Starting phenix.real_space_refine on Wed Feb 12 02:22:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ql4_14063/02_2025/7ql4_14063.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ql4_14063/02_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_14063/02_2025/7ql4_14063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ql4_14063/02_2025/7ql4_14063.map" model { file = "/net/cci-nas-00/data/ceres_data/7ql4_14063/02_2025/7ql4_14063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ql4_14063/02_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-5592/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: 3.84, per 1000 atoms: 0.54 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: 1.75 Conformation dependent library (CDL) restraints added in 633.0 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: 0.71 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: 2.44 Time building geometry restraints manager: 2.12 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: 0.680 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: 0.120 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.430 Find NCS groups from input model: 0.170 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.620 ------------------------------------------------------------------------------- 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= 0.738 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 *********************** 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 : 0.580 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: 0.2249 time to fit residues: 39.3909 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 : 0.580 ------------------------------------------------------------------------------- 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 = 33)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.121838 restraints weight = 13710.422| |-----------------------------------------------------------------------------| r_work (start): 0.4333 rms_B_bonded: 3.00 r_work: 0.4242 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5961 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= 0.280 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 *********************** 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 : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 352 SER cc_start: 0.8049 (OUTLIER) cc_final: 0.7663 (t) REVERT: B 342 GLU cc_start: 0.7975 (mm-30) cc_final: 0.6146 (pm20) REVERT: B 379 ARG cc_start: 0.4739 (mtm180) cc_final: 0.4123 (mtm-85) REVERT: C 379 ARG cc_start: 0.6504 (mtm180) cc_final: 0.5724 (mtm-85) outliers start: 11 outliers final: 9 residues processed: 92 average time/residue: 0.3202 time to fit residues: 35.9558 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 : 0.545 ------------------------------------------------------------------------------- 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: 0.8980 chunk 10 optimal weight: 0.0040 chunk 28 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 11 optimal weight: 0.0040 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: 0.9980 overall best weight: 0.9806 ------------------------------------------------------------------------------- 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 = 0.4655 r_free = 0.4655 target = 0.155076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.135323 restraints weight = 12913.172| |-----------------------------------------------------------------------------| r_work (start): 0.4460 rms_B_bonded: 3.07 r_work: 0.4347 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6306 moved from start: 0.6294 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= 0.190 Angle : 0.583 7.716 4710 Z= 0.315 Chirality : 0.052 0.139 528 Planarity : 0.005 0.050 600 Dihedral : 6.549 17.927 468 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.53 % Allowed : 8.84 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (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 0.003 0.001 HIS D 362 PHE 0.008 0.001 PHE C 346 TYR 0.015 0.002 TYR E 310 ARG 0.002 0.000 ARG F 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 80 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 342 GLU cc_start: 0.7957 (mm-30) cc_final: 0.6200 (pm20) REVERT: B 379 ARG cc_start: 0.4561 (mtm180) cc_final: 0.4258 (mtm-85) REVERT: C 379 ARG cc_start: 0.6613 (mtm180) cc_final: 0.5928 (mtm-85) REVERT: D 370 LYS cc_start: 0.7671 (tttp) cc_final: 0.6891 (ttmt) outliers start: 10 outliers final: 7 residues processed: 77 average time/residue: 0.2676 time to fit residues: 26.3213 Evaluate side-chains 70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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 C residue 352 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 359 ASN 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: 10.0000 chunk 24 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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 = 0.4545 r_free = 0.4545 target = 0.145907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.126175 restraints weight = 13561.458| |-----------------------------------------------------------------------------| r_work (start): 0.4334 rms_B_bonded: 3.01 r_work: 0.4236 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.4134 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.8114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3522 Z= 0.238 Angle : 0.613 8.930 4710 Z= 0.334 Chirality : 0.055 0.238 528 Planarity : 0.005 0.046 600 Dihedral : 6.373 18.999 468 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.78 % Allowed : 10.10 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.82 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 374 PHE 0.011 0.002 PHE B 378 TYR 0.015 0.002 TYR E 310 ARG 0.002 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: F 340 LYS cc_start: 0.6810 (ttmt) cc_final: 0.6549 (mttt) REVERT: B 342 GLU cc_start: 0.8425 (mm-30) cc_final: 0.6376 (pm20) REVERT: B 349 ARG cc_start: 0.7763 (mtm180) cc_final: 0.7509 (mtt180) REVERT: B 359 ASN cc_start: 0.8013 (OUTLIER) cc_final: 0.7580 (m-40) REVERT: C 379 ARG cc_start: 0.6736 (mtm180) cc_final: 0.5979 (mtm-85) REVERT: D 306 VAL cc_start: 0.6735 (OUTLIER) cc_final: 0.6352 (p) REVERT: E 379 ARG cc_start: 0.6409 (mtm180) cc_final: 0.5759 (mmm160) outliers start: 11 outliers final: 6 residues processed: 78 average time/residue: 0.4269 time to fit residues: 39.3631 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 : 0.587 ------------------------------------------------------------------------------- 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 359 ASN Chi-restraints excluded: chain E residue 320 SER 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: 0.4980 chunk 30 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 22 optimal weight: 0.3980 chunk 21 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.131952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.112838 restraints weight = 14107.823| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 2.80 r_work: 0.4095 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3985 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.9575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3522 Z= 0.239 Angle : 0.584 5.732 4710 Z= 0.313 Chirality : 0.052 0.136 528 Planarity : 0.005 0.055 600 Dihedral : 5.934 16.752 468 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.78 % Allowed : 12.88 % Favored : 84.34 % 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: -1.86 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS C 374 PHE 0.008 0.001 PHE A 378 TYR 0.012 0.002 TYR E 310 ARG 0.004 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 325 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8141 (mt) REVERT: F 336 GLN cc_start: 0.8183 (tp40) cc_final: 0.7957 (mm-40) REVERT: B 342 GLU cc_start: 0.8447 (mm-30) cc_final: 0.6488 (pm20) REVERT: B 349 ARG cc_start: 0.7830 (mtm180) cc_final: 0.7583 (mtt180) REVERT: C 342 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7309 (mm-30) REVERT: C 371 ILE cc_start: 0.8370 (mt) cc_final: 0.8095 (mp) REVERT: C 379 ARG cc_start: 0.6608 (mtm180) cc_final: 0.5631 (mtm-85) REVERT: D 306 VAL cc_start: 0.7122 (OUTLIER) cc_final: 0.6854 (p) REVERT: E 379 ARG cc_start: 0.6508 (mtm180) cc_final: 0.5982 (mmm160) outliers start: 11 outliers final: 8 residues processed: 78 average time/residue: 0.4492 time to fit residues: 40.8015 Evaluate side-chains 67 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain F residue 325 LEU 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 Chi-restraints excluded: chain E residue 361 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 5 optimal weight: 0.0970 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.131473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.112904 restraints weight = 14133.005| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 2.88 r_work: 0.4098 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3989 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 1.0137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3522 Z= 0.169 Angle : 0.546 6.784 4710 Z= 0.294 Chirality : 0.051 0.128 528 Planarity : 0.005 0.052 600 Dihedral : 5.743 16.525 468 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.27 % Allowed : 14.39 % Favored : 83.33 % 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 0.003 0.001 HIS A 362 PHE 0.009 0.001 PHE A 378 TYR 0.012 0.001 TYR E 310 ARG 0.002 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7709 (mttt) cc_final: 0.7282 (mttm) REVERT: F 336 GLN cc_start: 0.8180 (tp40) cc_final: 0.7776 (tp40) REVERT: F 356 SER cc_start: 0.8442 (m) cc_final: 0.8189 (p) REVERT: B 342 GLU cc_start: 0.8476 (mm-30) cc_final: 0.6456 (pm20) REVERT: B 349 ARG cc_start: 0.7796 (mtm180) cc_final: 0.7491 (mtt180) REVERT: C 342 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7284 (mm-30) REVERT: C 379 ARG cc_start: 0.6580 (mtm180) cc_final: 0.5572 (mtm-85) REVERT: D 306 VAL cc_start: 0.7119 (OUTLIER) cc_final: 0.6902 (p) REVERT: D 321 LYS cc_start: 0.7708 (mttt) cc_final: 0.7081 (mttp) REVERT: E 358 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7868 (p0) REVERT: E 379 ARG cc_start: 0.6444 (mtm180) cc_final: 0.6000 (mmm160) outliers start: 9 outliers final: 6 residues processed: 60 average time/residue: 0.4218 time to fit residues: 30.1873 Evaluate side-chains 58 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain B residue 356 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 358 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.4289 r_free = 0.4289 target = 0.121684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.103340 restraints weight = 14559.041| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 2.77 r_work: 0.3943 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3835 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 1.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3522 Z= 0.306 Angle : 0.621 6.506 4710 Z= 0.335 Chirality : 0.053 0.137 528 Planarity : 0.005 0.048 600 Dihedral : 5.844 17.218 468 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.27 % Allowed : 14.65 % Favored : 83.08 % 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: -1.92 (0.35), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 362 PHE 0.009 0.002 PHE E 378 TYR 0.016 0.003 TYR D 310 ARG 0.002 0.000 ARG B 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 63 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.7788 (mttt) cc_final: 0.7386 (mttp) REVERT: C 342 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7563 (mm-30) REVERT: C 369 LYS cc_start: 0.8249 (mtpt) cc_final: 0.7591 (mttm) REVERT: C 379 ARG cc_start: 0.6593 (mtm180) cc_final: 0.5676 (mtm-85) REVERT: D 306 VAL cc_start: 0.7373 (OUTLIER) cc_final: 0.7159 (p) REVERT: D 311 LYS cc_start: 0.7828 (tttt) cc_final: 0.7607 (mtpt) REVERT: D 321 LYS cc_start: 0.7871 (mttt) cc_final: 0.7268 (mttp) outliers start: 9 outliers final: 6 residues processed: 60 average time/residue: 0.4849 time to fit residues: 34.1606 Evaluate side-chains 55 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 356 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 14 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4365 r_free = 0.4365 target = 0.127119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.108528 restraints weight = 14054.223| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 2.83 r_work: 0.4021 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3914 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 1.1578 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= 0.165 Angle : 0.547 7.043 4710 Z= 0.293 Chirality : 0.051 0.134 528 Planarity : 0.005 0.051 600 Dihedral : 5.608 16.034 468 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.02 % Allowed : 14.90 % Favored : 83.08 % 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: -1.95 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.010 0.001 PHE A 378 TYR 0.011 0.001 TYR E 310 ARG 0.002 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7656 (ptmt) REVERT: A 321 LYS cc_start: 0.7739 (mttt) cc_final: 0.7342 (mttm) REVERT: A 369 LYS cc_start: 0.8034 (mtpt) cc_final: 0.7306 (mttt) REVERT: F 343 LYS cc_start: 0.8462 (tttt) cc_final: 0.8244 (mtpt) REVERT: C 342 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7608 (mm-30) REVERT: C 369 LYS cc_start: 0.8290 (mtpt) cc_final: 0.7954 (mtpt) REVERT: C 379 ARG cc_start: 0.6549 (mtm180) cc_final: 0.5545 (mtm-85) REVERT: D 306 VAL cc_start: 0.7300 (OUTLIER) cc_final: 0.7098 (p) REVERT: D 321 LYS cc_start: 0.7861 (mttt) cc_final: 0.7233 (mttp) outliers start: 8 outliers final: 5 residues processed: 57 average time/residue: 0.4894 time to fit residues: 32.4026 Evaluate side-chains 51 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain F residue 361 THR 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 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: 7.9990 chunk 6 optimal weight: 0.7980 chunk 19 optimal weight: 0.2980 chunk 31 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 368 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 = 0.4383 r_free = 0.4383 target = 0.127931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.109356 restraints weight = 14227.934| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 2.85 r_work: 0.4040 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3933 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 1.1694 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= 0.146 Angle : 0.529 6.839 4710 Z= 0.281 Chirality : 0.051 0.131 528 Planarity : 0.005 0.052 600 Dihedral : 5.438 16.241 468 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.26 % Allowed : 15.15 % Favored : 83.59 % 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: -1.87 (0.35), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.008 0.001 PHE A 378 TYR 0.014 0.001 TYR E 310 ARG 0.002 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7633 (ptmt) REVERT: A 321 LYS cc_start: 0.7782 (mttt) cc_final: 0.7398 (mttm) REVERT: A 369 LYS cc_start: 0.8020 (mtpt) cc_final: 0.7280 (mttt) REVERT: B 379 ARG cc_start: 0.3745 (mtm-85) cc_final: 0.3078 (mtm110) REVERT: C 342 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7618 (mm-30) REVERT: C 379 ARG cc_start: 0.6543 (mtm180) cc_final: 0.5536 (mtm-85) REVERT: D 321 LYS cc_start: 0.7852 (mttt) cc_final: 0.7218 (mttp) outliers start: 5 outliers final: 3 residues processed: 50 average time/residue: 0.4987 time to fit residues: 29.1829 Evaluate side-chains 47 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain F residue 361 THR 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: 6.9990 chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.4335 r_free = 0.4335 target = 0.124511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.105893 restraints weight = 14686.367| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 2.87 r_work: 0.3990 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3880 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 1.1985 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= 0.221 Angle : 0.548 6.684 4710 Z= 0.294 Chirality : 0.051 0.127 528 Planarity : 0.005 0.047 600 Dihedral : 5.440 15.885 468 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.52 % Allowed : 14.90 % Favored : 83.59 % 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: -1.92 (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 A 378 TYR 0.016 0.002 TYR E 310 ARG 0.001 0.000 ARG B 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.561 Fit side-chains REVERT: A 311 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7702 (ptmt) REVERT: A 321 LYS cc_start: 0.7801 (mttt) cc_final: 0.7408 (mttp) REVERT: A 369 LYS cc_start: 0.7862 (mtpt) cc_final: 0.7158 (mttt) REVERT: B 311 LYS cc_start: 0.8151 (tttt) cc_final: 0.7884 (mtpt) REVERT: B 379 ARG cc_start: 0.3757 (mtm-85) cc_final: 0.3089 (mtm110) REVERT: C 342 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7716 (mm-30) REVERT: C 369 LYS cc_start: 0.8335 (mtpt) cc_final: 0.8021 (mtpt) REVERT: C 379 ARG cc_start: 0.6500 (mtm180) cc_final: 0.5599 (mtm-85) REVERT: D 321 LYS cc_start: 0.7805 (mttt) cc_final: 0.7212 (mttp) REVERT: E 321 LYS cc_start: 0.7867 (mttt) cc_final: 0.7459 (mttp) outliers start: 6 outliers final: 4 residues processed: 51 average time/residue: 0.5704 time to fit residues: 33.4334 Evaluate side-chains 47 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 350 VAL 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: 0.0060 chunk 11 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 16 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 = 0.4331 r_free = 0.4331 target = 0.124245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.105646 restraints weight = 14538.857| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 2.87 r_work: 0.3981 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3874 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 1.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.226 3522 Z= 0.299 Angle : 1.210 59.173 4710 Z= 0.748 Chirality : 0.051 0.127 528 Planarity : 0.005 0.047 600 Dihedral : 5.504 15.956 468 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.01 % Allowed : 15.40 % Favored : 83.59 % 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: -1.94 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 362 PHE 0.006 0.001 PHE A 378 TYR 0.015 0.002 TYR E 310 ARG 0.001 0.000 ARG E 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4598.71 seconds wall clock time: 81 minutes 27.73 seconds (4887.73 seconds total)