Starting phenix.real_space_refine on Tue Feb 11 01:29:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q8f_18253/02_2025/8q8f_18253.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q8f_18253/02_2025/8q8f_18253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q8f_18253/02_2025/8q8f_18253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q8f_18253/02_2025/8q8f_18253.map" model { file = "/net/cci-nas-00/data/ceres_data/8q8f_18253/02_2025/8q8f_18253.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q8f_18253/02_2025/8q8f_18253.cif" } resolution = 2.93 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: 4 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 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3468 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "B" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "D" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "F" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 3.87, per 1000 atoms: 1.12 Number of scatterers: 3468 At special positions: 0 Unit cell: (111.24, 124.424, 36.256, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 648 8.00 N 642 7.00 C 2172 6.00 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: 0.86 Conformation dependent library (CDL) restraints added in 458.6 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, 47.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.520A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.514A 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: 7.713A 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: 6.853A 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 322 removed outlier: 6.441A pdb=" N LYS A 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N SER C 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR A 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N CYS C 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LYS A 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.441A pdb=" N LYS A 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N SER C 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR A 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N CYS C 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.353A 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: 6.302A 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: 6.614A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.417A 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: 7.958A pdb=" N PHE C 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.572A 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: 6.366A 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: 6.357A pdb=" N ASP A 358 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N THR C 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.498A 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: 6.379A 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: 6.716A 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: 6.083A pdb=" N THR A 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 8.010A 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: 7.902A 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: 8.383A pdb=" N LYS E 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N HIS A 374 " --> pdb=" O LYS E 375 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR E 377 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 6.500A 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: 6.492A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.424A 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: 6.783A 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 321 removed outlier: 6.245A pdb=" N LYS B 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N SER D 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR B 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.653A pdb=" N HIS B 329 " --> pdb=" O HIS F 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 336 through 340 removed outlier: 6.410A pdb=" N VAL B 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N LYS F 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL B 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 343 through 348 removed outlier: 6.831A pdb=" N ASP D 348 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N LYS B 343 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 10.105A pdb=" N PHE F 346 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 9.035A pdb=" N ASP B 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N ASP F 348 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N LYS B 347 " --> pdb=" O ASP F 348 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 351 through 354 removed outlier: 6.744A pdb=" N GLN B 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ILE D 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LYS B 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.580A pdb=" N THR B 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 368 through 378 removed outlier: 6.410A pdb=" N LYS B 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N GLU D 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE B 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N HIS D 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N THR B 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LEU D 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS B 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N PHE D 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR B 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) 54 hydrogen bonds defined for protein. 159 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: 0.86 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1030 1.33 - 1.45: 405 1.45 - 1.58: 2081 1.58 - 1.70: 0 1.70 - 1.82: 6 Bond restraints: 3522 Sorted by residual: bond pdb=" CZ ARG E 349 " pdb=" NH2 ARG E 349 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.24e+00 bond pdb=" CZ ARG A 349 " pdb=" NH2 ARG A 349 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.49e+00 bond pdb=" CZ ARG C 349 " pdb=" NH2 ARG C 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.40e+00 bond pdb=" CZ ARG B 379 " pdb=" NH2 ARG B 379 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.11e+00 bond pdb=" CZ ARG D 379 " pdb=" NH2 ARG D 379 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.91e+00 ... (remaining 3517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 3406 1.92 - 3.83: 1137 3.83 - 5.75: 150 5.75 - 7.66: 12 7.66 - 9.58: 5 Bond angle restraints: 4710 Sorted by residual: angle pdb=" O CYS D 322 " pdb=" C CYS D 322 " pdb=" N GLY D 323 " ideal model delta sigma weight residual 123.25 115.67 7.58 1.14e+00 7.69e-01 4.43e+01 angle pdb=" O CYS B 322 " pdb=" C CYS B 322 " pdb=" N GLY B 323 " ideal model delta sigma weight residual 123.17 115.44 7.73 1.21e+00 6.83e-01 4.08e+01 angle pdb=" CA CYS D 322 " pdb=" C CYS D 322 " pdb=" N GLY D 323 " ideal model delta sigma weight residual 115.36 124.74 -9.38 1.48e+00 4.57e-01 4.01e+01 angle pdb=" CA CYS B 322 " pdb=" C CYS B 322 " pdb=" N GLY B 323 " ideal model delta sigma weight residual 115.36 124.94 -9.58 1.53e+00 4.27e-01 3.92e+01 angle pdb=" CA PHE E 346 " pdb=" CB PHE E 346 " pdb=" CG PHE E 346 " ideal model delta sigma weight residual 113.80 119.35 -5.55 1.00e+00 1.00e+00 3.08e+01 ... (remaining 4705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.81: 1899 12.81 - 25.62: 176 25.62 - 38.43: 42 38.43 - 51.24: 12 51.24 - 64.05: 13 Dihedral angle restraints: 2142 sinusoidal: 894 harmonic: 1248 Sorted by residual: 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 180.00 151.23 28.77 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 180.00 151.61 28.39 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA LEU C 325 " pdb=" C LEU C 325 " pdb=" N GLY C 326 " pdb=" CA GLY C 326 " ideal model delta harmonic sigma weight residual -180.00 -151.64 -28.36 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 2139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 275 0.061 - 0.122: 188 0.122 - 0.183: 52 0.183 - 0.243: 9 0.243 - 0.304: 4 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA LYS B 347 " pdb=" N LYS B 347 " pdb=" C LYS B 347 " pdb=" CB LYS B 347 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+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 2.05e+00 chirality pdb=" CA LYS F 331 " pdb=" N LYS F 331 " pdb=" C LYS F 331 " pdb=" CB LYS F 331 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 525 not shown) Planarity restraints: 600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " 0.161 2.00e-02 2.50e+03 9.29e-02 1.73e+02 pdb=" CG TYR E 310 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " -0.075 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " -0.064 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " -0.059 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " -0.017 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " 0.156 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " 0.112 2.00e-02 2.50e+03 6.20e-02 7.69e+01 pdb=" CG TYR A 310 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " -0.055 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " -0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " -0.036 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " 0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 310 " -0.085 2.00e-02 2.50e+03 4.92e-02 4.84e+01 pdb=" CG TYR B 310 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR B 310 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR B 310 " 0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR B 310 " 0.037 2.00e-02 2.50e+03 pdb=" CE2 TYR B 310 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR B 310 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR B 310 " -0.081 2.00e-02 2.50e+03 ... (remaining 597 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 1592 2.98 - 3.46: 2729 3.46 - 3.94: 5654 3.94 - 4.42: 5646 4.42 - 4.90: 10814 Nonbonded interactions: 26435 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.504 3.040 nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.505 3.040 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.520 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.528 3.040 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.556 3.040 ... (remaining 26430 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: 2.380 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.340 Find NCS groups from input model: 0.120 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:12.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 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 0.037 3522 Z= 0.745 Angle : 1.823 9.579 4710 Z= 1.219 Chirality : 0.082 0.304 528 Planarity : 0.010 0.093 600 Dihedral : 12.076 64.052 1350 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.76 % Allowed : 1.77 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: -1.60 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.003 HIS F 330 PHE 0.032 0.011 PHE B 346 TYR 0.161 0.039 TYR E 310 ARG 0.004 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 142 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 139 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8664 (p) cc_final: 0.8446 (p) REVERT: A 321 LYS cc_start: 0.7354 (mttt) cc_final: 0.6833 (tttm) REVERT: A 338 GLU cc_start: 0.7668 (tt0) cc_final: 0.7362 (mt-10) REVERT: A 343 LYS cc_start: 0.7701 (mtmt) cc_final: 0.7459 (mtpp) REVERT: A 375 LYS cc_start: 0.7863 (ttmt) cc_final: 0.7600 (tttt) REVERT: B 321 LYS cc_start: 0.7366 (mttt) cc_final: 0.7128 (mttm) REVERT: B 369 LYS cc_start: 0.7593 (tttt) cc_final: 0.7187 (tttt) REVERT: C 314 ASP cc_start: 0.8341 (t0) cc_final: 0.7734 (t0) REVERT: C 321 LYS cc_start: 0.8086 (mttt) cc_final: 0.7591 (tttm) REVERT: C 375 LYS cc_start: 0.8500 (ttmt) cc_final: 0.8156 (ttmt) REVERT: D 310 TYR cc_start: 0.8866 (t80) cc_final: 0.8620 (t80) REVERT: D 316 SER cc_start: 0.8442 (p) cc_final: 0.8225 (p) REVERT: D 321 LYS cc_start: 0.7992 (mttt) cc_final: 0.7697 (mttm) REVERT: E 321 LYS cc_start: 0.7487 (mttt) cc_final: 0.6983 (tttt) REVERT: E 370 LYS cc_start: 0.8138 (tttt) cc_final: 0.7936 (tttm) REVERT: E 372 GLU cc_start: 0.8334 (tt0) cc_final: 0.8110 (tt0) REVERT: F 321 LYS cc_start: 0.7752 (mttt) cc_final: 0.7520 (mtmm) outliers start: 3 outliers final: 0 residues processed: 139 average time/residue: 1.3954 time to fit residues: 198.3781 Evaluate side-chains 109 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 21 optimal weight: 0.0770 chunk 32 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 24 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.7144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS C 336 GLN C 359 ASN C 362 HIS E 362 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.129824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.110482 restraints weight = 4626.196| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 1.90 r_work: 0.3588 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3522 Z= 0.222 Angle : 0.650 7.174 4710 Z= 0.319 Chirality : 0.050 0.148 528 Planarity : 0.003 0.026 600 Dihedral : 5.934 20.757 468 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.77 % Allowed : 14.90 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: -1.68 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 330 PHE 0.015 0.002 PHE E 378 TYR 0.020 0.003 TYR F 310 ARG 0.003 0.000 ARG B 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 119 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8225 (mttt) cc_final: 0.7936 (tttm) REVERT: A 343 LYS cc_start: 0.8079 (mtmt) cc_final: 0.7823 (tttt) REVERT: A 379 ARG cc_start: 0.7357 (mmm-85) cc_final: 0.7134 (mmt90) REVERT: B 321 LYS cc_start: 0.8456 (mttt) cc_final: 0.8227 (mttm) REVERT: B 342 GLU cc_start: 0.5997 (pm20) cc_final: 0.5462 (tp30) REVERT: B 369 LYS cc_start: 0.8574 (tttt) cc_final: 0.8332 (tttp) REVERT: C 343 LYS cc_start: 0.8379 (mtpp) cc_final: 0.8024 (tttt) REVERT: D 321 LYS cc_start: 0.8621 (mttt) cc_final: 0.8391 (mttm) REVERT: E 343 LYS cc_start: 0.8241 (mtpp) cc_final: 0.7873 (tttt) REVERT: E 349 ARG cc_start: 0.7296 (mtm180) cc_final: 0.6781 (mpt90) REVERT: E 369 LYS cc_start: 0.8762 (mtmt) cc_final: 0.8347 (mttt) REVERT: E 379 ARG cc_start: 0.7135 (mtt180) cc_final: 0.6071 (tpm170) outliers start: 7 outliers final: 1 residues processed: 114 average time/residue: 1.5659 time to fit residues: 182.3656 Evaluate side-chains 95 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 379 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 10.0000 chunk 28 optimal weight: 0.0670 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 overall best weight: 1.2920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.133278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.113146 restraints weight = 4527.568| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.91 r_work: 0.3615 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3522 Z= 0.172 Angle : 0.597 7.676 4710 Z= 0.286 Chirality : 0.048 0.120 528 Planarity : 0.002 0.021 600 Dihedral : 5.266 18.770 468 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.01 % Allowed : 23.74 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: -1.62 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 330 PHE 0.011 0.001 PHE E 378 TYR 0.014 0.002 TYR F 310 ARG 0.002 0.000 ARG B 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 102 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8148 (mttt) cc_final: 0.7844 (tttm) REVERT: A 343 LYS cc_start: 0.8223 (mtmt) cc_final: 0.7860 (ttmt) REVERT: B 321 LYS cc_start: 0.8520 (mttt) cc_final: 0.8277 (mttm) REVERT: B 342 GLU cc_start: 0.6062 (OUTLIER) cc_final: 0.5578 (tp30) REVERT: C 343 LYS cc_start: 0.8289 (mtpp) cc_final: 0.8027 (tttt) REVERT: D 321 LYS cc_start: 0.8517 (mttt) cc_final: 0.8273 (mttm) REVERT: D 349 ARG cc_start: 0.7510 (mtm-85) cc_final: 0.7049 (mtp85) REVERT: D 369 LYS cc_start: 0.8778 (tttt) cc_final: 0.8572 (tttp) REVERT: E 311 LYS cc_start: 0.8725 (mtpt) cc_final: 0.7727 (tppt) REVERT: E 343 LYS cc_start: 0.8249 (mtpp) cc_final: 0.7952 (tttt) REVERT: E 349 ARG cc_start: 0.7252 (mtm180) cc_final: 0.6799 (mpt180) REVERT: E 369 LYS cc_start: 0.8779 (mtmt) cc_final: 0.8427 (mtpt) REVERT: E 379 ARG cc_start: 0.7409 (mtt180) cc_final: 0.6367 (tpm170) REVERT: F 316 SER cc_start: 0.9157 (p) cc_final: 0.8946 (p) outliers start: 4 outliers final: 0 residues processed: 98 average time/residue: 1.5460 time to fit residues: 154.8648 Evaluate side-chains 87 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 342 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 32 optimal weight: 0.0570 chunk 22 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN B 330 HIS C 359 ASN D 336 GLN E 327 ASN F 307 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.127544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.106771 restraints weight = 4663.360| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.93 r_work: 0.3527 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3522 Z= 0.300 Angle : 0.643 7.435 4710 Z= 0.314 Chirality : 0.048 0.127 528 Planarity : 0.003 0.023 600 Dihedral : 5.483 21.156 468 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.03 % Allowed : 22.98 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: -1.74 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 330 PHE 0.008 0.002 PHE E 378 TYR 0.018 0.003 TYR A 310 ARG 0.002 0.000 ARG B 349 *********************** 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 106 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.457 Fit side-chains REVERT: A 321 LYS cc_start: 0.8334 (mttt) cc_final: 0.7960 (tttt) REVERT: A 338 GLU cc_start: 0.8241 (tt0) cc_final: 0.8017 (mt-10) REVERT: A 343 LYS cc_start: 0.8371 (mtmt) cc_final: 0.7899 (tttt) REVERT: A 379 ARG cc_start: 0.7549 (mmm-85) cc_final: 0.7055 (mpt-90) REVERT: B 316 SER cc_start: 0.9295 (p) cc_final: 0.9089 (p) REVERT: B 342 GLU cc_start: 0.6243 (OUTLIER) cc_final: 0.5867 (tp30) REVERT: B 353 LYS cc_start: 0.8612 (mtpt) cc_final: 0.7921 (ttpt) REVERT: C 321 LYS cc_start: 0.8582 (mttt) cc_final: 0.8248 (tttm) REVERT: C 343 LYS cc_start: 0.8333 (mtpp) cc_final: 0.8090 (tttt) REVERT: D 321 LYS cc_start: 0.8805 (mttt) cc_final: 0.8575 (mttm) REVERT: D 338 GLU cc_start: 0.4054 (pm20) cc_final: 0.3825 (pm20) REVERT: D 349 ARG cc_start: 0.7568 (mtm-85) cc_final: 0.7063 (mtp85) REVERT: E 343 LYS cc_start: 0.8344 (mtpp) cc_final: 0.8059 (tttt) REVERT: E 349 ARG cc_start: 0.7379 (mtm180) cc_final: 0.6989 (mpt90) REVERT: E 369 LYS cc_start: 0.8832 (mtmt) cc_final: 0.8413 (mttt) REVERT: E 379 ARG cc_start: 0.7781 (mtt180) cc_final: 0.6991 (mmp80) outliers start: 12 outliers final: 4 residues processed: 100 average time/residue: 1.6168 time to fit residues: 165.1362 Evaluate side-chains 87 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 338 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 19 optimal weight: 0.3980 chunk 15 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN D 336 GLN E 327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.129287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.108752 restraints weight = 4635.752| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.93 r_work: 0.3560 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3522 Z= 0.244 Angle : 0.602 7.783 4710 Z= 0.291 Chirality : 0.048 0.118 528 Planarity : 0.002 0.021 600 Dihedral : 5.213 16.865 468 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.03 % Allowed : 23.23 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: -1.87 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 330 PHE 0.007 0.001 PHE E 378 TYR 0.015 0.002 TYR A 310 ARG 0.001 0.000 ARG B 349 *********************** 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 96 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.446 Fit side-chains REVERT: A 321 LYS cc_start: 0.8372 (mttt) cc_final: 0.7998 (tttt) REVERT: A 338 GLU cc_start: 0.8275 (tt0) cc_final: 0.8032 (mt-10) REVERT: A 343 LYS cc_start: 0.8399 (mtmt) cc_final: 0.7945 (tttt) REVERT: A 379 ARG cc_start: 0.7579 (mmm-85) cc_final: 0.7097 (mpt-90) REVERT: B 340 LYS cc_start: 0.7733 (mttp) cc_final: 0.7153 (tmtt) REVERT: B 351 GLN cc_start: 0.8081 (tt0) cc_final: 0.7121 (mp10) REVERT: C 321 LYS cc_start: 0.8506 (mttt) cc_final: 0.8164 (tttm) REVERT: C 343 LYS cc_start: 0.8330 (mtpp) cc_final: 0.8094 (tttt) REVERT: D 349 ARG cc_start: 0.7576 (mtm-85) cc_final: 0.7071 (mtp85) REVERT: E 343 LYS cc_start: 0.8325 (mtpp) cc_final: 0.8037 (tttt) REVERT: E 349 ARG cc_start: 0.7419 (mtm180) cc_final: 0.6975 (mpt90) REVERT: E 369 LYS cc_start: 0.8819 (mtmt) cc_final: 0.8411 (mttt) REVERT: E 379 ARG cc_start: 0.7767 (mtt180) cc_final: 0.7099 (tpm170) outliers start: 12 outliers final: 5 residues processed: 90 average time/residue: 1.5733 time to fit residues: 144.7358 Evaluate side-chains 87 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 351 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 0.1980 chunk 3 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 41 optimal weight: 0.0050 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.135938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.115701 restraints weight = 4381.859| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 1.87 r_work: 0.3627 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3522 Z= 0.140 Angle : 0.558 8.186 4710 Z= 0.266 Chirality : 0.048 0.119 528 Planarity : 0.002 0.016 600 Dihedral : 4.751 15.405 468 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.27 % Allowed : 24.75 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: -1.83 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 330 PHE 0.006 0.001 PHE E 378 TYR 0.010 0.002 TYR F 310 ARG 0.001 0.000 ARG B 349 *********************** 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 92 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.475 Fit side-chains REVERT: A 321 LYS cc_start: 0.8143 (mttt) cc_final: 0.7836 (tttm) REVERT: A 343 LYS cc_start: 0.8358 (mtmt) cc_final: 0.7921 (tttt) REVERT: A 379 ARG cc_start: 0.7552 (mmm-85) cc_final: 0.7012 (mpt-90) REVERT: B 340 LYS cc_start: 0.7693 (mttp) cc_final: 0.7140 (tmtt) REVERT: B 351 GLN cc_start: 0.7989 (tt0) cc_final: 0.7112 (mp10) REVERT: B 356 SER cc_start: 0.8484 (m) cc_final: 0.8239 (p) REVERT: C 343 LYS cc_start: 0.8324 (mtpp) cc_final: 0.8124 (tttt) REVERT: D 321 LYS cc_start: 0.8492 (mttt) cc_final: 0.8215 (mttm) REVERT: D 349 ARG cc_start: 0.7585 (mtm-85) cc_final: 0.7095 (mtp85) REVERT: E 311 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.7444 (tppt) REVERT: E 343 LYS cc_start: 0.8316 (mtpp) cc_final: 0.8072 (tttt) REVERT: E 349 ARG cc_start: 0.7312 (mtm180) cc_final: 0.6874 (mpt180) REVERT: E 369 LYS cc_start: 0.8818 (mtmt) cc_final: 0.8387 (mttt) REVERT: E 379 ARG cc_start: 0.7693 (mtt180) cc_final: 0.7375 (mmp80) REVERT: F 379 ARG cc_start: 0.6545 (mmt180) cc_final: 0.5670 (mmp-170) outliers start: 9 outliers final: 3 residues processed: 86 average time/residue: 1.4984 time to fit residues: 131.9626 Evaluate side-chains 83 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain F residue 338 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 0.5980 chunk 25 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 32 optimal weight: 0.1980 chunk 13 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN C 359 ASN D 336 GLN E 327 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.128357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.107829 restraints weight = 4436.305| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.84 r_work: 0.3521 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3522 Z= 0.339 Angle : 0.637 8.439 4710 Z= 0.309 Chirality : 0.047 0.121 528 Planarity : 0.003 0.019 600 Dihedral : 5.246 17.830 468 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.79 % Allowed : 23.74 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: -1.91 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 330 PHE 0.006 0.002 PHE F 378 TYR 0.017 0.003 TYR A 310 ARG 0.002 0.000 ARG F 379 *********************** 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 100 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.418 Fit side-chains REVERT: A 321 LYS cc_start: 0.8338 (mttt) cc_final: 0.7999 (tttt) REVERT: A 338 GLU cc_start: 0.8299 (tt0) cc_final: 0.8061 (mt-10) REVERT: A 343 LYS cc_start: 0.8303 (mtmt) cc_final: 0.7838 (tttt) REVERT: A 379 ARG cc_start: 0.7518 (mmm-85) cc_final: 0.7083 (mmt90) REVERT: B 340 LYS cc_start: 0.7805 (mttp) cc_final: 0.7196 (tmtt) REVERT: B 351 GLN cc_start: 0.7973 (tt0) cc_final: 0.7125 (mp10) REVERT: B 356 SER cc_start: 0.8542 (m) cc_final: 0.8278 (p) REVERT: C 321 LYS cc_start: 0.8601 (mttt) cc_final: 0.8238 (tttm) REVERT: C 343 LYS cc_start: 0.8369 (mtpp) cc_final: 0.8123 (tttt) REVERT: D 321 LYS cc_start: 0.8847 (mttt) cc_final: 0.8608 (mttm) REVERT: D 379 ARG cc_start: 0.6630 (OUTLIER) cc_final: 0.5869 (ptt90) REVERT: E 343 LYS cc_start: 0.8335 (mtpp) cc_final: 0.8071 (tttt) REVERT: E 349 ARG cc_start: 0.7465 (mtm180) cc_final: 0.6881 (mpt90) REVERT: E 369 LYS cc_start: 0.8856 (mtmt) cc_final: 0.8446 (mttt) REVERT: E 379 ARG cc_start: 0.7759 (mtt180) cc_final: 0.7203 (tpm170) outliers start: 15 outliers final: 5 residues processed: 91 average time/residue: 1.5305 time to fit residues: 142.4478 Evaluate side-chains 88 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 351 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 ASN F 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.133808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.113495 restraints weight = 4348.054| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.86 r_work: 0.3594 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3522 Z= 0.171 Angle : 0.564 8.706 4710 Z= 0.267 Chirality : 0.047 0.117 528 Planarity : 0.002 0.015 600 Dihedral : 4.797 15.299 468 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.78 % Allowed : 25.00 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: -1.86 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 330 PHE 0.005 0.001 PHE E 378 TYR 0.010 0.002 TYR A 310 ARG 0.001 0.000 ARG B 349 *********************** 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 88 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.546 Fit side-chains REVERT: A 321 LYS cc_start: 0.8322 (mttt) cc_final: 0.7957 (tttt) REVERT: A 338 GLU cc_start: 0.8291 (tt0) cc_final: 0.8021 (mt-10) REVERT: A 343 LYS cc_start: 0.8348 (mtmt) cc_final: 0.7895 (tttt) REVERT: A 379 ARG cc_start: 0.7481 (mmm-85) cc_final: 0.7067 (mmt90) REVERT: B 340 LYS cc_start: 0.7701 (mttp) cc_final: 0.7136 (tmtt) REVERT: B 351 GLN cc_start: 0.7963 (tt0) cc_final: 0.7154 (mp10) REVERT: B 356 SER cc_start: 0.8476 (m) cc_final: 0.8221 (p) REVERT: C 321 LYS cc_start: 0.8504 (mttt) cc_final: 0.8114 (ttmt) REVERT: C 343 LYS cc_start: 0.8351 (mtpp) cc_final: 0.8129 (tttt) REVERT: D 379 ARG cc_start: 0.6782 (OUTLIER) cc_final: 0.4262 (mtm180) REVERT: E 311 LYS cc_start: 0.8715 (mtpt) cc_final: 0.7535 (tppt) REVERT: E 343 LYS cc_start: 0.8314 (mtpp) cc_final: 0.8072 (tttt) REVERT: E 349 ARG cc_start: 0.7471 (mtm180) cc_final: 0.6884 (mpt90) REVERT: E 369 LYS cc_start: 0.8829 (mtmt) cc_final: 0.8442 (mtpt) REVERT: E 379 ARG cc_start: 0.7796 (mtt180) cc_final: 0.7370 (mmp80) REVERT: F 379 ARG cc_start: 0.6256 (mmt180) cc_final: 0.5652 (mmp-170) outliers start: 11 outliers final: 6 residues processed: 82 average time/residue: 1.5406 time to fit residues: 129.3299 Evaluate side-chains 83 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 352 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 0.0040 chunk 9 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 overall best weight: 3.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.126675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.105978 restraints weight = 4580.792| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.91 r_work: 0.3515 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3522 Z= 0.355 Angle : 0.643 8.823 4710 Z= 0.312 Chirality : 0.048 0.121 528 Planarity : 0.003 0.020 600 Dihedral : 5.196 17.769 468 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.02 % Allowed : 27.27 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: -2.01 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 330 PHE 0.007 0.002 PHE F 378 TYR 0.017 0.003 TYR A 310 ARG 0.001 0.000 ARG B 349 *********************** 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 86 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.457 Fit side-chains REVERT: A 321 LYS cc_start: 0.8355 (mttt) cc_final: 0.8009 (tttt) REVERT: A 343 LYS cc_start: 0.8407 (mtmt) cc_final: 0.7889 (tttt) REVERT: A 379 ARG cc_start: 0.7565 (mmm-85) cc_final: 0.7200 (mtp180) REVERT: B 340 LYS cc_start: 0.7801 (mttp) cc_final: 0.7232 (tmtt) REVERT: B 351 GLN cc_start: 0.8011 (tt0) cc_final: 0.7226 (mp10) REVERT: C 321 LYS cc_start: 0.8606 (mttt) cc_final: 0.8229 (ttmt) REVERT: C 343 LYS cc_start: 0.8411 (mtpp) cc_final: 0.8155 (tttt) REVERT: D 321 LYS cc_start: 0.8850 (mttt) cc_final: 0.8614 (mttm) REVERT: D 379 ARG cc_start: 0.6643 (OUTLIER) cc_final: 0.4193 (mtm180) REVERT: E 343 LYS cc_start: 0.8352 (mtpp) cc_final: 0.8115 (tttt) REVERT: E 349 ARG cc_start: 0.7589 (mtm180) cc_final: 0.6923 (mpt90) REVERT: E 369 LYS cc_start: 0.8861 (mtmt) cc_final: 0.8506 (mtpt) REVERT: E 379 ARG cc_start: 0.7912 (mtt180) cc_final: 0.7272 (tpm170) outliers start: 8 outliers final: 4 residues processed: 83 average time/residue: 1.5483 time to fit residues: 131.4833 Evaluate side-chains 82 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 352 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 11 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 16 optimal weight: 0.0980 chunk 40 optimal weight: 4.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 ASN F 307 GLN F 359 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.130548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.110178 restraints weight = 4421.630| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.85 r_work: 0.3559 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.4674 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= 0.234 Angle : 0.598 10.132 4710 Z= 0.283 Chirality : 0.047 0.116 528 Planarity : 0.002 0.016 600 Dihedral : 4.983 16.340 468 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.52 % Allowed : 27.53 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: -2.03 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 330 PHE 0.005 0.001 PHE F 378 TYR 0.012 0.002 TYR A 310 ARG 0.001 0.000 ARG B 349 ********************** 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 83 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.444 Fit side-chains REVERT: A 321 LYS cc_start: 0.8351 (mttt) cc_final: 0.7993 (tttt) REVERT: A 343 LYS cc_start: 0.8457 (mtmt) cc_final: 0.7920 (tttt) REVERT: A 379 ARG cc_start: 0.7546 (mmm-85) cc_final: 0.7215 (mtp180) REVERT: B 340 LYS cc_start: 0.7819 (mttp) cc_final: 0.7220 (tmtt) REVERT: B 351 GLN cc_start: 0.8011 (tt0) cc_final: 0.7276 (mp10) REVERT: C 321 LYS cc_start: 0.8538 (mttt) cc_final: 0.8160 (ttmt) REVERT: C 343 LYS cc_start: 0.8410 (mtpp) cc_final: 0.8161 (tttt) REVERT: D 321 LYS cc_start: 0.8747 (mttt) cc_final: 0.8474 (mttm) REVERT: D 379 ARG cc_start: 0.6639 (OUTLIER) cc_final: 0.5178 (ptt90) REVERT: E 343 LYS cc_start: 0.8380 (mtpp) cc_final: 0.8121 (tttt) REVERT: E 349 ARG cc_start: 0.7599 (mtm180) cc_final: 0.6908 (mpt90) REVERT: E 369 LYS cc_start: 0.8825 (mtmt) cc_final: 0.8462 (mtpt) REVERT: E 379 ARG cc_start: 0.7894 (mtt180) cc_final: 0.7291 (tpm170) outliers start: 6 outliers final: 3 residues processed: 80 average time/residue: 1.5524 time to fit residues: 126.9841 Evaluate side-chains 81 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain F residue 352 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 0.1980 chunk 22 optimal weight: 9.9990 chunk 37 optimal weight: 0.3980 chunk 35 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 26 optimal weight: 0.0050 chunk 11 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.135065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.114809 restraints weight = 4382.862| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 1.86 r_work: 0.3631 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3522 Z= 0.151 Angle : 0.569 10.604 4710 Z= 0.266 Chirality : 0.047 0.117 528 Planarity : 0.002 0.014 600 Dihedral : 4.580 14.405 468 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.52 % Allowed : 27.78 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: -1.92 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS F 330 PHE 0.005 0.001 PHE E 378 TYR 0.009 0.002 TYR A 310 ARG 0.001 0.000 ARG B 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3704.11 seconds wall clock time: 66 minutes 12.05 seconds (3972.05 seconds total)