Starting phenix.real_space_refine on Wed Mar 12 04:06:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q9a_18273/03_2025/8q9a_18273.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q9a_18273/03_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_18273/03_2025/8q9a_18273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q9a_18273/03_2025/8q9a_18273.map" model { file = "/net/cci-nas-00/data/ceres_data/8q9a_18273/03_2025/8q9a_18273.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q9a_18273/03_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-5624/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: 5.21, per 1000 atoms: 0.73 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 644.4 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: 0.69 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: 2.63 Time building geometry restraints manager: 2.09 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: 3.570 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: 0.130 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.130 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.320 ------------------------------------------------------------------------------- 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 : 0.523 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: 0.6035 time to fit residues: 92.3839 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 : 0.548 ------------------------------------------------------------------------------- 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: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.4248 r_free = 0.4248 target = 0.147661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.129502 restraints weight = 13307.733| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 2.32 r_work: 0.3992 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3910 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3561 Z= 0.194 Angle : 0.559 4.951 4761 Z= 0.300 Chirality : 0.052 0.133 531 Planarity : 0.003 0.031 609 Dihedral : 5.819 19.058 474 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.38 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (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 0.008 0.002 TYR C 310 ARG 0.002 0.000 ARG D 379 *********************** 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 112 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.601 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: 0.8548 (mttt) cc_final: 0.8136 (mttm) REVERT: A 369 LYS cc_start: 0.8528 (mttt) cc_final: 0.8067 (mtpp) REVERT: B 307 GLN cc_start: 0.7992 (mt0) cc_final: 0.7517 (tt0) REVERT: B 331 LYS cc_start: 0.8371 (mttt) cc_final: 0.7962 (mtpp) REVERT: B 343 LYS cc_start: 0.9064 (mttt) cc_final: 0.8836 (mtpp) REVERT: C 321 LYS cc_start: 0.8556 (mttt) cc_final: 0.8170 (mttp) REVERT: C 369 LYS cc_start: 0.8688 (mttt) cc_final: 0.8311 (mtpp) REVERT: D 307 GLN cc_start: 0.8309 (tt0) cc_final: 0.7746 (tm-30) REVERT: D 311 LYS cc_start: 0.8644 (tttt) cc_final: 0.8260 (ttpt) REVERT: D 331 LYS cc_start: 0.8463 (mttt) cc_final: 0.8008 (mmmt) REVERT: D 375 LYS cc_start: 0.8594 (pttt) cc_final: 0.8168 (ptpp) REVERT: D 379 ARG cc_start: 0.7116 (mtt-85) cc_final: 0.5875 (mmp-170) REVERT: E 317 LYS cc_start: 0.8213 (mtmt) cc_final: 0.7683 (ptmt) REVERT: E 321 LYS cc_start: 0.8689 (mttt) cc_final: 0.8309 (mttm) REVERT: E 338 GLU cc_start: 0.8217 (tt0) cc_final: 0.7796 (mt-10) REVERT: E 343 LYS cc_start: 0.9125 (mttt) cc_final: 0.8913 (mttm) REVERT: E 349 ARG cc_start: 0.7158 (mtm180) cc_final: 0.6198 (mmp-170) REVERT: E 356 SER cc_start: 0.8227 (p) cc_final: 0.7900 (t) REVERT: E 369 LYS cc_start: 0.8518 (mttt) cc_final: 0.8163 (mtpp) REVERT: F 307 GLN cc_start: 0.8068 (mt0) cc_final: 0.7500 (tt0) REVERT: F 311 LYS cc_start: 0.8575 (tttt) cc_final: 0.8162 (ttpt) REVERT: F 331 LYS cc_start: 0.8498 (mttt) cc_final: 0.7534 (mmtt) REVERT: F 356 SER cc_start: 0.7475 (p) cc_final: 0.6725 (t) REVERT: F 374 HIS cc_start: 0.7747 (OUTLIER) cc_final: 0.7546 (p90) outliers start: 9 outliers final: 7 residues processed: 112 average time/residue: 0.6027 time to fit residues: 75.3783 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 : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 374 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 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: 0.8980 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.4282 r_free = 0.4282 target = 0.149599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.131003 restraints weight = 13215.681| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 2.42 r_work: 0.4031 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3943 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.4323 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= 0.126 Angle : 0.490 4.872 4761 Z= 0.259 Chirality : 0.052 0.133 531 Planarity : 0.003 0.042 609 Dihedral : 4.978 17.947 474 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.51 % Allowed : 9.02 % Favored : 88.47 % 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: -1.41 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 374 PHE 0.006 0.001 PHE B 346 TYR 0.007 0.001 TYR C 310 ARG 0.001 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 109 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8098 (mtpt) cc_final: 0.7737 (ttpt) REVERT: A 321 LYS cc_start: 0.8633 (mttt) cc_final: 0.8201 (mttm) REVERT: A 369 LYS cc_start: 0.8550 (mttt) cc_final: 0.8085 (mtpp) REVERT: B 307 GLN cc_start: 0.8097 (mt0) cc_final: 0.7577 (tt0) REVERT: B 331 LYS cc_start: 0.8342 (mttt) cc_final: 0.7933 (mtpp) REVERT: B 343 LYS cc_start: 0.9073 (mttt) cc_final: 0.8807 (mtpp) REVERT: B 375 LYS cc_start: 0.8258 (ptmt) cc_final: 0.7708 (ptpp) REVERT: C 321 LYS cc_start: 0.8497 (mttt) cc_final: 0.8097 (mttp) REVERT: C 369 LYS cc_start: 0.8710 (mttt) cc_final: 0.8311 (mtpp) REVERT: D 307 GLN cc_start: 0.8374 (tt0) cc_final: 0.7790 (tm-30) REVERT: D 311 LYS cc_start: 0.8624 (tttt) cc_final: 0.8259 (ttpt) REVERT: D 331 LYS cc_start: 0.8465 (mttt) cc_final: 0.8003 (mmmt) REVERT: D 340 LYS cc_start: 0.8583 (mttt) cc_final: 0.8259 (mtpp) REVERT: D 374 HIS cc_start: 0.7419 (OUTLIER) cc_final: 0.7181 (p-80) REVERT: D 375 LYS cc_start: 0.8587 (pttt) cc_final: 0.8108 (ptpp) REVERT: D 379 ARG cc_start: 0.6936 (mtt-85) cc_final: 0.5700 (mmp-170) REVERT: E 317 LYS cc_start: 0.8276 (mtmt) cc_final: 0.7791 (ptmt) REVERT: E 321 LYS cc_start: 0.8771 (mttt) cc_final: 0.8401 (mttm) REVERT: E 343 LYS cc_start: 0.9167 (mttt) cc_final: 0.8895 (mttm) REVERT: E 356 SER cc_start: 0.8091 (p) cc_final: 0.7864 (t) REVERT: E 369 LYS cc_start: 0.8517 (mttt) cc_final: 0.8126 (mtpp) REVERT: F 307 GLN cc_start: 0.8060 (mt0) cc_final: 0.7511 (tt0) REVERT: F 311 LYS cc_start: 0.8461 (tttt) cc_final: 0.8037 (ttpt) REVERT: F 331 LYS cc_start: 0.8467 (mttt) cc_final: 0.7477 (mmtt) REVERT: F 356 SER cc_start: 0.7408 (p) cc_final: 0.6778 (t) REVERT: F 375 LYS cc_start: 0.8096 (pttt) cc_final: 0.7607 (ptpt) outliers start: 10 outliers final: 7 residues processed: 109 average time/residue: 0.6419 time to fit residues: 77.4570 Evaluate side-chains 98 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 28 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.4173 r_free = 0.4173 target = 0.145954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.128754 restraints weight = 13616.103| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.17 r_work: 0.3877 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3786 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3561 Z= 0.304 Angle : 0.552 5.509 4761 Z= 0.295 Chirality : 0.052 0.134 531 Planarity : 0.004 0.041 609 Dihedral : 5.254 17.258 474 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.51 % Allowed : 10.78 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (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 HIS 0.002 0.001 HIS F 329 PHE 0.011 0.002 PHE F 346 TYR 0.014 0.003 TYR E 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 101 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.733 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: 0.8719 (mttt) cc_final: 0.8284 (mttp) REVERT: A 369 LYS cc_start: 0.8497 (mttt) cc_final: 0.8166 (mtpp) REVERT: B 307 GLN cc_start: 0.8180 (mt0) cc_final: 0.7674 (tt0) REVERT: B 331 LYS cc_start: 0.8463 (mttt) cc_final: 0.8153 (mtpp) REVERT: B 375 LYS cc_start: 0.8429 (ptmt) cc_final: 0.7866 (ptpp) REVERT: C 321 LYS cc_start: 0.8686 (mttt) cc_final: 0.8282 (mttp) REVERT: C 369 LYS cc_start: 0.8774 (mttt) cc_final: 0.8491 (mtpp) REVERT: D 311 LYS cc_start: 0.8706 (tttt) cc_final: 0.8346 (ttpt) REVERT: D 331 LYS cc_start: 0.8572 (mttt) cc_final: 0.8275 (mtpp) REVERT: D 340 LYS cc_start: 0.8650 (mttt) cc_final: 0.8376 (mtpp) REVERT: D 374 HIS cc_start: 0.7891 (OUTLIER) cc_final: 0.7335 (p-80) REVERT: D 375 LYS cc_start: 0.8541 (pttt) cc_final: 0.8070 (ptpp) REVERT: D 379 ARG cc_start: 0.7115 (mtt-85) cc_final: 0.6244 (mmp-170) REVERT: E 317 LYS cc_start: 0.8354 (mtmt) cc_final: 0.7738 (ptmt) REVERT: E 321 LYS cc_start: 0.8827 (mttt) cc_final: 0.8510 (mttm) REVERT: E 356 SER cc_start: 0.8288 (p) cc_final: 0.8077 (t) REVERT: E 369 LYS cc_start: 0.8565 (mttt) cc_final: 0.8179 (mtpp) REVERT: F 311 LYS cc_start: 0.8458 (tttt) cc_final: 0.7903 (mmtt) REVERT: F 331 LYS cc_start: 0.8650 (mttt) cc_final: 0.7736 (mmtt) REVERT: F 375 LYS cc_start: 0.8284 (pttt) cc_final: 0.7820 (ptpt) outliers start: 10 outliers final: 5 residues processed: 99 average time/residue: 0.6816 time to fit residues: 74.5210 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 : 0.540 ------------------------------------------------------------------------------- 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 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 34 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.4210 r_free = 0.4210 target = 0.153600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.136675 restraints weight = 12810.285| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.14 r_work: 0.3928 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3838 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.4948 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= 0.205 Angle : 0.492 4.424 4761 Z= 0.258 Chirality : 0.051 0.130 531 Planarity : 0.003 0.041 609 Dihedral : 4.961 17.321 474 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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: -1.42 (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 HIS 0.002 0.000 HIS B 374 PHE 0.006 0.001 PHE B 346 TYR 0.007 0.002 TYR C 310 ARG 0.001 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 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: 0.8753 (mttt) cc_final: 0.8313 (mttp) REVERT: A 369 LYS cc_start: 0.8549 (mttt) cc_final: 0.8240 (mtpp) REVERT: B 307 GLN cc_start: 0.8166 (mt0) cc_final: 0.7655 (tt0) REVERT: B 331 LYS cc_start: 0.8443 (mttt) cc_final: 0.8109 (mtpp) REVERT: B 375 LYS cc_start: 0.8389 (ptmt) cc_final: 0.7843 (ptpp) REVERT: C 321 LYS cc_start: 0.8664 (mttt) cc_final: 0.8240 (mttp) REVERT: C 369 LYS cc_start: 0.8742 (mttt) cc_final: 0.8431 (mtpp) REVERT: D 311 LYS cc_start: 0.8690 (tttt) cc_final: 0.8332 (ttpt) REVERT: D 331 LYS cc_start: 0.8563 (mttt) cc_final: 0.8083 (mmmt) REVERT: D 340 LYS cc_start: 0.8594 (mttt) cc_final: 0.8281 (mtpp) REVERT: D 374 HIS cc_start: 0.7671 (OUTLIER) cc_final: 0.7441 (p90) REVERT: D 375 LYS cc_start: 0.8532 (pttt) cc_final: 0.7973 (ptpp) REVERT: D 379 ARG cc_start: 0.7087 (mtt-85) cc_final: 0.6147 (mmp-170) REVERT: E 317 LYS cc_start: 0.8406 (mtmt) cc_final: 0.7783 (ptmt) REVERT: E 321 LYS cc_start: 0.8854 (mttt) cc_final: 0.8542 (mttm) REVERT: E 356 SER cc_start: 0.8335 (p) cc_final: 0.8127 (t) REVERT: E 369 LYS cc_start: 0.8594 (mttt) cc_final: 0.8213 (mtpp) REVERT: F 311 LYS cc_start: 0.8421 (tttt) cc_final: 0.7819 (mmtt) REVERT: F 331 LYS cc_start: 0.8631 (mttt) cc_final: 0.7673 (mmtt) REVERT: F 375 LYS cc_start: 0.8302 (pttt) cc_final: 0.7811 (ptpt) outliers start: 9 outliers final: 6 residues processed: 96 average time/residue: 0.6927 time to fit residues: 73.8567 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 : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP 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 374 HIS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 0.4980 chunk 4 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 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: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4295 r_free = 0.4295 target = 0.162239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.145153 restraints weight = 13008.232| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 2.15 r_work: 0.3992 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3900 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3561 Z= 0.110 Angle : 0.452 4.281 4761 Z= 0.232 Chirality : 0.051 0.132 531 Planarity : 0.003 0.045 609 Dihedral : 4.468 16.806 474 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.25 % Allowed : 12.53 % 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: -1.34 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 374 PHE 0.003 0.000 PHE B 346 TYR 0.005 0.001 TYR B 310 ARG 0.002 0.000 ARG C 349 *********************** 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 98 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.518 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: 0.8739 (mttt) cc_final: 0.8312 (mttp) REVERT: A 369 LYS cc_start: 0.8558 (mttt) cc_final: 0.8238 (mtpp) REVERT: B 307 GLN cc_start: 0.8191 (mt0) cc_final: 0.7638 (tt0) REVERT: B 331 LYS cc_start: 0.8447 (mttt) cc_final: 0.8025 (mtpp) REVERT: B 375 LYS cc_start: 0.8391 (ptmt) cc_final: 0.7920 (ptpp) REVERT: C 321 LYS cc_start: 0.8620 (mttt) cc_final: 0.8182 (mttp) REVERT: C 369 LYS cc_start: 0.8721 (mttt) cc_final: 0.8438 (mtpp) REVERT: D 311 LYS cc_start: 0.8573 (tttt) cc_final: 0.8200 (ttpt) REVERT: D 331 LYS cc_start: 0.8566 (mttt) cc_final: 0.8111 (mmmt) REVERT: D 340 LYS cc_start: 0.8603 (mttt) cc_final: 0.8294 (mtpp) REVERT: D 375 LYS cc_start: 0.8497 (pttt) cc_final: 0.7905 (ptpp) REVERT: D 379 ARG cc_start: 0.6866 (mtt-85) cc_final: 0.5771 (mmp-170) REVERT: E 317 LYS cc_start: 0.8456 (mtmt) cc_final: 0.7846 (ptmt) REVERT: E 321 LYS cc_start: 0.8838 (mttt) cc_final: 0.8530 (mttm) REVERT: E 369 LYS cc_start: 0.8580 (mttt) cc_final: 0.8252 (mtpp) REVERT: F 307 GLN cc_start: 0.8156 (mt0) cc_final: 0.7521 (tm-30) REVERT: F 311 LYS cc_start: 0.8298 (tttt) cc_final: 0.7680 (mmtt) REVERT: F 331 LYS cc_start: 0.8565 (mttt) cc_final: 0.7604 (mmtt) REVERT: F 356 SER cc_start: 0.7530 (p) cc_final: 0.6984 (t) outliers start: 5 outliers final: 4 residues processed: 95 average time/residue: 0.6151 time to fit residues: 65.1465 Evaluate side-chains 90 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.150906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.133976 restraints weight = 13397.485| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.16 r_work: 0.3914 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3822 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.5260 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= 0.190 Angle : 0.465 4.686 4761 Z= 0.243 Chirality : 0.051 0.130 531 Planarity : 0.003 0.042 609 Dihedral : 4.566 16.636 474 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % 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: -1.35 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.02 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 374 PHE 0.006 0.001 PHE F 346 TYR 0.009 0.002 TYR E 310 ARG 0.001 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8746 (mttt) cc_final: 0.8315 (mttp) REVERT: A 369 LYS cc_start: 0.8575 (mttt) cc_final: 0.8248 (mtpp) REVERT: B 307 GLN cc_start: 0.8189 (mt0) cc_final: 0.7679 (tt0) REVERT: B 331 LYS cc_start: 0.8451 (mttt) cc_final: 0.8097 (mtpp) REVERT: B 375 LYS cc_start: 0.8386 (ptmt) cc_final: 0.7899 (ptpp) REVERT: C 321 LYS cc_start: 0.8652 (mttt) cc_final: 0.8225 (mttp) REVERT: C 369 LYS cc_start: 0.8765 (mttt) cc_final: 0.8464 (mtpp) REVERT: D 311 LYS cc_start: 0.8636 (tttt) cc_final: 0.8265 (ttpt) REVERT: D 331 LYS cc_start: 0.8574 (mttt) cc_final: 0.8086 (mmmt) REVERT: D 340 LYS cc_start: 0.8625 (mttt) cc_final: 0.8291 (mtpp) REVERT: D 374 HIS cc_start: 0.7657 (OUTLIER) cc_final: 0.7442 (p90) REVERT: D 375 LYS cc_start: 0.8558 (pttt) cc_final: 0.7917 (ptpp) REVERT: D 379 ARG cc_start: 0.7001 (mtt-85) cc_final: 0.6082 (mmp-170) REVERT: E 317 LYS cc_start: 0.8420 (mtmt) cc_final: 0.7766 (ptmt) REVERT: E 321 LYS cc_start: 0.8822 (mttt) cc_final: 0.8520 (mttp) REVERT: E 369 LYS cc_start: 0.8561 (mttt) cc_final: 0.8231 (mtpp) REVERT: F 311 LYS cc_start: 0.8337 (tttt) cc_final: 0.7553 (mmtt) REVERT: F 331 LYS cc_start: 0.8661 (mttt) cc_final: 0.7701 (mmtt) REVERT: F 356 SER cc_start: 0.7530 (p) cc_final: 0.6977 (t) REVERT: F 375 LYS cc_start: 0.8337 (pttt) cc_final: 0.7845 (ptpp) outliers start: 7 outliers final: 5 residues processed: 92 average time/residue: 0.7486 time to fit residues: 76.5197 Evaluate side-chains 93 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 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 = 0.4220 r_free = 0.4220 target = 0.150875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.133615 restraints weight = 13458.575| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 2.24 r_work: 0.3923 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3832 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.5356 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= 0.175 Angle : 0.462 4.379 4761 Z= 0.240 Chirality : 0.051 0.129 531 Planarity : 0.003 0.044 609 Dihedral : 4.513 16.463 474 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.26 % Allowed : 12.53 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (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 0.003 0.000 HIS B 374 PHE 0.004 0.001 PHE B 378 TYR 0.009 0.002 TYR C 310 ARG 0.001 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.584 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: 0.8752 (mttt) cc_final: 0.8334 (mttp) REVERT: A 369 LYS cc_start: 0.8595 (mttt) cc_final: 0.8324 (mtpp) REVERT: B 307 GLN cc_start: 0.8191 (mt0) cc_final: 0.7701 (tt0) REVERT: B 331 LYS cc_start: 0.8474 (mttt) cc_final: 0.8148 (mtpp) REVERT: B 375 LYS cc_start: 0.8376 (ptmt) cc_final: 0.7887 (ptpp) REVERT: C 321 LYS cc_start: 0.8641 (mttt) cc_final: 0.8205 (mttp) REVERT: C 349 ARG cc_start: 0.7911 (mtm180) cc_final: 0.6234 (mtt-85) REVERT: C 369 LYS cc_start: 0.8732 (mttt) cc_final: 0.8462 (mtpp) REVERT: D 311 LYS cc_start: 0.8627 (tttt) cc_final: 0.8251 (ttpt) REVERT: D 331 LYS cc_start: 0.8539 (mttt) cc_final: 0.8220 (mtpp) REVERT: D 340 LYS cc_start: 0.8619 (mttt) cc_final: 0.8295 (mtpp) REVERT: D 374 HIS cc_start: 0.7624 (OUTLIER) cc_final: 0.7404 (p90) REVERT: D 375 LYS cc_start: 0.8586 (pttt) cc_final: 0.7930 (ptpp) REVERT: D 379 ARG cc_start: 0.7034 (mtt-85) cc_final: 0.6101 (mmp-170) REVERT: E 317 LYS cc_start: 0.8431 (mtmt) cc_final: 0.7769 (ptmt) REVERT: E 321 LYS cc_start: 0.8846 (mttt) cc_final: 0.8550 (mttm) REVERT: E 369 LYS cc_start: 0.8593 (mttt) cc_final: 0.8237 (mtpp) REVERT: F 311 LYS cc_start: 0.8312 (tttt) cc_final: 0.7586 (mmtt) REVERT: F 331 LYS cc_start: 0.8662 (mttt) cc_final: 0.7700 (mmtt) REVERT: F 356 SER cc_start: 0.7599 (p) cc_final: 0.7085 (t) REVERT: F 375 LYS cc_start: 0.8350 (pttt) cc_final: 0.7912 (ptpp) outliers start: 9 outliers final: 5 residues processed: 94 average time/residue: 0.6658 time to fit residues: 69.2675 Evaluate side-chains 93 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.4193 r_free = 0.4193 target = 0.152106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.135115 restraints weight = 12997.664| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 2.16 r_work: 0.3911 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3821 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3561 Z= 0.209 Angle : 0.479 5.773 4761 Z= 0.250 Chirality : 0.051 0.129 531 Planarity : 0.003 0.041 609 Dihedral : 4.582 16.412 474 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.75 % Allowed : 12.78 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (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 0.005 0.001 PHE F 346 TYR 0.010 0.002 TYR C 310 ARG 0.001 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.631 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: 0.8734 (mttt) cc_final: 0.8299 (mttp) REVERT: A 369 LYS cc_start: 0.8578 (mttt) cc_final: 0.8282 (mtpp) REVERT: B 307 GLN cc_start: 0.8189 (mt0) cc_final: 0.7694 (tt0) REVERT: B 331 LYS cc_start: 0.8448 (mttt) cc_final: 0.8116 (mtpp) REVERT: B 375 LYS cc_start: 0.8376 (ptmt) cc_final: 0.7855 (ptpp) REVERT: C 321 LYS cc_start: 0.8647 (mttt) cc_final: 0.8199 (mttp) REVERT: C 349 ARG cc_start: 0.7583 (mtm180) cc_final: 0.6233 (mtt-85) REVERT: C 369 LYS cc_start: 0.8745 (mttt) cc_final: 0.8454 (mtpp) REVERT: D 311 LYS cc_start: 0.8632 (tttt) cc_final: 0.8256 (ttpt) REVERT: D 331 LYS cc_start: 0.8499 (mttt) cc_final: 0.8163 (mtpp) REVERT: D 340 LYS cc_start: 0.8596 (mttt) cc_final: 0.8265 (mtpp) REVERT: D 374 HIS cc_start: 0.7703 (OUTLIER) cc_final: 0.7485 (p90) REVERT: D 375 LYS cc_start: 0.8578 (pttt) cc_final: 0.7902 (ptpp) REVERT: D 379 ARG cc_start: 0.7070 (mtt-85) cc_final: 0.6137 (mmp-170) REVERT: E 317 LYS cc_start: 0.8402 (mtmt) cc_final: 0.7665 (ptmt) REVERT: E 321 LYS cc_start: 0.8767 (mttt) cc_final: 0.8471 (mttm) REVERT: E 369 LYS cc_start: 0.8587 (mttt) cc_final: 0.8204 (mtpp) REVERT: F 311 LYS cc_start: 0.8342 (tttt) cc_final: 0.7651 (mmtt) REVERT: F 331 LYS cc_start: 0.8698 (mttt) cc_final: 0.7736 (mmtt) REVERT: F 356 SER cc_start: 0.7616 (p) cc_final: 0.7093 (t) REVERT: F 375 LYS cc_start: 0.8330 (pttt) cc_final: 0.7896 (ptpp) outliers start: 7 outliers final: 6 residues processed: 91 average time/residue: 0.9003 time to fit residues: 91.3846 Evaluate side-chains 92 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP 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 374 HIS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 14 optimal weight: 0.0870 chunk 11 optimal weight: 0.2980 overall best weight: 0.6360 ------------------------------------------------------------------------------- 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 = 0.4293 r_free = 0.4293 target = 0.161939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.144576 restraints weight = 13145.771| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 2.17 r_work: 0.3990 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3898 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.5553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3561 Z= 0.107 Angle : 0.446 5.606 4761 Z= 0.227 Chirality : 0.051 0.130 531 Planarity : 0.004 0.044 609 Dihedral : 4.185 15.852 474 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.50 % Allowed : 13.53 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (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 0.004 0.000 HIS B 374 PHE 0.004 0.000 PHE B 378 TYR 0.005 0.001 TYR B 310 ARG 0.001 0.000 ARG A 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.535 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: 0.8309 (mttp) REVERT: A 369 LYS cc_start: 0.8596 (mttt) cc_final: 0.8297 (mtpp) REVERT: B 307 GLN cc_start: 0.8186 (mt0) cc_final: 0.7662 (tt0) REVERT: B 331 LYS cc_start: 0.8477 (mttt) cc_final: 0.8114 (mtpp) REVERT: B 375 LYS cc_start: 0.8344 (ptmt) cc_final: 0.7871 (ptpp) REVERT: C 321 LYS cc_start: 0.8587 (mttt) cc_final: 0.8135 (mttp) REVERT: C 349 ARG cc_start: 0.7631 (mtm180) cc_final: 0.6184 (mtt-85) REVERT: C 369 LYS cc_start: 0.8620 (mttt) cc_final: 0.8391 (mtpp) REVERT: D 311 LYS cc_start: 0.8560 (tttt) cc_final: 0.8193 (ttpt) REVERT: D 331 LYS cc_start: 0.8526 (mttt) cc_final: 0.8072 (mmmt) REVERT: D 340 LYS cc_start: 0.8617 (mttt) cc_final: 0.8274 (mtpp) REVERT: D 375 LYS cc_start: 0.8491 (pttt) cc_final: 0.7797 (ptpp) REVERT: D 379 ARG cc_start: 0.6788 (mtt-85) cc_final: 0.5821 (mmp-170) REVERT: E 317 LYS cc_start: 0.8385 (mtmt) cc_final: 0.7774 (ptmt) REVERT: E 321 LYS cc_start: 0.8798 (mttt) cc_final: 0.8515 (mttm) REVERT: E 338 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8258 (mt-10) REVERT: E 369 LYS cc_start: 0.8617 (mttt) cc_final: 0.8282 (mtpp) REVERT: F 307 GLN cc_start: 0.8134 (mt0) cc_final: 0.7473 (tm-30) REVERT: F 311 LYS cc_start: 0.8240 (tttt) cc_final: 0.7491 (mmtt) REVERT: F 331 LYS cc_start: 0.8616 (mttt) cc_final: 0.7640 (mmtt) REVERT: F 356 SER cc_start: 0.7395 (p) cc_final: 0.6919 (t) outliers start: 6 outliers final: 5 residues processed: 99 average time/residue: 0.6112 time to fit residues: 67.5033 Evaluate side-chains 98 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 348 ASP 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: 0.8980 chunk 1 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 39 optimal weight: 0.2980 chunk 30 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4284 r_free = 0.4284 target = 0.156473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.139074 restraints weight = 13169.207| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 2.26 r_work: 0.3981 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3883 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.5612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3561 Z= 0.110 Angle : 0.436 5.663 4761 Z= 0.223 Chirality : 0.051 0.130 531 Planarity : 0.004 0.046 609 Dihedral : 4.079 15.615 474 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.75 % Allowed : 13.03 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS B 374 PHE 0.003 0.001 PHE B 378 TYR 0.005 0.001 TYR B 310 ARG 0.001 0.000 ARG D 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5805.23 seconds wall clock time: 102 minutes 43.29 seconds (6163.29 seconds total)