Starting phenix.real_space_refine on Tue Mar 11 23:33:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q9h_18281/03_2025/8q9h_18281.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q9h_18281/03_2025/8q9h_18281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q9h_18281/03_2025/8q9h_18281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q9h_18281/03_2025/8q9h_18281.map" model { file = "/net/cci-nas-00/data/ceres_data/8q9h_18281/03_2025/8q9h_18281.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q9h_18281/03_2025/8q9h_18281.cif" } resolution = 2.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2106 2.51 5 N 606 2.21 5 O 624 1.98 5 H 3480 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6822 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "B" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "C" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "D" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "E" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "G" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 4.79, per 1000 atoms: 0.70 Number of scatterers: 6822 At special positions: 0 Unit cell: (98.872, 137.403, 35.623, 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 624 8.00 N 606 7.00 C 2106 6.00 H 3480 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: 1.52 Conformation dependent library (CDL) restraints added in 584.6 milliseconds 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 49.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 307 through 310 removed outlier: 6.515A pdb=" N GLN A 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N TYR E 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL A 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.663A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 321 removed outlier: 6.345A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 325 through 330 removed outlier: 5.840A pdb=" N GLY A 326 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N HIS C 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY E 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN A 327 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 342 Processing sheet with id=AA6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.439A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 350 through 357 removed outlier: 6.567A pdb=" N GLN A 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ILE E 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LYS A 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N SER E 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLY A 355 " --> pdb=" O SER E 356 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.457A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 369 through 377 removed outlier: 6.365A pdb=" N LYS A 370 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N THR C 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLU A 372 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N LYS C 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N HIS A 374 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N THR C 377 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU A 376 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LYS A 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLU E 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE A 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N HIS E 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N THR A 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LEU E 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LYS A 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 307 through 310 removed outlier: 6.557A pdb=" N GLN B 307 " --> pdb=" O ILE G 308 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N TYR G 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL B 309 " --> pdb=" O TYR G 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.642A pdb=" N VAL B 313 " --> pdb=" O ASP G 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 317 through 321 removed outlier: 6.327A pdb=" N VAL D 318 " --> pdb=" O THR G 319 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N LYS G 321 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N SER D 320 " --> pdb=" O LYS G 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 325 through 330 removed outlier: 8.808A pdb=" N LEU B 325 " --> pdb=" O GLY G 326 " (cutoff:3.500A) removed outlier: 9.778A pdb=" N ILE G 328 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASN B 327 " --> pdb=" O ILE G 328 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N HIS G 330 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N HIS B 329 " --> pdb=" O HIS G 330 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N GLY D 326 " --> pdb=" O ASN G 327 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N HIS G 329 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE D 328 " --> pdb=" O HIS G 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 337 through 342 removed outlier: 6.532A pdb=" N GLU B 338 " --> pdb=" O VAL G 339 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N SER G 341 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LYS B 340 " --> pdb=" O SER G 341 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL D 337 " --> pdb=" O GLU G 338 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LYS G 340 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL D 339 " --> pdb=" O LYS G 340 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLU G 342 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N SER D 341 " --> pdb=" O GLU G 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 345 through 346 removed outlier: 6.422A pdb=" N ASP B 345 " --> pdb=" O PHE G 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 350 through 357 removed outlier: 6.574A pdb=" N GLN B 351 " --> pdb=" O SER G 352 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ILE G 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LYS B 353 " --> pdb=" O ILE G 354 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N SER G 356 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLY B 355 " --> pdb=" O SER G 356 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 360 through 362 removed outlier: 6.412A pdb=" N THR D 361 " --> pdb=" O HIS G 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 369 through 377 65 hydrogen bonds defined for protein. 195 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: 2.00 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 3474 1.12 - 1.29: 558 1.29 - 1.46: 992 1.46 - 1.64: 1846 1.64 - 1.81: 6 Bond restraints: 6876 Sorted by residual: bond pdb=" CE1 HIS A 330 " pdb=" HE1 HIS A 330 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N ASN E 359 " pdb=" H ASN E 359 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N LEU C 325 " pdb=" H LEU C 325 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" ND2 ASN B 359 " pdb="HD22 ASN B 359 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N VAL C 306 " pdb=" H VAL C 306 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 6871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 10566 2.42 - 4.85: 1493 4.85 - 7.27: 462 7.27 - 9.69: 19 9.69 - 12.12: 6 Bond angle restraints: 12546 Sorted by residual: angle pdb=" CB HIS G 329 " pdb=" CG HIS G 329 " pdb=" CD2 HIS G 329 " ideal model delta sigma weight residual 131.20 125.24 5.96 1.30e+00 5.92e-01 2.10e+01 angle pdb=" CB HIS A 329 " pdb=" CG HIS A 329 " pdb=" CD2 HIS A 329 " ideal model delta sigma weight residual 131.20 125.29 5.91 1.30e+00 5.92e-01 2.07e+01 angle pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " pdb=" CD2 HIS E 374 " ideal model delta sigma weight residual 131.20 125.44 5.76 1.30e+00 5.92e-01 1.97e+01 angle pdb=" N GLY G 326 " pdb=" CA GLY G 326 " pdb=" C GLY G 326 " ideal model delta sigma weight residual 110.69 116.56 -5.87 1.33e+00 5.65e-01 1.95e+01 angle pdb=" CB HIS D 329 " pdb=" CG HIS D 329 " pdb=" CD2 HIS D 329 " ideal model delta sigma weight residual 131.20 125.49 5.71 1.30e+00 5.92e-01 1.93e+01 ... (remaining 12541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.36: 2753 13.36 - 26.73: 203 26.73 - 40.09: 86 40.09 - 53.45: 40 53.45 - 66.81: 86 Dihedral angle restraints: 3168 sinusoidal: 1806 harmonic: 1362 Sorted by residual: dihedral pdb=" CA THR C 319 " pdb=" C THR C 319 " pdb=" N SER C 320 " pdb=" CA SER C 320 " ideal model delta harmonic sigma weight residual 180.00 157.49 22.51 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA THR A 319 " pdb=" C THR A 319 " pdb=" N SER A 320 " pdb=" CA SER A 320 " ideal model delta harmonic sigma weight residual 180.00 158.95 21.05 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA THR G 319 " pdb=" C THR G 319 " pdb=" N SER G 320 " pdb=" CA SER G 320 " ideal model delta harmonic sigma weight residual 180.00 160.23 19.77 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 3165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 198 0.046 - 0.093: 190 0.093 - 0.139: 79 0.139 - 0.185: 36 0.185 - 0.231: 13 Chirality restraints: 516 Sorted by residual: chirality pdb=" CA LYS C 347 " pdb=" N LYS C 347 " pdb=" C LYS C 347 " pdb=" CB LYS C 347 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA LYS B 331 " pdb=" N LYS B 331 " pdb=" C LYS B 331 " pdb=" CB LYS B 331 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA LYS C 331 " pdb=" N LYS C 331 " pdb=" C LYS C 331 " pdb=" CB LYS C 331 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 513 not shown) Planarity restraints: 990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 310 " 0.102 2.00e-02 2.50e+03 4.08e-02 5.01e+01 pdb=" CG TYR B 310 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR B 310 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR B 310 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR B 310 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR B 310 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR B 310 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 310 " 0.053 2.00e-02 2.50e+03 pdb=" HD1 TYR B 310 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR B 310 " -0.017 2.00e-02 2.50e+03 pdb=" HE1 TYR B 310 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 TYR B 310 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " -0.095 2.00e-02 2.50e+03 3.82e-02 4.38e+01 pdb=" CG TYR C 310 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " -0.050 2.00e-02 2.50e+03 pdb=" HD1 TYR C 310 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 TYR C 310 " 0.015 2.00e-02 2.50e+03 pdb=" HE1 TYR C 310 " -0.004 2.00e-02 2.50e+03 pdb=" HE2 TYR C 310 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " -0.091 2.00e-02 2.50e+03 3.75e-02 4.21e+01 pdb=" CG TYR A 310 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.063 2.00e-02 2.50e+03 pdb=" HD1 TYR A 310 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 TYR A 310 " 0.015 2.00e-02 2.50e+03 pdb=" HE1 TYR A 310 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR A 310 " -0.005 2.00e-02 2.50e+03 ... (remaining 987 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 542 2.18 - 2.79: 12035 2.79 - 3.39: 17518 3.39 - 4.00: 24456 4.00 - 4.60: 33284 Nonbonded interactions: 87835 Sorted by model distance: nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.580 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.587 2.450 nonbonded pdb=" OD1 ASP G 314 " pdb=" HG SER G 316 " model vdw 1.610 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.613 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.616 2.450 ... (remaining 87830 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 '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: 4.810 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.400 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:17.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 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 0.035 3396 Z= 0.725 Angle : 1.727 5.962 4548 Z= 1.150 Chirality : 0.083 0.231 516 Planarity : 0.010 0.049 576 Dihedral : 10.930 59.436 1296 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.90 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.004 HIS G 330 PHE 0.033 0.010 PHE C 378 TYR 0.096 0.031 TYR B 310 ARG 0.004 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.584 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: A 320 SER cc_start: 0.8009 (t) cc_final: 0.7790 (p) REVERT: A 340 LYS cc_start: 0.7620 (mtpt) cc_final: 0.7093 (mttt) REVERT: A 369 LYS cc_start: 0.7334 (mttt) cc_final: 0.6724 (mtpm) REVERT: A 372 GLU cc_start: 0.7210 (tt0) cc_final: 0.6830 (tt0) REVERT: B 311 LYS cc_start: 0.5947 (ttpt) cc_final: 0.5522 (mttm) REVERT: B 321 LYS cc_start: 0.7499 (ttpt) cc_final: 0.7117 (mtpm) REVERT: B 340 LYS cc_start: 0.7691 (mtpt) cc_final: 0.7208 (mttm) REVERT: B 343 LYS cc_start: 0.8258 (mttt) cc_final: 0.7770 (mtpt) REVERT: B 349 ARG cc_start: 0.7189 (mtt180) cc_final: 0.5521 (mmp-170) REVERT: B 369 LYS cc_start: 0.7307 (mttt) cc_final: 0.6725 (mtpm) REVERT: B 372 GLU cc_start: 0.7526 (tt0) cc_final: 0.7214 (tt0) REVERT: C 311 LYS cc_start: 0.5871 (ttpt) cc_final: 0.5476 (tptt) REVERT: C 340 LYS cc_start: 0.7646 (mtpt) cc_final: 0.7330 (mttm) REVERT: C 343 LYS cc_start: 0.8247 (mttt) cc_final: 0.7994 (mttm) REVERT: C 349 ARG cc_start: 0.7211 (mtt180) cc_final: 0.5500 (mmp-170) REVERT: C 372 GLU cc_start: 0.7646 (tt0) cc_final: 0.7124 (tp30) REVERT: D 311 LYS cc_start: 0.6851 (ttpt) cc_final: 0.6101 (ttpp) REVERT: D 316 SER cc_start: 0.6513 (m) cc_final: 0.6258 (p) REVERT: D 321 LYS cc_start: 0.8006 (ttpt) cc_final: 0.7806 (ttmm) REVERT: D 340 LYS cc_start: 0.7851 (mtpt) cc_final: 0.7480 (mttm) REVERT: D 349 ARG cc_start: 0.7353 (mtt180) cc_final: 0.5359 (pmt-80) REVERT: D 369 LYS cc_start: 0.7887 (mttt) cc_final: 0.7258 (mtpm) REVERT: D 375 LYS cc_start: 0.6772 (tttt) cc_final: 0.6371 (tttm) REVERT: E 311 LYS cc_start: 0.7090 (ttpt) cc_final: 0.6297 (ttpp) REVERT: E 340 LYS cc_start: 0.7809 (mtpt) cc_final: 0.7415 (mttp) REVERT: E 349 ARG cc_start: 0.7391 (mtt180) cc_final: 0.5307 (pmt-80) REVERT: G 340 LYS cc_start: 0.7460 (mtpt) cc_final: 0.7214 (mttm) REVERT: G 369 LYS cc_start: 0.7225 (mttt) cc_final: 0.6750 (mptt) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 3.0932 time to fit residues: 460.9820 Evaluate side-chains 126 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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: 6.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS D 351 GLN D 362 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.168945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.143649 restraints weight = 9808.834| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 1.36 r_work: 0.4088 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.4023 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3396 Z= 0.223 Angle : 0.601 4.520 4548 Z= 0.319 Chirality : 0.052 0.142 516 Planarity : 0.003 0.019 576 Dihedral : 5.851 15.350 444 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.56 % Allowed : 11.72 % Favored : 86.72 % 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: -1.20 (0.34), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.91 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 362 PHE 0.007 0.001 PHE G 346 TYR 0.018 0.004 TYR D 310 ARG 0.002 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 0.583 Fit side-chains REVERT: A 311 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8056 (ttpp) REVERT: A 343 LYS cc_start: 0.8587 (mtmt) cc_final: 0.8313 (mttm) REVERT: A 349 ARG cc_start: 0.7692 (mtt180) cc_final: 0.7368 (mtp85) REVERT: A 369 LYS cc_start: 0.8212 (mttt) cc_final: 0.7962 (mtpm) REVERT: B 349 ARG cc_start: 0.7745 (mtt180) cc_final: 0.6499 (mmp-170) REVERT: B 369 LYS cc_start: 0.8303 (mttt) cc_final: 0.8038 (mtpm) REVERT: C 311 LYS cc_start: 0.8299 (ttpt) cc_final: 0.7809 (tptt) REVERT: C 349 ARG cc_start: 0.7729 (mtt180) cc_final: 0.6596 (mmp-170) REVERT: C 369 LYS cc_start: 0.8605 (mttt) cc_final: 0.8256 (mtpm) REVERT: D 311 LYS cc_start: 0.8362 (ttpt) cc_final: 0.8044 (ttpp) REVERT: D 349 ARG cc_start: 0.7686 (mtt180) cc_final: 0.6473 (pmt-80) REVERT: D 369 LYS cc_start: 0.8231 (mttt) cc_final: 0.7992 (mtpm) REVERT: D 375 LYS cc_start: 0.7923 (tttt) cc_final: 0.7657 (mtpm) REVERT: E 311 LYS cc_start: 0.8358 (ttpt) cc_final: 0.7746 (ttpp) REVERT: E 349 ARG cc_start: 0.7868 (mtt180) cc_final: 0.6412 (pmt-80) REVERT: G 348 ASP cc_start: 0.7963 (t0) cc_final: 0.7713 (t0) REVERT: G 369 LYS cc_start: 0.8180 (mttt) cc_final: 0.7969 (mtpm) outliers start: 6 outliers final: 1 residues processed: 136 average time/residue: 3.1780 time to fit residues: 441.0173 Evaluate side-chains 127 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain G residue 331 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.166998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.141565 restraints weight = 9966.577| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 1.38 r_work: 0.4054 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3989 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3396 Z= 0.201 Angle : 0.576 4.399 4548 Z= 0.301 Chirality : 0.051 0.147 516 Planarity : 0.002 0.014 576 Dihedral : 5.084 14.202 444 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.30 % Allowed : 17.97 % Favored : 80.73 % 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: -1.41 (0.34), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.06 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 329 PHE 0.005 0.001 PHE G 346 TYR 0.015 0.004 TYR B 310 ARG 0.000 0.000 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 127 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 343 LYS cc_start: 0.8536 (mtmt) cc_final: 0.8306 (mttm) REVERT: A 349 ARG cc_start: 0.7752 (mtt180) cc_final: 0.7457 (mtp85) REVERT: A 369 LYS cc_start: 0.8201 (mttt) cc_final: 0.7956 (mtpm) REVERT: B 319 THR cc_start: 0.8270 (m) cc_final: 0.7962 (p) REVERT: B 340 LYS cc_start: 0.8009 (mtpp) cc_final: 0.7775 (mttm) REVERT: B 349 ARG cc_start: 0.7764 (mtt180) cc_final: 0.6501 (mmp-170) REVERT: B 369 LYS cc_start: 0.8337 (mttt) cc_final: 0.8026 (mtpm) REVERT: C 311 LYS cc_start: 0.8316 (ttpt) cc_final: 0.7800 (tptt) REVERT: C 349 ARG cc_start: 0.7837 (mtt180) cc_final: 0.6673 (mmp-170) REVERT: C 369 LYS cc_start: 0.8537 (mttt) cc_final: 0.8207 (mtpm) REVERT: D 311 LYS cc_start: 0.8451 (ttpt) cc_final: 0.8160 (ttpp) REVERT: D 349 ARG cc_start: 0.7722 (mtt180) cc_final: 0.6380 (pmt-80) REVERT: D 369 LYS cc_start: 0.8347 (mttt) cc_final: 0.8070 (mtpm) REVERT: E 311 LYS cc_start: 0.8462 (ttpt) cc_final: 0.7841 (ttpp) REVERT: E 349 ARG cc_start: 0.7919 (mtt180) cc_final: 0.6453 (pmt-80) REVERT: G 348 ASP cc_start: 0.8003 (t0) cc_final: 0.7778 (t0) REVERT: G 369 LYS cc_start: 0.8222 (mttt) cc_final: 0.7940 (mtpm) outliers start: 5 outliers final: 1 residues processed: 130 average time/residue: 3.0765 time to fit residues: 408.3201 Evaluate side-chains 123 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 331 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 0 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.168273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.142886 restraints weight = 10072.177| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 1.38 r_work: 0.4068 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.4003 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3396 Z= 0.177 Angle : 0.538 3.982 4548 Z= 0.277 Chirality : 0.051 0.141 516 Planarity : 0.002 0.015 576 Dihedral : 4.838 13.800 444 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.04 % Allowed : 20.57 % Favored : 78.39 % 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: -1.61 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.004 0.001 PHE G 346 TYR 0.011 0.003 TYR D 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8361 (ttpt) cc_final: 0.8101 (ttpp) REVERT: A 349 ARG cc_start: 0.7755 (mtt180) cc_final: 0.7439 (mtp85) REVERT: A 369 LYS cc_start: 0.8204 (mttt) cc_final: 0.7937 (mtpm) REVERT: B 319 THR cc_start: 0.8309 (m) cc_final: 0.7989 (p) REVERT: B 340 LYS cc_start: 0.7983 (mtpp) cc_final: 0.7774 (mttm) REVERT: B 349 ARG cc_start: 0.7732 (mtt180) cc_final: 0.6442 (mmp-170) REVERT: B 369 LYS cc_start: 0.8349 (mttt) cc_final: 0.8019 (mtpm) REVERT: C 311 LYS cc_start: 0.8324 (ttpt) cc_final: 0.7791 (mmtm) REVERT: C 319 THR cc_start: 0.8355 (m) cc_final: 0.8065 (p) REVERT: C 349 ARG cc_start: 0.7839 (mtt180) cc_final: 0.6645 (mmp-170) REVERT: C 369 LYS cc_start: 0.8518 (mttt) cc_final: 0.8182 (mtpm) REVERT: D 311 LYS cc_start: 0.8405 (ttpt) cc_final: 0.8106 (ttpp) REVERT: D 343 LYS cc_start: 0.8546 (mttt) cc_final: 0.8281 (mttm) REVERT: D 349 ARG cc_start: 0.7695 (mtt180) cc_final: 0.6355 (pmt-80) REVERT: D 369 LYS cc_start: 0.8321 (mttt) cc_final: 0.8030 (mtpm) REVERT: E 311 LYS cc_start: 0.8420 (ttpt) cc_final: 0.7721 (ttpp) REVERT: E 349 ARG cc_start: 0.7930 (mtt180) cc_final: 0.6463 (pmt-80) REVERT: G 369 LYS cc_start: 0.8260 (mttt) cc_final: 0.7914 (mtpm) outliers start: 4 outliers final: 1 residues processed: 120 average time/residue: 2.9629 time to fit residues: 363.4125 Evaluate side-chains 119 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 331 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.171238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.145876 restraints weight = 9911.149| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 1.36 r_work: 0.4103 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.4039 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3396 Z= 0.143 Angle : 0.502 4.064 4548 Z= 0.255 Chirality : 0.051 0.140 516 Planarity : 0.002 0.015 576 Dihedral : 4.496 12.293 444 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 0.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.26 % Allowed : 22.40 % Favored : 77.34 % 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: -1.67 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 362 PHE 0.003 0.000 PHE G 346 TYR 0.008 0.002 TYR D 310 ARG 0.001 0.000 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: A 349 ARG cc_start: 0.7742 (mtt180) cc_final: 0.7433 (mtp85) REVERT: A 369 LYS cc_start: 0.8228 (mttt) cc_final: 0.7965 (mtpm) REVERT: B 319 THR cc_start: 0.8292 (m) cc_final: 0.7990 (p) REVERT: B 349 ARG cc_start: 0.7713 (mtt180) cc_final: 0.6465 (mmp-170) REVERT: B 369 LYS cc_start: 0.8342 (mttt) cc_final: 0.7983 (mtpm) REVERT: C 311 LYS cc_start: 0.8273 (ttpt) cc_final: 0.7747 (mmtm) REVERT: C 319 THR cc_start: 0.8276 (m) cc_final: 0.8061 (p) REVERT: C 349 ARG cc_start: 0.7793 (mtt180) cc_final: 0.6649 (mmp-170) REVERT: D 311 LYS cc_start: 0.8380 (ttpt) cc_final: 0.8102 (ttpp) REVERT: D 343 LYS cc_start: 0.8552 (mttt) cc_final: 0.8280 (mttm) REVERT: D 349 ARG cc_start: 0.7704 (mtt180) cc_final: 0.6374 (pmt-80) REVERT: D 369 LYS cc_start: 0.8341 (mttt) cc_final: 0.8040 (mtpm) REVERT: E 311 LYS cc_start: 0.8393 (ttpt) cc_final: 0.7754 (ttpp) REVERT: E 349 ARG cc_start: 0.7913 (mtt180) cc_final: 0.6464 (pmt-80) REVERT: G 369 LYS cc_start: 0.8273 (mttt) cc_final: 0.7891 (mtpm) outliers start: 1 outliers final: 1 residues processed: 115 average time/residue: 2.6927 time to fit residues: 317.6437 Evaluate side-chains 103 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 331 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.164843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.139323 restraints weight = 10010.753| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 1.38 r_work: 0.4014 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3950 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3396 Z= 0.288 Angle : 0.602 4.303 4548 Z= 0.316 Chirality : 0.051 0.150 516 Planarity : 0.002 0.018 576 Dihedral : 4.875 13.929 444 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.52 % Allowed : 22.92 % Favored : 76.56 % 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 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 329 PHE 0.006 0.001 PHE G 346 TYR 0.017 0.004 TYR B 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.536 Fit side-chains REVERT: A 311 LYS cc_start: 0.8388 (ttpt) cc_final: 0.8084 (mtpt) REVERT: A 349 ARG cc_start: 0.7808 (mtt180) cc_final: 0.7476 (mtp85) REVERT: A 369 LYS cc_start: 0.8294 (mttt) cc_final: 0.8022 (mtpm) REVERT: B 319 THR cc_start: 0.8362 (m) cc_final: 0.8067 (p) REVERT: B 349 ARG cc_start: 0.7832 (mtt180) cc_final: 0.6527 (mmp-170) REVERT: B 369 LYS cc_start: 0.8374 (mttt) cc_final: 0.8028 (mtpm) REVERT: C 319 THR cc_start: 0.8357 (m) cc_final: 0.8082 (p) REVERT: C 349 ARG cc_start: 0.7861 (mtt180) cc_final: 0.6685 (mmp-170) REVERT: D 311 LYS cc_start: 0.8409 (ttpt) cc_final: 0.8064 (pttp) REVERT: D 349 ARG cc_start: 0.7762 (mtt180) cc_final: 0.6375 (pmt-80) REVERT: E 319 THR cc_start: 0.8437 (m) cc_final: 0.8067 (p) REVERT: E 349 ARG cc_start: 0.7954 (mtt180) cc_final: 0.6489 (pmt-80) outliers start: 2 outliers final: 2 residues processed: 98 average time/residue: 2.5727 time to fit residues: 258.6843 Evaluate side-chains 94 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain E residue 331 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.168138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.142938 restraints weight = 9905.421| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 1.37 r_work: 0.4057 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3993 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3396 Z= 0.177 Angle : 0.531 4.065 4548 Z= 0.273 Chirality : 0.051 0.142 516 Planarity : 0.002 0.018 576 Dihedral : 4.698 13.176 444 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.26 % Allowed : 23.44 % Favored : 76.30 % 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: -1.80 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.003 0.001 PHE D 378 TYR 0.010 0.003 TYR D 310 ARG 0.000 0.000 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.615 Fit side-chains REVERT: A 311 LYS cc_start: 0.8306 (ttpt) cc_final: 0.7982 (mtpt) REVERT: A 349 ARG cc_start: 0.7774 (mtt180) cc_final: 0.7450 (mtp85) REVERT: A 369 LYS cc_start: 0.8306 (mttt) cc_final: 0.8028 (mtpm) REVERT: B 311 LYS cc_start: 0.6605 (mttm) cc_final: 0.5913 (mtpp) REVERT: B 319 THR cc_start: 0.8322 (m) cc_final: 0.8028 (p) REVERT: B 349 ARG cc_start: 0.7816 (mtt180) cc_final: 0.6513 (mmp-170) REVERT: C 319 THR cc_start: 0.8339 (m) cc_final: 0.8107 (p) REVERT: C 349 ARG cc_start: 0.7867 (mtt180) cc_final: 0.6693 (mmp-170) REVERT: D 311 LYS cc_start: 0.8364 (ttpt) cc_final: 0.8043 (pttp) REVERT: D 349 ARG cc_start: 0.7768 (mtt180) cc_final: 0.6365 (pmt-80) REVERT: E 319 THR cc_start: 0.8386 (m) cc_final: 0.8029 (p) REVERT: E 349 ARG cc_start: 0.7898 (mtt180) cc_final: 0.6446 (pmt-80) outliers start: 1 outliers final: 1 residues processed: 94 average time/residue: 2.5032 time to fit residues: 242.4658 Evaluate side-chains 93 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 331 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.170702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.145455 restraints weight = 10031.901| |-----------------------------------------------------------------------------| r_work (start): 0.4158 rms_B_bonded: 1.38 r_work: 0.4088 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.4023 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3396 Z= 0.146 Angle : 0.497 3.879 4548 Z= 0.254 Chirality : 0.050 0.140 516 Planarity : 0.002 0.018 576 Dihedral : 4.465 12.162 444 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 0.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.52 % Allowed : 23.96 % Favored : 75.52 % 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: -1.78 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 362 PHE 0.003 0.001 PHE G 346 TYR 0.008 0.002 TYR D 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 84 time to evaluate : 0.618 Fit side-chains REVERT: A 349 ARG cc_start: 0.7767 (mtt180) cc_final: 0.7446 (mtp85) REVERT: A 369 LYS cc_start: 0.8310 (mttt) cc_final: 0.8016 (mtpm) REVERT: B 311 LYS cc_start: 0.6591 (mttm) cc_final: 0.6081 (mtpp) REVERT: B 319 THR cc_start: 0.8344 (m) cc_final: 0.8027 (p) REVERT: B 349 ARG cc_start: 0.7768 (mtt180) cc_final: 0.6492 (mmp-170) REVERT: C 349 ARG cc_start: 0.7836 (mtt180) cc_final: 0.6623 (mmp-170) REVERT: D 349 ARG cc_start: 0.7762 (mtt180) cc_final: 0.6363 (pmt-80) REVERT: E 319 THR cc_start: 0.8369 (m) cc_final: 0.8012 (p) REVERT: E 349 ARG cc_start: 0.7880 (mtt180) cc_final: 0.6431 (pmt-80) outliers start: 2 outliers final: 1 residues processed: 85 average time/residue: 2.3240 time to fit residues: 203.9595 Evaluate side-chains 83 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 331 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 7 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.165482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.140995 restraints weight = 10297.655| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 1.34 r_work: 0.4043 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3977 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3396 Z= 0.213 Angle : 0.547 4.078 4548 Z= 0.285 Chirality : 0.050 0.143 516 Planarity : 0.002 0.019 576 Dihedral : 4.655 13.046 444 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.26 % Allowed : 24.48 % Favored : 75.26 % 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: -1.79 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.004 0.001 PHE G 346 TYR 0.013 0.003 TYR D 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.695 Fit side-chains REVERT: A 349 ARG cc_start: 0.7776 (mtt180) cc_final: 0.7441 (mtp85) REVERT: A 369 LYS cc_start: 0.8346 (mttt) cc_final: 0.8037 (mtpm) REVERT: B 311 LYS cc_start: 0.6606 (mttm) cc_final: 0.6178 (mttm) REVERT: B 319 THR cc_start: 0.8333 (m) cc_final: 0.8042 (p) REVERT: B 349 ARG cc_start: 0.7805 (mtt180) cc_final: 0.6519 (mmp-170) REVERT: C 349 ARG cc_start: 0.7863 (mtt180) cc_final: 0.6690 (mmp-170) REVERT: D 349 ARG cc_start: 0.7791 (mtt180) cc_final: 0.6344 (pmt-80) REVERT: E 319 THR cc_start: 0.8397 (m) cc_final: 0.8035 (p) REVERT: E 349 ARG cc_start: 0.7890 (mtt180) cc_final: 0.6422 (pmt-80) outliers start: 1 outliers final: 1 residues processed: 86 average time/residue: 2.2656 time to fit residues: 201.2831 Evaluate side-chains 86 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 331 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 20 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 8.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.166135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.141703 restraints weight = 10405.490| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 1.34 r_work: 0.4052 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3989 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3396 Z= 0.196 Angle : 0.535 4.003 4548 Z= 0.278 Chirality : 0.050 0.143 516 Planarity : 0.002 0.022 576 Dihedral : 4.639 12.853 444 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.26 % Allowed : 24.48 % Favored : 75.26 % 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: -1.80 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.004 0.001 PHE G 346 TYR 0.012 0.003 TYR D 310 ARG 0.001 0.000 ARG A 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.590 Fit side-chains REVERT: A 349 ARG cc_start: 0.7778 (mtt180) cc_final: 0.7442 (mtp85) REVERT: A 369 LYS cc_start: 0.8357 (mttt) cc_final: 0.8048 (mtpm) REVERT: B 311 LYS cc_start: 0.6602 (mttm) cc_final: 0.6152 (mttm) REVERT: B 319 THR cc_start: 0.8290 (m) cc_final: 0.8018 (p) REVERT: B 349 ARG cc_start: 0.7817 (mtt180) cc_final: 0.6541 (mmp-170) REVERT: C 349 ARG cc_start: 0.7850 (mtt180) cc_final: 0.6693 (mmp-170) REVERT: D 349 ARG cc_start: 0.7762 (mtt180) cc_final: 0.6350 (pmt-80) REVERT: E 319 THR cc_start: 0.8388 (m) cc_final: 0.8046 (p) REVERT: E 349 ARG cc_start: 0.7884 (mtt180) cc_final: 0.6440 (pmt-80) outliers start: 1 outliers final: 1 residues processed: 85 average time/residue: 2.2214 time to fit residues: 194.5496 Evaluate side-chains 85 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 331 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.167705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.142348 restraints weight = 10067.272| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 1.39 r_work: 0.4051 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3987 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.5335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3396 Z= 0.189 Angle : 0.529 4.022 4548 Z= 0.274 Chirality : 0.051 0.141 516 Planarity : 0.002 0.022 576 Dihedral : 4.608 12.784 444 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.26 % Allowed : 24.74 % Favored : 75.00 % 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: -1.79 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.004 0.001 PHE G 346 TYR 0.011 0.003 TYR D 310 ARG 0.001 0.000 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8444.72 seconds wall clock time: 143 minutes 14.28 seconds (8594.28 seconds total)