Starting phenix.real_space_refine on Fri Aug 22 19:03:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q9b_18275/08_2025/8q9b_18275.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q9b_18275/08_2025/8q9b_18275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q9b_18275/08_2025/8q9b_18275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q9b_18275/08_2025/8q9b_18275.map" model { file = "/net/cci-nas-00/data/ceres_data/8q9b_18275/08_2025/8q9b_18275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q9b_18275/08_2025/8q9b_18275.cif" } resolution = 3.1 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 2160 2.51 5 N 636 2.21 5 O 642 1.98 5 H 3588 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 7032 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 1.27, per 1000 atoms: 0.18 Number of scatterers: 7032 At special positions: 0 Unit cell: (96.408, 150.792, 37.08, 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 642 8.00 N 636 7.00 C 2160 6.00 H 3588 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: 0.49 Conformation dependent library (CDL) restraints added in 234.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 57.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.585A pdb=" N VAL A 306 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL F 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE A 308 " --> pdb=" O VAL F 309 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLN E 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N TYR F 310 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL E 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.743A pdb=" N VAL E 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 325 removed outlier: 6.100A pdb=" N LYS E 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N SER F 320 " --> pdb=" O LYS E 317 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR E 319 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N CYS F 322 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LYS E 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N SER F 324 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLY E 323 " --> pdb=" O SER F 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 330 removed outlier: 6.627A pdb=" N ILE E 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 337 through 342 Processing sheet with id=AA6, first strand: chain 'A' and resid 345 through 346 removed outlier: 6.517A pdb=" N ASP E 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 350 through 362 removed outlier: 6.928A pdb=" N GLN A 351 " --> pdb=" O VAL F 350 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N SER F 352 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LYS A 353 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE F 354 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLY A 355 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N SER F 356 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER F 356 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU E 357 " --> pdb=" O SER F 356 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASP F 358 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASN E 359 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE F 360 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR E 361 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N HIS F 362 " --> pdb=" O THR E 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 368 through 378 removed outlier: 6.479A pdb=" N LYS E 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N GLU F 372 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE E 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N HIS F 374 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N THR E 373 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LEU F 376 " --> pdb=" O THR E 373 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LYS E 375 " --> pdb=" O LEU F 376 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N PHE F 378 " --> pdb=" O LYS E 375 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR E 377 " --> pdb=" O PHE F 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.441A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL C 306 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL D 309 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE C 308 " --> pdb=" O VAL D 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.722A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 317 through 325 removed outlier: 6.109A pdb=" N LYS B 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N SER D 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR B 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N CYS D 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LYS B 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N SER D 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY B 323 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.589A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 337 through 342 removed outlier: 6.472A pdb=" N GLU B 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N SER D 341 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS B 340 " --> pdb=" O SER D 341 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL C 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LYS D 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL C 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N GLU D 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N SER C 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 345 through 346 removed outlier: 6.414A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 350 through 362 removed outlier: 6.944A pdb=" N LEU B 357 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASP D 358 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASN B 359 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE D 360 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR B 361 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N HIS D 362 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL C 350 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LYS D 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER C 352 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N GLY D 355 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE C 354 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU D 357 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N SER C 356 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 10.428A pdb=" N ASN D 359 " --> pdb=" O SER C 356 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N ASP C 358 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 10.176A pdb=" N THR D 361 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N ILE C 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 368 through 378 removed outlier: 6.484A pdb=" N LYS B 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N GLU D 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE B 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N HIS D 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N THR B 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU D 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS B 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N PHE D 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR B 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) 71 hydrogen bonds defined for protein. 213 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.34 Time building geometry restraints manager: 0.73 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: 3582 1.12 - 1.29: 570 1.29 - 1.46: 1011 1.46 - 1.64: 1917 1.64 - 1.81: 6 Bond restraints: 7086 Sorted by residual: bond pdb=" N LEU F 325 " pdb=" H LEU F 325 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N GLU E 372 " pdb=" H GLU E 372 " 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 A 368 " pdb="HD21 ASN A 368 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N TYR F 310 " pdb=" H TYR F 310 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N LYS E 311 " pdb=" H LYS E 311 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 7081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 11012 2.54 - 5.07: 1447 5.07 - 7.61: 436 7.61 - 10.14: 11 10.14 - 12.68: 6 Bond angle restraints: 12912 Sorted by residual: angle pdb=" C ASP E 348 " pdb=" N ARG E 349 " pdb=" CA ARG E 349 " ideal model delta sigma weight residual 121.56 128.79 -7.23 1.56e+00 4.11e-01 2.15e+01 angle pdb=" CB HIS B 329 " pdb=" CG HIS B 329 " pdb=" CD2 HIS B 329 " ideal model delta sigma weight residual 131.20 125.24 5.96 1.30e+00 5.92e-01 2.10e+01 angle pdb=" C ASP B 348 " pdb=" N ARG B 349 " pdb=" CA ARG B 349 " ideal model delta sigma weight residual 121.56 128.65 -7.09 1.56e+00 4.11e-01 2.06e+01 angle pdb=" CB HIS B 330 " pdb=" CG HIS B 330 " pdb=" CD2 HIS B 330 " ideal model delta sigma weight residual 131.20 125.40 5.80 1.30e+00 5.92e-01 1.99e+01 angle pdb=" CB HIS D 329 " pdb=" CG HIS D 329 " pdb=" CD2 HIS D 329 " ideal model delta sigma weight residual 131.20 125.41 5.79 1.30e+00 5.92e-01 1.98e+01 ... (remaining 12907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.31: 2902 14.31 - 28.62: 164 28.62 - 42.93: 76 42.93 - 57.24: 64 57.24 - 71.55: 58 Dihedral angle restraints: 3264 sinusoidal: 1866 harmonic: 1398 Sorted by residual: dihedral pdb=" CA LYS C 317 " pdb=" C LYS C 317 " pdb=" N VAL C 318 " pdb=" CA VAL C 318 " ideal model delta harmonic sigma weight residual 180.00 154.37 25.63 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA LYS F 317 " pdb=" C LYS F 317 " pdb=" N VAL F 318 " pdb=" CA VAL F 318 " ideal model delta harmonic sigma weight residual 180.00 156.60 23.40 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA LYS D 317 " pdb=" C LYS D 317 " pdb=" N VAL D 318 " pdb=" CA VAL D 318 " ideal model delta harmonic sigma weight residual 180.00 157.34 22.66 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 3261 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.062: 296 0.062 - 0.123: 181 0.123 - 0.184: 36 0.184 - 0.245: 5 0.245 - 0.306: 10 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA LYS B 311 " pdb=" N LYS B 311 " pdb=" C LYS B 311 " pdb=" CB LYS B 311 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA LYS E 311 " pdb=" N LYS E 311 " pdb=" C LYS E 311 " pdb=" CB LYS E 311 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA LYS E 343 " pdb=" N LYS E 343 " pdb=" C LYS E 343 " pdb=" CB LYS E 343 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 525 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " 0.111 2.00e-02 2.50e+03 4.99e-02 7.48e+01 pdb=" CG TYR E 310 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " -0.036 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " 0.106 2.00e-02 2.50e+03 pdb=" HD1 TYR E 310 " -0.009 2.00e-02 2.50e+03 pdb=" HD2 TYR E 310 " -0.036 2.00e-02 2.50e+03 pdb=" HE1 TYR E 310 " -0.025 2.00e-02 2.50e+03 pdb=" HE2 TYR E 310 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 310 " 0.089 2.00e-02 2.50e+03 4.05e-02 4.91e+01 pdb=" CG TYR B 310 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR B 310 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR B 310 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR B 310 " -0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR B 310 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR B 310 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 310 " 0.086 2.00e-02 2.50e+03 pdb=" HD1 TYR B 310 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR B 310 " -0.029 2.00e-02 2.50e+03 pdb=" HE1 TYR B 310 " -0.025 2.00e-02 2.50e+03 pdb=" HE2 TYR B 310 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " 0.088 2.00e-02 2.50e+03 4.03e-02 4.86e+01 pdb=" CG TYR F 310 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " -0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " -0.018 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " 0.086 2.00e-02 2.50e+03 pdb=" HD1 TYR F 310 " -0.007 2.00e-02 2.50e+03 pdb=" HD2 TYR F 310 " -0.029 2.00e-02 2.50e+03 pdb=" HE1 TYR F 310 " -0.019 2.00e-02 2.50e+03 pdb=" HE2 TYR F 310 " -0.009 2.00e-02 2.50e+03 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 539 2.17 - 2.78: 12128 2.78 - 3.39: 17832 3.39 - 3.99: 24552 3.99 - 4.60: 34219 Nonbonded interactions: 89270 Sorted by model distance: nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.563 2.450 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.565 2.450 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.578 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.585 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.629 2.450 ... (remaining 89265 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 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.750 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.470 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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 3498 Z= 0.673 Angle : 1.788 7.231 4680 Z= 1.193 Chirality : 0.082 0.306 528 Planarity : 0.011 0.058 594 Dihedral : 10.912 67.422 1344 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % 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: -1.61 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 349 TYR 0.099 0.031 TYR E 310 PHE 0.038 0.012 PHE C 346 HIS 0.008 0.002 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.01076 ( 3498) covalent geometry : angle 1.78798 ( 4680) hydrogen bonds : bond 0.10822 ( 71) hydrogen bonds : angle 7.59037 ( 213) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.125 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 317 LYS cc_start: 0.7699 (mttt) cc_final: 0.7377 (mtpt) REVERT: A 321 LYS cc_start: 0.8409 (mttt) cc_final: 0.8085 (mttm) REVERT: A 349 ARG cc_start: 0.7435 (mtm180) cc_final: 0.6805 (ptt-90) REVERT: B 311 LYS cc_start: 0.7901 (mttt) cc_final: 0.7221 (mttm) REVERT: B 317 LYS cc_start: 0.6550 (mttt) cc_final: 0.5940 (mtpt) REVERT: B 340 LYS cc_start: 0.7548 (tttt) cc_final: 0.7052 (mmtt) REVERT: C 349 ARG cc_start: 0.7443 (mtm180) cc_final: 0.6917 (ptt-90) REVERT: D 311 LYS cc_start: 0.8244 (mttt) cc_final: 0.8013 (mtmt) REVERT: D 338 GLU cc_start: 0.7606 (tt0) cc_final: 0.7391 (tt0) REVERT: D 345 ASP cc_start: 0.8015 (t0) cc_final: 0.7813 (m-30) REVERT: D 349 ARG cc_start: 0.6871 (mtm180) cc_final: 0.6564 (mtt-85) REVERT: D 372 GLU cc_start: 0.7662 (tt0) cc_final: 0.7382 (tt0) REVERT: E 317 LYS cc_start: 0.6489 (mttt) cc_final: 0.6042 (mtpt) REVERT: E 340 LYS cc_start: 0.7682 (tttt) cc_final: 0.7180 (mmtt) REVERT: E 353 LYS cc_start: 0.6414 (mttt) cc_final: 0.6197 (tttm) REVERT: F 317 LYS cc_start: 0.6333 (mttt) cc_final: 0.5849 (mtpt) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.3032 time to fit residues: 41.1847 Evaluate side-chains 81 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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: 5.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 307 GLN C 307 GLN D 307 GLN E 307 GLN F 307 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.140715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.123625 restraints weight = 13269.906| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 1.86 r_work: 0.3918 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3838 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 3498 Z= 0.192 Angle : 0.533 3.975 4680 Z= 0.285 Chirality : 0.050 0.136 528 Planarity : 0.005 0.037 594 Dihedral : 6.081 20.997 462 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.52 % Allowed : 4.55 % Favored : 93.94 % 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: -1.49 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.007 0.002 TYR F 310 PHE 0.007 0.001 PHE D 346 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 3498) covalent geometry : angle 0.53264 ( 4680) hydrogen bonds : bond 0.02612 ( 71) hydrogen bonds : angle 5.54620 ( 213) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.7702 (mtm180) cc_final: 0.7075 (mtt180) REVERT: B 311 LYS cc_start: 0.8449 (mttt) cc_final: 0.7744 (mttm) REVERT: B 317 LYS cc_start: 0.7681 (mttt) cc_final: 0.7291 (mtpt) REVERT: B 340 LYS cc_start: 0.7864 (tttt) cc_final: 0.7417 (mmtt) REVERT: B 348 ASP cc_start: 0.8374 (t0) cc_final: 0.8161 (t0) REVERT: C 314 ASP cc_start: 0.8812 (t0) cc_final: 0.8530 (t0) REVERT: C 349 ARG cc_start: 0.7655 (mtm180) cc_final: 0.6828 (ptt-90) REVERT: D 349 ARG cc_start: 0.7151 (mtm180) cc_final: 0.6530 (mtt90) REVERT: E 317 LYS cc_start: 0.7673 (mttt) cc_final: 0.7200 (mtpt) REVERT: E 340 LYS cc_start: 0.7764 (tttt) cc_final: 0.7319 (mmtt) outliers start: 6 outliers final: 6 residues processed: 85 average time/residue: 0.2848 time to fit residues: 26.7867 Evaluate side-chains 76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 305 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 4.9990 chunk 28 optimal weight: 0.0970 chunk 12 optimal weight: 0.1980 chunk 22 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 1 optimal weight: 0.0670 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- 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 = 0.4245 r_free = 0.4245 target = 0.141440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.124255 restraints weight = 13315.649| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 1.81 r_work: 0.3992 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3916 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 3498 Z= 0.078 Angle : 0.459 3.861 4680 Z= 0.237 Chirality : 0.052 0.136 528 Planarity : 0.003 0.027 594 Dihedral : 5.292 17.224 462 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.52 % Allowed : 4.04 % Favored : 94.44 % 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: -1.16 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.88 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 379 TYR 0.005 0.001 TYR A 310 PHE 0.008 0.001 PHE D 346 HIS 0.001 0.000 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.00177 ( 3498) covalent geometry : angle 0.45906 ( 4680) hydrogen bonds : bond 0.02025 ( 71) hydrogen bonds : angle 5.14921 ( 213) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.8746 (t0) cc_final: 0.8489 (t0) REVERT: B 317 LYS cc_start: 0.7718 (mttt) cc_final: 0.7260 (mtpt) REVERT: B 340 LYS cc_start: 0.7844 (tttt) cc_final: 0.7448 (mmtt) REVERT: B 349 ARG cc_start: 0.5176 (mmp-170) cc_final: 0.4763 (tpm170) REVERT: C 314 ASP cc_start: 0.8812 (t0) cc_final: 0.8518 (t0) REVERT: C 349 ARG cc_start: 0.7668 (mtm180) cc_final: 0.6378 (pmt-80) REVERT: D 349 ARG cc_start: 0.7126 (mtm180) cc_final: 0.6575 (mtt90) REVERT: E 340 LYS cc_start: 0.7680 (tttt) cc_final: 0.7265 (mmtt) outliers start: 6 outliers final: 6 residues processed: 70 average time/residue: 0.2965 time to fit residues: 23.0973 Evaluate side-chains 65 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 305 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.4179 r_free = 0.4179 target = 0.135886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.118689 restraints weight = 13743.397| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 1.80 r_work: 0.3914 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3837 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3498 Z= 0.147 Angle : 0.458 3.920 4680 Z= 0.237 Chirality : 0.050 0.127 528 Planarity : 0.003 0.024 594 Dihedral : 5.158 15.277 462 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.52 % Allowed : 4.29 % Favored : 94.19 % 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: -1.03 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.77 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 349 TYR 0.009 0.002 TYR F 310 PHE 0.006 0.001 PHE D 346 HIS 0.002 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 3498) covalent geometry : angle 0.45772 ( 4680) hydrogen bonds : bond 0.02006 ( 71) hydrogen bonds : angle 4.68975 ( 213) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.7717 (mtm180) cc_final: 0.7074 (mtt180) REVERT: B 340 LYS cc_start: 0.7805 (tttt) cc_final: 0.7391 (mmtt) REVERT: C 314 ASP cc_start: 0.8786 (t0) cc_final: 0.8517 (t0) REVERT: C 349 ARG cc_start: 0.7698 (mtm180) cc_final: 0.6476 (pmt-80) REVERT: D 349 ARG cc_start: 0.7154 (mtm180) cc_final: 0.6498 (mtt90) REVERT: D 372 GLU cc_start: 0.8416 (tt0) cc_final: 0.8134 (tt0) REVERT: E 340 LYS cc_start: 0.7658 (tttt) cc_final: 0.7198 (mmtt) REVERT: E 349 ARG cc_start: 0.4696 (mmp-170) cc_final: 0.4492 (tpm170) outliers start: 6 outliers final: 6 residues processed: 75 average time/residue: 0.3115 time to fit residues: 25.9979 Evaluate side-chains 73 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 305 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.4173 r_free = 0.4173 target = 0.135348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.118170 restraints weight = 13617.084| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 1.80 r_work: 0.3908 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3831 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3498 Z= 0.142 Angle : 0.448 3.929 4680 Z= 0.230 Chirality : 0.050 0.128 528 Planarity : 0.003 0.024 594 Dihedral : 4.996 14.212 462 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.52 % Allowed : 5.56 % Favored : 92.93 % 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: -1.10 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.83 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.008 0.002 TYR F 310 PHE 0.004 0.001 PHE D 346 HIS 0.002 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 3498) covalent geometry : angle 0.44758 ( 4680) hydrogen bonds : bond 0.01800 ( 71) hydrogen bonds : angle 4.47829 ( 213) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.215 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: A 349 ARG cc_start: 0.7738 (mtm180) cc_final: 0.7083 (mtt180) REVERT: B 340 LYS cc_start: 0.7819 (tttt) cc_final: 0.7423 (mmtt) REVERT: C 314 ASP cc_start: 0.8791 (t0) cc_final: 0.8587 (t0) REVERT: C 349 ARG cc_start: 0.7835 (mtm180) cc_final: 0.6606 (pmt-80) REVERT: D 349 ARG cc_start: 0.7200 (mtm180) cc_final: 0.6581 (mtt90) REVERT: D 372 GLU cc_start: 0.8382 (tt0) cc_final: 0.8082 (tt0) REVERT: E 340 LYS cc_start: 0.7664 (tttt) cc_final: 0.7224 (mmtt) REVERT: E 349 ARG cc_start: 0.4710 (mmp-170) cc_final: 0.4500 (tpm170) outliers start: 6 outliers final: 6 residues processed: 73 average time/residue: 0.3282 time to fit residues: 26.4361 Evaluate side-chains 72 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 305 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 = 0.4142 r_free = 0.4142 target = 0.132802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.115637 restraints weight = 13863.590| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 1.79 r_work: 0.3872 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3796 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 3498 Z= 0.206 Angle : 0.468 4.029 4680 Z= 0.244 Chirality : 0.050 0.125 528 Planarity : 0.003 0.025 594 Dihedral : 5.160 14.134 462 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.52 % Allowed : 6.57 % Favored : 91.92 % 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: -1.17 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.88 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 349 TYR 0.010 0.002 TYR F 310 PHE 0.003 0.001 PHE B 346 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 3498) covalent geometry : angle 0.46817 ( 4680) hydrogen bonds : bond 0.01923 ( 71) hydrogen bonds : angle 4.45357 ( 213) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.206 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 349 ARG cc_start: 0.7766 (mtm180) cc_final: 0.7071 (mtt180) REVERT: B 340 LYS cc_start: 0.7761 (tttt) cc_final: 0.7313 (mmtt) REVERT: C 314 ASP cc_start: 0.8790 (t0) cc_final: 0.8578 (t0) REVERT: C 349 ARG cc_start: 0.7865 (mtm180) cc_final: 0.6574 (pmt-80) REVERT: D 349 ARG cc_start: 0.7184 (mtm180) cc_final: 0.6587 (mtt90) REVERT: D 372 GLU cc_start: 0.8387 (tt0) cc_final: 0.8064 (tt0) REVERT: E 340 LYS cc_start: 0.7641 (tttt) cc_final: 0.7175 (mmtt) outliers start: 6 outliers final: 6 residues processed: 75 average time/residue: 0.3156 time to fit residues: 26.2368 Evaluate side-chains 75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 305 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.4200 r_free = 0.4200 target = 0.143205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.126640 restraints weight = 13030.951| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 1.70 r_work: 0.3923 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3850 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3498 Z= 0.125 Angle : 0.438 3.949 4680 Z= 0.225 Chirality : 0.050 0.125 528 Planarity : 0.003 0.025 594 Dihedral : 4.874 13.324 462 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.52 % Allowed : 7.07 % Favored : 91.41 % 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 (0.39), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.89 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.008 0.002 TYR F 310 PHE 0.004 0.001 PHE F 378 HIS 0.002 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 3498) covalent geometry : angle 0.43809 ( 4680) hydrogen bonds : bond 0.01637 ( 71) hydrogen bonds : angle 4.29745 ( 213) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.209 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 349 ARG cc_start: 0.7772 (mtm180) cc_final: 0.7140 (mtt180) REVERT: B 340 LYS cc_start: 0.7841 (tttt) cc_final: 0.7410 (mmtt) REVERT: C 349 ARG cc_start: 0.7882 (mtm180) cc_final: 0.6644 (pmt-80) REVERT: D 349 ARG cc_start: 0.7262 (mtm180) cc_final: 0.6705 (mtt90) REVERT: D 372 GLU cc_start: 0.8295 (tt0) cc_final: 0.7989 (tt0) REVERT: E 340 LYS cc_start: 0.7698 (tttt) cc_final: 0.7293 (mmtt) outliers start: 6 outliers final: 6 residues processed: 74 average time/residue: 0.3238 time to fit residues: 26.5395 Evaluate side-chains 71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 305 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 = 0.4132 r_free = 0.4132 target = 0.132113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.114877 restraints weight = 13854.442| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 1.77 r_work: 0.3865 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3790 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3498 Z= 0.202 Angle : 0.464 4.058 4680 Z= 0.240 Chirality : 0.049 0.126 528 Planarity : 0.003 0.026 594 Dihedral : 5.062 13.968 462 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.52 % Allowed : 7.83 % Favored : 90.66 % 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: -1.25 (0.39), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.94 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 349 TYR 0.009 0.002 TYR D 310 PHE 0.003 0.001 PHE F 378 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 3498) covalent geometry : angle 0.46358 ( 4680) hydrogen bonds : bond 0.01845 ( 71) hydrogen bonds : angle 4.34544 ( 213) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.203 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 349 ARG cc_start: 0.7795 (mtm180) cc_final: 0.7121 (mtt180) REVERT: B 340 LYS cc_start: 0.7781 (tttt) cc_final: 0.7324 (mmtt) REVERT: C 349 ARG cc_start: 0.7851 (mtm180) cc_final: 0.6502 (pmt-80) REVERT: C 379 ARG cc_start: 0.5661 (mmt-90) cc_final: 0.5229 (mmt-90) REVERT: D 349 ARG cc_start: 0.7233 (mtm180) cc_final: 0.6707 (mtt180) REVERT: D 372 GLU cc_start: 0.8345 (tt0) cc_final: 0.8029 (tt0) REVERT: E 340 LYS cc_start: 0.7636 (tttt) cc_final: 0.7175 (mmtt) outliers start: 6 outliers final: 6 residues processed: 73 average time/residue: 0.3181 time to fit residues: 25.6607 Evaluate side-chains 72 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 305 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.4158 r_free = 0.4158 target = 0.134257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.117104 restraints weight = 13614.128| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 1.75 r_work: 0.3899 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3826 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3498 Z= 0.148 Angle : 0.442 3.986 4680 Z= 0.226 Chirality : 0.050 0.125 528 Planarity : 0.003 0.026 594 Dihedral : 4.869 13.436 462 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.52 % Allowed : 8.08 % Favored : 90.40 % 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: -1.24 (0.39), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.93 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 349 TYR 0.008 0.002 TYR F 310 PHE 0.003 0.001 PHE B 346 HIS 0.002 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 3498) covalent geometry : angle 0.44183 ( 4680) hydrogen bonds : bond 0.01650 ( 71) hydrogen bonds : angle 4.25547 ( 213) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.218 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 349 ARG cc_start: 0.7811 (mtm180) cc_final: 0.7130 (mtt180) REVERT: B 340 LYS cc_start: 0.7837 (tttt) cc_final: 0.7335 (mmtt) REVERT: C 349 ARG cc_start: 0.7828 (mtm180) cc_final: 0.6460 (pmt-80) REVERT: C 379 ARG cc_start: 0.5602 (mmt-90) cc_final: 0.5169 (mmt-90) REVERT: D 349 ARG cc_start: 0.7217 (mtm180) cc_final: 0.6740 (mtt180) REVERT: D 372 GLU cc_start: 0.8330 (tt0) cc_final: 0.7999 (tt0) REVERT: E 340 LYS cc_start: 0.7678 (tttt) cc_final: 0.7182 (mmtt) outliers start: 6 outliers final: 6 residues processed: 72 average time/residue: 0.3228 time to fit residues: 25.7672 Evaluate side-chains 72 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 305 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.131124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.113872 restraints weight = 13805.331| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 1.77 r_work: 0.3851 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3774 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3498 Z= 0.223 Angle : 0.476 4.064 4680 Z= 0.246 Chirality : 0.049 0.126 528 Planarity : 0.003 0.026 594 Dihedral : 5.110 13.838 462 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.52 % Allowed : 8.33 % Favored : 90.15 % 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: -1.34 (0.39), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 349 TYR 0.009 0.002 TYR D 310 PHE 0.003 0.001 PHE B 346 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 3498) covalent geometry : angle 0.47556 ( 4680) hydrogen bonds : bond 0.01914 ( 71) hydrogen bonds : angle 4.34397 ( 213) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.211 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 349 ARG cc_start: 0.7864 (mtm180) cc_final: 0.7166 (mtt180) REVERT: B 340 LYS cc_start: 0.7862 (tttt) cc_final: 0.7345 (mmtt) REVERT: C 349 ARG cc_start: 0.7836 (mtm180) cc_final: 0.6478 (pmt-80) REVERT: C 379 ARG cc_start: 0.5469 (mmt-90) cc_final: 0.5020 (mmt-90) REVERT: D 349 ARG cc_start: 0.7248 (mtm180) cc_final: 0.6745 (mtt180) REVERT: D 372 GLU cc_start: 0.8341 (tt0) cc_final: 0.8023 (tt0) REVERT: E 340 LYS cc_start: 0.7720 (tttt) cc_final: 0.7156 (mmtt) outliers start: 6 outliers final: 6 residues processed: 74 average time/residue: 0.2887 time to fit residues: 23.8857 Evaluate side-chains 73 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 305 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4232 r_free = 0.4232 target = 0.145856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.129286 restraints weight = 12748.439| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 1.68 r_work: 0.3967 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3896 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 3498 Z= 0.078 Angle : 0.425 3.925 4680 Z= 0.215 Chirality : 0.051 0.131 528 Planarity : 0.003 0.023 594 Dihedral : 4.553 13.456 462 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.76 % Allowed : 9.34 % Favored : 89.90 % 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: -1.26 (0.39), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.95 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 349 TYR 0.006 0.001 TYR F 310 PHE 0.004 0.001 PHE F 378 HIS 0.001 0.000 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00178 ( 3498) covalent geometry : angle 0.42518 ( 4680) hydrogen bonds : bond 0.01418 ( 71) hydrogen bonds : angle 4.13037 ( 213) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2215.40 seconds wall clock time: 38 minutes 16.86 seconds (2296.86 seconds total)