Starting phenix.real_space_refine on Fri Aug 22 19:11:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q8d_18251/08_2025/8q8d_18251.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q8d_18251/08_2025/8q8d_18251.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/8q8d_18251/08_2025/8q8d_18251.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q8d_18251/08_2025/8q8d_18251.map" model { file = "/net/cci-nas-00/data/ceres_data/8q8d_18251/08_2025/8q8d_18251.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q8d_18251/08_2025/8q8d_18251.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 2172 2.51 5 N 642 2.21 5 O 648 1.98 5 H 3606 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7074 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "B" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "D" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "E" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "F" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Time building chain proxies: 1.50, per 1000 atoms: 0.21 Number of scatterers: 7074 At special positions: 0 Unit cell: (119.48, 117.832, 39.552, 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 648 8.00 N 642 7.00 C 2172 6.00 H 3606 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: 0.33 Conformation dependent library (CDL) restraints added in 187.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 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 19 sheets defined 0.0% alpha, 48.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.519A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL A 306 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL E 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE A 308 " --> pdb=" O VAL E 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.852A 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: 6.441A 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: 6.385A pdb=" N LYS A 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.375A pdb=" N ILE A 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 336 through 340 removed outlier: 6.626A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 343 through 346 removed outlier: 6.267A pdb=" N LYS A 343 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N PHE C 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 351 through 354 removed outlier: 6.409A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE C 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LYS A 353 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.460A pdb=" N ASP A 358 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N THR C 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.480A 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: 6.380A pdb=" N LYS A 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N GLU C 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N HIS C 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N THR A 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N LEU C 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LYS A 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N PHE C 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR A 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LYS A 370 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N THR E 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLU A 372 " --> pdb=" O THR E 373 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N LYS E 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N HIS A 374 " --> pdb=" O LYS E 375 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N THR E 377 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU A 376 " --> pdb=" O THR E 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.491A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.450A 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: 6.800A 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 removed outlier: 6.243A pdb=" N LYS B 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N SER D 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR B 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N CYS D 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LYS B 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N SER D 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLY B 323 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 328 through 330 Processing sheet with id=AB6, first strand: chain 'D' and resid 336 through 342 removed outlier: 6.389A pdb=" N VAL B 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N LYS F 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL B 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N GLU F 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.626A 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: 6.817A 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: 6.730A pdb=" N GLN B 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ILE D 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LYS B 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 357 through 362 removed outlier: 6.514A pdb=" N ASP B 358 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N THR D 361 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE B 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 368 through 378 removed outlier: 6.424A pdb=" N LYS B 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N GLU D 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE B 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N HIS D 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR B 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N LEU D 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYS B 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N PHE D 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR B 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) 63 hydrogen bonds defined for protein. 189 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: 1.23 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 3600 1.12 - 1.29: 579 1.29 - 1.47: 1174 1.47 - 1.64: 1769 1.64 - 1.82: 6 Bond restraints: 7128 Sorted by residual: bond pdb=" N THR E 377 " pdb=" H THR E 377 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N GLU A 342 " pdb=" H GLU A 342 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ILE C 371 " pdb=" H ILE C 371 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N GLU E 342 " pdb=" H GLU E 342 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CZ PHE E 378 " pdb=" HZ PHE E 378 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 7123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 10932 2.51 - 5.02: 1556 5.02 - 7.53: 466 7.53 - 10.04: 21 10.04 - 12.55: 9 Bond angle restraints: 12984 Sorted by residual: angle pdb=" CA ASP D 358 " pdb=" CB ASP D 358 " pdb=" CG ASP D 358 " ideal model delta sigma weight residual 112.60 118.99 -6.39 1.00e+00 1.00e+00 4.08e+01 angle pdb=" CA ASP B 358 " pdb=" CB ASP B 358 " pdb=" CG ASP B 358 " ideal model delta sigma weight residual 112.60 118.59 -5.99 1.00e+00 1.00e+00 3.59e+01 angle pdb=" C LYS C 331 " pdb=" CA LYS C 331 " pdb=" CB LYS C 331 " ideal model delta sigma weight residual 110.55 120.21 -9.66 1.66e+00 3.63e-01 3.39e+01 angle pdb=" N SER C 324 " pdb=" CA SER C 324 " pdb=" CB SER C 324 " ideal model delta sigma weight residual 111.24 102.10 9.14 1.58e+00 4.01e-01 3.35e+01 angle pdb=" CA PHE E 346 " pdb=" CB PHE E 346 " pdb=" CG PHE E 346 " ideal model delta sigma weight residual 113.80 119.34 -5.54 1.00e+00 1.00e+00 3.07e+01 ... (remaining 12979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 2940 17.99 - 35.98: 158 35.98 - 53.98: 83 53.98 - 71.97: 96 71.97 - 89.96: 5 Dihedral angle restraints: 3282 sinusoidal: 1878 harmonic: 1404 Sorted by residual: dihedral pdb=" CA GLY C 323 " pdb=" C GLY C 323 " pdb=" N SER C 324 " pdb=" CA SER C 324 " ideal model delta harmonic sigma weight residual 180.00 150.83 29.17 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA SER A 341 " pdb=" C SER A 341 " pdb=" N GLU A 342 " pdb=" CA GLU A 342 " ideal model delta harmonic sigma weight residual 180.00 151.25 28.75 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA SER C 341 " pdb=" C SER C 341 " pdb=" N GLU C 342 " pdb=" CA GLU C 342 " ideal model delta harmonic sigma weight residual 180.00 151.64 28.36 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 3279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 323 0.073 - 0.145: 165 0.145 - 0.218: 34 0.218 - 0.290: 4 0.290 - 0.363: 2 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA CYS F 322 " pdb=" N CYS F 322 " pdb=" C CYS F 322 " pdb=" CB CYS F 322 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CA SER C 324 " pdb=" N SER C 324 " pdb=" C SER C 324 " pdb=" CB SER C 324 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA LYS E 347 " pdb=" N LYS E 347 " pdb=" C LYS E 347 " pdb=" CB LYS E 347 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 525 not shown) Planarity restraints: 1032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " 0.178 2.00e-02 2.50e+03 7.97e-02 1.91e+02 pdb=" CG TYR E 310 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " -0.051 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " -0.056 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " -0.035 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " 0.172 2.00e-02 2.50e+03 pdb=" HD1 TYR E 310 " -0.021 2.00e-02 2.50e+03 pdb=" HD2 TYR E 310 " -0.049 2.00e-02 2.50e+03 pdb=" HE1 TYR E 310 " -0.036 2.00e-02 2.50e+03 pdb=" HE2 TYR E 310 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " 0.127 2.00e-02 2.50e+03 5.36e-02 8.63e+01 pdb=" CG TYR A 310 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " -0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " 0.105 2.00e-02 2.50e+03 pdb=" HD1 TYR A 310 " -0.016 2.00e-02 2.50e+03 pdb=" HD2 TYR A 310 " -0.041 2.00e-02 2.50e+03 pdb=" HE1 TYR A 310 " -0.023 2.00e-02 2.50e+03 pdb=" HE2 TYR A 310 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 310 " -0.083 2.00e-02 2.50e+03 3.78e-02 4.28e+01 pdb=" CG TYR B 310 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR B 310 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR B 310 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR B 310 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR B 310 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR B 310 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 310 " -0.078 2.00e-02 2.50e+03 pdb=" HD1 TYR B 310 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR B 310 " 0.030 2.00e-02 2.50e+03 pdb=" HE1 TYR B 310 " 0.025 2.00e-02 2.50e+03 pdb=" HE2 TYR B 310 " 0.001 2.00e-02 2.50e+03 ... (remaining 1029 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.16: 504 2.16 - 2.77: 11738 2.77 - 3.38: 18515 3.38 - 3.99: 25771 3.99 - 4.60: 35517 Nonbonded interactions: 92045 Sorted by model distance: nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.545 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.545 2.450 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.548 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.556 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.585 2.450 ... (remaining 92040 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' 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: 3.370 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: 0.030 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.750 Find NCS groups from input model: 0.050 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 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 0.064 3522 Z= 0.692 Angle : 1.850 10.333 4710 Z= 1.226 Chirality : 0.085 0.363 528 Planarity : 0.011 0.093 600 Dihedral : 13.263 89.960 1350 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Cbeta Deviations : 0.51 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 349 TYR 0.161 0.038 TYR E 310 PHE 0.033 0.010 PHE F 346 HIS 0.010 0.003 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.01089 ( 3522) covalent geometry : angle 1.85038 ( 4710) hydrogen bonds : bond 0.10853 ( 63) hydrogen bonds : angle 8.40692 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.6939 (mttt) cc_final: 0.6655 (mtpt) REVERT: A 348 ASP cc_start: 0.7612 (t0) cc_final: 0.7404 (t70) REVERT: A 351 GLN cc_start: 0.7228 (mt0) cc_final: 0.6743 (mp10) REVERT: A 369 LYS cc_start: 0.7297 (mtmt) cc_final: 0.6864 (mttp) REVERT: B 307 GLN cc_start: 0.7224 (tt0) cc_final: 0.6683 (mt0) REVERT: B 321 LYS cc_start: 0.7258 (mttt) cc_final: 0.7020 (mttp) REVERT: B 336 GLN cc_start: 0.7944 (mt0) cc_final: 0.7739 (mt0) REVERT: B 338 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6598 (tp30) REVERT: B 369 LYS cc_start: 0.7696 (tttt) cc_final: 0.7074 (ttmm) REVERT: B 375 LYS cc_start: 0.6979 (ttmt) cc_final: 0.6374 (tttm) REVERT: C 317 LYS cc_start: 0.7787 (mttt) cc_final: 0.7431 (mtpt) REVERT: C 340 LYS cc_start: 0.8536 (mttt) cc_final: 0.8290 (mmmm) REVERT: C 351 GLN cc_start: 0.7709 (mt0) cc_final: 0.7392 (mp10) REVERT: C 375 LYS cc_start: 0.7984 (ttmt) cc_final: 0.7699 (ttmt) REVERT: D 307 GLN cc_start: 0.7800 (tt0) cc_final: 0.7331 (mt0) REVERT: D 347 LYS cc_start: 0.8391 (mptt) cc_final: 0.6752 (mtmm) REVERT: D 357 LEU cc_start: 0.7731 (tp) cc_final: 0.7526 (mp) REVERT: D 369 LYS cc_start: 0.8370 (tttt) cc_final: 0.7654 (ttmm) REVERT: D 375 LYS cc_start: 0.8365 (ttmt) cc_final: 0.7853 (tttp) REVERT: E 343 LYS cc_start: 0.7281 (mtmt) cc_final: 0.7012 (mtpp) REVERT: E 351 GLN cc_start: 0.7114 (mt0) cc_final: 0.6729 (mp10) REVERT: E 369 LYS cc_start: 0.7479 (mtmt) cc_final: 0.6987 (mttp) REVERT: F 307 GLN cc_start: 0.7055 (tt0) cc_final: 0.6523 (mt0) REVERT: F 311 LYS cc_start: 0.7808 (mttt) cc_final: 0.6517 (tppt) REVERT: F 336 GLN cc_start: 0.7699 (mt0) cc_final: 0.7390 (mt0) REVERT: F 340 LYS cc_start: 0.7593 (ttpp) cc_final: 0.6788 (mmtt) REVERT: F 358 ASP cc_start: 0.7695 (m-30) cc_final: 0.7339 (m-30) REVERT: F 375 LYS cc_start: 0.7523 (ttmt) cc_final: 0.7079 (tttm) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2582 time to fit residues: 38.0726 Evaluate side-chains 90 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.4109 r_free = 0.4109 target = 0.138369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.126058 restraints weight = 14206.028| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 1.81 r_work: 0.3823 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3522 Z= 0.131 Angle : 0.620 4.060 4710 Z= 0.331 Chirality : 0.053 0.163 528 Planarity : 0.004 0.055 600 Dihedral : 6.709 21.888 468 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.01 % Allowed : 8.08 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 349 TYR 0.011 0.002 TYR C 310 PHE 0.005 0.001 PHE E 346 HIS 0.003 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 3522) covalent geometry : angle 0.61964 ( 4710) hydrogen bonds : bond 0.02886 ( 63) hydrogen bonds : angle 5.68267 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.169 Fit side-chains revert: symmetry clash REVERT: A 314 ASP cc_start: 0.8062 (t0) cc_final: 0.7547 (t70) REVERT: A 348 ASP cc_start: 0.8032 (t0) cc_final: 0.7737 (t70) REVERT: A 351 GLN cc_start: 0.7768 (mt0) cc_final: 0.7443 (mp10) REVERT: A 369 LYS cc_start: 0.8225 (mtmt) cc_final: 0.7955 (mttp) REVERT: B 307 GLN cc_start: 0.7785 (tt0) cc_final: 0.7394 (mt0) REVERT: B 340 LYS cc_start: 0.7695 (mtpp) cc_final: 0.6785 (mtmm) REVERT: B 369 LYS cc_start: 0.8549 (tttt) cc_final: 0.8117 (ttmm) REVERT: B 375 LYS cc_start: 0.8107 (ttmt) cc_final: 0.7617 (tttm) REVERT: C 314 ASP cc_start: 0.8185 (t0) cc_final: 0.7877 (t0) REVERT: D 307 GLN cc_start: 0.7998 (tt0) cc_final: 0.7665 (mt0) REVERT: D 347 LYS cc_start: 0.8381 (mptt) cc_final: 0.6627 (mtmm) REVERT: D 375 LYS cc_start: 0.8571 (ttmt) cc_final: 0.8288 (tttp) REVERT: E 351 GLN cc_start: 0.7824 (mt0) cc_final: 0.7500 (mp10) REVERT: E 369 LYS cc_start: 0.8345 (mtmt) cc_final: 0.8121 (mttp) REVERT: E 372 GLU cc_start: 0.8436 (tt0) cc_final: 0.8130 (tt0) REVERT: F 307 GLN cc_start: 0.7788 (tt0) cc_final: 0.7346 (mt0) REVERT: F 311 LYS cc_start: 0.8374 (mttt) cc_final: 0.7340 (tppt) REVERT: F 340 LYS cc_start: 0.7832 (ttpp) cc_final: 0.7092 (mmpt) REVERT: F 342 GLU cc_start: 0.6946 (pm20) cc_final: 0.6732 (tp30) REVERT: F 358 ASP cc_start: 0.8099 (m-30) cc_final: 0.7848 (m-30) REVERT: F 375 LYS cc_start: 0.8410 (ttmt) cc_final: 0.8145 (tttm) outliers start: 4 outliers final: 4 residues processed: 97 average time/residue: 0.2536 time to fit residues: 27.4951 Evaluate side-chains 87 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain F residue 341 SER 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 4 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 0.1980 chunk 29 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 327 ASN E 327 ASN F 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.138712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.127084 restraints weight = 13832.804| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 1.64 r_work: 0.3864 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3794 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3522 Z= 0.116 Angle : 0.505 4.092 4710 Z= 0.264 Chirality : 0.052 0.138 528 Planarity : 0.003 0.027 600 Dihedral : 5.697 21.595 468 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.77 % Allowed : 8.59 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.009 0.002 TYR C 310 PHE 0.006 0.001 PHE E 346 HIS 0.003 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 3522) covalent geometry : angle 0.50461 ( 4710) hydrogen bonds : bond 0.01857 ( 63) hydrogen bonds : angle 4.71146 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.8206 (t0) cc_final: 0.7735 (t0) REVERT: A 351 GLN cc_start: 0.7792 (mt0) cc_final: 0.7576 (mp10) REVERT: A 369 LYS cc_start: 0.8269 (mtmt) cc_final: 0.8053 (mttp) REVERT: B 340 LYS cc_start: 0.7727 (mtpp) cc_final: 0.7000 (mtmm) REVERT: B 369 LYS cc_start: 0.8628 (tttt) cc_final: 0.8229 (ttmm) REVERT: B 375 LYS cc_start: 0.8246 (ttmt) cc_final: 0.7869 (tttm) REVERT: D 307 GLN cc_start: 0.8048 (tt0) cc_final: 0.7718 (mt0) REVERT: E 351 GLN cc_start: 0.7886 (mt0) cc_final: 0.7642 (mp10) REVERT: F 307 GLN cc_start: 0.7898 (tt0) cc_final: 0.7530 (mt0) REVERT: F 311 LYS cc_start: 0.8421 (mttt) cc_final: 0.7411 (tppt) REVERT: F 340 LYS cc_start: 0.7813 (ttpp) cc_final: 0.7168 (mmpt) REVERT: F 342 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6719 (tp30) REVERT: F 375 LYS cc_start: 0.8530 (ttmt) cc_final: 0.8320 (tttm) outliers start: 7 outliers final: 5 residues processed: 94 average time/residue: 0.2606 time to fit residues: 27.3458 Evaluate side-chains 89 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 345 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4086 r_free = 0.4086 target = 0.138777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.126978 restraints weight = 13861.759| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 1.75 r_work: 0.3862 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3786 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3522 Z= 0.086 Angle : 0.464 3.968 4710 Z= 0.239 Chirality : 0.051 0.132 528 Planarity : 0.003 0.041 600 Dihedral : 5.193 19.957 468 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.77 % Allowed : 9.85 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.87 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 349 TYR 0.010 0.001 TYR C 310 PHE 0.003 0.001 PHE E 346 HIS 0.002 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00199 ( 3522) covalent geometry : angle 0.46352 ( 4710) hydrogen bonds : bond 0.01599 ( 63) hydrogen bonds : angle 4.24600 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 314 ASP cc_start: 0.8233 (t0) cc_final: 0.7781 (t0) REVERT: A 349 ARG cc_start: 0.8135 (mmm-85) cc_final: 0.7880 (mtm180) REVERT: A 351 GLN cc_start: 0.7844 (mt0) cc_final: 0.7542 (mp10) REVERT: A 369 LYS cc_start: 0.8269 (mtmt) cc_final: 0.8006 (mttp) REVERT: B 340 LYS cc_start: 0.7790 (mtpp) cc_final: 0.6978 (mtmm) REVERT: B 369 LYS cc_start: 0.8650 (tttt) cc_final: 0.8252 (ttmm) REVERT: B 375 LYS cc_start: 0.8278 (ttmt) cc_final: 0.7896 (tttp) REVERT: C 314 ASP cc_start: 0.7961 (t0) cc_final: 0.7649 (t0) REVERT: C 372 GLU cc_start: 0.8297 (tt0) cc_final: 0.8038 (tt0) REVERT: D 307 GLN cc_start: 0.8097 (tt0) cc_final: 0.7743 (mt0) REVERT: E 311 LYS cc_start: 0.8084 (mttt) cc_final: 0.6900 (tppt) REVERT: E 340 LYS cc_start: 0.8614 (mtmt) cc_final: 0.8373 (mtmt) REVERT: E 351 GLN cc_start: 0.7881 (mt0) cc_final: 0.7489 (mp10) REVERT: F 307 GLN cc_start: 0.7851 (tt0) cc_final: 0.7484 (mt0) REVERT: F 311 LYS cc_start: 0.8394 (mttt) cc_final: 0.7316 (tppt) REVERT: F 340 LYS cc_start: 0.7953 (ttpp) cc_final: 0.7156 (mmpt) REVERT: F 342 GLU cc_start: 0.7025 (pm20) cc_final: 0.6676 (tp30) REVERT: F 375 LYS cc_start: 0.8537 (ttmt) cc_final: 0.8295 (tttm) outliers start: 7 outliers final: 7 residues processed: 88 average time/residue: 0.2462 time to fit residues: 24.2193 Evaluate side-chains 82 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 345 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.135135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.123210 restraints weight = 13940.036| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.76 r_work: 0.3819 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3741 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3522 Z= 0.114 Angle : 0.453 3.939 4710 Z= 0.235 Chirality : 0.051 0.129 528 Planarity : 0.004 0.046 600 Dihedral : 5.025 19.871 468 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.27 % Allowed : 9.85 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.35), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.81 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 349 TYR 0.018 0.002 TYR A 310 PHE 0.003 0.001 PHE F 346 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 3522) covalent geometry : angle 0.45284 ( 4710) hydrogen bonds : bond 0.01508 ( 63) hydrogen bonds : angle 3.99439 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 314 ASP cc_start: 0.8308 (t0) cc_final: 0.7820 (t0) REVERT: A 351 GLN cc_start: 0.7824 (mt0) cc_final: 0.7549 (mp10) REVERT: A 369 LYS cc_start: 0.8285 (mtmt) cc_final: 0.8047 (mttp) REVERT: B 340 LYS cc_start: 0.7794 (mtpp) cc_final: 0.6967 (mtmm) REVERT: B 369 LYS cc_start: 0.8660 (tttt) cc_final: 0.8224 (ttmm) REVERT: B 375 LYS cc_start: 0.8295 (ttmt) cc_final: 0.7937 (tttp) REVERT: C 348 ASP cc_start: 0.7500 (p0) cc_final: 0.6798 (p0) REVERT: C 372 GLU cc_start: 0.8303 (tt0) cc_final: 0.8093 (tt0) REVERT: D 307 GLN cc_start: 0.8209 (tt0) cc_final: 0.7790 (mt0) REVERT: E 311 LYS cc_start: 0.8129 (mttt) cc_final: 0.6904 (tppt) REVERT: E 340 LYS cc_start: 0.8647 (mtmt) cc_final: 0.8431 (mtmt) REVERT: E 343 LYS cc_start: 0.7775 (mtpp) cc_final: 0.7244 (ttpt) REVERT: E 351 GLN cc_start: 0.7851 (mt0) cc_final: 0.7526 (mp10) REVERT: F 307 GLN cc_start: 0.7897 (tt0) cc_final: 0.7533 (mt0) REVERT: F 311 LYS cc_start: 0.8440 (mttt) cc_final: 0.7421 (tppt) REVERT: F 340 LYS cc_start: 0.7964 (ttpp) cc_final: 0.7143 (mmtt) REVERT: F 342 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6719 (tp30) REVERT: F 375 LYS cc_start: 0.8597 (ttmt) cc_final: 0.8353 (tttm) outliers start: 9 outliers final: 8 residues processed: 84 average time/residue: 0.2404 time to fit residues: 22.5854 Evaluate side-chains 80 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 345 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.4013 r_free = 0.4013 target = 0.133431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.121564 restraints weight = 13931.994| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 1.75 r_work: 0.3792 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3716 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3522 Z= 0.155 Angle : 0.469 3.925 4710 Z= 0.243 Chirality : 0.050 0.124 528 Planarity : 0.003 0.042 600 Dihedral : 5.081 20.004 468 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.02 % Allowed : 10.86 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.35), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.84 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 349 TYR 0.009 0.001 TYR A 310 PHE 0.003 0.001 PHE F 346 HIS 0.002 0.000 HIS E 329 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 3522) covalent geometry : angle 0.46877 ( 4710) hydrogen bonds : bond 0.01592 ( 63) hydrogen bonds : angle 3.96976 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 314 ASP cc_start: 0.8311 (t0) cc_final: 0.7828 (t0) REVERT: A 369 LYS cc_start: 0.8348 (mtmt) cc_final: 0.8098 (mttp) REVERT: B 340 LYS cc_start: 0.7787 (mtpp) cc_final: 0.6902 (mttm) REVERT: B 369 LYS cc_start: 0.8669 (tttt) cc_final: 0.8224 (ttmm) REVERT: B 375 LYS cc_start: 0.8325 (ttmt) cc_final: 0.7973 (tttp) REVERT: C 348 ASP cc_start: 0.7542 (p0) cc_final: 0.6956 (p0) REVERT: C 372 GLU cc_start: 0.8354 (tt0) cc_final: 0.8129 (tt0) REVERT: D 307 GLN cc_start: 0.8255 (tt0) cc_final: 0.7794 (mt0) REVERT: E 340 LYS cc_start: 0.8671 (mtmt) cc_final: 0.8439 (mtmt) REVERT: E 343 LYS cc_start: 0.7782 (mtpp) cc_final: 0.7271 (ttpp) REVERT: E 351 GLN cc_start: 0.7872 (mt0) cc_final: 0.7542 (mp10) REVERT: F 307 GLN cc_start: 0.7976 (tt0) cc_final: 0.7563 (mt0) REVERT: F 311 LYS cc_start: 0.8472 (mttt) cc_final: 0.7429 (tppt) REVERT: F 340 LYS cc_start: 0.7942 (ttpp) cc_final: 0.7116 (mmtt) REVERT: F 342 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6726 (tp30) REVERT: F 375 LYS cc_start: 0.8576 (ttmt) cc_final: 0.8322 (tttm) outliers start: 8 outliers final: 7 residues processed: 75 average time/residue: 0.2546 time to fit residues: 21.4418 Evaluate side-chains 74 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 345 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 0.0270 chunk 7 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.133818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.122116 restraints weight = 13800.304| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 1.73 r_work: 0.3797 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3719 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3522 Z= 0.114 Angle : 0.462 4.160 4710 Z= 0.235 Chirality : 0.051 0.125 528 Planarity : 0.003 0.029 600 Dihedral : 4.897 19.737 468 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.02 % Allowed : 10.86 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.36), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.82 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 349 TYR 0.011 0.001 TYR A 310 PHE 0.003 0.001 PHE F 346 HIS 0.001 0.000 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 3522) covalent geometry : angle 0.46170 ( 4710) hydrogen bonds : bond 0.01424 ( 63) hydrogen bonds : angle 3.79568 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: A 314 ASP cc_start: 0.8238 (t0) cc_final: 0.7745 (t0) REVERT: A 369 LYS cc_start: 0.8361 (mtmt) cc_final: 0.8099 (mttp) REVERT: B 369 LYS cc_start: 0.8685 (tttt) cc_final: 0.8232 (ttmm) REVERT: B 375 LYS cc_start: 0.8381 (ttmt) cc_final: 0.8043 (tttp) REVERT: C 348 ASP cc_start: 0.7509 (p0) cc_final: 0.6873 (p0) REVERT: C 372 GLU cc_start: 0.8369 (tt0) cc_final: 0.8092 (tt0) REVERT: D 307 GLN cc_start: 0.8333 (tt0) cc_final: 0.7806 (mt0) REVERT: E 340 LYS cc_start: 0.8700 (mtmt) cc_final: 0.8481 (mtmt) REVERT: E 343 LYS cc_start: 0.7812 (mtpp) cc_final: 0.7308 (ttpt) REVERT: F 307 GLN cc_start: 0.8058 (tt0) cc_final: 0.7572 (mt0) REVERT: F 311 LYS cc_start: 0.8506 (mttt) cc_final: 0.7510 (tppt) REVERT: F 340 LYS cc_start: 0.7968 (ttpp) cc_final: 0.7115 (mmtt) REVERT: F 342 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6664 (tp30) REVERT: F 375 LYS cc_start: 0.8568 (ttmt) cc_final: 0.8323 (tttm) outliers start: 8 outliers final: 6 residues processed: 77 average time/residue: 0.2542 time to fit residues: 22.0262 Evaluate side-chains 74 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 345 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.133712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.122094 restraints weight = 13932.035| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 1.74 r_work: 0.3796 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3719 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.5708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3522 Z= 0.112 Angle : 0.442 3.879 4710 Z= 0.227 Chirality : 0.050 0.123 528 Planarity : 0.003 0.027 600 Dihedral : 4.794 19.280 468 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.27 % Allowed : 10.61 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.36), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.82 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.009 0.001 TYR A 310 PHE 0.003 0.001 PHE F 346 HIS 0.002 0.000 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 3522) covalent geometry : angle 0.44201 ( 4710) hydrogen bonds : bond 0.01365 ( 63) hydrogen bonds : angle 3.68503 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: A 314 ASP cc_start: 0.8210 (t0) cc_final: 0.7676 (t0) REVERT: A 369 LYS cc_start: 0.8371 (mtmt) cc_final: 0.8098 (mttp) REVERT: B 369 LYS cc_start: 0.8680 (tttt) cc_final: 0.8211 (ttmm) REVERT: B 375 LYS cc_start: 0.8358 (ttmt) cc_final: 0.8036 (tttm) REVERT: C 314 ASP cc_start: 0.7896 (t0) cc_final: 0.7566 (t70) REVERT: C 348 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.6827 (p0) REVERT: C 372 GLU cc_start: 0.8376 (tt0) cc_final: 0.8144 (tt0) REVERT: D 307 GLN cc_start: 0.8288 (tt0) cc_final: 0.7794 (mt0) REVERT: E 343 LYS cc_start: 0.7864 (mtpp) cc_final: 0.7437 (ttpp) REVERT: E 349 ARG cc_start: 0.8020 (mmm-85) cc_final: 0.7812 (mmm-85) REVERT: F 307 GLN cc_start: 0.8042 (tt0) cc_final: 0.7560 (mt0) REVERT: F 311 LYS cc_start: 0.8531 (mttt) cc_final: 0.7504 (tppt) REVERT: F 340 LYS cc_start: 0.7945 (ttpp) cc_final: 0.7119 (mmtt) REVERT: F 342 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6655 (tp30) REVERT: F 375 LYS cc_start: 0.8586 (ttmt) cc_final: 0.8356 (tttm) outliers start: 9 outliers final: 6 residues processed: 78 average time/residue: 0.2240 time to fit residues: 20.0530 Evaluate side-chains 77 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 345 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 34 optimal weight: 0.0000 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 overall best weight: 2.7992 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.130311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.118678 restraints weight = 13907.888| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 1.74 r_work: 0.3748 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3669 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.5831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3522 Z= 0.184 Angle : 0.485 4.303 4710 Z= 0.249 Chirality : 0.050 0.123 528 Planarity : 0.003 0.029 600 Dihedral : 4.982 19.291 468 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.02 % Allowed : 11.36 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.36), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.84 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.011 0.001 TYR A 310 PHE 0.005 0.001 PHE C 346 HIS 0.002 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 3522) covalent geometry : angle 0.48474 ( 4710) hydrogen bonds : bond 0.01619 ( 63) hydrogen bonds : angle 3.75358 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.8218 (t0) cc_final: 0.7683 (t0) REVERT: A 369 LYS cc_start: 0.8405 (mtmt) cc_final: 0.8092 (mttp) REVERT: B 369 LYS cc_start: 0.8702 (tttt) cc_final: 0.8211 (ttmm) REVERT: B 375 LYS cc_start: 0.8396 (ttmt) cc_final: 0.8066 (tttm) REVERT: C 314 ASP cc_start: 0.7916 (t0) cc_final: 0.7448 (t0) REVERT: C 372 GLU cc_start: 0.8364 (tt0) cc_final: 0.8085 (tt0) REVERT: D 307 GLN cc_start: 0.8345 (tt0) cc_final: 0.7813 (mt0) REVERT: E 343 LYS cc_start: 0.7898 (mtpp) cc_final: 0.7474 (ttpp) REVERT: F 307 GLN cc_start: 0.8119 (tt0) cc_final: 0.7599 (mt0) REVERT: F 324 SER cc_start: 0.8839 (m) cc_final: 0.8605 (t) REVERT: F 340 LYS cc_start: 0.7917 (ttpp) cc_final: 0.7093 (mmtt) REVERT: F 342 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6727 (tp30) REVERT: F 375 LYS cc_start: 0.8585 (ttmt) cc_final: 0.8349 (tttm) outliers start: 8 outliers final: 6 residues processed: 73 average time/residue: 0.2493 time to fit residues: 20.5699 Evaluate side-chains 72 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 345 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 23 optimal weight: 0.0170 chunk 11 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.5622 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.131988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.120448 restraints weight = 14030.088| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.74 r_work: 0.3773 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3697 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.5925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3522 Z= 0.110 Angle : 0.462 4.389 4710 Z= 0.235 Chirality : 0.051 0.124 528 Planarity : 0.003 0.025 600 Dihedral : 4.813 18.894 468 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.77 % Allowed : 12.37 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.36), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.82 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 349 TYR 0.009 0.001 TYR A 310 PHE 0.003 0.001 PHE F 346 HIS 0.001 0.000 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 3522) covalent geometry : angle 0.46224 ( 4710) hydrogen bonds : bond 0.01399 ( 63) hydrogen bonds : angle 3.65906 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 314 ASP cc_start: 0.8216 (t0) cc_final: 0.7671 (t0) REVERT: A 369 LYS cc_start: 0.8402 (mtmt) cc_final: 0.8089 (mttp) REVERT: B 369 LYS cc_start: 0.8699 (tttt) cc_final: 0.8208 (ttmm) REVERT: B 375 LYS cc_start: 0.8373 (ttmt) cc_final: 0.8070 (tttm) REVERT: C 314 ASP cc_start: 0.7888 (t0) cc_final: 0.7389 (t0) REVERT: C 372 GLU cc_start: 0.8380 (tt0) cc_final: 0.8105 (tt0) REVERT: D 307 GLN cc_start: 0.8335 (tt0) cc_final: 0.7789 (mt0) REVERT: E 343 LYS cc_start: 0.7904 (mtpp) cc_final: 0.7557 (ttpp) REVERT: F 307 GLN cc_start: 0.8071 (tt0) cc_final: 0.7592 (mt0) REVERT: F 324 SER cc_start: 0.8809 (m) cc_final: 0.8572 (t) REVERT: F 340 LYS cc_start: 0.7939 (ttpp) cc_final: 0.7051 (mmtt) REVERT: F 342 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6628 (tp30) REVERT: F 375 LYS cc_start: 0.8561 (ttmt) cc_final: 0.8319 (tttm) outliers start: 7 outliers final: 6 residues processed: 76 average time/residue: 0.2045 time to fit residues: 17.7216 Evaluate side-chains 73 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 345 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 0.0370 chunk 19 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 30 optimal weight: 0.0870 overall best weight: 0.8240 ------------------------------------------------------------------------------- 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 = 0.4019 r_free = 0.4019 target = 0.134465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.123097 restraints weight = 13861.723| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 1.74 r_work: 0.3810 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3734 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.6039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3522 Z= 0.082 Angle : 0.432 3.938 4710 Z= 0.218 Chirality : 0.051 0.127 528 Planarity : 0.003 0.027 600 Dihedral : 4.499 17.830 468 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.52 % Allowed : 13.13 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.37), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.80 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 349 TYR 0.010 0.001 TYR A 310 PHE 0.003 0.000 PHE F 346 HIS 0.002 0.000 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00191 ( 3522) covalent geometry : angle 0.43240 ( 4710) hydrogen bonds : bond 0.01284 ( 63) hydrogen bonds : angle 3.50510 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2197.77 seconds wall clock time: 37 minutes 56.40 seconds (2276.40 seconds total)