Starting phenix.real_space_refine on Tue Feb 11 23:56:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q9j_18283/02_2025/8q9j_18283.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q9j_18283/02_2025/8q9j_18283.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q9j_18283/02_2025/8q9j_18283.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q9j_18283/02_2025/8q9j_18283.map" model { file = "/net/cci-nas-00/data/ceres_data/8q9j_18283/02_2025/8q9j_18283.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q9j_18283/02_2025/8q9j_18283.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2106 2.51 5 N 606 2.21 5 O 624 1.98 5 H 3480 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 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: "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: "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: "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: "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: "F" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 4.89, per 1000 atoms: 0.72 Number of scatterers: 6822 At special positions: 0 Unit cell: (119.228, 100.326, 50.163, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 624 8.00 N 606 7.00 C 2106 6.00 H 3480 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 623.3 milliseconds 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 50.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 307 through 310 removed outlier: 6.376A pdb=" N ILE A 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 7.127A 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 322 removed outlier: 6.375A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.676A 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: 5.771A pdb=" N GLY A 326 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N HIS C 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY E 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.769A 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 removed outlier: 6.459A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LYS C 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL A 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N GLU C 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER A 341 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLU A 338 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N SER E 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LYS A 340 " --> pdb=" O SER E 341 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.525A 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 Processing sheet with id=AA8, first strand: chain 'C' and resid 360 through 362 Processing sheet with id=AA9, first strand: chain 'C' and resid 369 through 377 removed outlier: 6.426A pdb=" N LYS A 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLU E 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE A 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N HIS E 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N THR A 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N LEU E 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LYS A 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 307 through 310 removed outlier: 6.598A pdb=" N GLN B 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N TYR F 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL B 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 313 through 314 removed outlier: 7.090A pdb=" N VAL B 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 317 through 322 removed outlier: 6.466A pdb=" N LYS B 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N SER F 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR B 319 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N CYS F 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LYS B 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 325 through 330 removed outlier: 5.905A pdb=" N GLY B 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N HIS D 329 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLY F 326 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN B 327 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 337 through 342 removed outlier: 6.433A pdb=" N VAL B 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N LYS D 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL B 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLU D 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER B 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.592A pdb=" N ASP B 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 350 through 357 removed outlier: 6.490A pdb=" N GLN B 351 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ILE F 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LYS B 353 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N SER F 356 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLY B 355 " --> pdb=" O SER F 356 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.484A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 369 through 377 removed outlier: 6.447A pdb=" N LYS B 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N GLU F 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE B 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N HIS F 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N THR B 373 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N LEU F 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS B 375 " --> pdb=" O LEU F 376 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 222 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 3474 1.12 - 1.29: 560 1.29 - 1.47: 1022 1.47 - 1.64: 1814 1.64 - 1.81: 6 Bond restraints: 6876 Sorted by residual: bond pdb=" CD2 HIS E 330 " pdb=" HD2 HIS E 330 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N LYS D 353 " pdb=" H LYS D 353 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" ND2 ASN C 327 " pdb="HD21 ASN C 327 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N GLY E 323 " pdb=" H GLY E 323 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CE2 TYR D 310 " pdb=" HE2 TYR D 310 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 6871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 10491 2.49 - 4.98: 1573 4.98 - 7.47: 457 7.47 - 9.96: 20 9.96 - 12.45: 5 Bond angle restraints: 12546 Sorted by residual: angle pdb=" C GLY F 334 " pdb=" N GLY F 335 " pdb=" CA GLY F 335 " ideal model delta sigma weight residual 120.60 125.80 -5.20 1.01e+00 9.80e-01 2.65e+01 angle pdb=" CB HIS F 374 " pdb=" CG HIS F 374 " pdb=" CD2 HIS F 374 " ideal model delta sigma weight residual 131.20 124.53 6.67 1.30e+00 5.92e-01 2.64e+01 angle pdb=" CB HIS B 374 " pdb=" CG HIS B 374 " pdb=" CD2 HIS B 374 " ideal model delta sigma weight residual 131.20 125.03 6.17 1.30e+00 5.92e-01 2.25e+01 angle pdb=" CB HIS C 329 " pdb=" CG HIS C 329 " pdb=" CD2 HIS C 329 " ideal model delta sigma weight residual 131.20 125.31 5.89 1.30e+00 5.92e-01 2.06e+01 angle pdb=" CB HIS A 329 " pdb=" CG HIS A 329 " pdb=" CD2 HIS A 329 " ideal model delta sigma weight residual 131.20 125.32 5.88 1.30e+00 5.92e-01 2.05e+01 ... (remaining 12541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.69: 2747 13.69 - 27.38: 214 27.38 - 41.07: 69 41.07 - 54.76: 53 54.76 - 68.45: 85 Dihedral angle restraints: 3168 sinusoidal: 1806 harmonic: 1362 Sorted by residual: dihedral pdb=" CA GLY F 323 " pdb=" C GLY F 323 " pdb=" N SER F 324 " pdb=" CA SER F 324 " ideal model delta harmonic sigma weight residual 180.00 155.29 24.71 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA ILE E 360 " pdb=" C ILE E 360 " pdb=" N THR E 361 " pdb=" CA THR E 361 " ideal model delta harmonic sigma weight residual 180.00 155.37 24.63 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA GLY E 323 " pdb=" C GLY E 323 " pdb=" N SER E 324 " pdb=" CA SER E 324 " ideal model delta harmonic sigma weight residual 180.00 155.42 24.58 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 3165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 296 0.067 - 0.134: 165 0.134 - 0.202: 45 0.202 - 0.269: 7 0.269 - 0.336: 3 Chirality restraints: 516 Sorted by residual: chirality pdb=" CA LYS B 317 " pdb=" N LYS B 317 " pdb=" C LYS B 317 " pdb=" CB LYS B 317 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA LYS D 343 " pdb=" N LYS D 343 " pdb=" C LYS D 343 " pdb=" CB LYS D 343 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA LYS A 317 " pdb=" N LYS A 317 " pdb=" C LYS A 317 " pdb=" CB LYS A 317 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 513 not shown) Planarity restraints: 990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " -0.099 2.00e-02 2.50e+03 4.49e-02 6.06e+01 pdb=" CG TYR C 310 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " 0.025 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " -0.098 2.00e-02 2.50e+03 pdb=" HD1 TYR C 310 " 0.012 2.00e-02 2.50e+03 pdb=" HD2 TYR C 310 " 0.020 2.00e-02 2.50e+03 pdb=" HE1 TYR C 310 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 TYR C 310 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 310 " -0.102 2.00e-02 2.50e+03 4.34e-02 5.65e+01 pdb=" CG TYR D 310 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR D 310 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR D 310 " 0.035 2.00e-02 2.50e+03 pdb=" CE1 TYR D 310 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR D 310 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR D 310 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 310 " -0.084 2.00e-02 2.50e+03 pdb=" HD1 TYR D 310 " 0.007 2.00e-02 2.50e+03 pdb=" HD2 TYR D 310 " 0.030 2.00e-02 2.50e+03 pdb=" HE1 TYR D 310 " 0.017 2.00e-02 2.50e+03 pdb=" HE2 TYR D 310 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " -0.090 2.00e-02 2.50e+03 3.94e-02 4.65e+01 pdb=" CG TYR A 310 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " 0.018 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.081 2.00e-02 2.50e+03 pdb=" HD1 TYR A 310 " 0.004 2.00e-02 2.50e+03 pdb=" HD2 TYR A 310 " 0.023 2.00e-02 2.50e+03 pdb=" HE1 TYR A 310 " 0.014 2.00e-02 2.50e+03 pdb=" HE2 TYR A 310 " 0.004 2.00e-02 2.50e+03 ... (remaining 987 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 503 2.18 - 2.79: 11907 2.79 - 3.39: 17566 3.39 - 4.00: 24456 4.00 - 4.60: 33504 Nonbonded interactions: 87936 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.577 2.450 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.578 2.450 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.581 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.598 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.600 2.450 ... (remaining 87931 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.350 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: 0.110 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.320 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 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 0.039 3396 Z= 0.751 Angle : 1.860 9.801 4548 Z= 1.236 Chirality : 0.087 0.336 516 Planarity : 0.011 0.062 576 Dihedral : 10.827 61.776 1296 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.34), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.94 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.004 HIS A 330 PHE 0.035 0.010 PHE A 346 TYR 0.093 0.031 TYR D 310 ARG 0.005 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 LYS cc_start: 0.8164 (mttt) cc_final: 0.7955 (mttp) REVERT: A 369 LYS cc_start: 0.7068 (mttt) cc_final: 0.6703 (mtpt) REVERT: A 370 LYS cc_start: 0.6981 (tttm) cc_final: 0.6741 (tttp) REVERT: A 372 GLU cc_start: 0.6509 (tt0) cc_final: 0.6164 (tp30) REVERT: C 321 LYS cc_start: 0.6612 (ttpt) cc_final: 0.6290 (ptpp) REVERT: C 340 LYS cc_start: 0.7883 (mtpt) cc_final: 0.7417 (tppt) REVERT: C 347 LYS cc_start: 0.7812 (mttt) cc_final: 0.7100 (mmpt) REVERT: C 349 ARG cc_start: 0.7390 (mtt180) cc_final: 0.5704 (mmp-170) REVERT: C 369 LYS cc_start: 0.7035 (mttt) cc_final: 0.6763 (mtpt) REVERT: C 370 LYS cc_start: 0.8097 (tttm) cc_final: 0.7155 (mptt) REVERT: C 372 GLU cc_start: 0.7646 (tt0) cc_final: 0.7197 (mp0) REVERT: C 375 LYS cc_start: 0.5780 (tttt) cc_final: 0.5237 (tppt) REVERT: E 311 LYS cc_start: 0.7113 (ttpt) cc_final: 0.6611 (pttp) REVERT: E 340 LYS cc_start: 0.8295 (mtpt) cc_final: 0.7915 (ttpt) REVERT: E 342 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7509 (tm-30) REVERT: E 372 GLU cc_start: 0.5843 (tt0) cc_final: 0.5550 (tp30) REVERT: E 375 LYS cc_start: 0.7300 (tttt) cc_final: 0.6876 (ttmt) REVERT: B 310 TYR cc_start: 0.4789 (t80) cc_final: 0.4539 (t80) REVERT: B 321 LYS cc_start: 0.7361 (ttpt) cc_final: 0.7004 (mttm) REVERT: B 342 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7732 (mt-10) REVERT: B 349 ARG cc_start: 0.7404 (mtt180) cc_final: 0.7168 (mtp85) REVERT: D 342 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7903 (mt-10) REVERT: D 349 ARG cc_start: 0.7546 (mtt180) cc_final: 0.5794 (mmp-170) REVERT: D 372 GLU cc_start: 0.7736 (tt0) cc_final: 0.7404 (tt0) REVERT: F 317 LYS cc_start: 0.7346 (pttt) cc_final: 0.7128 (ptpp) REVERT: F 320 SER cc_start: 0.7986 (t) cc_final: 0.7425 (p) REVERT: F 321 LYS cc_start: 0.8009 (ttpt) cc_final: 0.7645 (mttm) REVERT: F 342 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8007 (mt-10) REVERT: F 349 ARG cc_start: 0.7596 (mtt180) cc_final: 0.5966 (mtm180) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 3.1464 time to fit residues: 404.8250 Evaluate side-chains 79 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS C 362 HIS E 362 HIS B 362 HIS D 362 HIS F 307 GLN F 351 GLN F 362 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.157960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.138089 restraints weight = 10703.068| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 1.64 r_work: 0.3999 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3920 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3396 Z= 0.203 Angle : 0.581 4.899 4548 Z= 0.301 Chirality : 0.052 0.157 516 Planarity : 0.003 0.025 576 Dihedral : 6.544 19.806 444 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.56 % Allowed : 11.98 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.009 0.001 PHE B 346 TYR 0.010 0.002 TYR F 310 ARG 0.002 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 THR cc_start: 0.7679 (m) cc_final: 0.7199 (p) REVERT: C 342 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7107 (tm-30) REVERT: C 349 ARG cc_start: 0.7151 (mtt180) cc_final: 0.5763 (mtp180) REVERT: E 311 LYS cc_start: 0.7953 (ttpt) cc_final: 0.7731 (pttp) REVERT: E 338 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7634 (tt0) REVERT: E 347 LYS cc_start: 0.8038 (mttt) cc_final: 0.7014 (mtmt) REVERT: E 372 GLU cc_start: 0.6975 (tt0) cc_final: 0.6749 (mt-10) REVERT: D 349 ARG cc_start: 0.7887 (mtt180) cc_final: 0.6392 (mmp-170) REVERT: F 320 SER cc_start: 0.8410 (t) cc_final: 0.8063 (p) REVERT: F 342 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7825 (mt-10) REVERT: F 349 ARG cc_start: 0.7842 (mtt180) cc_final: 0.6386 (mtm180) outliers start: 6 outliers final: 1 residues processed: 75 average time/residue: 3.3226 time to fit residues: 254.8860 Evaluate side-chains 50 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain E residue 338 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 10.0000 chunk 12 optimal weight: 0.0000 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.153953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.135286 restraints weight = 11038.182| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 1.55 r_work: 0.3957 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3883 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3396 Z= 0.195 Angle : 0.543 3.848 4548 Z= 0.282 Chirality : 0.052 0.140 516 Planarity : 0.003 0.028 576 Dihedral : 5.675 17.794 444 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.34 % Allowed : 15.10 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 374 PHE 0.007 0.001 PHE D 346 TYR 0.016 0.002 TYR B 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 THR cc_start: 0.7808 (m) cc_final: 0.7375 (p) REVERT: C 342 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7244 (tm-30) REVERT: C 349 ARG cc_start: 0.7110 (mtt180) cc_final: 0.5851 (mtp180) REVERT: E 338 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7716 (tm-30) REVERT: E 347 LYS cc_start: 0.8040 (mttt) cc_final: 0.7052 (mtmt) REVERT: B 342 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7589 (mt-10) REVERT: D 342 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7415 (mp0) REVERT: D 349 ARG cc_start: 0.7849 (mtt180) cc_final: 0.6427 (mmp-170) REVERT: F 320 SER cc_start: 0.8538 (t) cc_final: 0.8207 (t) REVERT: F 342 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7894 (mt-10) REVERT: F 349 ARG cc_start: 0.7848 (mtt180) cc_final: 0.6470 (mtm180) outliers start: 9 outliers final: 1 residues processed: 61 average time/residue: 2.7451 time to fit residues: 172.1158 Evaluate side-chains 56 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain B residue 342 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.154998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.136749 restraints weight = 11080.129| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 1.55 r_work: 0.3962 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3887 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3396 Z= 0.188 Angle : 0.516 3.824 4548 Z= 0.266 Chirality : 0.051 0.136 516 Planarity : 0.003 0.027 576 Dihedral : 5.364 17.523 444 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 0.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.34 % Allowed : 16.15 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 374 PHE 0.004 0.001 PHE E 378 TYR 0.017 0.002 TYR B 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 LYS cc_start: 0.8262 (mttm) cc_final: 0.8023 (mttt) REVERT: A 373 THR cc_start: 0.7839 (m) cc_final: 0.7405 (p) REVERT: C 342 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7197 (tm-30) REVERT: E 338 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7123 (tt0) REVERT: E 347 LYS cc_start: 0.8080 (mttt) cc_final: 0.7076 (mtmt) REVERT: B 342 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7696 (mt-10) REVERT: D 342 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7805 (tt0) REVERT: D 349 ARG cc_start: 0.7884 (mtt180) cc_final: 0.6472 (mmp-170) REVERT: F 320 SER cc_start: 0.8544 (t) cc_final: 0.8195 (t) REVERT: F 342 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7898 (mt-10) REVERT: F 349 ARG cc_start: 0.7856 (mtt180) cc_final: 0.6461 (mtm180) outliers start: 9 outliers final: 1 residues processed: 56 average time/residue: 2.8585 time to fit residues: 164.3337 Evaluate side-chains 52 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain B residue 342 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 8.9990 chunk 35 optimal weight: 0.3980 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.157706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.139508 restraints weight = 10805.879| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 1.57 r_work: 0.4031 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3960 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3396 Z= 0.140 Angle : 0.483 4.359 4548 Z= 0.246 Chirality : 0.052 0.137 516 Planarity : 0.003 0.024 576 Dihedral : 4.843 16.148 444 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 1.04 % Allowed : 18.49 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.11 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 374 PHE 0.003 0.000 PHE C 346 TYR 0.017 0.002 TYR B 310 ARG 0.002 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 353 LYS cc_start: 0.8271 (mttm) cc_final: 0.8035 (mttt) REVERT: A 373 THR cc_start: 0.7911 (m) cc_final: 0.7557 (p) REVERT: C 342 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7192 (tm-30) REVERT: E 338 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7266 (mp0) REVERT: E 347 LYS cc_start: 0.8037 (mttt) cc_final: 0.7043 (mtmt) REVERT: B 342 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7703 (mt-10) REVERT: D 342 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7770 (tt0) REVERT: D 349 ARG cc_start: 0.7820 (mtt180) cc_final: 0.6405 (mmp-170) REVERT: F 320 SER cc_start: 0.8495 (t) cc_final: 0.8140 (t) REVERT: F 342 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7882 (mt-10) REVERT: F 349 ARG cc_start: 0.7858 (mtt180) cc_final: 0.6453 (mtm180) outliers start: 4 outliers final: 0 residues processed: 58 average time/residue: 2.6026 time to fit residues: 155.4032 Evaluate side-chains 53 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain B residue 342 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.4266 r_free = 0.4266 target = 0.155241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.137083 restraints weight = 10958.168| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 1.58 r_work: 0.3996 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3924 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3396 Z= 0.165 Angle : 0.494 4.113 4548 Z= 0.251 Chirality : 0.051 0.136 516 Planarity : 0.003 0.023 576 Dihedral : 4.812 16.230 444 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.56 % Allowed : 18.23 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 329 PHE 0.004 0.001 PHE C 346 TYR 0.017 0.002 TYR B 310 ARG 0.000 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 353 LYS cc_start: 0.8262 (mttm) cc_final: 0.8050 (mttt) REVERT: A 373 THR cc_start: 0.7966 (m) cc_final: 0.7566 (p) REVERT: C 342 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7142 (tm-30) REVERT: E 347 LYS cc_start: 0.8028 (mttt) cc_final: 0.7024 (mtmt) REVERT: B 342 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7716 (mt-10) REVERT: D 342 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7782 (tt0) REVERT: D 349 ARG cc_start: 0.7869 (mtt180) cc_final: 0.6466 (mmp-170) REVERT: F 320 SER cc_start: 0.8519 (t) cc_final: 0.8123 (t) REVERT: F 342 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7857 (mt-10) REVERT: F 349 ARG cc_start: 0.7887 (mtt180) cc_final: 0.6469 (mtm180) outliers start: 6 outliers final: 2 residues processed: 61 average time/residue: 2.7848 time to fit residues: 174.5993 Evaluate side-chains 53 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 342 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 40 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.149911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.131881 restraints weight = 11026.333| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 1.58 r_work: 0.3922 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3847 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.5319 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= 0.246 Angle : 0.535 4.452 4548 Z= 0.276 Chirality : 0.052 0.140 516 Planarity : 0.003 0.025 576 Dihedral : 5.144 17.509 444 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.56 % Allowed : 18.75 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.31), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 330 PHE 0.007 0.001 PHE D 346 TYR 0.018 0.002 TYR B 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 353 LYS cc_start: 0.8278 (mttm) cc_final: 0.8049 (mttt) REVERT: A 373 THR cc_start: 0.8036 (m) cc_final: 0.7626 (p) REVERT: E 338 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7515 (tt0) REVERT: E 347 LYS cc_start: 0.8108 (mttt) cc_final: 0.7073 (mtmt) REVERT: B 342 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7661 (mt-10) REVERT: D 342 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7782 (tt0) REVERT: D 349 ARG cc_start: 0.7918 (mtt180) cc_final: 0.6480 (mmp-170) REVERT: F 342 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7809 (mt-10) REVERT: F 349 ARG cc_start: 0.7932 (mtt180) cc_final: 0.6609 (mtm180) outliers start: 6 outliers final: 3 residues processed: 57 average time/residue: 2.7639 time to fit residues: 161.9419 Evaluate side-chains 55 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain B residue 342 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.151078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.133158 restraints weight = 11185.519| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 1.59 r_work: 0.3944 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3874 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3396 Z= 0.218 Angle : 0.521 4.390 4548 Z= 0.267 Chirality : 0.051 0.137 516 Planarity : 0.003 0.026 576 Dihedral : 5.063 17.662 444 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.08 % Allowed : 19.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.31), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.005 0.001 PHE E 378 TYR 0.018 0.002 TYR B 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 353 LYS cc_start: 0.8282 (mttm) cc_final: 0.8055 (mttt) REVERT: A 373 THR cc_start: 0.8039 (m) cc_final: 0.7628 (p) REVERT: E 338 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7515 (tt0) REVERT: E 347 LYS cc_start: 0.8099 (mttt) cc_final: 0.7058 (mtmt) REVERT: B 342 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7732 (mt-10) REVERT: D 349 ARG cc_start: 0.7904 (mtt180) cc_final: 0.6494 (mmp-170) REVERT: F 342 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7892 (mt-10) REVERT: F 349 ARG cc_start: 0.7905 (mtt180) cc_final: 0.6583 (mtm180) outliers start: 8 outliers final: 3 residues processed: 54 average time/residue: 2.8646 time to fit residues: 159.0396 Evaluate side-chains 57 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain B residue 342 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.4260 r_free = 0.4260 target = 0.154765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.136990 restraints weight = 10943.478| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 1.59 r_work: 0.3997 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3926 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.5565 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= 0.145 Angle : 0.482 4.344 4548 Z= 0.245 Chirality : 0.051 0.136 516 Planarity : 0.003 0.025 576 Dihedral : 4.673 16.403 444 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.52 % Allowed : 21.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 374 PHE 0.003 0.000 PHE C 346 TYR 0.014 0.002 TYR B 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 353 LYS cc_start: 0.8249 (mttm) cc_final: 0.8034 (mttt) REVERT: A 373 THR cc_start: 0.8038 (m) cc_final: 0.7638 (p) REVERT: C 311 LYS cc_start: 0.7975 (pttt) cc_final: 0.7675 (ptpt) REVERT: E 347 LYS cc_start: 0.8059 (mttt) cc_final: 0.7049 (mtmt) REVERT: E 372 GLU cc_start: 0.7343 (mp0) cc_final: 0.6927 (mp0) REVERT: B 342 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7745 (mt-10) REVERT: D 342 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7525 (mp0) REVERT: D 349 ARG cc_start: 0.7878 (mtt180) cc_final: 0.6456 (mmp-170) REVERT: F 342 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7836 (mt-10) REVERT: F 349 ARG cc_start: 0.7855 (mtt180) cc_final: 0.6580 (mtm180) outliers start: 2 outliers final: 1 residues processed: 52 average time/residue: 2.5984 time to fit residues: 139.2377 Evaluate side-chains 51 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain B residue 342 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 4.9990 chunk 33 optimal weight: 0.1980 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 37 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.156654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.138790 restraints weight = 11022.135| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 1.61 r_work: 0.4020 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3949 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.5671 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= 0.138 Angle : 0.475 4.331 4548 Z= 0.240 Chirality : 0.051 0.135 516 Planarity : 0.003 0.023 576 Dihedral : 4.445 15.212 444 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.52 % Allowed : 21.61 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 374 PHE 0.004 0.000 PHE C 346 TYR 0.014 0.002 TYR B 310 ARG 0.001 0.000 ARG C 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 353 LYS cc_start: 0.8264 (mttm) cc_final: 0.8048 (mttt) REVERT: A 373 THR cc_start: 0.8047 (m) cc_final: 0.7651 (p) REVERT: C 311 LYS cc_start: 0.7940 (pttt) cc_final: 0.7644 (ptpt) REVERT: E 347 LYS cc_start: 0.8045 (mttt) cc_final: 0.7024 (mtmt) REVERT: E 372 GLU cc_start: 0.7371 (mp0) cc_final: 0.6987 (mp0) REVERT: B 342 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7740 (mt-10) REVERT: D 342 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7724 (tt0) REVERT: D 349 ARG cc_start: 0.7874 (mtt180) cc_final: 0.6382 (mmp-170) REVERT: F 342 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7852 (mt-10) REVERT: F 349 ARG cc_start: 0.7823 (mtt180) cc_final: 0.6583 (mtm180) outliers start: 2 outliers final: 1 residues processed: 52 average time/residue: 2.3647 time to fit residues: 127.0490 Evaluate side-chains 51 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain B residue 342 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.4233 r_free = 0.4233 target = 0.152393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.134556 restraints weight = 11212.154| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 1.60 r_work: 0.3961 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3890 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.5617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3396 Z= 0.195 Angle : 0.503 4.238 4548 Z= 0.258 Chirality : 0.051 0.138 516 Planarity : 0.003 0.024 576 Dihedral : 4.699 16.226 444 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.30 % Allowed : 20.83 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.005 0.001 PHE C 346 TYR 0.017 0.002 TYR B 310 ARG 0.001 0.000 ARG E 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5843.20 seconds wall clock time: 103 minutes 50.34 seconds (6230.34 seconds total)