Starting phenix.real_space_refine on Sat May 2 16:14:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uq7_42463/05_2026/8uq7_42463_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uq7_42463/05_2026/8uq7_42463.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8uq7_42463/05_2026/8uq7_42463_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uq7_42463/05_2026/8uq7_42463_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8uq7_42463/05_2026/8uq7_42463.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uq7_42463/05_2026/8uq7_42463.map" } resolution = 2.31 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: 6 Type Number sf(0) Gaussians S 6 5.16 5 C 2256 2.51 5 N 660 2.21 5 O 642 1.98 5 F 6 1.80 5 H 3600 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7170 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1174 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1174 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1174 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1174 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1174 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1174 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'X6R': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'X6R': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'X6R': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'X6R': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.83, per 1000 atoms: 0.26 Number of scatterers: 7170 At special positions: 0 Unit cell: (148.57, 80.51, 36.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 6 16.00 F 6 9.00 O 642 8.00 N 660 7.00 C 2256 6.00 H 3600 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: 0.56 Conformation dependent library (CDL) restraints added in 313.7 milliseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 53.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.568A pdb=" N GLN A 307 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N TYR B 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.765A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 322 removed outlier: 6.250A pdb=" N LYS A 317 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N SER B 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR A 319 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N CYS B 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYS A 321 " --> pdb=" O CYS B 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 325 through 330 removed outlier: 8.835A pdb=" N LEU A 325 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 9.640A pdb=" N ILE B 328 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN A 327 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N HIS B 330 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N HIS A 329 " --> pdb=" O HIS B 330 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLY A 326 " --> pdb=" O LEU F 325 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASN F 327 " --> pdb=" O GLY A 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 336 through 340 removed outlier: 6.498A pdb=" N VAL A 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N LYS F 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL A 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 343 through 346 removed outlier: 6.410A pdb=" N LEU A 344 " --> pdb=" O ASP F 345 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 350 through 356 removed outlier: 6.821A pdb=" N SER B 356 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL A 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N LYS F 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER A 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N GLY F 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ILE A 354 " --> pdb=" O GLY F 355 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 359 through 362 removed outlier: 6.543A pdb=" N ASN A 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N HIS F 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N THR A 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 369 through 378 removed outlier: 6.550A pdb=" N LYS A 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N GLU B 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE A 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N HIS B 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N THR A 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LEU B 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LYS A 375 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N PHE B 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N THR A 377 " --> pdb=" O PHE B 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.535A pdb=" N GLN C 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N TYR D 310 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL C 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL C 306 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL E 309 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ILE C 308 " --> pdb=" O VAL E 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.767A pdb=" N VAL C 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 317 through 322 removed outlier: 6.207A pdb=" N LYS C 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N SER D 320 " --> pdb=" O LYS C 317 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR C 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N CYS D 322 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS C 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 325 through 330 removed outlier: 8.862A pdb=" N LEU C 325 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 9.593A pdb=" N ILE D 328 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN C 327 " --> pdb=" O ILE D 328 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N HIS D 330 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N HIS C 329 " --> pdb=" O HIS D 330 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLY C 326 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASN E 327 " --> pdb=" O GLY C 326 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 336 through 340 Processing sheet with id=AB6, first strand: chain 'D' and resid 343 through 346 removed outlier: 6.571A pdb=" N LEU C 344 " --> pdb=" O ASP E 345 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 350 through 356 removed outlier: 6.805A pdb=" N SER D 356 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL C 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N LYS E 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N SER C 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N GLY E 355 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ILE C 354 " --> pdb=" O GLY E 355 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 359 through 362 removed outlier: 6.502A pdb=" N ASN C 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N HIS E 362 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N THR C 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 369 through 378 removed outlier: 6.548A pdb=" N LYS C 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N GLU D 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE C 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N HIS D 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N THR C 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LEU D 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS C 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N PHE D 378 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR C 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 222 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: 1.16 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: 0.95 - 1.12: 3594 1.12 - 1.29: 574 1.29 - 1.47: 1253 1.47 - 1.64: 1815 1.64 - 1.81: 6 Bond restraints: 7242 Sorted by residual: bond pdb=" ND2 ASN E 327 " pdb="HD22 ASN E 327 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" ND1 HIS B 330 " pdb=" HD1 HIS B 330 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N LYS D 340 " pdb=" H LYS D 340 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" NH2 ARG B 379 " pdb="HH22 ARG B 379 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NE ARG F 349 " pdb=" HE ARG F 349 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 7237 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 10755 2.29 - 4.58: 1780 4.58 - 6.87: 565 6.87 - 9.16: 46 9.16 - 11.45: 6 Bond angle restraints: 13152 Sorted by residual: angle pdb=" CA PHE F 346 " pdb=" CB PHE F 346 " pdb=" CG PHE F 346 " ideal model delta sigma weight residual 113.80 118.80 -5.00 1.00e+00 1.00e+00 2.50e+01 angle pdb=" CA PHE A 346 " pdb=" CB PHE A 346 " pdb=" CG PHE A 346 " ideal model delta sigma weight residual 113.80 118.78 -4.98 1.00e+00 1.00e+00 2.48e+01 angle pdb=" CA PHE D 346 " pdb=" CB PHE D 346 " pdb=" CG PHE D 346 " ideal model delta sigma weight residual 113.80 118.74 -4.94 1.00e+00 1.00e+00 2.44e+01 angle pdb=" N GLY C 326 " pdb=" CA GLY C 326 " pdb=" C GLY C 326 " ideal model delta sigma weight residual 110.69 117.15 -6.46 1.33e+00 5.65e-01 2.36e+01 angle pdb=" N GLY E 326 " pdb=" CA GLY E 326 " pdb=" C GLY E 326 " ideal model delta sigma weight residual 110.69 117.12 -6.43 1.33e+00 5.65e-01 2.34e+01 ... (remaining 13147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.02: 2832 14.02 - 28.04: 210 28.04 - 42.06: 67 42.06 - 56.08: 82 56.08 - 70.09: 67 Dihedral angle restraints: 3258 sinusoidal: 1860 harmonic: 1398 Sorted by residual: dihedral pdb=" CA HIS C 330 " pdb=" C HIS C 330 " pdb=" N LYS C 331 " pdb=" CA LYS C 331 " ideal model delta harmonic sigma weight residual 180.00 -157.30 -22.70 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA HIS E 330 " pdb=" C HIS E 330 " pdb=" N LYS E 331 " pdb=" CA LYS E 331 " ideal model delta harmonic sigma weight residual -180.00 -157.33 -22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA HIS D 330 " pdb=" C HIS D 330 " pdb=" N LYS D 331 " pdb=" CA LYS D 331 " ideal model delta harmonic sigma weight residual -180.00 -157.52 -22.48 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 3255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 240 0.053 - 0.105: 197 0.105 - 0.157: 68 0.157 - 0.209: 18 0.209 - 0.261: 5 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA ASP A 348 " pdb=" N ASP A 348 " pdb=" C ASP A 348 " pdb=" CB ASP A 348 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA ASP F 348 " pdb=" N ASP F 348 " pdb=" C ASP F 348 " pdb=" CB ASP F 348 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA ASP C 348 " pdb=" N ASP C 348 " pdb=" C ASP C 348 " pdb=" CB ASP C 348 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 525 not shown) Planarity restraints: 1032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " -0.125 2.00e-02 2.50e+03 5.14e-02 7.92e+01 pdb=" CG TYR E 310 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " 0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " -0.091 2.00e-02 2.50e+03 pdb=" HD1 TYR E 310 " 0.008 2.00e-02 2.50e+03 pdb=" HD2 TYR E 310 " 0.049 2.00e-02 2.50e+03 pdb=" HE1 TYR E 310 " 0.026 2.00e-02 2.50e+03 pdb=" HE2 TYR E 310 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " -0.106 2.00e-02 2.50e+03 4.37e-02 5.72e+01 pdb=" CG TYR C 310 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " -0.077 2.00e-02 2.50e+03 pdb=" HD1 TYR C 310 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR C 310 " 0.037 2.00e-02 2.50e+03 pdb=" HE1 TYR C 310 " 0.014 2.00e-02 2.50e+03 pdb=" HE2 TYR C 310 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 371 " 0.031 2.00e-02 2.50e+03 5.70e-02 3.25e+01 pdb=" N GLU C 372 " -0.098 2.00e-02 2.50e+03 pdb=" CA GLU C 372 " 0.028 2.00e-02 2.50e+03 pdb=" H GLU C 372 " 0.039 2.00e-02 2.50e+03 ... (remaining 1029 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 632 2.18 - 2.79: 12385 2.79 - 3.39: 18642 3.39 - 4.00: 25921 4.00 - 4.60: 35547 Nonbonded interactions: 93127 Sorted by model distance: nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.581 2.450 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.596 2.450 nonbonded pdb=" HZ3 LYS B 353 " pdb=" N4 X6R B 401 " model vdw 1.598 2.600 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.599 2.450 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.600 2.450 ... (remaining 93122 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 305 through 379) selection = (chain 'B' and resid 305 through 379) selection = (chain 'C' and resid 305 through 379) selection = (chain 'D' and resid 305 through 379) selection = chain 'E' selection = chain 'F' } 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: 3.890 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: 0.040 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.910 Find NCS groups from input model: 0.090 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:7.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6225 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 : 0.012 0.069 3642 Z= 0.739 Angle : 1.836 7.069 4890 Z= 1.198 Chirality : 0.078 0.261 528 Planarity : 0.009 0.059 606 Dihedral : 11.754 67.823 1344 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 0.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % 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 are not related in a simple way. whole: -1.44 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG F 379 TYR 0.109 0.027 TYR E 310 PHE 0.039 0.012 PHE D 378 HIS 0.009 0.003 HIS F 362 Details of bonding type rmsd covalent geometry : bond 0.01226 ( 3642) covalent geometry : angle 1.83633 ( 4890) hydrogen bonds : bond 0.09098 ( 74) hydrogen bonds : angle 7.93242 ( 222) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7319 (mt0) cc_final: 0.7001 (mt0) REVERT: A 338 GLU cc_start: 0.7397 (tt0) cc_final: 0.7046 (tt0) REVERT: A 369 LYS cc_start: 0.7034 (mttt) cc_final: 0.6577 (mtpm) REVERT: A 375 LYS cc_start: 0.7381 (tttt) cc_final: 0.6811 (ttmm) REVERT: B 369 LYS cc_start: 0.7715 (mttt) cc_final: 0.7321 (mtpm) REVERT: B 375 LYS cc_start: 0.8079 (tttt) cc_final: 0.7554 (ttmm) REVERT: C 338 GLU cc_start: 0.7203 (tt0) cc_final: 0.6877 (tt0) REVERT: C 369 LYS cc_start: 0.7075 (mttt) cc_final: 0.6462 (mtpm) REVERT: C 375 LYS cc_start: 0.7212 (tttt) cc_final: 0.6528 (ttmm) REVERT: D 369 LYS cc_start: 0.7888 (mttt) cc_final: 0.7353 (mtpm) REVERT: D 375 LYS cc_start: 0.8142 (tttt) cc_final: 0.7501 (ttmp) REVERT: E 311 LYS cc_start: 0.7529 (mttt) cc_final: 0.7098 (mttm) REVERT: E 369 LYS cc_start: 0.7247 (mttt) cc_final: 0.6599 (mtpm) REVERT: E 370 LYS cc_start: 0.6431 (tttm) cc_final: 0.6171 (tttp) REVERT: E 375 LYS cc_start: 0.7095 (tttt) cc_final: 0.6603 (ttmp) REVERT: F 307 GLN cc_start: 0.7614 (mt0) cc_final: 0.7082 (mt0) REVERT: F 311 LYS cc_start: 0.7750 (mttt) cc_final: 0.7347 (mttm) REVERT: F 338 GLU cc_start: 0.7114 (tt0) cc_final: 0.6542 (tt0) REVERT: F 340 LYS cc_start: 0.5992 (mttt) cc_final: 0.5782 (mmtm) REVERT: F 369 LYS cc_start: 0.7243 (mttt) cc_final: 0.6751 (mtpm) REVERT: F 375 LYS cc_start: 0.7322 (tttt) cc_final: 0.6836 (ttmp) outliers start: 0 outliers final: 1 residues processed: 145 average time/residue: 1.5767 time to fit residues: 233.2597 Evaluate side-chains 113 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 348 ASP 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: 0.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 327 ASN F 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.158410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.134601 restraints weight = 11302.910| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 1.57 r_work: 0.3997 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3913 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3642 Z= 0.118 Angle : 0.612 4.188 4890 Z= 0.322 Chirality : 0.051 0.135 528 Planarity : 0.004 0.039 606 Dihedral : 6.777 21.287 464 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.77 % Allowed : 13.64 % Favored : 84.60 % 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 are not related in a simple way. whole: -1.54 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 379 TYR 0.010 0.002 TYR C 310 PHE 0.006 0.001 PHE D 346 HIS 0.007 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 3642) covalent geometry : angle 0.61150 ( 4890) hydrogen bonds : bond 0.02195 ( 74) hydrogen bonds : angle 5.60696 ( 222) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 369 LYS cc_start: 0.8635 (mttt) cc_final: 0.8268 (mtpm) REVERT: A 375 LYS cc_start: 0.8269 (tttt) cc_final: 0.7820 (ttmm) REVERT: B 369 LYS cc_start: 0.8536 (mttt) cc_final: 0.8284 (mtpm) REVERT: B 375 LYS cc_start: 0.8380 (tttt) cc_final: 0.7998 (ttmm) REVERT: C 331 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8699 (ttmt) REVERT: C 340 LYS cc_start: 0.8397 (mtpp) cc_final: 0.7961 (mmtm) REVERT: C 369 LYS cc_start: 0.8640 (mttt) cc_final: 0.8285 (mtpm) REVERT: C 375 LYS cc_start: 0.8185 (tttt) cc_final: 0.7641 (ttmm) REVERT: D 369 LYS cc_start: 0.8582 (mttt) cc_final: 0.8309 (mtpm) REVERT: D 375 LYS cc_start: 0.8390 (tttt) cc_final: 0.8015 (ttmp) REVERT: E 307 GLN cc_start: 0.7925 (mt0) cc_final: 0.7514 (mt0) REVERT: E 311 LYS cc_start: 0.8617 (mttt) cc_final: 0.7802 (mttm) REVERT: E 369 LYS cc_start: 0.8655 (mttt) cc_final: 0.8354 (mtpm) REVERT: E 375 LYS cc_start: 0.8053 (tttt) cc_final: 0.7697 (ttmp) REVERT: F 311 LYS cc_start: 0.8743 (mttt) cc_final: 0.7870 (mttm) REVERT: F 331 LYS cc_start: 0.8873 (mtpt) cc_final: 0.7968 (tptp) REVERT: F 340 LYS cc_start: 0.8498 (mttt) cc_final: 0.8118 (mmtt) REVERT: F 369 LYS cc_start: 0.8665 (mttt) cc_final: 0.8351 (mtpm) REVERT: F 375 LYS cc_start: 0.8252 (tttt) cc_final: 0.7929 (ttmp) outliers start: 7 outliers final: 1 residues processed: 122 average time/residue: 1.6662 time to fit residues: 207.3189 Evaluate side-chains 100 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain F residue 345 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN D 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.150377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.124836 restraints weight = 10755.563| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 1.60 r_work: 0.3875 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3792 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3642 Z= 0.224 Angle : 0.650 4.692 4890 Z= 0.344 Chirality : 0.052 0.129 528 Planarity : 0.005 0.042 606 Dihedral : 6.523 20.245 462 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.27 % Allowed : 16.41 % Favored : 81.31 % 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 are not related in a simple way. whole: -1.60 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 379 TYR 0.020 0.004 TYR E 310 PHE 0.010 0.002 PHE D 346 HIS 0.005 0.002 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00503 ( 3642) covalent geometry : angle 0.64952 ( 4890) hydrogen bonds : bond 0.02304 ( 74) hydrogen bonds : angle 5.42381 ( 222) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 369 LYS cc_start: 0.8676 (mttt) cc_final: 0.8327 (mtpm) REVERT: A 375 LYS cc_start: 0.8291 (tttt) cc_final: 0.7863 (ttmm) REVERT: B 369 LYS cc_start: 0.8594 (mttt) cc_final: 0.8354 (mtpm) REVERT: B 375 LYS cc_start: 0.8461 (tttt) cc_final: 0.8072 (ttmm) REVERT: C 340 LYS cc_start: 0.8500 (mtpp) cc_final: 0.7948 (mmtm) REVERT: C 369 LYS cc_start: 0.8676 (mttt) cc_final: 0.8321 (mtpm) REVERT: C 375 LYS cc_start: 0.8276 (tttt) cc_final: 0.7723 (ttmm) REVERT: D 369 LYS cc_start: 0.8725 (mttt) cc_final: 0.8427 (mtpm) REVERT: D 375 LYS cc_start: 0.8459 (tttt) cc_final: 0.8086 (ttmp) REVERT: E 307 GLN cc_start: 0.7898 (mt0) cc_final: 0.7623 (mt0) REVERT: E 311 LYS cc_start: 0.8720 (mttt) cc_final: 0.7820 (mmtm) REVERT: E 331 LYS cc_start: 0.8865 (ttmt) cc_final: 0.8619 (mtpp) REVERT: E 369 LYS cc_start: 0.8699 (mttt) cc_final: 0.8367 (mtpm) REVERT: E 375 LYS cc_start: 0.8131 (tttt) cc_final: 0.7730 (ttmp) REVERT: F 311 LYS cc_start: 0.8854 (mttt) cc_final: 0.7940 (mmtm) REVERT: F 331 LYS cc_start: 0.9028 (mtpt) cc_final: 0.8047 (tptp) REVERT: F 340 LYS cc_start: 0.8556 (mttt) cc_final: 0.8113 (mmtt) REVERT: F 369 LYS cc_start: 0.8743 (mttt) cc_final: 0.8435 (mtpm) REVERT: F 375 LYS cc_start: 0.8230 (tttt) cc_final: 0.7895 (ttmp) outliers start: 9 outliers final: 2 residues processed: 108 average time/residue: 1.7886 time to fit residues: 196.7618 Evaluate side-chains 103 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain F residue 316 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.4373 r_free = 0.4373 target = 0.155201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.130510 restraints weight = 10843.483| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 1.65 r_work: 0.3955 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3868 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3642 Z= 0.100 Angle : 0.534 4.163 4890 Z= 0.277 Chirality : 0.051 0.131 528 Planarity : 0.004 0.037 606 Dihedral : 5.801 17.329 462 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.26 % Allowed : 16.41 % Favored : 82.32 % 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 are not related in a simple way. whole: -1.64 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 379 TYR 0.008 0.002 TYR E 310 PHE 0.003 0.000 PHE F 378 HIS 0.007 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 3642) covalent geometry : angle 0.53360 ( 4890) hydrogen bonds : bond 0.01494 ( 74) hydrogen bonds : angle 4.68278 ( 222) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 369 LYS cc_start: 0.8674 (mttt) cc_final: 0.8341 (mtpm) REVERT: A 375 LYS cc_start: 0.8313 (tttt) cc_final: 0.7892 (ttmm) REVERT: B 340 LYS cc_start: 0.8585 (mtpp) cc_final: 0.8171 (mmtt) REVERT: B 342 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7263 (mp0) REVERT: B 369 LYS cc_start: 0.8490 (mttt) cc_final: 0.8276 (mtpm) REVERT: B 375 LYS cc_start: 0.8445 (tttt) cc_final: 0.8063 (ttmm) REVERT: C 369 LYS cc_start: 0.8664 (mttt) cc_final: 0.8338 (mtpm) REVERT: C 375 LYS cc_start: 0.8311 (tttt) cc_final: 0.7914 (ttmp) REVERT: D 331 LYS cc_start: 0.8752 (mtmt) cc_final: 0.8463 (mmmt) REVERT: D 369 LYS cc_start: 0.8572 (mttt) cc_final: 0.8316 (mtpm) REVERT: D 375 LYS cc_start: 0.8386 (tttt) cc_final: 0.8041 (ttmp) REVERT: E 307 GLN cc_start: 0.7883 (mt0) cc_final: 0.7546 (mt0) REVERT: E 311 LYS cc_start: 0.8615 (mttt) cc_final: 0.7745 (mmtm) REVERT: E 331 LYS cc_start: 0.8897 (ttmt) cc_final: 0.8671 (mtpp) REVERT: E 369 LYS cc_start: 0.8633 (mttt) cc_final: 0.8321 (mtpm) REVERT: E 375 LYS cc_start: 0.8118 (tttt) cc_final: 0.7703 (ttmp) REVERT: F 311 LYS cc_start: 0.8788 (mttt) cc_final: 0.7962 (mttm) REVERT: F 331 LYS cc_start: 0.9022 (mtpt) cc_final: 0.8013 (tmtt) REVERT: F 340 LYS cc_start: 0.8540 (mttt) cc_final: 0.8129 (mmtt) REVERT: F 342 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7490 (mt-10) REVERT: F 369 LYS cc_start: 0.8692 (mttt) cc_final: 0.8406 (mtpm) REVERT: F 375 LYS cc_start: 0.8226 (tttt) cc_final: 0.7909 (ttmp) outliers start: 5 outliers final: 0 residues processed: 107 average time/residue: 1.7150 time to fit residues: 186.9045 Evaluate side-chains 101 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 28 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 39 optimal weight: 0.0370 chunk 0 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- 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 = 0.4343 r_free = 0.4343 target = 0.152942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.128028 restraints weight = 10796.018| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 1.64 r_work: 0.3915 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3827 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3642 Z= 0.122 Angle : 0.533 4.523 4890 Z= 0.278 Chirality : 0.051 0.125 528 Planarity : 0.004 0.036 606 Dihedral : 5.674 16.799 462 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.77 % Allowed : 17.42 % Favored : 80.81 % 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 are not related in a simple way. whole: -1.60 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 379 TYR 0.012 0.002 TYR E 310 PHE 0.004 0.001 PHE D 346 HIS 0.006 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 3642) covalent geometry : angle 0.53293 ( 4890) hydrogen bonds : bond 0.01666 ( 74) hydrogen bonds : angle 4.55830 ( 222) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.182 Fit side-chains REVERT: A 369 LYS cc_start: 0.8685 (mttt) cc_final: 0.8343 (mtpm) REVERT: A 375 LYS cc_start: 0.8303 (tttt) cc_final: 0.7874 (ttmm) REVERT: B 340 LYS cc_start: 0.8537 (mtpp) cc_final: 0.8074 (mmtt) REVERT: B 342 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7233 (mp0) REVERT: B 369 LYS cc_start: 0.8529 (mttt) cc_final: 0.8320 (mtpm) REVERT: B 375 LYS cc_start: 0.8435 (tttt) cc_final: 0.8070 (ttmm) REVERT: C 340 LYS cc_start: 0.8493 (mtpp) cc_final: 0.7994 (mmtm) REVERT: C 375 LYS cc_start: 0.8300 (tttt) cc_final: 0.7893 (ttmp) REVERT: D 317 LYS cc_start: 0.8548 (mtpt) cc_final: 0.8338 (mtpp) REVERT: D 331 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8612 (mtpt) REVERT: D 369 LYS cc_start: 0.8584 (mttt) cc_final: 0.8336 (mtpm) REVERT: D 375 LYS cc_start: 0.8378 (tttt) cc_final: 0.8058 (ttmp) REVERT: E 307 GLN cc_start: 0.7871 (mt0) cc_final: 0.7506 (mt0) REVERT: E 311 LYS cc_start: 0.8675 (mttt) cc_final: 0.7806 (mmtm) REVERT: E 369 LYS cc_start: 0.8621 (mttt) cc_final: 0.8309 (mtpm) REVERT: E 375 LYS cc_start: 0.8098 (tttt) cc_final: 0.7671 (ttmp) REVERT: F 311 LYS cc_start: 0.8827 (mttt) cc_final: 0.7975 (mmtm) REVERT: F 327 ASN cc_start: 0.8672 (OUTLIER) cc_final: 0.8295 (m110) REVERT: F 331 LYS cc_start: 0.9070 (mtpt) cc_final: 0.8091 (tptp) REVERT: F 340 LYS cc_start: 0.8525 (mttt) cc_final: 0.8095 (mmtt) REVERT: F 369 LYS cc_start: 0.8669 (mttt) cc_final: 0.8383 (mtpm) REVERT: F 375 LYS cc_start: 0.8211 (tttt) cc_final: 0.7917 (ttmp) outliers start: 7 outliers final: 2 residues processed: 104 average time/residue: 1.8956 time to fit residues: 200.5516 Evaluate side-chains 104 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 327 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.154768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.130660 restraints weight = 11396.743| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 1.58 r_work: 0.3951 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3864 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3642 Z= 0.106 Angle : 0.518 4.340 4890 Z= 0.269 Chirality : 0.050 0.127 528 Planarity : 0.004 0.031 606 Dihedral : 5.460 15.121 462 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.52 % Allowed : 17.42 % Favored : 81.06 % 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 are not related in a simple way. whole: -1.60 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 379 TYR 0.009 0.002 TYR E 310 PHE 0.002 0.001 PHE F 378 HIS 0.006 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 3642) covalent geometry : angle 0.51757 ( 4890) hydrogen bonds : bond 0.01475 ( 74) hydrogen bonds : angle 4.32234 ( 222) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 369 LYS cc_start: 0.8669 (mttt) cc_final: 0.8332 (mtpm) REVERT: A 375 LYS cc_start: 0.8308 (tttt) cc_final: 0.7880 (ttmm) REVERT: B 342 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7287 (mp0) REVERT: B 375 LYS cc_start: 0.8414 (tttt) cc_final: 0.8172 (ttmp) REVERT: C 331 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8543 (mtpp) REVERT: C 340 LYS cc_start: 0.8492 (mtpp) cc_final: 0.8024 (mmtm) REVERT: C 375 LYS cc_start: 0.8306 (tttt) cc_final: 0.7901 (ttmp) REVERT: D 369 LYS cc_start: 0.8544 (mttt) cc_final: 0.8310 (mtpm) REVERT: D 375 LYS cc_start: 0.8332 (tttt) cc_final: 0.8032 (ttmp) REVERT: E 307 GLN cc_start: 0.7863 (mt0) cc_final: 0.7558 (mt0) REVERT: E 311 LYS cc_start: 0.8653 (mttt) cc_final: 0.7767 (mmtm) REVERT: E 369 LYS cc_start: 0.8618 (mttt) cc_final: 0.8306 (mtpm) REVERT: E 375 LYS cc_start: 0.8076 (tttt) cc_final: 0.7636 (ttmp) REVERT: F 311 LYS cc_start: 0.8810 (mttt) cc_final: 0.7944 (mmtm) REVERT: F 331 LYS cc_start: 0.9056 (mtpt) cc_final: 0.8043 (tmtt) REVERT: F 340 LYS cc_start: 0.8524 (mttt) cc_final: 0.8082 (mmtt) REVERT: F 369 LYS cc_start: 0.8665 (mttt) cc_final: 0.8383 (mtpm) REVERT: F 375 LYS cc_start: 0.8207 (tttt) cc_final: 0.7925 (ttmp) outliers start: 6 outliers final: 2 residues processed: 103 average time/residue: 1.8637 time to fit residues: 195.4169 Evaluate side-chains 101 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain E residue 345 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.4335 r_free = 0.4335 target = 0.151990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.126686 restraints weight = 10843.761| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 1.66 r_work: 0.3905 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3818 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3642 Z= 0.141 Angle : 0.550 4.436 4890 Z= 0.285 Chirality : 0.050 0.125 528 Planarity : 0.004 0.031 606 Dihedral : 5.644 15.567 462 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.01 % Allowed : 18.43 % Favored : 80.56 % 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 are not related in a simple way. whole: -1.58 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 379 TYR 0.012 0.002 TYR E 310 PHE 0.005 0.001 PHE D 346 HIS 0.006 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 3642) covalent geometry : angle 0.55016 ( 4890) hydrogen bonds : bond 0.01766 ( 74) hydrogen bonds : angle 4.47192 ( 222) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.198 Fit side-chains REVERT: A 369 LYS cc_start: 0.8714 (mttt) cc_final: 0.8357 (mtpm) REVERT: A 375 LYS cc_start: 0.8319 (tttt) cc_final: 0.7776 (ttmm) REVERT: B 340 LYS cc_start: 0.8531 (mtpp) cc_final: 0.8089 (mmtm) REVERT: B 342 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7314 (mp0) REVERT: B 375 LYS cc_start: 0.8460 (tttt) cc_final: 0.8199 (ttmp) REVERT: C 331 LYS cc_start: 0.8837 (ttmt) cc_final: 0.8564 (mtpp) REVERT: C 340 LYS cc_start: 0.8505 (mtpp) cc_final: 0.7993 (mmtm) REVERT: C 375 LYS cc_start: 0.8282 (tttt) cc_final: 0.7729 (ttmm) REVERT: D 342 GLU cc_start: 0.8142 (tt0) cc_final: 0.7860 (mp0) REVERT: D 369 LYS cc_start: 0.8659 (mttt) cc_final: 0.8389 (mtpm) REVERT: D 375 LYS cc_start: 0.8392 (tttt) cc_final: 0.8069 (ttmp) REVERT: E 307 GLN cc_start: 0.7843 (mt0) cc_final: 0.7544 (mt0) REVERT: E 311 LYS cc_start: 0.8733 (mttt) cc_final: 0.7850 (mmtm) REVERT: E 369 LYS cc_start: 0.8634 (mttt) cc_final: 0.8311 (mtpm) REVERT: E 375 LYS cc_start: 0.8081 (tttt) cc_final: 0.7645 (ttmp) REVERT: F 311 LYS cc_start: 0.8835 (mttt) cc_final: 0.7905 (mmtm) REVERT: F 331 LYS cc_start: 0.9096 (mtpt) cc_final: 0.8091 (tptp) REVERT: F 340 LYS cc_start: 0.8537 (mttt) cc_final: 0.8074 (mmtt) REVERT: F 369 LYS cc_start: 0.8701 (mttt) cc_final: 0.8418 (mtpm) REVERT: F 375 LYS cc_start: 0.8236 (tttt) cc_final: 0.7943 (ttmp) outliers start: 4 outliers final: 2 residues processed: 99 average time/residue: 1.8032 time to fit residues: 181.7606 Evaluate side-chains 99 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 372 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 0.0370 chunk 8 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 overall best weight: 1.5664 ------------------------------------------------------------------------------- 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 = 0.4371 r_free = 0.4371 target = 0.154972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.129862 restraints weight = 10726.213| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 1.66 r_work: 0.3951 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3863 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3642 Z= 0.105 Angle : 0.518 4.269 4890 Z= 0.268 Chirality : 0.050 0.125 528 Planarity : 0.004 0.028 606 Dihedral : 5.391 14.692 462 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.76 % Allowed : 18.69 % Favored : 80.56 % 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 are not related in a simple way. whole: -1.63 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 379 TYR 0.008 0.002 TYR E 310 PHE 0.002 0.000 PHE F 378 HIS 0.007 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 3642) covalent geometry : angle 0.51811 ( 4890) hydrogen bonds : bond 0.01425 ( 74) hydrogen bonds : angle 4.24758 ( 222) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 103 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 369 LYS cc_start: 0.8650 (mttt) cc_final: 0.8310 (mtpm) REVERT: A 375 LYS cc_start: 0.8318 (tttt) cc_final: 0.7778 (ttmm) REVERT: B 342 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7309 (mp0) REVERT: B 375 LYS cc_start: 0.8423 (tttt) cc_final: 0.8179 (ttmp) REVERT: C 331 LYS cc_start: 0.8813 (ttmt) cc_final: 0.8561 (mtpp) REVERT: C 340 LYS cc_start: 0.8488 (mtpp) cc_final: 0.8003 (mmtm) REVERT: C 375 LYS cc_start: 0.8301 (tttt) cc_final: 0.7924 (ttmp) REVERT: D 342 GLU cc_start: 0.8130 (tt0) cc_final: 0.7847 (mp0) REVERT: D 369 LYS cc_start: 0.8547 (mttt) cc_final: 0.8307 (mtpm) REVERT: D 375 LYS cc_start: 0.8346 (tttt) cc_final: 0.8047 (ttmp) REVERT: E 307 GLN cc_start: 0.7877 (mt0) cc_final: 0.7592 (mt0) REVERT: E 311 LYS cc_start: 0.8684 (mttt) cc_final: 0.7815 (mmtm) REVERT: E 369 LYS cc_start: 0.8627 (mttt) cc_final: 0.8308 (mtpm) REVERT: E 375 LYS cc_start: 0.8086 (tttt) cc_final: 0.7645 (ttmp) REVERT: F 311 LYS cc_start: 0.8823 (mttt) cc_final: 0.7890 (mmtm) REVERT: F 331 LYS cc_start: 0.9065 (mtpt) cc_final: 0.8020 (tmtt) REVERT: F 340 LYS cc_start: 0.8524 (mttt) cc_final: 0.8081 (mmtt) REVERT: F 369 LYS cc_start: 0.8695 (mttt) cc_final: 0.8409 (mtpm) REVERT: F 375 LYS cc_start: 0.8235 (tttt) cc_final: 0.7945 (ttmp) outliers start: 3 outliers final: 2 residues processed: 104 average time/residue: 1.8884 time to fit residues: 199.9135 Evaluate side-chains 101 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain D residue 345 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 0.7980 chunk 3 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 overall best weight: 1.4982 ------------------------------------------------------------------------------- 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 = 0.4381 r_free = 0.4381 target = 0.155499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.130551 restraints weight = 10715.481| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 1.65 r_work: 0.3954 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3866 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3642 Z= 0.105 Angle : 0.521 4.445 4890 Z= 0.267 Chirality : 0.050 0.125 528 Planarity : 0.004 0.028 606 Dihedral : 5.302 14.672 462 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.01 % Allowed : 18.69 % Favored : 80.30 % 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 are not related in a simple way. whole: -1.64 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 379 TYR 0.008 0.002 TYR E 310 PHE 0.003 0.001 PHE D 346 HIS 0.006 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 3642) covalent geometry : angle 0.52124 ( 4890) hydrogen bonds : bond 0.01416 ( 74) hydrogen bonds : angle 4.17006 ( 222) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 369 LYS cc_start: 0.8615 (mttt) cc_final: 0.8296 (mtpm) REVERT: A 375 LYS cc_start: 0.8315 (tttt) cc_final: 0.7769 (ttmm) REVERT: B 342 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7303 (mp0) REVERT: B 375 LYS cc_start: 0.8439 (tttt) cc_final: 0.8186 (ttmp) REVERT: C 331 LYS cc_start: 0.8782 (ttmt) cc_final: 0.8528 (mtpp) REVERT: C 340 LYS cc_start: 0.8491 (mtpp) cc_final: 0.8001 (mmtm) REVERT: C 375 LYS cc_start: 0.8285 (tttt) cc_final: 0.7899 (ttmp) REVERT: D 342 GLU cc_start: 0.8120 (tt0) cc_final: 0.7867 (mp0) REVERT: D 369 LYS cc_start: 0.8544 (mttt) cc_final: 0.8305 (mtpm) REVERT: D 375 LYS cc_start: 0.8356 (tttt) cc_final: 0.8090 (ttmp) REVERT: E 307 GLN cc_start: 0.7820 (mt0) cc_final: 0.7536 (mt0) REVERT: E 311 LYS cc_start: 0.8686 (mttt) cc_final: 0.7810 (mmtm) REVERT: E 369 LYS cc_start: 0.8603 (mttt) cc_final: 0.8290 (mtpm) REVERT: E 375 LYS cc_start: 0.8081 (tttt) cc_final: 0.7637 (ttmp) REVERT: F 311 LYS cc_start: 0.8828 (mttt) cc_final: 0.7963 (mmtm) REVERT: F 331 LYS cc_start: 0.9065 (mtpt) cc_final: 0.8022 (tmtt) REVERT: F 340 LYS cc_start: 0.8537 (mttt) cc_final: 0.8091 (mmtt) REVERT: F 369 LYS cc_start: 0.8696 (mttt) cc_final: 0.8405 (mtpm) REVERT: F 375 LYS cc_start: 0.8225 (tttt) cc_final: 0.7937 (ttmp) outliers start: 4 outliers final: 3 residues processed: 100 average time/residue: 1.8681 time to fit residues: 190.1040 Evaluate side-chains 102 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 372 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 0.3980 chunk 13 optimal weight: 0.7980 chunk 40 optimal weight: 0.3980 chunk 24 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.4429 r_free = 0.4429 target = 0.159487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.136062 restraints weight = 11427.122| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 1.58 r_work: 0.4029 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3944 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3642 Z= 0.085 Angle : 0.497 4.573 4890 Z= 0.254 Chirality : 0.051 0.126 528 Planarity : 0.004 0.028 606 Dihedral : 4.933 13.669 462 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.25 % Allowed : 19.95 % Favored : 79.80 % 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 are not related in a simple way. whole: -1.68 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 379 TYR 0.005 0.001 TYR A 310 PHE 0.002 0.000 PHE F 378 HIS 0.007 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 3642) covalent geometry : angle 0.49672 ( 4890) hydrogen bonds : bond 0.01152 ( 74) hydrogen bonds : angle 3.88948 ( 222) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 ASN cc_start: 0.8814 (m110) cc_final: 0.8576 (m-40) REVERT: A 369 LYS cc_start: 0.8557 (mttt) cc_final: 0.8268 (mtpm) REVERT: A 375 LYS cc_start: 0.8330 (tttt) cc_final: 0.7801 (ttmm) REVERT: B 342 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7294 (mp0) REVERT: B 375 LYS cc_start: 0.8383 (tttt) cc_final: 0.8161 (ttmp) REVERT: C 331 LYS cc_start: 0.8738 (ttmt) cc_final: 0.8516 (mtpp) REVERT: C 375 LYS cc_start: 0.8306 (tttt) cc_final: 0.7915 (ttmp) REVERT: D 340 LYS cc_start: 0.8604 (mttm) cc_final: 0.8230 (mmtm) REVERT: D 369 LYS cc_start: 0.8490 (mttt) cc_final: 0.8263 (mtpm) REVERT: D 375 LYS cc_start: 0.8320 (tttt) cc_final: 0.8077 (ttmp) REVERT: E 307 GLN cc_start: 0.7754 (mt0) cc_final: 0.7517 (mt0) REVERT: E 311 LYS cc_start: 0.8633 (mttt) cc_final: 0.7754 (mmtm) REVERT: E 369 LYS cc_start: 0.8563 (mttt) cc_final: 0.8266 (mtpm) REVERT: E 375 LYS cc_start: 0.8076 (tttt) cc_final: 0.7651 (ttmp) REVERT: F 311 LYS cc_start: 0.8770 (mttt) cc_final: 0.7948 (mttm) REVERT: F 331 LYS cc_start: 0.9015 (mtpt) cc_final: 0.7988 (tmtt) REVERT: F 340 LYS cc_start: 0.8513 (mttt) cc_final: 0.8095 (mmtt) REVERT: F 369 LYS cc_start: 0.8669 (mttt) cc_final: 0.8390 (mtpm) REVERT: F 375 LYS cc_start: 0.8217 (tttt) cc_final: 0.7945 (ttmp) outliers start: 1 outliers final: 0 residues processed: 108 average time/residue: 1.8217 time to fit residues: 200.3782 Evaluate side-chains 100 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.151845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.126855 restraints weight = 10820.932| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 1.63 r_work: 0.3915 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3828 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3642 Z= 0.150 Angle : 0.550 4.403 4890 Z= 0.285 Chirality : 0.050 0.124 528 Planarity : 0.004 0.030 606 Dihedral : 5.404 14.828 462 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.25 % Allowed : 20.71 % Favored : 79.04 % 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 are not related in a simple way. whole: -1.61 (0.35), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 379 TYR 0.012 0.002 TYR E 310 PHE 0.004 0.001 PHE D 346 HIS 0.005 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 3642) covalent geometry : angle 0.54987 ( 4890) hydrogen bonds : bond 0.01679 ( 74) hydrogen bonds : angle 4.28862 ( 222) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4662.09 seconds wall clock time: 79 minutes 37.90 seconds (4777.90 seconds total)