Starting phenix.real_space_refine on Wed Mar 12 02:50:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q8d_18251/03_2025/8q8d_18251.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q8d_18251/03_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_18251/03_2025/8q8d_18251.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q8d_18251/03_2025/8q8d_18251.map" model { file = "/net/cci-nas-00/data/ceres_data/8q8d_18251/03_2025/8q8d_18251.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q8d_18251/03_2025/8q8d_18251.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.49, per 1000 atoms: 0.63 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: 1.55 Conformation dependent library (CDL) restraints added in 661.6 milliseconds 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: 0.67 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: 2.15 Time building geometry restraints manager: 1.94 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: 0.01 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: 4.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.130 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.050 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.870 ------------------------------------------------------------------------------- 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= 0.745 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (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 HIS 0.010 0.003 HIS A 330 PHE 0.033 0.010 PHE F 346 TYR 0.161 0.038 TYR E 310 ARG 0.003 0.001 ARG E 349 *********************** 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 : 0.543 Fit side-chains revert: symmetry clash 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: 0.7332 (mt0) REVERT: D 347 LYS cc_start: 0.8391 (mptt) cc_final: 0.6751 (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: 0.6728 (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: 0.6524 (mt0) REVERT: F 311 LYS cc_start: 0.7808 (mttt) cc_final: 0.6518 (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: 0.6789 (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: 0.7080 (tttm) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.5827 time to fit residues: 86.7005 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 : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 362 HIS E 362 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.137681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.125740 restraints weight = 13759.752| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 1.68 r_work: 0.3852 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3778 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3522 Z= 0.300 Angle : 0.614 4.226 4710 Z= 0.326 Chirality : 0.052 0.149 528 Planarity : 0.004 0.052 600 Dihedral : 6.562 23.129 468 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.01 % Allowed : 8.59 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 330 PHE 0.007 0.001 PHE E 346 TYR 0.014 0.002 TYR A 310 ARG 0.002 0.000 ARG F 349 *********************** 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 102 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.8138 (t0) cc_final: 0.7702 (t0) REVERT: A 351 GLN cc_start: 0.7819 (mt0) cc_final: 0.7567 (mp10) REVERT: A 369 LYS cc_start: 0.8273 (mtmt) cc_final: 0.8019 (mttp) REVERT: A 372 GLU cc_start: 0.8122 (tt0) cc_final: 0.7914 (tt0) REVERT: B 307 GLN cc_start: 0.7721 (tt0) cc_final: 0.7500 (mt0) REVERT: B 340 LYS cc_start: 0.7780 (mtpp) cc_final: 0.6905 (mtmm) REVERT: B 369 LYS cc_start: 0.8582 (tttt) cc_final: 0.8190 (ttmm) REVERT: B 375 LYS cc_start: 0.8179 (ttmt) cc_final: 0.7742 (tttm) REVERT: D 307 GLN cc_start: 0.8008 (tt0) cc_final: 0.7719 (mt0) REVERT: D 347 LYS cc_start: 0.8406 (mptt) cc_final: 0.6828 (mtmt) REVERT: D 375 LYS cc_start: 0.8516 (ttmt) cc_final: 0.8304 (tttp) REVERT: E 351 GLN cc_start: 0.7816 (mt0) cc_final: 0.7582 (mp10) REVERT: E 372 GLU cc_start: 0.8425 (tt0) cc_final: 0.8116 (tt0) REVERT: F 307 GLN cc_start: 0.7852 (tt0) cc_final: 0.7487 (mt0) REVERT: F 311 LYS cc_start: 0.8430 (mttt) cc_final: 0.7425 (tppt) REVERT: F 338 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7614 (tp30) REVERT: F 340 LYS cc_start: 0.7832 (ttpp) cc_final: 0.7080 (mmtt) REVERT: F 375 LYS cc_start: 0.8509 (ttmt) cc_final: 0.8295 (tttm) outliers start: 4 outliers final: 4 residues processed: 101 average time/residue: 0.6229 time to fit residues: 70.0912 Evaluate side-chains 88 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 17 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 34 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.135103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.123686 restraints weight = 14047.023| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 1.65 r_work: 0.3810 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3738 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3522 Z= 0.233 Angle : 0.524 4.065 4710 Z= 0.276 Chirality : 0.052 0.132 528 Planarity : 0.003 0.026 600 Dihedral : 5.766 22.564 468 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.52 % Allowed : 9.85 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.97 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.004 0.001 PHE F 346 TYR 0.009 0.002 TYR C 310 ARG 0.006 0.001 ARG A 349 *********************** 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 94 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: A 314 ASP cc_start: 0.8228 (t0) cc_final: 0.7719 (t0) REVERT: A 348 ASP cc_start: 0.8088 (t0) cc_final: 0.7837 (t70) REVERT: A 349 ARG cc_start: 0.7859 (mtm180) cc_final: 0.7587 (mtm180) REVERT: A 351 GLN cc_start: 0.7815 (mt0) cc_final: 0.7558 (mp10) REVERT: B 307 GLN cc_start: 0.7923 (tt0) cc_final: 0.7628 (mt0) REVERT: B 340 LYS cc_start: 0.7822 (mtpp) cc_final: 0.6994 (mtmm) REVERT: B 369 LYS cc_start: 0.8633 (tttt) cc_final: 0.8248 (ttmm) REVERT: B 375 LYS cc_start: 0.8303 (ttmt) cc_final: 0.7954 (tttp) REVERT: C 348 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7196 (p0) REVERT: D 307 GLN cc_start: 0.8171 (tt0) cc_final: 0.7836 (mt0) REVERT: D 336 GLN cc_start: 0.8425 (mt0) cc_final: 0.8218 (tt0) REVERT: D 375 LYS cc_start: 0.8593 (ttmt) cc_final: 0.8377 (tttp) REVERT: E 351 GLN cc_start: 0.7853 (mt0) cc_final: 0.7594 (mp10) REVERT: F 307 GLN cc_start: 0.7865 (tt0) cc_final: 0.7570 (mt0) REVERT: F 311 LYS cc_start: 0.8482 (mttt) cc_final: 0.7457 (tppt) REVERT: F 340 LYS cc_start: 0.7666 (ttpp) cc_final: 0.7128 (mmtt) REVERT: F 375 LYS cc_start: 0.8574 (ttmt) cc_final: 0.8358 (tttm) outliers start: 6 outliers final: 5 residues processed: 90 average time/residue: 0.6024 time to fit residues: 60.5942 Evaluate side-chains 80 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 348 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.134396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.122802 restraints weight = 14052.468| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 1.76 r_work: 0.3796 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3720 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.5202 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= 0.191 Angle : 0.481 4.023 4710 Z= 0.250 Chirality : 0.051 0.134 528 Planarity : 0.004 0.046 600 Dihedral : 5.304 21.301 468 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.02 % Allowed : 10.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.35), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.89 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 374 PHE 0.003 0.001 PHE B 378 TYR 0.009 0.001 TYR C 310 ARG 0.005 0.001 ARG B 379 *********************** 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 83 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.556 Fit side-chains REVERT: A 314 ASP cc_start: 0.8235 (t0) cc_final: 0.7840 (t0) REVERT: A 351 GLN cc_start: 0.7868 (mt0) cc_final: 0.7579 (mp10) REVERT: A 372 GLU cc_start: 0.8404 (tt0) cc_final: 0.8145 (tt0) REVERT: B 307 GLN cc_start: 0.8038 (tt0) cc_final: 0.7599 (mt0) REVERT: B 340 LYS cc_start: 0.7814 (mtpp) cc_final: 0.6974 (mtmm) REVERT: B 369 LYS cc_start: 0.8642 (tttt) cc_final: 0.8216 (ttmm) REVERT: B 375 LYS cc_start: 0.8332 (ttmt) cc_final: 0.7974 (tttp) REVERT: C 348 ASP cc_start: 0.7662 (OUTLIER) cc_final: 0.6863 (p0) REVERT: D 307 GLN cc_start: 0.8225 (tt0) cc_final: 0.7803 (mt0) REVERT: D 336 GLN cc_start: 0.8433 (mt0) cc_final: 0.8214 (tt0) REVERT: D 375 LYS cc_start: 0.8648 (ttmt) cc_final: 0.8386 (tttp) REVERT: E 340 LYS cc_start: 0.8654 (mtmt) cc_final: 0.8415 (mtmt) REVERT: E 343 LYS cc_start: 0.7763 (mtpp) cc_final: 0.6565 (mmmt) REVERT: E 351 GLN cc_start: 0.7896 (mt0) cc_final: 0.7556 (mp10) REVERT: F 307 GLN cc_start: 0.7923 (tt0) cc_final: 0.7558 (mt0) REVERT: F 311 LYS cc_start: 0.8492 (mttt) cc_final: 0.7458 (tppt) REVERT: F 340 LYS cc_start: 0.7711 (ttpp) cc_final: 0.7054 (mmtt) REVERT: F 347 LYS cc_start: 0.8098 (mmtm) cc_final: 0.7889 (mmtm) REVERT: F 375 LYS cc_start: 0.8569 (ttmt) cc_final: 0.8325 (tttm) outliers start: 8 outliers final: 7 residues processed: 81 average time/residue: 0.5825 time to fit residues: 53.1949 Evaluate side-chains 78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 348 ASP 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 12 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.129178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.117551 restraints weight = 14108.181| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.75 r_work: 0.3728 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3522 Z= 0.351 Angle : 0.514 4.073 4710 Z= 0.272 Chirality : 0.050 0.125 528 Planarity : 0.003 0.023 600 Dihedral : 5.453 22.033 468 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.27 % Allowed : 11.36 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.35), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.89 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 362 PHE 0.004 0.001 PHE A 378 TYR 0.006 0.001 TYR A 310 ARG 0.003 0.000 ARG B 379 *********************** 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 78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.540 Fit side-chains REVERT: A 314 ASP cc_start: 0.8234 (t0) cc_final: 0.7804 (t0) REVERT: A 372 GLU cc_start: 0.8443 (tt0) cc_final: 0.8137 (tt0) REVERT: B 340 LYS cc_start: 0.7894 (mtpp) cc_final: 0.7012 (mtmm) REVERT: B 369 LYS cc_start: 0.8686 (tttt) cc_final: 0.8225 (ttmm) REVERT: B 375 LYS cc_start: 0.8392 (ttmt) cc_final: 0.8036 (tttp) REVERT: C 314 ASP cc_start: 0.8219 (t0) cc_final: 0.8011 (t0) REVERT: D 307 GLN cc_start: 0.8401 (tt0) cc_final: 0.7879 (mt0) REVERT: D 336 GLN cc_start: 0.8521 (mt0) cc_final: 0.8289 (tt0) REVERT: D 369 LYS cc_start: 0.8677 (tttt) cc_final: 0.8202 (ttmm) REVERT: D 375 LYS cc_start: 0.8711 (ttmt) cc_final: 0.8446 (tttp) REVERT: E 340 LYS cc_start: 0.8705 (mtmt) cc_final: 0.8464 (mtmt) REVERT: E 343 LYS cc_start: 0.7899 (mtpp) cc_final: 0.7403 (ttpp) REVERT: F 307 GLN cc_start: 0.8052 (tt0) cc_final: 0.7574 (mt0) REVERT: F 324 SER cc_start: 0.8867 (m) cc_final: 0.8639 (t) REVERT: F 340 LYS cc_start: 0.7727 (ttpp) cc_final: 0.7085 (mmtt) REVERT: F 347 LYS cc_start: 0.8116 (mmtm) cc_final: 0.7901 (mmtm) REVERT: F 375 LYS cc_start: 0.8601 (ttmt) cc_final: 0.8347 (tttm) outliers start: 9 outliers final: 8 residues processed: 75 average time/residue: 0.5441 time to fit residues: 46.4155 Evaluate side-chains 72 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 358 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.132099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.120667 restraints weight = 13971.178| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 1.75 r_work: 0.3769 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3694 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.5632 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= 0.172 Angle : 0.465 3.963 4710 Z= 0.241 Chirality : 0.051 0.130 528 Planarity : 0.003 0.034 600 Dihedral : 5.150 20.625 468 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.26 % Allowed : 12.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.35), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.92 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.002 0.001 PHE B 346 TYR 0.007 0.001 TYR C 310 ARG 0.005 0.000 ARG B 379 *********************** 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 79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.631 Fit side-chains REVERT: A 314 ASP cc_start: 0.8239 (t0) cc_final: 0.7768 (t0) REVERT: A 372 GLU cc_start: 0.8432 (tt0) cc_final: 0.8132 (tt0) REVERT: B 340 LYS cc_start: 0.7818 (mtpp) cc_final: 0.6993 (mtmm) REVERT: B 369 LYS cc_start: 0.8692 (tttt) cc_final: 0.8223 (ttmm) REVERT: B 375 LYS cc_start: 0.8356 (ttmt) cc_final: 0.8034 (tttp) REVERT: D 307 GLN cc_start: 0.8369 (tt0) cc_final: 0.7838 (mt0) REVERT: D 336 GLN cc_start: 0.8489 (mt0) cc_final: 0.8243 (tt0) REVERT: D 375 LYS cc_start: 0.8670 (ttmt) cc_final: 0.8410 (tttp) REVERT: E 340 LYS cc_start: 0.8719 (mtmt) cc_final: 0.8497 (mtmt) REVERT: E 343 LYS cc_start: 0.7915 (mtpp) cc_final: 0.7496 (ttpp) REVERT: F 307 GLN cc_start: 0.8024 (tt0) cc_final: 0.7561 (mt0) REVERT: F 324 SER cc_start: 0.8793 (m) cc_final: 0.8587 (t) REVERT: F 340 LYS cc_start: 0.7732 (ttpp) cc_final: 0.7079 (mmtt) REVERT: F 347 LYS cc_start: 0.8141 (mmtm) cc_final: 0.7928 (mmtm) REVERT: F 375 LYS cc_start: 0.8621 (ttmt) cc_final: 0.8370 (tttm) outliers start: 5 outliers final: 5 residues processed: 77 average time/residue: 0.5846 time to fit residues: 51.2470 Evaluate side-chains 75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 325 LEU 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 36 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3976 r_free = 0.3976 target = 0.132431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.121312 restraints weight = 13779.085| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 1.71 r_work: 0.3771 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3699 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.5769 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= 0.169 Angle : 0.447 3.920 4710 Z= 0.232 Chirality : 0.051 0.126 528 Planarity : 0.003 0.030 600 Dihedral : 4.917 19.920 468 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.02 % Allowed : 12.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.36), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.90 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 330 PHE 0.002 0.000 PHE F 378 TYR 0.005 0.001 TYR C 310 ARG 0.005 0.001 ARG A 349 *********************** 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 : 0.601 Fit side-chains REVERT: A 314 ASP cc_start: 0.8204 (t0) cc_final: 0.7654 (t0) REVERT: A 372 GLU cc_start: 0.8429 (tt0) cc_final: 0.8198 (tt0) REVERT: B 340 LYS cc_start: 0.7773 (mtpp) cc_final: 0.6860 (mttm) REVERT: B 369 LYS cc_start: 0.8687 (tttt) cc_final: 0.8208 (ttmm) REVERT: B 375 LYS cc_start: 0.8354 (ttmt) cc_final: 0.8048 (tttm) REVERT: C 348 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.6847 (p0) REVERT: D 307 GLN cc_start: 0.8300 (tt0) cc_final: 0.7815 (mt0) REVERT: D 336 GLN cc_start: 0.8469 (mt0) cc_final: 0.8211 (tt0) REVERT: D 375 LYS cc_start: 0.8667 (ttmt) cc_final: 0.8418 (tttp) REVERT: E 343 LYS cc_start: 0.7914 (mtpp) cc_final: 0.7524 (ttpp) REVERT: F 307 GLN cc_start: 0.8031 (tt0) cc_final: 0.7569 (mt0) REVERT: F 324 SER cc_start: 0.8795 (m) cc_final: 0.8574 (t) REVERT: F 340 LYS cc_start: 0.7716 (ttpp) cc_final: 0.7097 (mmtt) REVERT: F 347 LYS cc_start: 0.8177 (mmtm) cc_final: 0.7968 (mmtm) REVERT: F 375 LYS cc_start: 0.8609 (ttmt) cc_final: 0.8361 (tttm) outliers start: 8 outliers final: 6 residues processed: 76 average time/residue: 0.5047 time to fit residues: 44.3670 Evaluate side-chains 76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 14 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.134022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.123063 restraints weight = 13724.342| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 1.69 r_work: 0.3800 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3729 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.5878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3522 Z= 0.134 Angle : 0.437 3.867 4710 Z= 0.225 Chirality : 0.051 0.126 528 Planarity : 0.003 0.033 600 Dihedral : 4.729 19.039 468 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.02 % Allowed : 12.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.36), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.89 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 362 PHE 0.002 0.000 PHE A 346 TYR 0.006 0.001 TYR C 310 ARG 0.003 0.000 ARG B 379 *********************** 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 79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.593 Fit side-chains REVERT: A 314 ASP cc_start: 0.8148 (t0) cc_final: 0.7599 (t0) REVERT: A 372 GLU cc_start: 0.8438 (tt0) cc_final: 0.8205 (tt0) REVERT: B 340 LYS cc_start: 0.7744 (mtpp) cc_final: 0.6806 (mttm) REVERT: B 369 LYS cc_start: 0.8689 (tttt) cc_final: 0.8199 (ttmm) REVERT: B 375 LYS cc_start: 0.8352 (ttmt) cc_final: 0.8055 (tttm) REVERT: C 348 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.6600 (p0) REVERT: D 307 GLN cc_start: 0.8306 (tt0) cc_final: 0.7782 (mt0) REVERT: D 336 GLN cc_start: 0.8447 (mt0) cc_final: 0.8191 (tt0) REVERT: D 375 LYS cc_start: 0.8657 (ttmt) cc_final: 0.8410 (tttp) REVERT: E 343 LYS cc_start: 0.7941 (mtpp) cc_final: 0.7579 (ttpp) REVERT: F 307 GLN cc_start: 0.8000 (tt0) cc_final: 0.7505 (mt0) REVERT: F 324 SER cc_start: 0.8785 (m) cc_final: 0.8553 (t) REVERT: F 340 LYS cc_start: 0.7718 (ttpp) cc_final: 0.7094 (mmtt) REVERT: F 347 LYS cc_start: 0.8175 (mmtm) cc_final: 0.7969 (mmtm) REVERT: F 369 LYS cc_start: 0.8422 (ttmm) cc_final: 0.7963 (ttmm) REVERT: F 375 LYS cc_start: 0.8580 (ttmt) cc_final: 0.8331 (tttm) outliers start: 8 outliers final: 7 residues processed: 77 average time/residue: 0.5076 time to fit residues: 45.4760 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 : 0.598 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.127918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.116759 restraints weight = 14267.034| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.70 r_work: 0.3713 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3640 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.5990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3522 Z= 0.351 Angle : 0.514 4.117 4710 Z= 0.269 Chirality : 0.050 0.126 528 Planarity : 0.004 0.036 600 Dihedral : 5.154 19.600 468 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.27 % Allowed : 13.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.36), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.94 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 330 PHE 0.007 0.001 PHE C 346 TYR 0.004 0.001 TYR F 310 ARG 0.004 0.001 ARG B 379 *********************** 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 79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: A 314 ASP cc_start: 0.8191 (t0) cc_final: 0.7660 (t0) REVERT: A 372 GLU cc_start: 0.8453 (tt0) cc_final: 0.8142 (tt0) REVERT: B 340 LYS cc_start: 0.7812 (mtpp) cc_final: 0.6898 (mttm) REVERT: B 375 LYS cc_start: 0.8391 (ttmt) cc_final: 0.8082 (tttm) REVERT: D 307 GLN cc_start: 0.8358 (tt0) cc_final: 0.7803 (mt0) REVERT: D 336 GLN cc_start: 0.8543 (mt0) cc_final: 0.8269 (tt0) REVERT: D 369 LYS cc_start: 0.8674 (tttt) cc_final: 0.8358 (tttm) REVERT: D 375 LYS cc_start: 0.8737 (ttmt) cc_final: 0.8482 (tttp) REVERT: E 343 LYS cc_start: 0.7955 (mtpp) cc_final: 0.7506 (ttpt) REVERT: E 375 LYS cc_start: 0.8300 (ttmt) cc_final: 0.7810 (ttmm) REVERT: F 307 GLN cc_start: 0.8049 (tt0) cc_final: 0.7505 (mt0) REVERT: F 324 SER cc_start: 0.8839 (m) cc_final: 0.8605 (t) REVERT: F 340 LYS cc_start: 0.7724 (ttpp) cc_final: 0.7009 (mmtt) REVERT: F 347 LYS cc_start: 0.8189 (mmtm) cc_final: 0.7982 (mmtm) REVERT: F 369 LYS cc_start: 0.8435 (ttmm) cc_final: 0.7976 (ttmm) REVERT: F 375 LYS cc_start: 0.8600 (ttmt) cc_final: 0.8348 (tttm) outliers start: 9 outliers final: 8 residues processed: 76 average time/residue: 0.5378 time to fit residues: 46.8937 Evaluate side-chains 72 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 345 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 5 optimal weight: 6.9990 chunk 14 optimal weight: 0.1980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.131493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.120692 restraints weight = 14153.144| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 1.65 r_work: 0.3771 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.6072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3522 Z= 0.136 Angle : 0.455 3.888 4710 Z= 0.235 Chirality : 0.051 0.130 528 Planarity : 0.003 0.036 600 Dihedral : 4.826 19.000 468 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.36), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.95 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 362 PHE 0.002 0.000 PHE F 378 TYR 0.006 0.001 TYR C 310 ARG 0.005 0.000 ARG B 379 ********************** 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 75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.543 Fit side-chains REVERT: A 314 ASP cc_start: 0.8164 (t0) cc_final: 0.7603 (t0) REVERT: A 348 ASP cc_start: 0.7997 (t0) cc_final: 0.7699 (t70) REVERT: A 372 GLU cc_start: 0.8426 (tt0) cc_final: 0.8194 (tt0) REVERT: B 369 LYS cc_start: 0.8701 (tttt) cc_final: 0.8202 (ttmm) REVERT: B 375 LYS cc_start: 0.8388 (ttmt) cc_final: 0.8090 (tttm) REVERT: D 307 GLN cc_start: 0.8317 (tt0) cc_final: 0.7792 (mt0) REVERT: D 336 GLN cc_start: 0.8479 (mt0) cc_final: 0.8199 (tt0) REVERT: D 375 LYS cc_start: 0.8685 (ttmt) cc_final: 0.8453 (tttp) REVERT: E 343 LYS cc_start: 0.7969 (mtpp) cc_final: 0.7679 (ttpt) REVERT: F 307 GLN cc_start: 0.8014 (tt0) cc_final: 0.7498 (mt0) REVERT: F 324 SER cc_start: 0.8779 (m) cc_final: 0.8556 (t) REVERT: F 340 LYS cc_start: 0.7717 (ttpp) cc_final: 0.7114 (mmtt) REVERT: F 347 LYS cc_start: 0.8202 (mmtm) cc_final: 0.7997 (mmtm) REVERT: F 369 LYS cc_start: 0.8429 (ttmm) cc_final: 0.7974 (ttmm) REVERT: F 375 LYS cc_start: 0.8574 (ttmt) cc_final: 0.8333 (tttm) outliers start: 7 outliers final: 7 residues processed: 73 average time/residue: 0.5055 time to fit residues: 42.3285 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 : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 345 ASP 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 345 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.130624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.119739 restraints weight = 14006.317| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.69 r_work: 0.3751 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.6142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3522 Z= 0.197 Angle : 0.468 5.323 4710 Z= 0.244 Chirality : 0.050 0.124 528 Planarity : 0.003 0.037 600 Dihedral : 4.791 18.726 468 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.02 % Allowed : 13.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.36), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.94 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 330 PHE 0.003 0.001 PHE C 346 TYR 0.004 0.001 TYR C 310 ARG 0.004 0.000 ARG B 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4599.93 seconds wall clock time: 78 minutes 55.98 seconds (4735.98 seconds total)