Starting phenix.real_space_refine on Fri Aug 22 19:21:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q9a_18273/08_2025/8q9a_18273.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q9a_18273/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8q9a_18273/08_2025/8q9a_18273.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q9a_18273/08_2025/8q9a_18273.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8q9a_18273/08_2025/8q9a_18273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q9a_18273/08_2025/8q9a_18273.map" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.62, per 1000 atoms: 0.23 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: 0.54 Conformation dependent library (CDL) restraints added in 328.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.25 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: 1.30 Time building geometry restraints manager: 0.79 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: 3.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.610 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.970 ------------------------------------------------------------------------------- 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= 0.672 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.32), 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 ARG 0.005 0.001 ARG D 349 TYR 0.085 0.021 TYR A 310 PHE 0.045 0.016 PHE B 346 HIS 0.013 0.004 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.01079 ( 3561) covalent geometry : angle 1.79770 ( 4761) hydrogen bonds : bond 0.12407 ( 85) hydrogen bonds : angle 7.65598 ( 255) *********************** 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 : 0.208 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: symmetry clash REVERT: A 321 LYS cc_start: 0.7789 (mttt) cc_final: 0.7152 (mttp) REVERT: A 338 GLU cc_start: 0.7652 (tt0) cc_final: 0.7370 (mt-10) REVERT: A 343 LYS cc_start: 0.8885 (mttt) cc_final: 0.8667 (mttm) REVERT: A 369 LYS cc_start: 0.7496 (mttt) cc_final: 0.6700 (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: 0.7187 (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: 0.6252 (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: 0.7106 (mt-10) REVERT: E 343 LYS cc_start: 0.9039 (mttt) cc_final: 0.8817 (mttm) REVERT: E 349 ARG cc_start: 0.6732 (mtm180) cc_final: 0.6023 (mmp-170) REVERT: E 353 LYS cc_start: 0.8327 (tttt) cc_final: 0.8127 (tttt) REVERT: E 356 SER cc_start: 0.7968 (p) cc_final: 0.7241 (t) REVERT: E 369 LYS cc_start: 0.7691 (mttt) cc_final: 0.6960 (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: 0.2886 time to fit residues: 44.1122 Evaluate side-chains 98 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS B 327 ASN C 362 HIS C 368 ASN D 307 GLN D 327 ASN E 362 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.148442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.130161 restraints weight = 13368.291| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 2.34 r_work: 0.3997 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3914 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3356 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= 0.117 Angle : 0.563 4.952 4761 Z= 0.305 Chirality : 0.052 0.135 531 Planarity : 0.003 0.031 609 Dihedral : 5.758 19.118 474 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 379 TYR 0.008 0.002 TYR D 310 PHE 0.013 0.001 PHE B 378 HIS 0.006 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 3561) covalent geometry : angle 0.56301 ( 4761) hydrogen bonds : bond 0.03287 ( 85) hydrogen bonds : angle 5.78266 ( 255) *********************** 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 115 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.208 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: 0.8522 (mttt) cc_final: 0.8097 (mttm) REVERT: A 369 LYS cc_start: 0.8524 (mttt) cc_final: 0.8054 (mtpp) REVERT: B 307 GLN cc_start: 0.7978 (mt0) cc_final: 0.7518 (tt0) REVERT: B 331 LYS cc_start: 0.8366 (mttt) cc_final: 0.7955 (mtpp) REVERT: B 343 LYS cc_start: 0.9060 (mttt) cc_final: 0.8831 (mtpp) REVERT: C 321 LYS cc_start: 0.8547 (mttt) cc_final: 0.8161 (mttp) REVERT: C 369 LYS cc_start: 0.8680 (mttt) cc_final: 0.8300 (mtpp) REVERT: D 307 GLN cc_start: 0.8318 (tt0) cc_final: 0.7750 (tm-30) REVERT: D 311 LYS cc_start: 0.8630 (tttt) cc_final: 0.8252 (ttpt) REVERT: D 331 LYS cc_start: 0.8455 (mttt) cc_final: 0.8007 (mmmt) REVERT: D 375 LYS cc_start: 0.8581 (pttt) cc_final: 0.8155 (ptpp) REVERT: D 379 ARG cc_start: 0.7109 (mtt-85) cc_final: 0.5885 (mmp-170) REVERT: E 317 LYS cc_start: 0.8207 (mtmt) cc_final: 0.7671 (ptmt) REVERT: E 321 LYS cc_start: 0.8674 (mttt) cc_final: 0.8299 (mttm) REVERT: E 338 GLU cc_start: 0.8200 (tt0) cc_final: 0.7778 (mt-10) REVERT: E 349 ARG cc_start: 0.7183 (mtm180) cc_final: 0.6216 (mmp-170) REVERT: E 356 SER cc_start: 0.8154 (p) cc_final: 0.7831 (t) REVERT: E 369 LYS cc_start: 0.8524 (mttt) cc_final: 0.8149 (mtpp) REVERT: F 307 GLN cc_start: 0.8064 (mt0) cc_final: 0.7520 (tt0) REVERT: F 311 LYS cc_start: 0.8569 (tttt) cc_final: 0.7805 (mmtm) REVERT: F 331 LYS cc_start: 0.8485 (mttt) cc_final: 0.7521 (mmtt) REVERT: F 356 SER cc_start: 0.7497 (p) cc_final: 0.6750 (t) REVERT: F 375 LYS cc_start: 0.8166 (pttt) cc_final: 0.7691 (ptpt) outliers start: 9 outliers final: 7 residues processed: 115 average time/residue: 0.3009 time to fit residues: 38.4304 Evaluate side-chains 98 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 0 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.138010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.119937 restraints weight = 13776.501| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 2.27 r_work: 0.3883 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3797 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3561 Z= 0.208 Angle : 0.573 5.294 4761 Z= 0.307 Chirality : 0.053 0.135 531 Planarity : 0.003 0.035 609 Dihedral : 5.420 18.004 474 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.26 % Allowed : 10.53 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 379 TYR 0.014 0.003 TYR D 310 PHE 0.010 0.002 PHE B 346 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 3561) covalent geometry : angle 0.57343 ( 4761) hydrogen bonds : bond 0.02674 ( 85) hydrogen bonds : angle 5.05129 ( 255) *********************** 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 106 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.236 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: 0.8598 (mttt) cc_final: 0.8162 (mttm) REVERT: A 349 ARG cc_start: 0.7831 (mtm110) cc_final: 0.7301 (mtm110) REVERT: A 369 LYS cc_start: 0.8512 (mttt) cc_final: 0.8047 (mtpp) REVERT: B 307 GLN cc_start: 0.8073 (mt0) cc_final: 0.7591 (tt0) REVERT: B 331 LYS cc_start: 0.8318 (mttt) cc_final: 0.7871 (mtpp) REVERT: B 375 LYS cc_start: 0.8391 (ptmt) cc_final: 0.7828 (ptpp) REVERT: C 321 LYS cc_start: 0.8617 (mttt) cc_final: 0.8191 (mttp) REVERT: C 369 LYS cc_start: 0.8712 (mttt) cc_final: 0.8322 (mtpp) REVERT: D 311 LYS cc_start: 0.8688 (tttt) cc_final: 0.8290 (ttpt) REVERT: D 331 LYS cc_start: 0.8483 (mttt) cc_final: 0.7941 (mmmt) REVERT: D 340 LYS cc_start: 0.8613 (mttt) cc_final: 0.8315 (mtpp) REVERT: D 374 HIS cc_start: 0.7796 (OUTLIER) cc_final: 0.7520 (p90) REVERT: D 375 LYS cc_start: 0.8571 (pttt) cc_final: 0.8071 (ptpp) REVERT: D 379 ARG cc_start: 0.7156 (mtt-85) cc_final: 0.5906 (mmp-170) REVERT: E 317 LYS cc_start: 0.8269 (mtmt) cc_final: 0.7614 (ptmt) REVERT: E 321 LYS cc_start: 0.8734 (mttt) cc_final: 0.8369 (mttm) REVERT: E 356 SER cc_start: 0.8182 (p) cc_final: 0.7843 (t) REVERT: E 369 LYS cc_start: 0.8532 (mttt) cc_final: 0.8104 (mtpp) REVERT: F 311 LYS cc_start: 0.8449 (tttt) cc_final: 0.7746 (mmtm) REVERT: F 331 LYS cc_start: 0.8565 (mttt) cc_final: 0.7581 (mmtt) REVERT: F 356 SER cc_start: 0.7421 (p) cc_final: 0.6667 (t) REVERT: F 375 LYS cc_start: 0.8303 (pttt) cc_final: 0.7787 (ptpt) outliers start: 9 outliers final: 8 residues processed: 105 average time/residue: 0.3053 time to fit residues: 35.2810 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 : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 372 GLU Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.152580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.135792 restraints weight = 13072.380| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 2.15 r_work: 0.3917 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3828 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3561 Z= 0.153 Angle : 0.502 4.253 4761 Z= 0.265 Chirality : 0.051 0.131 531 Planarity : 0.003 0.041 609 Dihedral : 5.113 17.588 474 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.51 % Allowed : 11.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.34), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.08 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 379 TYR 0.008 0.002 TYR C 310 PHE 0.007 0.001 PHE F 346 HIS 0.002 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 3561) covalent geometry : angle 0.50233 ( 4761) hydrogen bonds : bond 0.02289 ( 85) hydrogen bonds : angle 4.69247 ( 255) *********************** 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 102 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.143 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: 0.8760 (mttt) cc_final: 0.8313 (mttp) REVERT: A 369 LYS cc_start: 0.8527 (mttt) cc_final: 0.8178 (mtpp) REVERT: B 307 GLN cc_start: 0.8173 (mt0) cc_final: 0.7635 (tt0) REVERT: B 331 LYS cc_start: 0.8458 (mttt) cc_final: 0.8050 (mtpp) REVERT: B 375 LYS cc_start: 0.8416 (ptmt) cc_final: 0.7862 (ptpp) REVERT: C 321 LYS cc_start: 0.8636 (mttt) cc_final: 0.8217 (mttp) REVERT: C 349 ARG cc_start: 0.7845 (mtm180) cc_final: 0.6192 (mtt-85) REVERT: C 369 LYS cc_start: 0.8773 (mttt) cc_final: 0.8444 (mtpp) REVERT: D 311 LYS cc_start: 0.8681 (tttt) cc_final: 0.8303 (ttpt) REVERT: D 331 LYS cc_start: 0.8582 (mttt) cc_final: 0.8103 (mmmt) REVERT: D 340 LYS cc_start: 0.8613 (mttt) cc_final: 0.8334 (mtpp) REVERT: D 374 HIS cc_start: 0.7656 (OUTLIER) cc_final: 0.7412 (p90) REVERT: D 375 LYS cc_start: 0.8581 (pttt) cc_final: 0.8064 (ptpp) REVERT: D 379 ARG cc_start: 0.7092 (mtt-85) cc_final: 0.6152 (mmp-170) REVERT: E 317 LYS cc_start: 0.8415 (mtmt) cc_final: 0.7806 (ptmt) REVERT: E 321 LYS cc_start: 0.8844 (mttt) cc_final: 0.8526 (mttm) REVERT: E 356 SER cc_start: 0.8325 (p) cc_final: 0.8113 (t) REVERT: E 369 LYS cc_start: 0.8618 (mttt) cc_final: 0.8241 (mtpp) REVERT: F 311 LYS cc_start: 0.8435 (tttt) cc_final: 0.7755 (mmtm) REVERT: F 331 LYS cc_start: 0.8628 (mttt) cc_final: 0.7664 (mmtt) REVERT: F 375 LYS cc_start: 0.8303 (pttt) cc_final: 0.7830 (ptpt) outliers start: 10 outliers final: 5 residues processed: 100 average time/residue: 0.2516 time to fit residues: 27.8057 Evaluate side-chains 96 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.125 ------------------------------------------------------------------------------- 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 372 GLU Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.155365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.138448 restraints weight = 12968.798| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 2.17 r_work: 0.3954 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3864 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3561 Z= 0.114 Angle : 0.469 4.493 4761 Z= 0.243 Chirality : 0.051 0.130 531 Planarity : 0.003 0.040 609 Dihedral : 4.746 17.383 474 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.76 % Allowed : 10.28 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.34), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.05 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 379 TYR 0.008 0.002 TYR C 310 PHE 0.005 0.001 PHE B 346 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 3561) covalent geometry : angle 0.46862 ( 4761) hydrogen bonds : bond 0.01923 ( 85) hydrogen bonds : angle 4.42593 ( 255) *********************** 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 104 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.211 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: 0.8761 (mttt) cc_final: 0.8320 (mttp) REVERT: A 369 LYS cc_start: 0.8569 (mttt) cc_final: 0.8235 (mtpp) REVERT: B 307 GLN cc_start: 0.8161 (mt0) cc_final: 0.7636 (tt0) REVERT: B 331 LYS cc_start: 0.8440 (mttt) cc_final: 0.8032 (mtpp) REVERT: B 375 LYS cc_start: 0.8381 (ptmt) cc_final: 0.7891 (ptpp) REVERT: C 321 LYS cc_start: 0.8651 (mttt) cc_final: 0.8214 (mttp) REVERT: C 349 ARG cc_start: 0.7609 (mtm180) cc_final: 0.6180 (mtt-85) REVERT: C 369 LYS cc_start: 0.8735 (mttt) cc_final: 0.8451 (mtpp) REVERT: D 311 LYS cc_start: 0.8662 (tttt) cc_final: 0.8296 (ttpt) REVERT: D 331 LYS cc_start: 0.8557 (mttt) cc_final: 0.8086 (mmmt) REVERT: D 340 LYS cc_start: 0.8598 (mttt) cc_final: 0.8308 (mtpp) REVERT: D 372 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7899 (mt-10) REVERT: D 375 LYS cc_start: 0.8512 (pttt) cc_final: 0.7942 (ptpp) REVERT: D 379 ARG cc_start: 0.7010 (mtt-85) cc_final: 0.5893 (mmp-170) REVERT: E 317 LYS cc_start: 0.8434 (mtmt) cc_final: 0.7882 (ttpt) REVERT: E 321 LYS cc_start: 0.8848 (mttt) cc_final: 0.8538 (mttm) REVERT: E 369 LYS cc_start: 0.8563 (mttt) cc_final: 0.8228 (mtpp) REVERT: F 311 LYS cc_start: 0.8387 (tttt) cc_final: 0.7653 (mmtt) REVERT: F 331 LYS cc_start: 0.8597 (mttt) cc_final: 0.7616 (mmtt) REVERT: F 356 SER cc_start: 0.7551 (p) cc_final: 0.6974 (t) REVERT: F 375 LYS cc_start: 0.8300 (pttt) cc_final: 0.7833 (ptpt) outliers start: 11 outliers final: 5 residues processed: 100 average time/residue: 0.2989 time to fit residues: 32.9821 Evaluate side-chains 94 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 372 GLU 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 8 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.146070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.128935 restraints weight = 13529.499| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.25 r_work: 0.3867 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3775 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 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 : 0.004 0.026 3561 Z= 0.189 Angle : 0.508 4.859 4761 Z= 0.265 Chirality : 0.051 0.130 531 Planarity : 0.003 0.041 609 Dihedral : 4.935 17.206 474 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.51 % Allowed : 11.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.34), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.11 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 379 TYR 0.012 0.003 TYR C 310 PHE 0.008 0.001 PHE F 346 HIS 0.002 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 3561) covalent geometry : angle 0.50765 ( 4761) hydrogen bonds : bond 0.02153 ( 85) hydrogen bonds : angle 4.40983 ( 255) *********************** 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: 10 poor density : 86 time to evaluate : 0.238 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: 0.8704 (mttt) cc_final: 0.8259 (mttp) REVERT: A 369 LYS cc_start: 0.8559 (mttt) cc_final: 0.8194 (mtpp) REVERT: B 307 GLN cc_start: 0.8226 (mt0) cc_final: 0.7653 (tt0) REVERT: B 331 LYS cc_start: 0.8418 (mttt) cc_final: 0.8084 (mtpp) REVERT: B 375 LYS cc_start: 0.8393 (ptmt) cc_final: 0.7866 (ptpp) REVERT: C 321 LYS cc_start: 0.8667 (mttt) cc_final: 0.8219 (mttp) REVERT: C 349 ARG cc_start: 0.7612 (mtm180) cc_final: 0.6134 (mtt-85) REVERT: C 369 LYS cc_start: 0.8763 (mttt) cc_final: 0.8432 (mtpp) REVERT: D 311 LYS cc_start: 0.8744 (tttt) cc_final: 0.8317 (ttpt) REVERT: D 331 LYS cc_start: 0.8505 (mttt) cc_final: 0.8172 (mtpp) REVERT: D 340 LYS cc_start: 0.8598 (mttt) cc_final: 0.8289 (mtpp) REVERT: D 375 LYS cc_start: 0.8557 (pttt) cc_final: 0.7908 (ptpp) REVERT: D 379 ARG cc_start: 0.7083 (mtt-85) cc_final: 0.6128 (mmp-170) REVERT: E 317 LYS cc_start: 0.8400 (mtmt) cc_final: 0.7622 (ptmt) REVERT: E 321 LYS cc_start: 0.8822 (mttt) cc_final: 0.8508 (mttp) REVERT: E 369 LYS cc_start: 0.8548 (mttt) cc_final: 0.8167 (mtpp) REVERT: F 311 LYS cc_start: 0.8395 (tttt) cc_final: 0.7584 (mmtm) REVERT: F 331 LYS cc_start: 0.8683 (mttt) cc_final: 0.7704 (mmtt) REVERT: F 375 LYS cc_start: 0.8317 (pttt) cc_final: 0.7817 (ptpp) outliers start: 10 outliers final: 8 residues processed: 93 average time/residue: 0.3060 time to fit residues: 31.3585 Evaluate side-chains 94 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain D residue 372 GLU 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 29 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.155927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.138950 restraints weight = 12754.125| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 2.17 r_work: 0.3953 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3860 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.5351 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= 0.094 Angle : 0.455 4.881 4761 Z= 0.232 Chirality : 0.051 0.131 531 Planarity : 0.003 0.044 609 Dihedral : 4.488 16.930 474 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.06 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 379 TYR 0.007 0.001 TYR C 310 PHE 0.003 0.001 PHE B 378 HIS 0.003 0.000 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 3561) covalent geometry : angle 0.45503 ( 4761) hydrogen bonds : bond 0.01750 ( 85) hydrogen bonds : angle 4.24210 ( 255) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.177 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: 0.8718 (mttt) cc_final: 0.8273 (mttp) REVERT: A 369 LYS cc_start: 0.8588 (mttt) cc_final: 0.8258 (mtpp) REVERT: B 307 GLN cc_start: 0.8200 (mt0) cc_final: 0.7658 (tt0) REVERT: B 331 LYS cc_start: 0.8429 (mttt) cc_final: 0.7991 (mtpp) REVERT: B 375 LYS cc_start: 0.8370 (ptmt) cc_final: 0.7868 (ptpp) REVERT: C 321 LYS cc_start: 0.8605 (mttt) cc_final: 0.8165 (mttp) REVERT: C 349 ARG cc_start: 0.7573 (mtm180) cc_final: 0.6157 (mtt-85) REVERT: C 369 LYS cc_start: 0.8703 (mttt) cc_final: 0.8418 (mtpp) REVERT: D 311 LYS cc_start: 0.8641 (tttt) cc_final: 0.8222 (ttpt) REVERT: D 331 LYS cc_start: 0.8532 (mttt) cc_final: 0.8052 (mmmt) REVERT: D 375 LYS cc_start: 0.8529 (pttt) cc_final: 0.7857 (ptpp) REVERT: D 379 ARG cc_start: 0.6922 (mtt-85) cc_final: 0.5891 (mmp-170) REVERT: E 317 LYS cc_start: 0.8419 (mtmt) cc_final: 0.7818 (ttpt) REVERT: E 321 LYS cc_start: 0.8827 (mttt) cc_final: 0.8514 (mttm) REVERT: E 369 LYS cc_start: 0.8562 (mttt) cc_final: 0.8213 (mtpp) REVERT: F 311 LYS cc_start: 0.8356 (tttt) cc_final: 0.7619 (mmtt) REVERT: F 331 LYS cc_start: 0.8618 (mttt) cc_final: 0.7623 (mmtt) REVERT: F 356 SER cc_start: 0.7517 (p) cc_final: 0.6948 (t) outliers start: 9 outliers final: 6 residues processed: 94 average time/residue: 0.2701 time to fit residues: 28.3245 Evaluate side-chains 94 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 369 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 7 optimal weight: 0.0570 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.7502 ------------------------------------------------------------------------------- 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 = 0.4215 r_free = 0.4215 target = 0.149907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.132714 restraints weight = 13590.178| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 2.26 r_work: 0.3923 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3831 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.5377 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= 0.127 Angle : 0.464 4.674 4761 Z= 0.240 Chirality : 0.051 0.129 531 Planarity : 0.003 0.045 609 Dihedral : 4.517 16.958 474 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.76 % Allowed : 12.53 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 379 TYR 0.008 0.002 TYR E 310 PHE 0.005 0.001 PHE F 346 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 3561) covalent geometry : angle 0.46405 ( 4761) hydrogen bonds : bond 0.01812 ( 85) hydrogen bonds : angle 4.18542 ( 255) *********************** 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 99 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.160 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: 0.8718 (mttt) cc_final: 0.8281 (mttp) REVERT: A 369 LYS cc_start: 0.8596 (mttt) cc_final: 0.8238 (mtpp) REVERT: B 307 GLN cc_start: 0.8186 (mt0) cc_final: 0.7664 (tt0) REVERT: B 331 LYS cc_start: 0.8421 (mttt) cc_final: 0.8086 (mtpp) REVERT: B 375 LYS cc_start: 0.8372 (ptmt) cc_final: 0.7847 (ptpp) REVERT: C 321 LYS cc_start: 0.8633 (mttt) cc_final: 0.8181 (mttp) REVERT: C 349 ARG cc_start: 0.7576 (mtm180) cc_final: 0.6145 (mtt-85) REVERT: C 369 LYS cc_start: 0.8739 (mttt) cc_final: 0.8440 (mtpp) REVERT: D 311 LYS cc_start: 0.8665 (tttt) cc_final: 0.8216 (ttpt) REVERT: D 331 LYS cc_start: 0.8480 (mttt) cc_final: 0.8158 (mtpp) REVERT: D 375 LYS cc_start: 0.8527 (pttt) cc_final: 0.7851 (ptpp) REVERT: D 379 ARG cc_start: 0.7019 (mtt-85) cc_final: 0.6094 (mmp-170) REVERT: E 317 LYS cc_start: 0.8373 (mtmt) cc_final: 0.7620 (ptmt) REVERT: E 321 LYS cc_start: 0.8776 (mttt) cc_final: 0.8478 (mttm) REVERT: E 369 LYS cc_start: 0.8533 (mttt) cc_final: 0.8167 (mtpp) REVERT: F 311 LYS cc_start: 0.8391 (tttt) cc_final: 0.7657 (mmtt) REVERT: F 331 LYS cc_start: 0.8662 (mttt) cc_final: 0.7689 (mmtt) REVERT: F 356 SER cc_start: 0.7498 (p) cc_final: 0.6903 (t) REVERT: F 375 LYS cc_start: 0.8336 (pttt) cc_final: 0.7857 (ptpp) outliers start: 11 outliers final: 5 residues processed: 93 average time/residue: 0.2664 time to fit residues: 27.4751 Evaluate side-chains 93 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 369 LYS 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 5 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.4203 r_free = 0.4203 target = 0.152900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.135847 restraints weight = 12978.004| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 2.17 r_work: 0.3908 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3817 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.5430 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= 0.128 Angle : 0.462 4.606 4761 Z= 0.238 Chirality : 0.051 0.128 531 Planarity : 0.003 0.046 609 Dihedral : 4.499 17.005 474 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.75 % Allowed : 13.53 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 379 TYR 0.007 0.002 TYR E 310 PHE 0.004 0.001 PHE F 346 HIS 0.003 0.000 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 3561) covalent geometry : angle 0.46199 ( 4761) hydrogen bonds : bond 0.01794 ( 85) hydrogen bonds : angle 4.18548 ( 255) *********************** 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 95 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.215 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: 0.8733 (mttt) cc_final: 0.8300 (mttp) REVERT: A 369 LYS cc_start: 0.8596 (mttt) cc_final: 0.8268 (mtpp) REVERT: B 307 GLN cc_start: 0.8184 (mt0) cc_final: 0.7636 (tt0) REVERT: B 331 LYS cc_start: 0.8421 (mttt) cc_final: 0.8081 (mtpp) REVERT: B 375 LYS cc_start: 0.8367 (ptmt) cc_final: 0.7836 (ptpp) REVERT: C 321 LYS cc_start: 0.8632 (mttt) cc_final: 0.8182 (mttp) REVERT: C 349 ARG cc_start: 0.7586 (mtm180) cc_final: 0.6158 (mtt-85) REVERT: C 369 LYS cc_start: 0.8727 (mttt) cc_final: 0.8438 (mtpp) REVERT: D 311 LYS cc_start: 0.8673 (tttt) cc_final: 0.8243 (ttpt) REVERT: D 331 LYS cc_start: 0.8510 (mttt) cc_final: 0.8171 (mtpp) REVERT: D 372 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7914 (mm-30) REVERT: D 375 LYS cc_start: 0.8507 (pttt) cc_final: 0.7831 (ptpp) REVERT: D 379 ARG cc_start: 0.7032 (mtt-85) cc_final: 0.6103 (mmp-170) REVERT: E 317 LYS cc_start: 0.8367 (mtmt) cc_final: 0.7607 (ptmt) REVERT: E 321 LYS cc_start: 0.8739 (mttt) cc_final: 0.8447 (mttm) REVERT: E 369 LYS cc_start: 0.8599 (mttt) cc_final: 0.8223 (mtpp) REVERT: F 311 LYS cc_start: 0.8382 (tttt) cc_final: 0.7571 (mmtt) REVERT: F 331 LYS cc_start: 0.8680 (mttt) cc_final: 0.7698 (mmtt) REVERT: F 356 SER cc_start: 0.7556 (p) cc_final: 0.7009 (t) REVERT: F 375 LYS cc_start: 0.8313 (pttt) cc_final: 0.7863 (ptpp) outliers start: 7 outliers final: 6 residues processed: 93 average time/residue: 0.2762 time to fit residues: 28.5738 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 : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 372 GLU 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 39 optimal weight: 0.0770 chunk 24 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.156971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.139837 restraints weight = 12867.866| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 2.18 r_work: 0.3958 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3865 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.5544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3561 Z= 0.088 Angle : 0.445 5.897 4761 Z= 0.227 Chirality : 0.051 0.129 531 Planarity : 0.003 0.047 609 Dihedral : 4.242 16.646 474 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.75 % Allowed : 14.04 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.08 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 379 TYR 0.006 0.001 TYR B 310 PHE 0.003 0.000 PHE B 378 HIS 0.004 0.000 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00196 ( 3561) covalent geometry : angle 0.44523 ( 4761) hydrogen bonds : bond 0.01597 ( 85) hydrogen bonds : angle 4.07781 ( 255) ********************** 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 100 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.123 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: 0.8723 (mttt) cc_final: 0.8294 (mttp) REVERT: A 369 LYS cc_start: 0.8587 (mttt) cc_final: 0.8279 (mtpp) REVERT: B 307 GLN cc_start: 0.8174 (mt0) cc_final: 0.7591 (tt0) REVERT: B 331 LYS cc_start: 0.8420 (mttt) cc_final: 0.8076 (mtpp) REVERT: B 375 LYS cc_start: 0.8343 (ptmt) cc_final: 0.7817 (ptpp) REVERT: C 321 LYS cc_start: 0.8600 (mttt) cc_final: 0.8149 (mttp) REVERT: C 349 ARG cc_start: 0.7567 (mtm180) cc_final: 0.6145 (mtt-85) REVERT: C 369 LYS cc_start: 0.8651 (mttt) cc_final: 0.8386 (mtpp) REVERT: D 311 LYS cc_start: 0.8595 (tttt) cc_final: 0.8167 (ttpt) REVERT: D 331 LYS cc_start: 0.8484 (mttt) cc_final: 0.8152 (mtpp) REVERT: D 375 LYS cc_start: 0.8520 (pttt) cc_final: 0.7822 (ptpp) REVERT: D 379 ARG cc_start: 0.6872 (mtt-85) cc_final: 0.5822 (mmp-170) REVERT: E 317 LYS cc_start: 0.8368 (mtmt) cc_final: 0.7700 (ptmt) REVERT: E 321 LYS cc_start: 0.8776 (mttt) cc_final: 0.8500 (mttm) REVERT: E 369 LYS cc_start: 0.8594 (mttt) cc_final: 0.8229 (mtpp) REVERT: F 307 GLN cc_start: 0.8121 (mt0) cc_final: 0.7417 (tm-30) REVERT: F 311 LYS cc_start: 0.8299 (tttt) cc_final: 0.7481 (mmtt) REVERT: F 331 LYS cc_start: 0.8642 (mttt) cc_final: 0.7643 (mmtt) REVERT: F 356 SER cc_start: 0.7432 (p) cc_final: 0.6903 (t) REVERT: F 375 LYS cc_start: 0.8275 (pttt) cc_final: 0.7841 (ptpp) outliers start: 7 outliers final: 4 residues processed: 98 average time/residue: 0.2236 time to fit residues: 24.3825 Evaluate side-chains 96 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.118 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 overall best weight: 2.3784 ------------------------------------------------------------------------------- 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 = 0.4195 r_free = 0.4195 target = 0.148252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.131018 restraints weight = 13462.310| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 2.28 r_work: 0.3890 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3799 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.5475 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= 0.160 Angle : 0.491 5.860 4761 Z= 0.253 Chirality : 0.050 0.128 531 Planarity : 0.004 0.044 609 Dihedral : 4.523 17.096 474 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.50 % Allowed : 14.29 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.11 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 379 TYR 0.010 0.002 TYR E 310 PHE 0.005 0.001 PHE F 346 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 3561) covalent geometry : angle 0.49081 ( 4761) hydrogen bonds : bond 0.01879 ( 85) hydrogen bonds : angle 4.16562 ( 255) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2381.72 seconds wall clock time: 41 minutes 3.55 seconds (2463.55 seconds total)