Starting phenix.real_space_refine on Tue Feb 3 21:53:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9shs_54909/02_2026/9shs_54909.cif Found real_map, /net/cci-nas-00/data/ceres_data/9shs_54909/02_2026/9shs_54909.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9shs_54909/02_2026/9shs_54909.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9shs_54909/02_2026/9shs_54909.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9shs_54909/02_2026/9shs_54909.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9shs_54909/02_2026/9shs_54909.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2172 2.51 5 N 642 2.21 5 O 648 1.98 5 H 3606 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7074 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Modifications used: {'NH1NOTPRO': 1} 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} Modifications used: {'NH1NOTPRO': 1} 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} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "G" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1179 Classifications: {'peptide': 76} Modifications used: {'NH1NOTPRO': 1} 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} Modifications used: {'NH1NOTPRO': 1} 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} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Time building chain proxies: 1.03, per 1000 atoms: 0.15 Number of scatterers: 7074 At special positions: 0 Unit cell: (144.15, 114.39, 39.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 648 8.00 N 642 7.00 C 2172 6.00 H 3606 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 315.8 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 18 sheets defined 0.0% alpha, 52.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 305 through 310 removed outlier: 6.653A pdb=" N SER A 305 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ILE C 308 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.693A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 324 removed outlier: 6.527A pdb=" N LYS A 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N SER C 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR A 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N CYS C 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LYS A 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N SER C 324 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLY A 323 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N SER A 324 " --> pdb=" O GLY E 323 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 327 through 330 removed outlier: 6.608A pdb=" N ASN A 327 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N HIS C 330 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N HIS A 329 " --> pdb=" O HIS C 330 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE A 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 340 removed outlier: 6.579A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 343 through 347 removed outlier: 6.767A pdb=" N LEU A 344 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LYS E 347 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE A 346 " --> pdb=" O LYS E 347 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 350 through 354 removed outlier: 6.775A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N ILE C 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS A 353 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL A 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N LYS E 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N SER A 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 358 through 362 removed outlier: 6.678A pdb=" N ASN A 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N HIS E 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR A 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 369 through 378 removed outlier: 6.730A pdb=" N LYS A 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N GLU C 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N HIS C 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR A 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N LEU C 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LYS A 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N PHE C 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR A 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 305 through 310 removed outlier: 6.654A pdb=" N SER G 305 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ILE B 308 " --> pdb=" O SER G 305 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLN G 307 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N TYR B 310 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL G 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.693A pdb=" N VAL G 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 317 through 324 removed outlier: 6.552A pdb=" N LYS G 317 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N SER B 320 " --> pdb=" O LYS G 317 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR G 319 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N CYS B 322 " --> pdb=" O THR G 319 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LYS G 321 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N SER B 324 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLY G 323 " --> pdb=" O SER B 324 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N SER G 324 " --> pdb=" O GLY D 323 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 327 through 330 removed outlier: 6.455A pdb=" N ILE G 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 337 through 340 removed outlier: 6.548A pdb=" N VAL G 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N LYS D 340 " --> pdb=" O VAL G 337 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL G 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 343 through 347 removed outlier: 6.726A pdb=" N LEU G 344 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LYS D 347 " --> pdb=" O LEU G 344 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N PHE G 346 " --> pdb=" O LYS D 347 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 350 through 354 removed outlier: 6.356A pdb=" N VAL G 350 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N LYS D 353 " --> pdb=" O VAL G 350 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N SER G 352 " --> pdb=" O LYS D 353 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 358 through 362 removed outlier: 6.550A pdb=" N ASP G 358 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N THR B 361 " --> pdb=" O ASP G 358 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE G 360 " --> pdb=" O THR B 361 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 369 through 378 removed outlier: 6.760A pdb=" N LYS G 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N GLU B 372 " --> pdb=" O LYS G 369 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE G 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N HIS B 374 " --> pdb=" O ILE G 371 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR G 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N LEU B 376 " --> pdb=" O THR G 373 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LYS G 375 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N PHE B 378 " --> pdb=" O LYS G 375 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR G 377 " --> pdb=" O PHE B 378 " (cutoff:3.500A) 71 hydrogen bonds defined for protein. 213 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.24 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.11: 3600 1.11 - 1.29: 576 1.29 - 1.46: 898 1.46 - 1.63: 2048 1.63 - 1.81: 6 Bond restraints: 7128 Sorted by residual: bond pdb=" N HIS D 374 " pdb=" H HIS D 374 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N SER C 316 " pdb=" H SER C 316 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N SER E 316 " pdb=" H SER E 316 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N LYS G 321 " pdb=" H LYS G 321 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N ASP C 314 " pdb=" H ASP C 314 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 7123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 10666 2.41 - 4.83: 1754 4.83 - 7.24: 510 7.24 - 9.65: 48 9.65 - 12.07: 6 Bond angle restraints: 12984 Sorted by residual: angle pdb=" CA ASP D 314 " pdb=" CB ASP D 314 " pdb=" CG ASP D 314 " ideal model delta sigma weight residual 112.60 118.24 -5.64 1.00e+00 1.00e+00 3.18e+01 angle pdb=" CA ASP E 314 " pdb=" CB ASP E 314 " pdb=" CG ASP E 314 " ideal model delta sigma weight residual 112.60 118.20 -5.60 1.00e+00 1.00e+00 3.13e+01 angle pdb=" C LYS D 331 " pdb=" CA LYS D 331 " pdb=" CB LYS D 331 " ideal model delta sigma weight residual 111.11 117.86 -6.75 1.28e+00 6.10e-01 2.78e+01 angle pdb=" N LYS A 369 " pdb=" CA LYS A 369 " pdb=" C LYS A 369 " ideal model delta sigma weight residual 109.07 116.92 -7.85 1.52e+00 4.33e-01 2.67e+01 angle pdb=" C LYS D 331 " pdb=" N PRO D 332 " pdb=" CA PRO D 332 " ideal model delta sigma weight residual 119.85 124.91 -5.06 1.01e+00 9.80e-01 2.51e+01 ... (remaining 12979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.84: 2855 13.84 - 27.69: 205 27.69 - 41.53: 69 41.53 - 55.37: 68 55.37 - 69.21: 79 Dihedral angle restraints: 3276 sinusoidal: 1872 harmonic: 1404 Sorted by residual: dihedral pdb=" CA LEU B 357 " pdb=" C LEU B 357 " pdb=" N ASP B 358 " pdb=" CA ASP B 358 " ideal model delta harmonic sigma weight residual -180.00 -154.17 -25.83 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA LEU C 357 " pdb=" C LEU C 357 " pdb=" N ASP C 358 " pdb=" CA ASP C 358 " ideal model delta harmonic sigma weight residual -180.00 -155.33 -24.67 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA VAL D 318 " pdb=" C VAL D 318 " pdb=" N THR D 319 " pdb=" CA THR D 319 " ideal model delta harmonic sigma weight residual 180.00 -155.64 -24.36 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 3273 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.079: 307 0.079 - 0.158: 187 0.158 - 0.236: 29 0.236 - 0.314: 3 0.314 - 0.393: 2 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA LEU B 325 " pdb=" N LEU B 325 " pdb=" C LEU B 325 " pdb=" CB LEU B 325 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CA LEU C 325 " pdb=" N LEU C 325 " pdb=" C LEU C 325 " pdb=" CB LEU C 325 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CA LEU G 325 " pdb=" N LEU G 325 " pdb=" C LEU G 325 " pdb=" CB LEU G 325 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 525 not shown) Planarity restraints: 1032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 362 " -0.069 2.00e-02 2.50e+03 4.02e-02 3.63e+01 pdb=" CG HIS B 362 " 0.057 2.00e-02 2.50e+03 pdb=" ND1 HIS B 362 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 HIS B 362 " 0.047 2.00e-02 2.50e+03 pdb=" CE1 HIS B 362 " 0.010 2.00e-02 2.50e+03 pdb=" NE2 HIS B 362 " 0.024 2.00e-02 2.50e+03 pdb=" HD2 HIS B 362 " -0.014 2.00e-02 2.50e+03 pdb=" HE1 HIS B 362 " -0.033 2.00e-02 2.50e+03 pdb=" HE2 HIS B 362 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU G 357 " -0.033 2.00e-02 2.50e+03 6.02e-02 3.62e+01 pdb=" N ASP G 358 " 0.104 2.00e-02 2.50e+03 pdb=" CA ASP G 358 " -0.030 2.00e-02 2.50e+03 pdb=" H ASP G 358 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 362 " 0.065 2.00e-02 2.50e+03 3.78e-02 3.21e+01 pdb=" CG HIS C 362 " -0.054 2.00e-02 2.50e+03 pdb=" ND1 HIS C 362 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 HIS C 362 " -0.040 2.00e-02 2.50e+03 pdb=" CE1 HIS C 362 " -0.014 2.00e-02 2.50e+03 pdb=" NE2 HIS C 362 " -0.025 2.00e-02 2.50e+03 pdb=" HD2 HIS C 362 " 0.008 2.00e-02 2.50e+03 pdb=" HE1 HIS C 362 " 0.029 2.00e-02 2.50e+03 pdb=" HE2 HIS C 362 " 0.046 2.00e-02 2.50e+03 ... (remaining 1029 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 803 2.26 - 2.84: 13822 2.84 - 3.43: 17367 3.43 - 4.01: 22576 4.01 - 4.60: 32622 Nonbonded interactions: 87190 Sorted by model distance: nonbonded pdb=" HZ3 LYS A 370 " pdb=" OE1 GLU A 372 " model vdw 1.669 2.450 nonbonded pdb=" HG SER G 320 " pdb=" O GLY B 365 " model vdw 1.673 2.450 nonbonded pdb=" HG SER A 320 " pdb=" O GLY C 365 " model vdw 1.674 2.450 nonbonded pdb=" HZ3 LYS G 370 " pdb=" OE1 GLU G 372 " model vdw 1.674 2.450 nonbonded pdb=" O GLY A 365 " pdb=" HG SER E 320 " model vdw 1.684 2.450 ... (remaining 87185 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.680 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 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 0.040 3522 Z= 0.714 Angle : 1.998 7.982 4710 Z= 1.300 Chirality : 0.094 0.393 528 Planarity : 0.011 0.070 600 Dihedral : 11.174 54.555 1350 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 1.58 % Allowed : 9.23 % Favored : 89.19 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 349 TYR 0.057 0.018 TYR D 310 PHE 0.015 0.006 PHE D 346 HIS 0.010 0.003 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.01119 ( 3522) covalent geometry : angle 1.99779 ( 4710) hydrogen bonds : bond 0.15391 ( 71) hydrogen bonds : angle 6.49126 ( 213) *********************** 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 93 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8158 (mtpt) cc_final: 0.7917 (mttm) REVERT: A 340 LYS cc_start: 0.8466 (mttt) cc_final: 0.8135 (tttm) REVERT: G 321 LYS cc_start: 0.8140 (mtpt) cc_final: 0.7929 (mttm) REVERT: G 338 GLU cc_start: 0.8087 (tt0) cc_final: 0.7746 (tt0) REVERT: G 340 LYS cc_start: 0.8448 (mttt) cc_final: 0.8087 (tttm) REVERT: G 349 ARG cc_start: 0.7749 (mtt-85) cc_final: 0.7359 (mtm-85) REVERT: D 349 ARG cc_start: 0.7769 (mtt-85) cc_final: 0.7563 (mtm180) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.2967 time to fit residues: 30.4025 Evaluate side-chains 56 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS C 327 ASN C 362 HIS E 362 HIS G 362 HIS B 362 HIS B 368 ASN D 362 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.158804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.139932 restraints weight = 15023.176| |-----------------------------------------------------------------------------| r_work (start): 0.4260 rms_B_bonded: 2.72 r_work: 0.4169 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.4071 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3975 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= 0.145 Angle : 0.677 4.427 4710 Z= 0.355 Chirality : 0.051 0.142 528 Planarity : 0.003 0.038 600 Dihedral : 7.313 19.968 468 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 0.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.02 % Allowed : 9.60 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.28), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.22), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 349 TYR 0.012 0.003 TYR B 310 PHE 0.008 0.001 PHE E 378 HIS 0.004 0.001 HIS G 362 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 3522) covalent geometry : angle 0.67722 ( 4710) hydrogen bonds : bond 0.02953 ( 71) hydrogen bonds : angle 5.04950 ( 213) *********************** 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 72 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8217 (mtpt) cc_final: 0.7978 (mttm) REVERT: A 338 GLU cc_start: 0.8374 (tt0) cc_final: 0.7923 (tt0) REVERT: A 340 LYS cc_start: 0.8384 (mttt) cc_final: 0.7830 (tttm) REVERT: E 372 GLU cc_start: 0.8567 (tt0) cc_final: 0.8313 (tt0) REVERT: G 321 LYS cc_start: 0.8240 (mtpt) cc_final: 0.7941 (mttm) REVERT: G 340 LYS cc_start: 0.8337 (mttt) cc_final: 0.7771 (tttm) REVERT: G 349 ARG cc_start: 0.7106 (mtt-85) cc_final: 0.6723 (mtm-85) REVERT: D 349 ARG cc_start: 0.7547 (mtt-85) cc_final: 0.7151 (mtm180) outliers start: 8 outliers final: 4 residues processed: 72 average time/residue: 0.2140 time to fit residues: 17.7328 Evaluate side-chains 51 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 368 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.160891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.142409 restraints weight = 14913.115| |-----------------------------------------------------------------------------| r_work (start): 0.4383 rms_B_bonded: 2.51 r_work: 0.4278 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.4177 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4837 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= 0.181 Angle : 0.652 4.205 4710 Z= 0.347 Chirality : 0.053 0.137 528 Planarity : 0.003 0.020 600 Dihedral : 6.610 17.904 468 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.77 % Allowed : 10.86 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.28), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.21), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 349 TYR 0.021 0.005 TYR D 310 PHE 0.010 0.001 PHE E 378 HIS 0.004 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 3522) covalent geometry : angle 0.65194 ( 4710) hydrogen bonds : bond 0.03278 ( 71) hydrogen bonds : angle 4.69622 ( 213) *********************** 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 64 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8486 (mttt) cc_final: 0.7900 (tttm) REVERT: E 349 ARG cc_start: 0.8375 (mtm180) cc_final: 0.8129 (mtm180) REVERT: E 372 GLU cc_start: 0.8534 (tt0) cc_final: 0.8211 (tt0) REVERT: E 379 ARG cc_start: 0.7226 (mtt180) cc_final: 0.6211 (tpm170) REVERT: G 321 LYS cc_start: 0.8243 (mtpt) cc_final: 0.8030 (mttm) REVERT: G 338 GLU cc_start: 0.8310 (tt0) cc_final: 0.7835 (tt0) REVERT: G 340 LYS cc_start: 0.8339 (mttt) cc_final: 0.7813 (tttm) REVERT: G 349 ARG cc_start: 0.7220 (mtt-85) cc_final: 0.6968 (mtm180) REVERT: B 379 ARG cc_start: 0.6819 (mtt180) cc_final: 0.6613 (mtt-85) REVERT: D 349 ARG cc_start: 0.7596 (mtt-85) cc_final: 0.7375 (mtm180) outliers start: 7 outliers final: 5 residues processed: 61 average time/residue: 0.3174 time to fit residues: 21.2978 Evaluate side-chains 50 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain G residue 344 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.157838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.138898 restraints weight = 14082.808| |-----------------------------------------------------------------------------| r_work (start): 0.4366 rms_B_bonded: 2.50 r_work: 0.4275 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.4173 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3522 Z= 0.170 Angle : 0.608 3.870 4710 Z= 0.318 Chirality : 0.051 0.135 528 Planarity : 0.003 0.017 600 Dihedral : 6.390 17.330 468 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.53 % Allowed : 11.87 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.29), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.22), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 379 TYR 0.018 0.005 TYR D 310 PHE 0.008 0.001 PHE E 378 HIS 0.002 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 3522) covalent geometry : angle 0.60830 ( 4710) hydrogen bonds : bond 0.02686 ( 71) hydrogen bonds : angle 4.78168 ( 213) *********************** 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 59 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8344 (mttt) cc_final: 0.7776 (tttm) REVERT: A 349 ARG cc_start: 0.7304 (mtt-85) cc_final: 0.7071 (mtm180) REVERT: E 349 ARG cc_start: 0.8362 (mtm180) cc_final: 0.7981 (mtm180) REVERT: E 372 GLU cc_start: 0.8509 (tt0) cc_final: 0.8230 (tt0) REVERT: G 340 LYS cc_start: 0.8307 (mttt) cc_final: 0.7778 (tttm) REVERT: G 349 ARG cc_start: 0.7295 (mtt-85) cc_final: 0.7049 (mtm180) outliers start: 10 outliers final: 10 residues processed: 55 average time/residue: 0.2657 time to fit residues: 16.4778 Evaluate side-chains 53 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 368 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 13 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.161308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.142186 restraints weight = 13970.543| |-----------------------------------------------------------------------------| r_work (start): 0.4406 rms_B_bonded: 2.55 r_work: 0.4312 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4210 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.5763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3522 Z= 0.104 Angle : 0.545 3.891 4710 Z= 0.279 Chirality : 0.051 0.138 528 Planarity : 0.003 0.020 600 Dihedral : 5.787 15.165 468 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.52 % Allowed : 13.13 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 379 TYR 0.010 0.002 TYR E 310 PHE 0.003 0.001 PHE C 378 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 3522) covalent geometry : angle 0.54542 ( 4710) hydrogen bonds : bond 0.02036 ( 71) hydrogen bonds : angle 4.62424 ( 213) *********************** 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 54 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8443 (tt0) cc_final: 0.8012 (tt0) REVERT: A 340 LYS cc_start: 0.8317 (mttt) cc_final: 0.7771 (tttm) REVERT: A 349 ARG cc_start: 0.7240 (mtt-85) cc_final: 0.6992 (mtm180) REVERT: E 349 ARG cc_start: 0.8353 (mtm180) cc_final: 0.8072 (mtm-85) REVERT: G 340 LYS cc_start: 0.8278 (mttt) cc_final: 0.7731 (tttm) REVERT: G 349 ARG cc_start: 0.7250 (mtt-85) cc_final: 0.6935 (mtm180) REVERT: B 375 LYS cc_start: 0.8676 (ttmt) cc_final: 0.8442 (ttmm) REVERT: D 349 ARG cc_start: 0.8422 (mtm180) cc_final: 0.8067 (mtm-85) outliers start: 6 outliers final: 6 residues processed: 52 average time/residue: 0.2569 time to fit residues: 15.1128 Evaluate side-chains 51 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain D residue 320 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.158486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.139613 restraints weight = 14087.753| |-----------------------------------------------------------------------------| r_work (start): 0.4379 rms_B_bonded: 2.51 r_work: 0.4286 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.4187 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.5880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3522 Z= 0.151 Angle : 0.566 4.043 4710 Z= 0.294 Chirality : 0.051 0.134 528 Planarity : 0.003 0.019 600 Dihedral : 5.890 15.440 468 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.27 % Allowed : 12.88 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.29), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.22), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 379 TYR 0.017 0.004 TYR E 310 PHE 0.007 0.001 PHE C 378 HIS 0.002 0.001 HIS G 330 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 3522) covalent geometry : angle 0.56611 ( 4710) hydrogen bonds : bond 0.02375 ( 71) hydrogen bonds : angle 4.68476 ( 213) *********************** 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 58 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8420 (tt0) cc_final: 0.7995 (tt0) REVERT: A 340 LYS cc_start: 0.8345 (mttt) cc_final: 0.7787 (tttm) REVERT: A 349 ARG cc_start: 0.7260 (mtt-85) cc_final: 0.7007 (mtm180) REVERT: E 349 ARG cc_start: 0.8419 (mtm180) cc_final: 0.8164 (mtm-85) REVERT: G 338 GLU cc_start: 0.8282 (tt0) cc_final: 0.7835 (tt0) REVERT: G 340 LYS cc_start: 0.8299 (mttt) cc_final: 0.7791 (tttm) REVERT: G 349 ARG cc_start: 0.7254 (mtt-85) cc_final: 0.6994 (mtm180) REVERT: B 375 LYS cc_start: 0.8733 (ttmt) cc_final: 0.8475 (ttmm) REVERT: D 349 ARG cc_start: 0.8435 (mtm180) cc_final: 0.8108 (mtm-85) outliers start: 9 outliers final: 9 residues processed: 54 average time/residue: 0.2618 time to fit residues: 16.1125 Evaluate side-chains 55 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 344 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.161317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.142282 restraints weight = 13834.572| |-----------------------------------------------------------------------------| r_work (start): 0.4409 rms_B_bonded: 2.54 r_work: 0.4315 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4212 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.6060 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= 0.094 Angle : 0.516 4.400 4710 Z= 0.264 Chirality : 0.051 0.132 528 Planarity : 0.002 0.016 600 Dihedral : 5.521 14.593 468 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.52 % Allowed : 13.64 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 379 TYR 0.009 0.002 TYR A 310 PHE 0.004 0.001 PHE D 378 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 3522) covalent geometry : angle 0.51608 ( 4710) hydrogen bonds : bond 0.01878 ( 71) hydrogen bonds : angle 4.57214 ( 213) *********************** 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 56 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.227 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: A 340 LYS cc_start: 0.8304 (mttt) cc_final: 0.7750 (tttm) REVERT: G 338 GLU cc_start: 0.8297 (tt0) cc_final: 0.7844 (tt0) REVERT: G 340 LYS cc_start: 0.8290 (mttt) cc_final: 0.7753 (tttm) REVERT: B 375 LYS cc_start: 0.8715 (ttmt) cc_final: 0.8492 (ttmm) outliers start: 6 outliers final: 5 residues processed: 54 average time/residue: 0.2505 time to fit residues: 15.3298 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 : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain D residue 320 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.157634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.138549 restraints weight = 14075.728| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 2.53 r_work: 0.4268 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4168 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.6236 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= 0.142 Angle : 0.549 4.553 4710 Z= 0.285 Chirality : 0.051 0.138 528 Planarity : 0.002 0.014 600 Dihedral : 5.676 14.751 468 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.53 % Allowed : 13.64 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 379 TYR 0.015 0.004 TYR B 310 PHE 0.006 0.001 PHE D 378 HIS 0.003 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 3522) covalent geometry : angle 0.54936 ( 4710) hydrogen bonds : bond 0.02250 ( 71) hydrogen bonds : angle 4.58681 ( 213) *********************** 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 51 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8352 (mttt) cc_final: 0.7758 (tttm) REVERT: G 338 GLU cc_start: 0.8355 (tt0) cc_final: 0.7907 (tt0) REVERT: G 340 LYS cc_start: 0.8275 (mttt) cc_final: 0.7750 (tttm) REVERT: B 375 LYS cc_start: 0.8753 (ttmt) cc_final: 0.8502 (ttmm) outliers start: 10 outliers final: 8 residues processed: 49 average time/residue: 0.2317 time to fit residues: 13.1634 Evaluate side-chains 48 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 344 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 368 ASN B 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.154924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.136130 restraints weight = 14086.431| |-----------------------------------------------------------------------------| r_work (start): 0.4328 rms_B_bonded: 2.49 r_work: 0.4237 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.4139 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.6284 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= 0.177 Angle : 0.579 4.748 4710 Z= 0.301 Chirality : 0.051 0.135 528 Planarity : 0.002 0.014 600 Dihedral : 5.962 15.516 468 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.53 % Allowed : 13.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG E 379 TYR 0.019 0.005 TYR E 310 PHE 0.007 0.001 PHE D 378 HIS 0.002 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 3522) covalent geometry : angle 0.57937 ( 4710) hydrogen bonds : bond 0.02498 ( 71) hydrogen bonds : angle 4.76742 ( 213) *********************** 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 49 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8387 (mttt) cc_final: 0.7760 (tttm) REVERT: G 338 GLU cc_start: 0.8402 (tt0) cc_final: 0.7982 (tt0) REVERT: G 340 LYS cc_start: 0.8332 (mttt) cc_final: 0.7800 (tttm) REVERT: B 375 LYS cc_start: 0.8780 (ttmt) cc_final: 0.8525 (ttmm) outliers start: 10 outliers final: 10 residues processed: 47 average time/residue: 0.2298 time to fit residues: 12.4878 Evaluate side-chains 48 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 368 ASN Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 344 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.155406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.136536 restraints weight = 14258.482| |-----------------------------------------------------------------------------| r_work (start): 0.4339 rms_B_bonded: 2.50 r_work: 0.4247 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.4150 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.6313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.224 3522 Z= 0.409 Angle : 1.623 59.200 4710 Z= 1.008 Chirality : 0.055 0.348 528 Planarity : 0.003 0.020 600 Dihedral : 6.075 18.174 468 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.02 % Allowed : 12.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 379 TYR 0.018 0.004 TYR E 310 PHE 0.007 0.001 PHE D 378 HIS 0.002 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00826 ( 3522) covalent geometry : angle 1.62295 ( 4710) hydrogen bonds : bond 0.02351 ( 71) hydrogen bonds : angle 4.77034 ( 213) ********************** 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 46 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8445 (tt0) cc_final: 0.8012 (tt0) REVERT: A 340 LYS cc_start: 0.8382 (mttt) cc_final: 0.7784 (tttm) REVERT: G 338 GLU cc_start: 0.8399 (tt0) cc_final: 0.7985 (tt0) REVERT: G 340 LYS cc_start: 0.8337 (mttt) cc_final: 0.7803 (tttm) REVERT: B 375 LYS cc_start: 0.8777 (ttmt) cc_final: 0.8524 (ttmm) outliers start: 8 outliers final: 8 residues processed: 44 average time/residue: 0.2248 time to fit residues: 11.4284 Evaluate side-chains 46 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 344 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 7.9990 chunk 19 optimal weight: 0.0770 chunk 26 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 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 = 0.4541 r_free = 0.4541 target = 0.155482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.136636 restraints weight = 14159.500| |-----------------------------------------------------------------------------| r_work (start): 0.4339 rms_B_bonded: 2.49 r_work: 0.4250 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.4151 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.6313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.224 3522 Z= 0.409 Angle : 1.623 59.200 4710 Z= 1.008 Chirality : 0.055 0.348 528 Planarity : 0.003 0.020 600 Dihedral : 6.075 18.174 468 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.02 % Allowed : 12.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 379 TYR 0.018 0.004 TYR E 310 PHE 0.007 0.001 PHE D 378 HIS 0.002 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00826 ( 3522) covalent geometry : angle 1.62295 ( 4710) hydrogen bonds : bond 0.02351 ( 71) hydrogen bonds : angle 4.77034 ( 213) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2269.03 seconds wall clock time: 39 minutes 14.16 seconds (2354.16 seconds total)