) cc_final: 0.8288 (mttp) REVERT: A 369 LYS cc_start: 0.8585 (mttt) cc_final: 0.8293 (mtpp) REVERT: B 307 GLN cc_start: 0.8180 (mt0) cc_final: 0.7607 (tt0) REVERT: B 331 LYS cc_start: 0.8446 (mttt) cc_final: 0.8080 (mtpp) REVERT: B 375 LYS cc_start: 0.8318 (ptmt) cc_final: 0.7818 (ptpp) REVERT: C 321 LYS cc_start: 0.8621 (mttt) cc_final: 0.8167 (mttp) REVERT: C 349 ARG cc_start: 0.7648 (mtm180) cc_final: 0.6234 (mtt-85) REVERT: C 369 LYS cc_start: 0.8658 (mttt) cc_final: 0.8416 (mtpp) REVERT: D 311 LYS cc_start: 0.8561 (tttt) cc_final: 0.8174 (ttpt) REVERT: D 331 LYS cc_start: 0.8539 (mttt) cc_final: 0.8041 (mmmt) REVERT: D 340 LYS cc_start: 0.8602 (mttt) cc_final: 0.8261 (mtpp) REVERT: D 375 LYS cc_start: 0.8564 (pttt) cc_final: 0.7900 (ptpp) REVERT: D 379 ARG cc_start: 0.6911 (mtt-85) cc_final: 0.5974 (mmp-170) REVERT: E 317 LYS cc_start: 0.8386 (mtmt) cc_final: 0.7754 (ptmt) REVERT: E 321 LYS cc_start: 0.8795 (mttt) cc_final: 0.8508 (mttm) REVERT: E 369 LYS cc_start: 0.8587 (mttt) cc_final: 0.8254 (mtpp) REVERT: F 307 GLN cc_start: 0.8129 (mt0) cc_final: 0.7460 (tm-30) REVERT: F 311 LYS cc_start: 0.8264 (tttt) cc_final: 0.7498 (mmtt) REVERT: F 331 LYS cc_start: 0.8620 (mttt) cc_final: 0.7647 (mmtt) REVERT: F 356 SER cc_start: 0.7461 (p) cc_final: 0.6987 (t) REVERT: F 375 LYS cc_start: 0.8304 (pttt) cc_final: 0.7861 (ptpp) outliers start: 7 outliers final: 7 residues processed: 101 average time/residue: 0.6772 time to fit residues: 75.7248 Evaluate side-chains 104 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 374 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 = 0.4216 r_free = 0.4216 target = 0.154162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.137035 restraints weight = 12745.767| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 2.14 r_work: 0.3933 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3843 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.5554 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= 0.174 Angle : 0.463 5.873 4761 Z= 0.238 Chirality : 0.051 0.129 531 Planarity : 0.004 0.041 609 Dihedral : 4.320 15.929 474 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.26 % Allowed : 12.03 % Favored : 85.71 % 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: -1.46 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 374 PHE 0.005 0.001 PHE B 378 TYR 0.008 0.002 TYR E 310 ARG 0.004 0.000 ARG B 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5020.01 seconds wall clock time: 89 minutes 2.09 seconds (5342.09 seconds total)