Starting phenix.real_space_refine on Fri Aug 22 19:04:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q98_18271/08_2025/8q98_18271.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q98_18271/08_2025/8q98_18271.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q98_18271/08_2025/8q98_18271.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q98_18271/08_2025/8q98_18271.map" model { file = "/net/cci-nas-00/data/ceres_data/8q98_18271/08_2025/8q98_18271.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q98_18271/08_2025/8q98_18271.cif" } resolution = 1.75 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= 0.003 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 15 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: 1.67, per 1000 atoms: 0.24 Number of scatterers: 7032 At special positions: 0 Unit cell: (114.139, 115.593, 41.439, 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: 0.61 Conformation dependent library (CDL) restraints added in 297.7 milliseconds Enol-peptide restraints added in 476.8 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 18 sheets defined 0.0% alpha, 53.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.534A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.912A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 325 removed outlier: 6.356A pdb=" N LYS A 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N SER C 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR A 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N CYS C 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LYS A 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N SER C 324 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N GLY A 323 " --> pdb=" O SER C 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.588A pdb=" N HIS A 329 " --> pdb=" O HIS E 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 342 removed outlier: 6.535A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N GLU E 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N SER A 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.494A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 350 through 354 Processing sheet with id=AA8, first strand: chain 'C' and resid 357 through 362 Processing sheet with id=AA9, first strand: chain 'C' and resid 368 through 378 removed outlier: 6.445A pdb=" N LYS A 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N GLU C 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N HIS C 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N THR A 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N LEU C 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LYS A 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N PHE C 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR A 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.522A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.931A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 317 through 325 removed outlier: 6.358A pdb=" N LYS B 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N SER D 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR B 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N CYS D 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LYS B 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N SER D 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLY B 323 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.582A pdb=" N HIS B 329 " --> pdb=" O HIS F 330 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 337 through 342 removed outlier: 6.533A pdb=" N GLU B 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N SER D 341 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LYS B 340 " --> pdb=" O SER D 341 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL B 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LYS F 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL B 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N GLU F 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER B 341 " --> pdb=" O GLU F 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.529A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 350 through 354 removed outlier: 6.304A pdb=" N VAL B 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N LYS F 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N SER B 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 357 through 362 removed outlier: 6.590A pdb=" N LEU B 357 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE F 360 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASN B 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N HIS F 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N THR B 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 368 through 378 removed outlier: 6.506A pdb=" N LYS B 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLU D 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE B 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N HIS D 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N THR B 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N LEU D 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS B 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N PHE D 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR B 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) 84 hydrogen bonds defined for protein. 252 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: 0.89 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: 3582 1.12 - 1.29: 570 1.29 - 1.47: 1228 1.47 - 1.64: 1700 1.64 - 1.82: 6 Bond restraints: 7086 Sorted by residual: bond pdb=" CE1 PHE F 378 " pdb=" HE1 PHE F 378 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N ASN B 327 " pdb=" H ASN B 327 " 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 B 327 " pdb="HD21 ASN B 327 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N VAL E 363 " pdb=" H VAL E 363 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N SER D 320 " pdb=" H SER D 320 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 7081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 11186 2.60 - 5.21: 1370 5.21 - 7.81: 343 7.81 - 10.41: 7 10.41 - 13.02: 6 Bond angle restraints: 12912 Sorted by residual: angle pdb=" CB HIS D 374 " pdb=" CG HIS D 374 " pdb=" CD2 HIS D 374 " ideal model delta sigma weight residual 131.20 124.08 7.12 1.30e+00 5.92e-01 3.00e+01 angle pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " pdb=" CD2 HIS C 374 " ideal model delta sigma weight residual 131.20 124.13 7.07 1.30e+00 5.92e-01 2.96e+01 angle pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " pdb=" CD2 HIS A 374 " ideal model delta sigma weight residual 131.20 124.17 7.03 1.30e+00 5.92e-01 2.92e+01 angle pdb=" CB HIS B 374 " pdb=" CG HIS B 374 " pdb=" CD2 HIS B 374 " ideal model delta sigma weight residual 131.20 124.17 7.03 1.30e+00 5.92e-01 2.92e+01 angle pdb=" CA ASP D 358 " pdb=" CB ASP D 358 " pdb=" CG ASP D 358 " ideal model delta sigma weight residual 112.60 117.68 -5.08 1.00e+00 1.00e+00 2.58e+01 ... (remaining 12907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.22: 2911 15.22 - 30.44: 190 30.44 - 45.66: 46 45.66 - 60.88: 66 60.88 - 76.10: 51 Dihedral angle restraints: 3264 sinusoidal: 1866 harmonic: 1398 Sorted by residual: dihedral pdb=" CA ASP B 358 " pdb=" C ASP B 358 " pdb=" N ASN B 359 " pdb=" CA ASN B 359 " ideal model delta harmonic sigma weight residual 180.00 158.87 21.13 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA ASP C 358 " pdb=" C ASP C 358 " pdb=" N ASN C 359 " pdb=" CA ASN C 359 " ideal model delta harmonic sigma weight residual 180.00 159.93 20.07 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA ASP D 358 " pdb=" C ASP D 358 " pdb=" N ASN D 359 " pdb=" CA ASN D 359 " ideal model delta harmonic sigma weight residual 180.00 161.09 18.91 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 3261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 193 0.042 - 0.084: 210 0.084 - 0.126: 87 0.126 - 0.168: 24 0.168 - 0.210: 14 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA LYS F 331 " pdb=" N LYS F 331 " pdb=" C LYS F 331 " pdb=" CB LYS F 331 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ARG B 379 " pdb=" N ARG B 379 " pdb=" C ARG B 379 " pdb=" CB ARG B 379 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+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 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 525 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 374 " 0.105 2.00e-02 2.50e+03 5.96e-02 7.99e+01 pdb=" CG HIS C 374 " -0.049 2.00e-02 2.50e+03 pdb=" ND1 HIS C 374 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 HIS C 374 " -0.072 2.00e-02 2.50e+03 pdb=" CE1 HIS C 374 " -0.023 2.00e-02 2.50e+03 pdb=" NE2 HIS C 374 " -0.030 2.00e-02 2.50e+03 pdb=" HD2 HIS C 374 " -0.022 2.00e-02 2.50e+03 pdb=" HE1 HIS C 374 " 0.027 2.00e-02 2.50e+03 pdb=" HE2 HIS C 374 " 0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 374 " -0.102 2.00e-02 2.50e+03 5.80e-02 7.56e+01 pdb=" CG HIS D 374 " 0.045 2.00e-02 2.50e+03 pdb=" ND1 HIS D 374 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 HIS D 374 " 0.070 2.00e-02 2.50e+03 pdb=" CE1 HIS D 374 " 0.024 2.00e-02 2.50e+03 pdb=" NE2 HIS D 374 " 0.028 2.00e-02 2.50e+03 pdb=" HD2 HIS D 374 " 0.023 2.00e-02 2.50e+03 pdb=" HE1 HIS D 374 " -0.024 2.00e-02 2.50e+03 pdb=" HE2 HIS D 374 " -0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 374 " 0.096 2.00e-02 2.50e+03 5.42e-02 6.60e+01 pdb=" CG HIS A 374 " -0.046 2.00e-02 2.50e+03 pdb=" ND1 HIS A 374 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 HIS A 374 " -0.065 2.00e-02 2.50e+03 pdb=" CE1 HIS A 374 " -0.022 2.00e-02 2.50e+03 pdb=" NE2 HIS A 374 " -0.022 2.00e-02 2.50e+03 pdb=" HD2 HIS A 374 " -0.022 2.00e-02 2.50e+03 pdb=" HE1 HIS A 374 " 0.021 2.00e-02 2.50e+03 pdb=" HE2 HIS A 374 " 0.089 2.00e-02 2.50e+03 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 656 2.19 - 2.79: 12468 2.79 - 3.39: 18092 3.39 - 4.00: 25495 4.00 - 4.60: 34046 Nonbonded interactions: 90757 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.583 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.585 2.450 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.603 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.605 2.450 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.611 2.450 ... (remaining 90752 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: 5.530 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: 0.060 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.990 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6371 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= 0.666 Angle : 1.661 7.119 4680 Z= 1.100 Chirality : 0.074 0.210 528 Planarity : 0.010 0.054 594 Dihedral : 9.830 68.403 1344 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: -0.80 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.60 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 349 TYR 0.058 0.017 TYR E 310 PHE 0.057 0.017 PHE C 346 HIS 0.015 0.004 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.01078 ( 3498) covalent geometry : angle 1.66145 ( 4680) hydrogen bonds : bond 0.04900 ( 84) hydrogen bonds : angle 8.03849 ( 252) *********************** 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 154 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.205 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: symmetry clash REVERT: A 317 LYS cc_start: 0.5894 (mttt) cc_final: 0.5567 (mttm) REVERT: A 331 LYS cc_start: 0.6621 (mttt) cc_final: 0.6088 (mtpp) REVERT: A 338 GLU cc_start: 0.6437 (tt0) cc_final: 0.5936 (mt-10) REVERT: A 340 LYS cc_start: 0.6208 (tttt) cc_final: 0.5539 (mttt) REVERT: A 342 GLU cc_start: 0.6324 (tt0) cc_final: 0.5840 (tt0) REVERT: A 343 LYS cc_start: 0.7321 (mttp) cc_final: 0.7037 (mtmm) REVERT: A 351 GLN cc_start: 0.6069 (tt0) cc_final: 0.5793 (mt0) REVERT: A 353 LYS cc_start: 0.5879 (mttt) cc_final: 0.5561 (tttp) REVERT: A 369 LYS cc_start: 0.6261 (tttt) cc_final: 0.5896 (tttp) REVERT: A 372 GLU cc_start: 0.6605 (tt0) cc_final: 0.5820 (mt-10) REVERT: A 373 THR cc_start: 0.6658 (m) cc_final: 0.6100 (p) REVERT: A 375 LYS cc_start: 0.6443 (tttt) cc_final: 0.5853 (ttpt) REVERT: B 307 GLN cc_start: 0.6760 (tt0) cc_final: 0.6551 (tt0) REVERT: B 317 LYS cc_start: 0.6087 (mttt) cc_final: 0.5834 (mttm) REVERT: B 331 LYS cc_start: 0.6754 (mttt) cc_final: 0.6327 (mtpt) REVERT: B 338 GLU cc_start: 0.6216 (tt0) cc_final: 0.5884 (mt-10) REVERT: B 340 LYS cc_start: 0.6241 (tttt) cc_final: 0.5565 (mttt) REVERT: B 351 GLN cc_start: 0.6158 (tt0) cc_final: 0.5856 (mt0) REVERT: B 353 LYS cc_start: 0.5732 (mttt) cc_final: 0.5459 (tttp) REVERT: B 369 LYS cc_start: 0.6166 (tttt) cc_final: 0.5930 (tttp) REVERT: B 373 THR cc_start: 0.6845 (m) cc_final: 0.6253 (p) REVERT: C 307 GLN cc_start: 0.7271 (tt0) cc_final: 0.7045 (tt0) REVERT: C 331 LYS cc_start: 0.6600 (mttt) cc_final: 0.6130 (mtpt) REVERT: C 338 GLU cc_start: 0.6526 (tt0) cc_final: 0.6183 (mt-10) REVERT: C 340 LYS cc_start: 0.6892 (tttt) cc_final: 0.6182 (mttt) REVERT: C 342 GLU cc_start: 0.6581 (tt0) cc_final: 0.6289 (tt0) REVERT: C 345 ASP cc_start: 0.7047 (t0) cc_final: 0.6674 (m-30) REVERT: C 347 LYS cc_start: 0.6654 (mttt) cc_final: 0.5618 (mppt) REVERT: C 369 LYS cc_start: 0.6794 (tttt) cc_final: 0.6501 (tttp) REVERT: C 372 GLU cc_start: 0.6573 (tt0) cc_final: 0.6355 (tt0) REVERT: C 373 THR cc_start: 0.7236 (m) cc_final: 0.6906 (p) REVERT: C 375 LYS cc_start: 0.7106 (tttt) cc_final: 0.6639 (tttp) REVERT: D 317 LYS cc_start: 0.6511 (mttt) cc_final: 0.6241 (mttm) REVERT: D 331 LYS cc_start: 0.6724 (mttt) cc_final: 0.6260 (mtpt) REVERT: D 342 GLU cc_start: 0.6670 (tt0) cc_final: 0.6457 (tt0) REVERT: D 343 LYS cc_start: 0.7413 (mttp) cc_final: 0.7180 (mttm) REVERT: D 345 ASP cc_start: 0.7229 (t0) cc_final: 0.6891 (m-30) REVERT: D 349 ARG cc_start: 0.5501 (mtm180) cc_final: 0.5257 (mtm180) REVERT: D 351 GLN cc_start: 0.6629 (tt0) cc_final: 0.6424 (mt0) REVERT: D 358 ASP cc_start: 0.6645 (m-30) cc_final: 0.6444 (m-30) REVERT: D 369 LYS cc_start: 0.6711 (tttt) cc_final: 0.6355 (tttp) REVERT: D 372 GLU cc_start: 0.6544 (tt0) cc_final: 0.5937 (mt-10) REVERT: D 373 THR cc_start: 0.7197 (m) cc_final: 0.6824 (p) REVERT: D 375 LYS cc_start: 0.6939 (tttt) cc_final: 0.6374 (ttpt) REVERT: D 379 ARG cc_start: 0.6002 (mtp180) cc_final: 0.5737 (mtp85) REVERT: E 331 LYS cc_start: 0.6802 (mttt) cc_final: 0.6309 (mtpp) REVERT: E 336 GLN cc_start: 0.6979 (tt0) cc_final: 0.6733 (tt0) REVERT: E 338 GLU cc_start: 0.6241 (tt0) cc_final: 0.5812 (mt-10) REVERT: E 340 LYS cc_start: 0.6362 (tttt) cc_final: 0.5646 (mttt) REVERT: E 351 GLN cc_start: 0.6137 (tt0) cc_final: 0.5813 (mt0) REVERT: E 369 LYS cc_start: 0.6271 (tttt) cc_final: 0.6007 (tttp) REVERT: E 373 THR cc_start: 0.6988 (m) cc_final: 0.6325 (p) REVERT: E 375 LYS cc_start: 0.6594 (tttt) cc_final: 0.6175 (ttpt) REVERT: F 331 LYS cc_start: 0.6641 (mttt) cc_final: 0.6433 (mtpp) REVERT: F 338 GLU cc_start: 0.6355 (tt0) cc_final: 0.5918 (mt-10) REVERT: F 340 LYS cc_start: 0.6214 (tttt) cc_final: 0.5586 (mttt) REVERT: F 345 ASP cc_start: 0.6878 (t0) cc_final: 0.6484 (t0) REVERT: F 351 GLN cc_start: 0.6260 (tt0) cc_final: 0.5980 (mt0) REVERT: F 372 GLU cc_start: 0.6660 (tt0) cc_final: 0.6225 (tt0) REVERT: F 373 THR cc_start: 0.6841 (m) cc_final: 0.6216 (p) REVERT: F 375 LYS cc_start: 0.6582 (tttt) cc_final: 0.6211 (tttp) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 1.5800 time to fit residues: 247.8990 Evaluate side-chains 126 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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: 5.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN D 362 HIS E 330 HIS F 330 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.155202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.141191 restraints weight = 7777.493| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 0.74 r_work: 0.3917 rms_B_bonded: 0.69 restraints_weight: 0.5000 r_work: 0.3856 rms_B_bonded: 1.20 restraints_weight: 0.2500 r_work: 0.3692 rms_B_bonded: 3.44 restraints_weight: 0.1250 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3498 Z= 0.206 Angle : 0.609 4.236 4680 Z= 0.313 Chirality : 0.052 0.141 528 Planarity : 0.005 0.032 594 Dihedral : 5.563 14.201 462 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.76 % Allowed : 4.29 % Favored : 94.95 % 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: -0.42 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.31 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 349 TYR 0.007 0.002 TYR E 310 PHE 0.007 0.002 PHE E 346 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 3498) covalent geometry : angle 0.60904 ( 4680) hydrogen bonds : bond 0.02958 ( 84) hydrogen bonds : angle 5.99038 ( 252) *********************** 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 127 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 124 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 347 LYS cc_start: 0.7923 (mttt) cc_final: 0.7532 (mppt) REVERT: E 379 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.7170 (mtt-85) outliers start: 3 outliers final: 1 residues processed: 124 average time/residue: 2.0860 time to fit residues: 262.8057 Evaluate side-chains 97 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN C 336 GLN F 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.151814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.138807 restraints weight = 8021.581| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 0.73 r_work: 0.3902 rms_B_bonded: 0.66 restraints_weight: 0.5000 r_work: 0.3841 rms_B_bonded: 1.17 restraints_weight: 0.2500 r_work: 0.3682 rms_B_bonded: 3.33 restraints_weight: 0.1250 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.4934 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= 0.133 Angle : 0.530 4.067 4680 Z= 0.271 Chirality : 0.053 0.139 528 Planarity : 0.003 0.023 594 Dihedral : 5.169 13.779 462 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.01 % Allowed : 9.34 % Favored : 89.65 % 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: -0.43 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.32 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 379 TYR 0.007 0.001 TYR B 310 PHE 0.006 0.001 PHE E 346 HIS 0.002 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 3498) covalent geometry : angle 0.52986 ( 4680) hydrogen bonds : bond 0.02350 ( 84) hydrogen bonds : angle 5.60925 ( 252) *********************** 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 99 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 347 LYS cc_start: 0.7927 (mttt) cc_final: 0.7655 (mppt) REVERT: E 379 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.7188 (mtt-85) outliers start: 4 outliers final: 1 residues processed: 95 average time/residue: 1.8737 time to fit residues: 181.2195 Evaluate side-chains 85 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 379 ARG 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: 5.9990 chunk 27 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 32 optimal weight: 0.4980 chunk 38 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 336 GLN E 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.150868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.137920 restraints weight = 8094.068| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 0.73 r_work: 0.3891 rms_B_bonded: 0.66 restraints_weight: 0.5000 r_work: 0.3832 rms_B_bonded: 1.16 restraints_weight: 0.2500 r_work: 0.3672 rms_B_bonded: 3.33 restraints_weight: 0.1250 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3498 Z= 0.143 Angle : 0.512 3.958 4680 Z= 0.262 Chirality : 0.053 0.134 528 Planarity : 0.003 0.023 594 Dihedral : 5.023 13.505 462 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.76 % Allowed : 10.86 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.36 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 379 TYR 0.007 0.001 TYR B 310 PHE 0.007 0.002 PHE E 346 HIS 0.003 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 3498) covalent geometry : angle 0.51177 ( 4680) hydrogen bonds : bond 0.02297 ( 84) hydrogen bonds : angle 5.49306 ( 252) *********************** 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 87 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 345 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.8179 (t70) REVERT: C 347 LYS cc_start: 0.7935 (mttt) cc_final: 0.7672 (mppt) REVERT: D 345 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8184 (t70) outliers start: 3 outliers final: 1 residues processed: 84 average time/residue: 1.6874 time to fit residues: 144.4039 Evaluate side-chains 85 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 82 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain E 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: 6.9990 chunk 9 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 32 optimal weight: 0.1980 chunk 6 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.4133 r_free = 0.4133 target = 0.152780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.139894 restraints weight = 8018.925| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 0.73 r_work: 0.3915 rms_B_bonded: 0.66 restraints_weight: 0.5000 r_work: 0.3856 rms_B_bonded: 1.16 restraints_weight: 0.2500 r_work: 0.3697 rms_B_bonded: 3.34 restraints_weight: 0.1250 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.5272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3498 Z= 0.106 Angle : 0.478 3.972 4680 Z= 0.244 Chirality : 0.053 0.136 528 Planarity : 0.002 0.019 594 Dihedral : 4.813 13.714 462 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.01 % Allowed : 10.61 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.32 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.006 0.001 TYR B 310 PHE 0.005 0.001 PHE E 346 HIS 0.002 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 3498) covalent geometry : angle 0.47813 ( 4680) hydrogen bonds : bond 0.01953 ( 84) hydrogen bonds : angle 5.28040 ( 252) *********************** 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 90 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 345 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.8159 (t70) REVERT: C 347 LYS cc_start: 0.7927 (mttt) cc_final: 0.7658 (mppt) REVERT: E 379 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.7182 (mtt-85) outliers start: 4 outliers final: 0 residues processed: 86 average time/residue: 1.6976 time to fit residues: 148.7482 Evaluate side-chains 86 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 84 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 6.9990 chunk 23 optimal weight: 0.0770 chunk 39 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 18 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.9144 ------------------------------------------------------------------------------- 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 = 0.4150 r_free = 0.4150 target = 0.154040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.141235 restraints weight = 8098.558| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 0.72 r_work: 0.3935 rms_B_bonded: 0.66 restraints_weight: 0.5000 r_work: 0.3876 rms_B_bonded: 1.17 restraints_weight: 0.2500 r_work: 0.3719 rms_B_bonded: 3.36 restraints_weight: 0.1250 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3498 Z= 0.090 Angle : 0.463 3.922 4680 Z= 0.234 Chirality : 0.052 0.135 528 Planarity : 0.002 0.014 594 Dihedral : 4.634 13.508 462 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 0.76 % Allowed : 10.86 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.39), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.26 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.006 0.001 TYR B 310 PHE 0.004 0.001 PHE B 378 HIS 0.002 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00185 ( 3498) covalent geometry : angle 0.46338 ( 4680) hydrogen bonds : bond 0.01770 ( 84) hydrogen bonds : angle 5.08487 ( 252) *********************** 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 91 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 345 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.8100 (t70) REVERT: C 347 LYS cc_start: 0.7901 (mttt) cc_final: 0.7634 (mppt) REVERT: D 345 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8173 (t70) outliers start: 3 outliers final: 0 residues processed: 88 average time/residue: 1.5447 time to fit residues: 138.7225 Evaluate side-chains 85 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain D residue 345 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.153297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.140556 restraints weight = 8004.836| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 0.71 r_work: 0.3923 rms_B_bonded: 0.64 restraints_weight: 0.5000 r_work: 0.3865 rms_B_bonded: 1.13 restraints_weight: 0.2500 r_work: 0.3706 rms_B_bonded: 3.28 restraints_weight: 0.1250 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.5343 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= 0.110 Angle : 0.478 3.966 4680 Z= 0.243 Chirality : 0.052 0.133 528 Planarity : 0.002 0.017 594 Dihedral : 4.679 13.268 462 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.26 % Allowed : 9.85 % Favored : 88.89 % 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: -0.40 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.29 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 379 TYR 0.006 0.001 TYR B 310 PHE 0.005 0.001 PHE E 346 HIS 0.002 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 3498) covalent geometry : angle 0.47788 ( 4680) hydrogen bonds : bond 0.01945 ( 84) hydrogen bonds : angle 5.07211 ( 252) *********************** 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 90 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 345 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.8086 (t70) REVERT: C 347 LYS cc_start: 0.7906 (mttt) cc_final: 0.7651 (mppt) REVERT: D 345 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8133 (t70) REVERT: E 379 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.7188 (mtt-85) outliers start: 5 outliers final: 1 residues processed: 85 average time/residue: 1.7725 time to fit residues: 153.4827 Evaluate side-chains 86 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain E residue 379 ARG Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.151797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.139019 restraints weight = 8012.978| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 0.70 r_work: 0.3901 rms_B_bonded: 0.64 restraints_weight: 0.5000 r_work: 0.3843 rms_B_bonded: 1.12 restraints_weight: 0.2500 r_work: 0.3683 rms_B_bonded: 3.28 restraints_weight: 0.1250 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.5326 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= 0.137 Angle : 0.511 6.265 4680 Z= 0.261 Chirality : 0.052 0.135 528 Planarity : 0.003 0.021 594 Dihedral : 4.794 14.044 462 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.52 % Allowed : 9.85 % Favored : 88.64 % 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: -0.43 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.32 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 379 TYR 0.007 0.001 TYR B 310 PHE 0.006 0.001 PHE E 346 HIS 0.002 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 3498) covalent geometry : angle 0.51120 ( 4680) hydrogen bonds : bond 0.02148 ( 84) hydrogen bonds : angle 5.21140 ( 252) *********************** 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 87 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 345 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.8085 (t70) REVERT: C 347 LYS cc_start: 0.7939 (mttt) cc_final: 0.7684 (mppt) REVERT: D 345 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8166 (t70) REVERT: E 345 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7929 (t70) REVERT: E 379 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.7229 (mtt-85) outliers start: 6 outliers final: 1 residues processed: 81 average time/residue: 1.6691 time to fit residues: 137.7733 Evaluate side-chains 86 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 379 ARG Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.150005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.136872 restraints weight = 7965.283| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 0.73 r_work: 0.3868 rms_B_bonded: 0.67 restraints_weight: 0.5000 r_work: 0.3807 rms_B_bonded: 1.17 restraints_weight: 0.2500 r_work: 0.3648 rms_B_bonded: 3.37 restraints_weight: 0.1250 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.5354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3498 Z= 0.200 Angle : 0.563 6.439 4680 Z= 0.292 Chirality : 0.052 0.135 528 Planarity : 0.004 0.025 594 Dihedral : 5.015 13.477 462 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.01 % Allowed : 10.35 % Favored : 88.64 % 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: -0.56 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.41 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 379 TYR 0.009 0.002 TYR B 310 PHE 0.008 0.002 PHE E 346 HIS 0.004 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 3498) covalent geometry : angle 0.56263 ( 4680) hydrogen bonds : bond 0.02599 ( 84) hydrogen bonds : angle 5.51015 ( 252) *********************** 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 85 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 345 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.8096 (t70) REVERT: C 347 LYS cc_start: 0.7935 (mttt) cc_final: 0.7690 (mppt) REVERT: D 345 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.8214 (t70) REVERT: E 345 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7893 (t70) REVERT: E 379 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.7222 (mtt-85) outliers start: 4 outliers final: 0 residues processed: 81 average time/residue: 1.7138 time to fit residues: 141.5221 Evaluate side-chains 85 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 = 0.4104 r_free = 0.4104 target = 0.150739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.137895 restraints weight = 8040.591| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 0.72 r_work: 0.3887 rms_B_bonded: 0.66 restraints_weight: 0.5000 r_work: 0.3828 rms_B_bonded: 1.16 restraints_weight: 0.2500 r_work: 0.3667 rms_B_bonded: 3.34 restraints_weight: 0.1250 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.5365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3498 Z= 0.156 Angle : 0.523 4.791 4680 Z= 0.270 Chirality : 0.052 0.140 528 Planarity : 0.003 0.025 594 Dihedral : 4.923 13.447 462 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.01 % Allowed : 10.35 % Favored : 88.64 % 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: -0.53 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.39 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 379 TYR 0.007 0.002 TYR B 310 PHE 0.007 0.002 PHE F 346 HIS 0.002 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 3498) covalent geometry : angle 0.52349 ( 4680) hydrogen bonds : bond 0.02273 ( 84) hydrogen bonds : angle 5.38302 ( 252) ********************** 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 87 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 345 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.8069 (t70) REVERT: C 347 LYS cc_start: 0.7955 (mttt) cc_final: 0.7707 (mppt) REVERT: E 345 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7912 (t70) REVERT: E 379 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.7203 (mtt-85) outliers start: 4 outliers final: 0 residues processed: 83 average time/residue: 1.6933 time to fit residues: 143.2838 Evaluate side-chains 87 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain E residue 345 ASP Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 28 optimal weight: 0.0970 chunk 35 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 overall best weight: 1.5782 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.152288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.139616 restraints weight = 7933.966| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 0.70 r_work: 0.3910 rms_B_bonded: 0.63 restraints_weight: 0.5000 r_work: 0.3852 rms_B_bonded: 1.11 restraints_weight: 0.2500 r_work: 0.3692 rms_B_bonded: 3.25 restraints_weight: 0.1250 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.5382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3498 Z= 0.121 Angle : 0.514 6.982 4680 Z= 0.260 Chirality : 0.052 0.132 528 Planarity : 0.003 0.020 594 Dihedral : 4.803 13.393 462 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 0.51 % Allowed : 10.86 % Favored : 88.64 % 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: -0.48 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.35 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.007 0.001 TYR B 310 PHE 0.006 0.001 PHE F 346 HIS 0.002 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 3498) covalent geometry : angle 0.51444 ( 4680) hydrogen bonds : bond 0.02017 ( 84) hydrogen bonds : angle 5.16887 ( 252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5466.42 seconds wall clock time: 93 minutes 2.04 seconds (5582.04 seconds total)