Starting phenix.real_space_refine on Fri Jun 6 02:26:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ql4_14063/06_2025/7ql4_14063.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ql4_14063/06_2025/7ql4_14063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ql4_14063/06_2025/7ql4_14063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ql4_14063/06_2025/7ql4_14063.map" model { file = "/net/cci-nas-00/data/ceres_data/7ql4_14063/06_2025/7ql4_14063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ql4_14063/06_2025/7ql4_14063.cif" } resolution = 3.2 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= 0.001 sd= 0.005 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 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: "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} 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} Time building chain proxies: 4.38, per 1000 atoms: 0.62 Number of scatterers: 7074 At special positions: 0 Unit cell: (158.7, 77.05, 40.25, 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: 1.81 Conformation dependent library (CDL) restraints added in 685.4 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 16 sheets defined 0.0% alpha, 52.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.253A pdb=" N GLN A 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N TYR D 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL A 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 322 removed outlier: 5.904A pdb=" N ASP B 314 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LYS D 317 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N SER B 316 " --> pdb=" O LYS D 317 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N THR D 319 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL B 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N LYS D 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N SER B 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 330 removed outlier: 8.911A pdb=" N LEU A 325 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 9.619A pdb=" N ILE D 328 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN A 327 " --> pdb=" O ILE D 328 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N HIS D 330 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N HIS A 329 " --> pdb=" O HIS D 330 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLY B 326 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASN D 327 " --> pdb=" O GLY B 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 340 removed outlier: 6.429A pdb=" N GLN A 336 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N VAL D 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLU A 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 346 removed outlier: 6.313A pdb=" N LYS A 343 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N PHE D 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASP A 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 351 through 354 removed outlier: 6.572A pdb=" N GLN A 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ILE D 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LYS A 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 359 through 362 removed outlier: 6.486A pdb=" N ASN B 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N HIS D 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 369 through 378 removed outlier: 6.377A pdb=" N LYS A 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N GLU D 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE A 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N HIS D 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N THR A 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N LEU D 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS A 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N PHE D 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR A 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 306 through 310 Processing sheet with id=AB1, first strand: chain 'F' and resid 313 through 322 removed outlier: 5.901A pdb=" N ASP C 314 " --> pdb=" O LEU E 315 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LYS E 317 " --> pdb=" O ASP C 314 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N SER C 316 " --> pdb=" O LYS E 317 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N THR E 319 " --> pdb=" O SER C 316 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL C 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N LYS E 321 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N SER C 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 325 through 330 removed outlier: 8.963A pdb=" N LEU F 325 " --> pdb=" O GLY E 326 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N ILE E 328 " --> pdb=" O LEU F 325 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ASN F 327 " --> pdb=" O ILE E 328 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N HIS E 330 " --> pdb=" O ASN F 327 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N HIS F 329 " --> pdb=" O HIS E 330 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLY C 326 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN E 327 " --> pdb=" O GLY C 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 336 through 340 removed outlier: 6.440A pdb=" N GLN F 336 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL E 339 " --> pdb=" O GLN F 336 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU F 338 " --> pdb=" O VAL E 339 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 343 through 346 removed outlier: 6.777A pdb=" N LYS F 343 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N PHE E 346 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASP F 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 351 through 354 removed outlier: 6.581A pdb=" N GLN F 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ILE E 354 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LYS F 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 359 through 362 removed outlier: 6.543A pdb=" N ASN C 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N HIS E 362 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N THR C 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 369 through 378 removed outlier: 6.490A pdb=" N LYS F 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N GLU E 372 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE F 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N HIS E 374 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N THR F 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N LEU E 376 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LYS F 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N PHE E 378 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR F 377 " --> pdb=" O PHE E 378 " (cutoff:3.500A) 80 hydrogen bonds defined for protein. 240 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: 2.35 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 3600 1.12 - 1.29: 576 1.29 - 1.46: 1117 1.46 - 1.63: 1829 1.63 - 1.81: 6 Bond restraints: 7128 Sorted by residual: bond pdb=" N ASN E 368 " pdb=" H ASN E 368 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ARG E 379 " pdb=" H ARG E 379 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N GLY E 366 " pdb=" H GLY E 366 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CE2 TYR C 310 " pdb=" HE2 TYR C 310 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" NH1 ARG C 379 " pdb="HH11 ARG C 379 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 7123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 10802 2.46 - 4.93: 1670 4.93 - 7.39: 482 7.39 - 9.86: 22 9.86 - 12.32: 8 Bond angle restraints: 12984 Sorted by residual: angle pdb=" N GLY E 326 " pdb=" CA GLY E 326 " pdb=" C GLY E 326 " ideal model delta sigma weight residual 110.42 118.06 -7.64 1.49e+00 4.50e-01 2.63e+01 angle pdb=" CA PHE F 346 " pdb=" CB PHE F 346 " pdb=" CG PHE F 346 " ideal model delta sigma weight residual 113.80 118.91 -5.11 1.00e+00 1.00e+00 2.61e+01 angle pdb=" CA PHE A 346 " pdb=" CB PHE A 346 " pdb=" CG PHE A 346 " ideal model delta sigma weight residual 113.80 118.85 -5.05 1.00e+00 1.00e+00 2.55e+01 angle pdb=" CA PHE E 346 " pdb=" CB PHE E 346 " pdb=" CG PHE E 346 " ideal model delta sigma weight residual 113.80 118.71 -4.91 1.00e+00 1.00e+00 2.41e+01 angle pdb=" N GLY D 326 " pdb=" CA GLY D 326 " pdb=" C GLY D 326 " ideal model delta sigma weight residual 110.75 117.80 -7.05 1.46e+00 4.69e-01 2.33e+01 ... (remaining 12979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.26: 2759 14.26 - 28.52: 289 28.52 - 42.78: 95 42.78 - 57.04: 74 57.04 - 71.30: 65 Dihedral angle restraints: 3282 sinusoidal: 1878 harmonic: 1404 Sorted by residual: dihedral pdb=" CA VAL A 318 " pdb=" C VAL A 318 " pdb=" N THR A 319 " pdb=" CA THR A 319 " ideal model delta harmonic sigma weight residual -180.00 -153.75 -26.25 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA VAL F 318 " pdb=" C VAL F 318 " pdb=" N THR F 319 " pdb=" CA THR F 319 " ideal model delta harmonic sigma weight residual 180.00 -155.24 -24.76 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA SER C 324 " pdb=" C SER C 324 " pdb=" N LEU C 325 " pdb=" CA LEU C 325 " ideal model delta harmonic sigma weight residual 180.00 155.40 24.60 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 3279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 301 0.070 - 0.140: 144 0.140 - 0.210: 63 0.210 - 0.281: 10 0.281 - 0.351: 10 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA LYS E 317 " pdb=" N LYS E 317 " pdb=" C LYS E 317 " pdb=" CB LYS E 317 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA ARG B 349 " pdb=" N ARG B 349 " pdb=" C ARG B 349 " pdb=" CB ARG B 349 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA LYS A 317 " pdb=" N LYS A 317 " pdb=" C LYS A 317 " pdb=" CB LYS A 317 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.33 2.00e-01 2.50e+01 2.64e+00 ... (remaining 525 not shown) Planarity restraints: 1032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 346 " -0.076 2.00e-02 2.50e+03 3.33e-02 3.32e+01 pdb=" CG PHE E 346 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE E 346 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE E 346 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 PHE E 346 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE E 346 " 0.025 2.00e-02 2.50e+03 pdb=" CZ PHE E 346 " -0.014 2.00e-02 2.50e+03 pdb=" HD1 PHE E 346 " 0.055 2.00e-02 2.50e+03 pdb=" HD2 PHE E 346 " 0.018 2.00e-02 2.50e+03 pdb=" HE1 PHE E 346 " -0.005 2.00e-02 2.50e+03 pdb=" HE2 PHE E 346 " 0.009 2.00e-02 2.50e+03 pdb=" HZ PHE E 346 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 330 " -0.053 2.00e-02 2.50e+03 3.82e-02 3.28e+01 pdb=" CG HIS B 330 " 0.067 2.00e-02 2.50e+03 pdb=" ND1 HIS B 330 " 0.043 2.00e-02 2.50e+03 pdb=" CD2 HIS B 330 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 HIS B 330 " 0.010 2.00e-02 2.50e+03 pdb=" NE2 HIS B 330 " -0.006 2.00e-02 2.50e+03 pdb=" HD1 HIS B 330 " -0.017 2.00e-02 2.50e+03 pdb=" HD2 HIS B 330 " -0.032 2.00e-02 2.50e+03 pdb=" HE1 HIS B 330 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 346 " -0.069 2.00e-02 2.50e+03 2.97e-02 2.65e+01 pdb=" CG PHE F 346 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE F 346 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE F 346 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 PHE F 346 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE F 346 " 0.021 2.00e-02 2.50e+03 pdb=" CZ PHE F 346 " -0.013 2.00e-02 2.50e+03 pdb=" HD1 PHE F 346 " 0.050 2.00e-02 2.50e+03 pdb=" HD2 PHE F 346 " 0.021 2.00e-02 2.50e+03 pdb=" HE1 PHE F 346 " -0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE F 346 " 0.006 2.00e-02 2.50e+03 pdb=" HZ PHE F 346 " -0.037 2.00e-02 2.50e+03 ... (remaining 1029 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 493 2.16 - 2.77: 12208 2.77 - 3.38: 19044 3.38 - 3.99: 25536 3.99 - 4.60: 36722 Nonbonded interactions: 94003 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.555 2.450 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.561 2.450 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.595 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.607 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.630 2.450 ... (remaining 93998 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: 0.990 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.390 Find NCS groups from input model: 0.190 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5027 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 0.036 3522 Z= 0.709 Angle : 1.857 7.638 4710 Z= 1.212 Chirality : 0.100 0.351 528 Planarity : 0.011 0.053 600 Dihedral : 12.284 58.792 1350 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: -1.77 (0.29), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.22), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.005 HIS E 330 PHE 0.038 0.013 PHE E 346 TYR 0.059 0.019 TYR F 310 ARG 0.004 0.001 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.10786 ( 80) hydrogen bonds : angle 6.99052 ( 240) covalent geometry : bond 0.01102 ( 3522) covalent geometry : angle 1.85679 ( 4710) *********************** 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 135 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 379 ARG cc_start: 0.5666 (mtm180) cc_final: 0.5423 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2206 time to fit residues: 38.9283 Evaluate side-chains 92 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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: 5.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.141287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.121845 restraints weight = 13710.421| |-----------------------------------------------------------------------------| r_work (start): 0.4333 rms_B_bonded: 2.99 r_work: 0.4244 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5967 moved from start: 0.4872 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= 0.190 Angle : 0.694 5.401 4710 Z= 0.386 Chirality : 0.056 0.167 528 Planarity : 0.006 0.056 600 Dihedral : 7.609 21.222 468 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.78 % Allowed : 7.83 % Favored : 89.39 % 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: -1.74 (0.32), 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 0.002 HIS F 330 PHE 0.014 0.002 PHE F 346 TYR 0.007 0.001 TYR A 310 ARG 0.007 0.002 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.03252 ( 80) hydrogen bonds : angle 5.85326 ( 240) covalent geometry : bond 0.00413 ( 3522) covalent geometry : angle 0.69405 ( 4710) *********************** 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 97 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 352 SER cc_start: 0.8053 (OUTLIER) cc_final: 0.7667 (t) REVERT: B 342 GLU cc_start: 0.7980 (mm-30) cc_final: 0.6154 (pm20) REVERT: B 379 ARG cc_start: 0.4741 (mtm180) cc_final: 0.4127 (mtm-85) REVERT: C 379 ARG cc_start: 0.6498 (mtm180) cc_final: 0.5725 (mtm-85) outliers start: 11 outliers final: 9 residues processed: 92 average time/residue: 0.3281 time to fit residues: 36.7487 Evaluate side-chains 79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 352 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 11 optimal weight: 0.0770 chunk 15 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 0 optimal weight: 0.6980 overall best weight: 1.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 ASN C 368 ASN D 359 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.154277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.134406 restraints weight = 13114.642| |-----------------------------------------------------------------------------| r_work (start): 0.4442 rms_B_bonded: 3.14 r_work: 0.4332 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6327 moved from start: 0.6551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3522 Z= 0.131 Angle : 0.600 7.912 4710 Z= 0.324 Chirality : 0.052 0.140 528 Planarity : 0.005 0.049 600 Dihedral : 6.473 17.601 468 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.53 % Allowed : 9.09 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.73 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 362 PHE 0.009 0.001 PHE C 346 TYR 0.015 0.002 TYR E 310 ARG 0.001 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.02666 ( 80) hydrogen bonds : angle 5.23049 ( 240) covalent geometry : bond 0.00295 ( 3522) covalent geometry : angle 0.59976 ( 4710) *********************** 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 81 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 342 GLU cc_start: 0.7978 (mm-30) cc_final: 0.6194 (pm20) REVERT: B 379 ARG cc_start: 0.4668 (mtm180) cc_final: 0.4299 (mtm-85) REVERT: C 379 ARG cc_start: 0.6682 (mtm180) cc_final: 0.5986 (mtm-85) REVERT: D 306 VAL cc_start: 0.6577 (OUTLIER) cc_final: 0.6138 (p) REVERT: D 370 LYS cc_start: 0.7736 (tttp) cc_final: 0.6946 (ttmt) outliers start: 10 outliers final: 5 residues processed: 78 average time/residue: 0.3258 time to fit residues: 31.2574 Evaluate side-chains 68 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 320 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.4477 r_free = 0.4477 target = 0.138133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.119085 restraints weight = 13991.671| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 2.95 r_work: 0.4149 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.4048 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.9299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3522 Z= 0.205 Angle : 0.667 9.768 4710 Z= 0.364 Chirality : 0.055 0.264 528 Planarity : 0.006 0.046 600 Dihedral : 6.484 21.611 468 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.03 % Allowed : 10.10 % Favored : 86.87 % 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: -1.90 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 374 PHE 0.011 0.002 PHE B 378 TYR 0.015 0.003 TYR E 310 ARG 0.003 0.000 ARG A 379 Details of bonding type rmsd hydrogen bonds : bond 0.02468 ( 80) hydrogen bonds : angle 4.98179 ( 240) covalent geometry : bond 0.00449 ( 3522) covalent geometry : angle 0.66673 ( 4710) *********************** 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 96 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLN cc_start: 0.7265 (mt0) cc_final: 0.6359 (tt0) REVERT: F 340 LYS cc_start: 0.7061 (ttmt) cc_final: 0.6771 (mttt) REVERT: F 358 ASP cc_start: 0.7769 (m-30) cc_final: 0.7327 (p0) REVERT: B 342 GLU cc_start: 0.8458 (mm-30) cc_final: 0.6443 (pm20) REVERT: B 379 ARG cc_start: 0.5341 (mtm180) cc_final: 0.4893 (mpp-170) REVERT: C 340 LYS cc_start: 0.8029 (ttmt) cc_final: 0.7747 (mmtp) REVERT: C 342 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7187 (mm-30) REVERT: C 371 ILE cc_start: 0.8472 (mt) cc_final: 0.8188 (mp) REVERT: C 379 ARG cc_start: 0.6624 (mtm180) cc_final: 0.5667 (mtm-85) REVERT: D 306 VAL cc_start: 0.7081 (OUTLIER) cc_final: 0.6835 (p) REVERT: D 319 THR cc_start: 0.7426 (m) cc_final: 0.7224 (m) REVERT: E 336 GLN cc_start: 0.8390 (tp40) cc_final: 0.8006 (tp40) REVERT: E 340 LYS cc_start: 0.6933 (ttmt) cc_final: 0.6606 (mmtp) REVERT: E 359 ASN cc_start: 0.7890 (m-40) cc_final: 0.7664 (m-40) REVERT: E 379 ARG cc_start: 0.6349 (mtm180) cc_final: 0.5902 (mmm160) outliers start: 12 outliers final: 8 residues processed: 94 average time/residue: 0.4758 time to fit residues: 51.5587 Evaluate side-chains 80 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 361 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN C 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.122526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.104973 restraints weight = 15376.230| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 2.83 r_work: 0.3988 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3894 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 1.0274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3522 Z= 0.180 Angle : 0.600 6.468 4710 Z= 0.323 Chirality : 0.053 0.144 528 Planarity : 0.005 0.051 600 Dihedral : 6.087 17.220 468 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.53 % Allowed : 12.37 % Favored : 85.10 % 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: -1.93 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 362 PHE 0.007 0.001 PHE B 378 TYR 0.012 0.002 TYR E 310 ARG 0.001 0.000 ARG D 379 Details of bonding type rmsd hydrogen bonds : bond 0.02538 ( 80) hydrogen bonds : angle 4.92905 ( 240) covalent geometry : bond 0.00397 ( 3522) covalent geometry : angle 0.60036 ( 4710) *********************** 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 75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7701 (mttt) cc_final: 0.7272 (mttp) REVERT: F 358 ASP cc_start: 0.7860 (m-30) cc_final: 0.7623 (p0) REVERT: C 342 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7320 (mm-30) REVERT: C 358 ASP cc_start: 0.8243 (p0) cc_final: 0.7953 (p0) REVERT: C 379 ARG cc_start: 0.6622 (mtm180) cc_final: 0.5618 (mtm-85) REVERT: D 306 VAL cc_start: 0.7195 (OUTLIER) cc_final: 0.6952 (p) REVERT: D 311 LYS cc_start: 0.7866 (tttt) cc_final: 0.7582 (mtpt) REVERT: D 321 LYS cc_start: 0.7853 (mttt) cc_final: 0.7088 (mptt) REVERT: E 379 ARG cc_start: 0.6203 (mtm180) cc_final: 0.5959 (mmm160) outliers start: 10 outliers final: 7 residues processed: 73 average time/residue: 0.5025 time to fit residues: 42.1516 Evaluate side-chains 65 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 320 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 368 ASN E 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.126321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.106952 restraints weight = 14304.936| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 2.78 r_work: 0.4012 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3899 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 1.1231 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= 0.172 Angle : 0.598 7.364 4710 Z= 0.319 Chirality : 0.052 0.182 528 Planarity : 0.005 0.046 600 Dihedral : 5.953 17.646 468 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.78 % Allowed : 14.65 % Favored : 82.58 % 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: -2.01 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 362 PHE 0.010 0.001 PHE B 378 TYR 0.013 0.002 TYR E 310 ARG 0.002 0.000 ARG F 379 Details of bonding type rmsd hydrogen bonds : bond 0.02479 ( 80) hydrogen bonds : angle 4.74132 ( 240) covalent geometry : bond 0.00375 ( 3522) covalent geometry : angle 0.59806 ( 4710) *********************** 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 64 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7754 (mttt) cc_final: 0.7294 (mttp) REVERT: A 369 LYS cc_start: 0.7988 (mtpt) cc_final: 0.7329 (mttt) REVERT: C 342 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7488 (mm-30) REVERT: C 369 LYS cc_start: 0.8315 (mtpt) cc_final: 0.7662 (mttm) REVERT: C 379 ARG cc_start: 0.6520 (mtm180) cc_final: 0.5564 (mtm-85) REVERT: D 306 VAL cc_start: 0.7391 (OUTLIER) cc_final: 0.7172 (p) REVERT: D 311 LYS cc_start: 0.7842 (tttt) cc_final: 0.7632 (mtpt) REVERT: D 321 LYS cc_start: 0.7847 (mttt) cc_final: 0.7159 (mttp) outliers start: 11 outliers final: 8 residues processed: 61 average time/residue: 0.4694 time to fit residues: 33.4660 Evaluate side-chains 58 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 356 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.124101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.105056 restraints weight = 14191.223| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 2.75 r_work: 0.3990 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3876 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 1.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3522 Z= 0.181 Angle : 0.599 9.365 4710 Z= 0.317 Chirality : 0.052 0.142 528 Planarity : 0.005 0.045 600 Dihedral : 5.773 17.699 468 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.78 % Allowed : 14.39 % Favored : 82.83 % 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: -2.05 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 362 PHE 0.005 0.001 PHE C 378 TYR 0.012 0.002 TYR A 310 ARG 0.003 0.000 ARG E 379 Details of bonding type rmsd hydrogen bonds : bond 0.02458 ( 80) hydrogen bonds : angle 4.76088 ( 240) covalent geometry : bond 0.00398 ( 3522) covalent geometry : angle 0.59906 ( 4710) *********************** 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 64 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.592 Fit side-chains REVERT: A 321 LYS cc_start: 0.7770 (mttt) cc_final: 0.7400 (mttp) REVERT: A 369 LYS cc_start: 0.8022 (mtpt) cc_final: 0.7337 (mttt) REVERT: B 311 LYS cc_start: 0.8158 (tttt) cc_final: 0.7904 (mtpt) REVERT: C 342 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7573 (mm-30) REVERT: C 369 LYS cc_start: 0.8321 (mtpt) cc_final: 0.7663 (mttm) REVERT: C 379 ARG cc_start: 0.6603 (mtm180) cc_final: 0.5688 (mtm-85) REVERT: D 321 LYS cc_start: 0.7917 (mttt) cc_final: 0.7350 (mttp) REVERT: E 321 LYS cc_start: 0.7932 (mttt) cc_final: 0.7544 (mttp) REVERT: E 342 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6779 (mm-30) REVERT: E 358 ASP cc_start: 0.8486 (p0) cc_final: 0.8026 (p0) outliers start: 11 outliers final: 6 residues processed: 60 average time/residue: 0.5110 time to fit residues: 35.4056 Evaluate side-chains 52 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 368 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 14 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 359 ASN E 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.125318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.106430 restraints weight = 14112.258| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 2.78 r_work: 0.4023 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3911 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 1.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3522 Z= 0.113 Angle : 0.556 7.394 4710 Z= 0.293 Chirality : 0.051 0.132 528 Planarity : 0.005 0.048 600 Dihedral : 5.635 16.572 468 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.26 % Allowed : 16.67 % Favored : 82.07 % 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: -2.08 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.005 0.001 PHE C 378 TYR 0.013 0.002 TYR E 310 ARG 0.002 0.000 ARG E 379 Details of bonding type rmsd hydrogen bonds : bond 0.02294 ( 80) hydrogen bonds : angle 4.70682 ( 240) covalent geometry : bond 0.00259 ( 3522) covalent geometry : angle 0.55613 ( 4710) *********************** 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 52 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.557 Fit side-chains REVERT: A 321 LYS cc_start: 0.7786 (mttt) cc_final: 0.7421 (mttp) REVERT: A 369 LYS cc_start: 0.7920 (mtpt) cc_final: 0.7242 (mttt) REVERT: C 342 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7564 (mm-30) REVERT: C 369 LYS cc_start: 0.8242 (mtpt) cc_final: 0.7589 (mttm) REVERT: C 379 ARG cc_start: 0.6530 (mtm180) cc_final: 0.5523 (mtm-85) REVERT: D 321 LYS cc_start: 0.7919 (mttt) cc_final: 0.7349 (mttp) outliers start: 5 outliers final: 4 residues processed: 51 average time/residue: 0.4971 time to fit residues: 29.3012 Evaluate side-chains 48 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 368 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.125600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.106776 restraints weight = 14344.253| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 2.81 r_work: 0.4011 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3896 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 1.1969 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= 0.134 Angle : 0.550 7.588 4710 Z= 0.292 Chirality : 0.050 0.133 528 Planarity : 0.005 0.053 600 Dihedral : 5.562 16.448 468 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.26 % Allowed : 16.16 % Favored : 82.58 % 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: -2.07 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.005 0.001 PHE C 378 TYR 0.011 0.002 TYR E 310 ARG 0.002 0.000 ARG E 379 Details of bonding type rmsd hydrogen bonds : bond 0.02277 ( 80) hydrogen bonds : angle 4.66037 ( 240) covalent geometry : bond 0.00298 ( 3522) covalent geometry : angle 0.55019 ( 4710) *********************** 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 53 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.628 Fit side-chains REVERT: A 321 LYS cc_start: 0.7807 (mttt) cc_final: 0.7425 (mttp) REVERT: A 369 LYS cc_start: 0.7932 (mtpt) cc_final: 0.7245 (mttt) REVERT: B 311 LYS cc_start: 0.8197 (tttt) cc_final: 0.7909 (mtpt) REVERT: C 342 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7595 (mm-30) REVERT: C 369 LYS cc_start: 0.8260 (mtpt) cc_final: 0.7606 (mttm) REVERT: C 379 ARG cc_start: 0.6533 (mtm180) cc_final: 0.5624 (mtm-85) REVERT: D 321 LYS cc_start: 0.7940 (mttt) cc_final: 0.7369 (mttp) REVERT: E 321 LYS cc_start: 0.7889 (mttt) cc_final: 0.7469 (mttp) REVERT: E 342 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6732 (mm-30) REVERT: E 358 ASP cc_start: 0.8101 (p0) cc_final: 0.7837 (p0) outliers start: 5 outliers final: 5 residues processed: 51 average time/residue: 0.5680 time to fit residues: 33.1200 Evaluate side-chains 51 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 368 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 368 ASN E 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.128864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.109749 restraints weight = 14246.368| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 2.83 r_work: 0.4067 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3953 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 1.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3522 Z= 0.095 Angle : 0.524 8.180 4710 Z= 0.275 Chirality : 0.050 0.128 528 Planarity : 0.005 0.054 600 Dihedral : 5.327 16.440 468 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.76 % Allowed : 16.92 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.06 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 374 PHE 0.007 0.001 PHE E 346 TYR 0.012 0.001 TYR E 310 ARG 0.002 0.000 ARG E 379 Details of bonding type rmsd hydrogen bonds : bond 0.02157 ( 80) hydrogen bonds : angle 4.51055 ( 240) covalent geometry : bond 0.00216 ( 3522) covalent geometry : angle 0.52440 ( 4710) ********************** 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 53 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.640 Fit side-chains REVERT: A 321 LYS cc_start: 0.7811 (mttt) cc_final: 0.7414 (mttp) REVERT: A 369 LYS cc_start: 0.7836 (mtpt) cc_final: 0.7166 (mttt) REVERT: C 342 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7621 (mm-30) REVERT: C 369 LYS cc_start: 0.8268 (mtpt) cc_final: 0.7590 (mttm) REVERT: C 379 ARG cc_start: 0.6504 (mtm180) cc_final: 0.5496 (mtm-85) REVERT: D 321 LYS cc_start: 0.7922 (mttt) cc_final: 0.7354 (mttp) REVERT: E 358 ASP cc_start: 0.8187 (p0) cc_final: 0.7927 (p0) outliers start: 3 outliers final: 2 residues processed: 52 average time/residue: 0.5386 time to fit residues: 32.6003 Evaluate side-chains 46 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 0.0020 chunk 11 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 16 optimal weight: 0.2980 chunk 41 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN E 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.129902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.111062 restraints weight = 14078.299| |-----------------------------------------------------------------------------| r_work (start): 0.4222 rms_B_bonded: 2.83 r_work: 0.4101 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3988 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 1.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3522 Z= 0.084 Angle : 0.516 7.873 4710 Z= 0.272 Chirality : 0.050 0.126 528 Planarity : 0.005 0.058 600 Dihedral : 5.153 16.601 468 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.76 % Allowed : 18.18 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.00 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 362 PHE 0.006 0.001 PHE E 346 TYR 0.023 0.002 TYR C 310 ARG 0.001 0.000 ARG E 379 Details of bonding type rmsd hydrogen bonds : bond 0.02134 ( 80) hydrogen bonds : angle 4.46253 ( 240) covalent geometry : bond 0.00199 ( 3522) covalent geometry : angle 0.51641 ( 4710) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4550.16 seconds wall clock time: 78 minutes 1.44 seconds (4681.44 seconds total)