Starting phenix.real_space_refine on Fri Aug 22 18:31:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q9h_18281/08_2025/8q9h_18281.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q9h_18281/08_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_18281/08_2025/8q9h_18281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q9h_18281/08_2025/8q9h_18281.map" model { file = "/net/cci-nas-00/data/ceres_data/8q9h_18281/08_2025/8q9h_18281.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q9h_18281/08_2025/8q9h_18281.cif" } resolution = 2.18 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 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.57, per 1000 atoms: 0.23 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: 0.47 Conformation dependent library (CDL) restraints added in 230.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.24 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: 1.20 Time building geometry restraints manager: 0.70 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: 0.00 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: 3.980 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: 0.040 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.590 Find NCS groups from input model: 0.090 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:8.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.920 ------------------------------------------------------------------------------- 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= 0.662 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.001 ARG E 349 TYR 0.096 0.031 TYR B 310 PHE 0.033 0.010 PHE C 378 HIS 0.016 0.004 HIS G 330 Details of bonding type rmsd covalent geometry : bond 0.01069 ( 3396) covalent geometry : angle 1.72700 ( 4548) hydrogen bonds : bond 0.09322 ( 65) hydrogen bonds : angle 7.44417 ( 195) *********************** 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 : 0.181 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: 0.5517 (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: 0.5361 (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: 1.3303 time to fit residues: 198.1476 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 : 0.128 ------------------------------------------------------------------------------- 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: 2.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.171723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.147959 restraints weight = 10343.770| |-----------------------------------------------------------------------------| r_work (start): 0.4227 rms_B_bonded: 1.33 r_work: 0.4157 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.4091 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3396 Z= 0.104 Angle : 0.554 3.752 4548 Z= 0.295 Chirality : 0.052 0.144 516 Planarity : 0.002 0.018 576 Dihedral : 5.858 15.160 444 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 0.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.30 % Allowed : 11.20 % Favored : 87.50 % 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 aren not related in a simple way. whole: -1.19 (0.34), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.90 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.012 0.002 TYR D 310 PHE 0.006 0.001 PHE G 346 HIS 0.004 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 3396) covalent geometry : angle 0.55357 ( 4548) hydrogen bonds : bond 0.02206 ( 65) hydrogen bonds : angle 4.94586 ( 195) *********************** 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 138 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 133 time to evaluate : 0.143 Fit side-chains REVERT: A 311 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7845 (ttpp) REVERT: A 343 LYS cc_start: 0.8550 (mtmt) cc_final: 0.8303 (mttm) REVERT: A 349 ARG cc_start: 0.7686 (mtt180) cc_final: 0.7390 (mtp85) REVERT: A 369 LYS cc_start: 0.8204 (mttt) cc_final: 0.7948 (mtpm) REVERT: B 349 ARG cc_start: 0.7638 (mtt180) cc_final: 0.6450 (mmp-170) REVERT: B 369 LYS cc_start: 0.8310 (mttt) cc_final: 0.8050 (mtpm) REVERT: C 311 LYS cc_start: 0.8047 (ttpt) cc_final: 0.7597 (tptt) REVERT: C 349 ARG cc_start: 0.7665 (mtt180) cc_final: 0.6541 (mmp-170) REVERT: C 369 LYS cc_start: 0.8549 (mttt) cc_final: 0.8188 (mtpm) REVERT: C 378 PHE cc_start: 0.6172 (t80) cc_final: 0.5961 (t80) REVERT: D 311 LYS cc_start: 0.8155 (ttpt) cc_final: 0.7772 (ttpp) REVERT: D 349 ARG cc_start: 0.7687 (mtt180) cc_final: 0.6413 (pmt-80) REVERT: D 369 LYS cc_start: 0.8211 (mttt) cc_final: 0.7977 (mtpm) REVERT: D 375 LYS cc_start: 0.7856 (tttt) cc_final: 0.7650 (mtpm) REVERT: E 311 LYS cc_start: 0.8103 (ttpt) cc_final: 0.7541 (ttpp) REVERT: E 349 ARG cc_start: 0.7758 (mtt180) cc_final: 0.6364 (pmt-80) REVERT: G 369 LYS cc_start: 0.8180 (mttt) cc_final: 0.7934 (mtpm) outliers start: 5 outliers final: 0 residues processed: 135 average time/residue: 1.3921 time to fit residues: 191.6108 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 : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.171634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.146346 restraints weight = 9913.353| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 1.36 r_work: 0.4115 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.4051 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3396 Z= 0.103 Angle : 0.544 5.114 4548 Z= 0.276 Chirality : 0.051 0.141 516 Planarity : 0.002 0.012 576 Dihedral : 4.845 13.142 444 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 0.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.78 % Allowed : 18.23 % Favored : 80.99 % 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 aren not related in a simple way. whole: -1.36 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.03 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 349 TYR 0.011 0.002 TYR D 310 PHE 0.012 0.001 PHE A 378 HIS 0.002 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 3396) covalent geometry : angle 0.54399 ( 4548) hydrogen bonds : bond 0.01792 ( 65) hydrogen bonds : angle 4.39964 ( 195) *********************** 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 134 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 131 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7976 (ttpp) REVERT: A 343 LYS cc_start: 0.8524 (mtmt) cc_final: 0.8291 (mttm) REVERT: A 349 ARG cc_start: 0.7722 (mtt180) cc_final: 0.7468 (mtp85) REVERT: A 369 LYS cc_start: 0.8174 (mttt) cc_final: 0.7938 (mtpm) REVERT: B 340 LYS cc_start: 0.7959 (mtpp) cc_final: 0.7757 (mttm) REVERT: B 349 ARG cc_start: 0.7619 (mtt180) cc_final: 0.6449 (mmp-170) REVERT: B 369 LYS cc_start: 0.8289 (mttt) cc_final: 0.7998 (mtpm) REVERT: C 311 LYS cc_start: 0.8158 (ttpt) cc_final: 0.7685 (tptt) REVERT: C 349 ARG cc_start: 0.7718 (mtt180) cc_final: 0.6597 (mmp-170) REVERT: C 369 LYS cc_start: 0.8548 (mttt) cc_final: 0.8208 (mtpm) REVERT: D 311 LYS cc_start: 0.8284 (ttpt) cc_final: 0.7914 (ttpp) REVERT: D 349 ARG cc_start: 0.7649 (mtt180) cc_final: 0.6484 (pmt-80) REVERT: D 369 LYS cc_start: 0.8228 (mttt) cc_final: 0.7987 (mtpm) REVERT: E 311 LYS cc_start: 0.8219 (ttpt) cc_final: 0.7593 (ttpp) REVERT: E 349 ARG cc_start: 0.7830 (mtt180) cc_final: 0.6485 (pmt-80) REVERT: G 369 LYS cc_start: 0.8207 (mttt) cc_final: 0.7922 (mtpm) outliers start: 3 outliers final: 1 residues processed: 133 average time/residue: 1.3200 time to fit residues: 179.0675 Evaluate side-chains 129 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain G residue 331 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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 = 0.4374 r_free = 0.4374 target = 0.163439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.138337 restraints weight = 10058.416| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 1.33 r_work: 0.3994 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3929 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3396 Z= 0.248 Angle : 0.676 5.216 4548 Z= 0.358 Chirality : 0.052 0.151 516 Planarity : 0.003 0.018 576 Dihedral : 5.244 14.716 444 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.30 % Allowed : 20.57 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.021 0.005 TYR D 310 PHE 0.008 0.002 PHE G 346 HIS 0.005 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00534 ( 3396) covalent geometry : angle 0.67605 ( 4548) hydrogen bonds : bond 0.02471 ( 65) hydrogen bonds : angle 4.57260 ( 195) *********************** 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 128 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 123 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8198 (ttpt) REVERT: A 349 ARG cc_start: 0.7784 (mtt180) cc_final: 0.7461 (mtp85) REVERT: A 369 LYS cc_start: 0.8220 (mttt) cc_final: 0.7980 (mtpm) REVERT: B 319 THR cc_start: 0.8294 (m) cc_final: 0.8023 (p) REVERT: B 349 ARG cc_start: 0.7780 (mtt180) cc_final: 0.6528 (mmp-170) REVERT: B 369 LYS cc_start: 0.8342 (mttt) cc_final: 0.8024 (mtpm) REVERT: C 311 LYS cc_start: 0.8383 (ttpt) cc_final: 0.7909 (mmtt) REVERT: C 319 THR cc_start: 0.8406 (m) cc_final: 0.8042 (p) REVERT: C 349 ARG cc_start: 0.7890 (mtt180) cc_final: 0.6638 (mmp-170) REVERT: C 369 LYS cc_start: 0.8521 (mttt) cc_final: 0.8205 (mtpm) REVERT: C 373 THR cc_start: 0.8544 (m) cc_final: 0.8341 (p) REVERT: D 311 LYS cc_start: 0.8433 (ttpt) cc_final: 0.8202 (ttpp) REVERT: D 349 ARG cc_start: 0.7774 (mtt180) cc_final: 0.6402 (pmt-80) REVERT: D 369 LYS cc_start: 0.8368 (mttt) cc_final: 0.8072 (mtpm) REVERT: E 311 LYS cc_start: 0.8536 (ttpt) cc_final: 0.7960 (ttpp) REVERT: E 349 ARG cc_start: 0.7967 (mtt180) cc_final: 0.6482 (pmt-80) REVERT: G 369 LYS cc_start: 0.8289 (mttt) cc_final: 0.8001 (mtpm) outliers start: 5 outliers final: 1 residues processed: 125 average time/residue: 1.4055 time to fit residues: 179.3498 Evaluate side-chains 118 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain G residue 331 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 31 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 = 0.4433 r_free = 0.4433 target = 0.168451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.143270 restraints weight = 10046.369| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 1.36 r_work: 0.4068 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.4004 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.4927 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= 0.119 Angle : 0.540 4.185 4548 Z= 0.276 Chirality : 0.051 0.142 516 Planarity : 0.002 0.021 576 Dihedral : 4.822 13.467 444 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.78 % Allowed : 22.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 349 TYR 0.010 0.003 TYR D 310 PHE 0.004 0.001 PHE G 346 HIS 0.002 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 3396) covalent geometry : angle 0.54033 ( 4548) hydrogen bonds : bond 0.01846 ( 65) hydrogen bonds : angle 4.05089 ( 195) *********************** 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 111 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 108 time to evaluate : 0.210 Fit side-chains REVERT: A 349 ARG cc_start: 0.7764 (mtt180) cc_final: 0.7458 (mtp85) REVERT: A 369 LYS cc_start: 0.8252 (mttt) cc_final: 0.7984 (mtpm) REVERT: B 319 THR cc_start: 0.8266 (m) cc_final: 0.7995 (p) REVERT: B 349 ARG cc_start: 0.7763 (mtt180) cc_final: 0.6501 (mmp-170) REVERT: B 369 LYS cc_start: 0.8349 (mttt) cc_final: 0.8020 (mtpm) REVERT: C 311 LYS cc_start: 0.8340 (ttpt) cc_final: 0.7830 (mmtt) REVERT: C 319 THR cc_start: 0.8335 (m) cc_final: 0.8074 (p) REVERT: C 349 ARG cc_start: 0.7850 (mtt180) cc_final: 0.6679 (mmp-170) REVERT: D 311 LYS cc_start: 0.8408 (ttpt) cc_final: 0.8135 (ttpp) REVERT: D 343 LYS cc_start: 0.8523 (mtmt) cc_final: 0.8284 (mttm) REVERT: D 349 ARG cc_start: 0.7732 (mtt180) cc_final: 0.6378 (pmt-80) REVERT: D 369 LYS cc_start: 0.8347 (mttt) cc_final: 0.8046 (mtpm) REVERT: E 311 LYS cc_start: 0.8445 (ttpt) cc_final: 0.7887 (ttpp) REVERT: E 349 ARG cc_start: 0.7903 (mtt180) cc_final: 0.6476 (pmt-80) REVERT: G 369 LYS cc_start: 0.8252 (mttt) cc_final: 0.7936 (mtpm) outliers start: 3 outliers final: 2 residues processed: 110 average time/residue: 1.3432 time to fit residues: 151.0540 Evaluate side-chains 102 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain G residue 331 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.167273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.141846 restraints weight = 10019.449| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 1.37 r_work: 0.4042 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3976 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.5083 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= 0.141 Angle : 0.560 4.632 4548 Z= 0.288 Chirality : 0.051 0.144 516 Planarity : 0.002 0.021 576 Dihedral : 4.750 13.501 444 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 0.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.78 % Allowed : 22.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 349 TYR 0.013 0.003 TYR D 310 PHE 0.005 0.001 PHE G 346 HIS 0.002 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 3396) covalent geometry : angle 0.55954 ( 4548) hydrogen bonds : bond 0.01826 ( 65) hydrogen bonds : angle 4.00901 ( 195) *********************** 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 108 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 105 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 349 ARG cc_start: 0.7770 (mtt180) cc_final: 0.7464 (mtp85) REVERT: A 369 LYS cc_start: 0.8292 (mttt) cc_final: 0.8011 (mtpm) REVERT: B 319 THR cc_start: 0.8283 (m) cc_final: 0.8028 (p) REVERT: B 349 ARG cc_start: 0.7776 (mtt180) cc_final: 0.6511 (mmp-170) REVERT: C 311 LYS cc_start: 0.8338 (ttpt) cc_final: 0.7837 (mmtt) REVERT: C 319 THR cc_start: 0.8336 (m) cc_final: 0.8115 (p) REVERT: C 349 ARG cc_start: 0.7833 (mtt180) cc_final: 0.6669 (mmp-170) REVERT: D 311 LYS cc_start: 0.8397 (ttpt) cc_final: 0.8164 (ttpp) REVERT: D 343 LYS cc_start: 0.8539 (mtmt) cc_final: 0.8291 (mttm) REVERT: D 349 ARG cc_start: 0.7752 (mtt180) cc_final: 0.6379 (pmt-80) REVERT: D 369 LYS cc_start: 0.8324 (mttt) cc_final: 0.8022 (mtpm) REVERT: E 349 ARG cc_start: 0.7908 (mtt180) cc_final: 0.6485 (pmt-80) outliers start: 3 outliers final: 2 residues processed: 108 average time/residue: 1.2312 time to fit residues: 135.9710 Evaluate side-chains 102 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain G residue 331 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 = 0.4402 r_free = 0.4402 target = 0.165774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.140605 restraints weight = 9936.251| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 1.37 r_work: 0.4037 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3971 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.5170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3396 Z= 0.157 Angle : 0.573 4.565 4548 Z= 0.297 Chirality : 0.051 0.144 516 Planarity : 0.002 0.024 576 Dihedral : 4.810 13.777 444 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 0.59 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 349 TYR 0.013 0.003 TYR D 310 PHE 0.005 0.001 PHE G 346 HIS 0.002 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 3396) covalent geometry : angle 0.57270 ( 4548) hydrogen bonds : bond 0.02001 ( 65) hydrogen bonds : angle 4.03810 ( 195) *********************** 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 96 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 94 time to evaluate : 0.186 Fit side-chains REVERT: A 314 ASP cc_start: 0.8365 (t70) cc_final: 0.8136 (t70) REVERT: A 349 ARG cc_start: 0.7786 (mtt180) cc_final: 0.7462 (mtp85) REVERT: A 369 LYS cc_start: 0.8325 (mttt) cc_final: 0.8030 (mtpm) REVERT: B 311 LYS cc_start: 0.6616 (mttm) cc_final: 0.6076 (mtpp) REVERT: B 319 THR cc_start: 0.8323 (m) cc_final: 0.8064 (p) REVERT: B 349 ARG cc_start: 0.7799 (mtt180) cc_final: 0.6511 (mmp-170) REVERT: C 319 THR cc_start: 0.8360 (m) cc_final: 0.8154 (p) REVERT: C 349 ARG cc_start: 0.7862 (mtt180) cc_final: 0.6683 (mmp-170) REVERT: D 311 LYS cc_start: 0.8379 (ttpt) cc_final: 0.8044 (pttp) REVERT: D 349 ARG cc_start: 0.7757 (mtt180) cc_final: 0.6349 (pmt-80) REVERT: E 349 ARG cc_start: 0.7896 (mtt180) cc_final: 0.6432 (pmt-80) outliers start: 2 outliers final: 2 residues processed: 96 average time/residue: 1.0446 time to fit residues: 102.9126 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 : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain G residue 331 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 = 0.4440 r_free = 0.4440 target = 0.169176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.144090 restraints weight = 10109.556| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 1.39 r_work: 0.4077 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.4011 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3396 Z= 0.114 Angle : 0.519 3.953 4548 Z= 0.267 Chirality : 0.051 0.141 516 Planarity : 0.002 0.022 576 Dihedral : 4.618 13.064 444 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.78 % Allowed : 23.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG G 349 TYR 0.010 0.003 TYR D 310 PHE 0.004 0.001 PHE G 346 HIS 0.002 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 3396) covalent geometry : angle 0.51854 ( 4548) hydrogen bonds : bond 0.01779 ( 65) hydrogen bonds : angle 3.82982 ( 195) *********************** 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 92 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 0.200 Fit side-chains REVERT: A 314 ASP cc_start: 0.8377 (t70) cc_final: 0.8168 (t70) REVERT: A 349 ARG cc_start: 0.7774 (mtt180) cc_final: 0.7459 (mtp85) REVERT: A 369 LYS cc_start: 0.8333 (mttt) cc_final: 0.8040 (mtpm) REVERT: B 311 LYS cc_start: 0.6565 (mttm) cc_final: 0.6035 (mtpp) REVERT: B 319 THR cc_start: 0.8297 (m) cc_final: 0.8035 (p) REVERT: B 349 ARG cc_start: 0.7792 (mtt180) cc_final: 0.6517 (mmp-170) REVERT: C 349 ARG cc_start: 0.7852 (mtt180) cc_final: 0.6681 (mmp-170) REVERT: D 349 ARG cc_start: 0.7771 (mtt180) cc_final: 0.6353 (pmt-80) REVERT: E 349 ARG cc_start: 0.7874 (mtt180) cc_final: 0.6422 (pmt-80) outliers start: 3 outliers final: 1 residues processed: 91 average time/residue: 0.9702 time to fit residues: 90.9980 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 : 0.167 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 40 optimal weight: 0.5980 chunk 35 optimal weight: 8.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- 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 = 0.4378 r_free = 0.4378 target = 0.163762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.138603 restraints weight = 10077.081| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 1.38 r_work: 0.4008 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3942 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3396 Z= 0.213 Angle : 0.609 4.604 4548 Z= 0.322 Chirality : 0.051 0.151 516 Planarity : 0.002 0.023 576 Dihedral : 4.944 13.913 444 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.52 % Allowed : 24.74 % Favored : 74.74 % 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 aren not related in a simple way. whole: -1.82 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 349 TYR 0.017 0.004 TYR B 310 PHE 0.006 0.001 PHE G 346 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 3396) covalent geometry : angle 0.60895 ( 4548) hydrogen bonds : bond 0.02308 ( 65) hydrogen bonds : angle 4.24226 ( 195) *********************** 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 88 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.126 Fit side-chains REVERT: A 314 ASP cc_start: 0.8367 (t70) cc_final: 0.8147 (t70) REVERT: A 349 ARG cc_start: 0.7812 (mtt180) cc_final: 0.7448 (mtp85) REVERT: A 369 LYS cc_start: 0.8367 (mttt) cc_final: 0.8062 (mtpm) REVERT: B 311 LYS cc_start: 0.6659 (mttm) cc_final: 0.6163 (mttm) REVERT: B 319 THR cc_start: 0.8318 (m) cc_final: 0.8061 (p) REVERT: B 349 ARG cc_start: 0.7834 (mtt180) cc_final: 0.6530 (mmp-170) REVERT: C 349 ARG cc_start: 0.7854 (mtt180) cc_final: 0.6662 (mmp-170) REVERT: D 349 ARG cc_start: 0.7824 (mtt180) cc_final: 0.6331 (pmt-80) REVERT: E 349 ARG cc_start: 0.7909 (mtt180) cc_final: 0.6441 (pmt-80) outliers start: 2 outliers final: 2 residues processed: 87 average time/residue: 0.9189 time to fit residues: 82.2825 Evaluate side-chains 87 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER 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 10 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.165053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.139986 restraints weight = 10119.363| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 1.38 r_work: 0.4024 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3959 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3396 Z= 0.178 Angle : 0.576 4.334 4548 Z= 0.302 Chirality : 0.051 0.147 516 Planarity : 0.002 0.023 576 Dihedral : 4.891 13.606 444 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.26 % Allowed : 25.00 % Favored : 74.74 % 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 aren not related in a simple way. whole: -1.84 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 349 TYR 0.014 0.004 TYR D 310 PHE 0.005 0.001 PHE G 346 HIS 0.002 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 3396) covalent geometry : angle 0.57644 ( 4548) hydrogen bonds : bond 0.02154 ( 65) hydrogen bonds : angle 4.17387 ( 195) ********************** 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 86 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.145 Fit side-chains REVERT: A 314 ASP cc_start: 0.8356 (t70) cc_final: 0.8144 (t70) REVERT: A 349 ARG cc_start: 0.7811 (mtt180) cc_final: 0.7473 (mtp85) REVERT: B 311 LYS cc_start: 0.6668 (mttm) cc_final: 0.6188 (mttm) REVERT: B 319 THR cc_start: 0.8307 (m) cc_final: 0.8058 (p) REVERT: B 349 ARG cc_start: 0.7826 (mtt180) cc_final: 0.6533 (mmp-170) REVERT: C 349 ARG cc_start: 0.7841 (mtt180) cc_final: 0.6686 (mmp-170) REVERT: D 349 ARG cc_start: 0.7794 (mtt180) cc_final: 0.6295 (pmt-80) REVERT: E 349 ARG cc_start: 0.7883 (mtt180) cc_final: 0.6418 (pmt-80) outliers start: 1 outliers final: 1 residues processed: 86 average time/residue: 1.0158 time to fit residues: 89.9175 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 : 0.197 ------------------------------------------------------------------------------- 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: 0.5980 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.170087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.145068 restraints weight = 10083.031| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 1.39 r_work: 0.4094 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.4029 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.5384 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= 0.096 Angle : 0.502 4.070 4548 Z= 0.257 Chirality : 0.051 0.140 516 Planarity : 0.002 0.021 576 Dihedral : 4.581 12.575 444 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.26 % Allowed : 25.52 % Favored : 74.22 % 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 aren not related in a simple way. whole: -1.81 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 349 TYR 0.008 0.002 TYR A 310 PHE 0.003 0.001 PHE E 378 HIS 0.002 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 3396) covalent geometry : angle 0.50157 ( 4548) hydrogen bonds : bond 0.01689 ( 65) hydrogen bonds : angle 3.79793 ( 195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3818.81 seconds wall clock time: 65 minutes 13.76 seconds (3913.76 seconds total)