Starting phenix.real_space_refine on Sat Aug 3 05:31:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q98_18271/08_2024/8q98_18271.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q98_18271/08_2024/8q98_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q98_18271/08_2024/8q98_18271.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q98_18271/08_2024/8q98_18271.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q98_18271/08_2024/8q98_18271.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q98_18271/08_2024/8q98_18271.cif" } resolution = 1.75 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= 0.003 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 Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 358": "OD1" <-> "OD2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 358": "OD1" <-> "OD2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 358": "OD1" <-> "OD2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 358": "OD1" <-> "OD2" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 358": "OD1" <-> "OD2" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 358": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/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: 5.33, per 1000 atoms: 0.76 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 - 3.50 Amino acid : False - 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: 5.63 Conformation dependent library (CDL) restraints added in 939.1 milliseconds 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: 0.69 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: 2.37 Time building geometry restraints manager: 5.89 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: 95.98 - 102.72: 17 102.72 - 109.46: 5118 109.46 - 116.20: 4141 116.20 - 122.94: 3013 122.94 - 129.67: 623 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: 16.480 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 28.810 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:13.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.850 ------------------------------------------------------------------------------- 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= 0.748 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 (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: -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 HIS 0.015 0.004 HIS E 362 PHE 0.057 0.017 PHE C 346 TYR 0.058 0.017 TYR E 310 ARG 0.005 0.001 ARG F 349 *********************** 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 fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.638 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: 0.6550 (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: 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: 3.3043 time to fit residues: 519.0625 Evaluate side-chains 126 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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: 0.9990 chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS B 336 GLN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 HIS F 330 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 3498 Z= 0.324 Angle : 0.629 4.350 4680 Z= 0.325 Chirality : 0.052 0.141 528 Planarity : 0.005 0.034 594 Dihedral : 5.553 14.047 462 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.76 % Allowed : 4.55 % Favored : 94.70 % 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: -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 HIS 0.004 0.001 HIS A 330 PHE 0.007 0.002 PHE E 346 TYR 0.008 0.002 TYR E 310 ARG 0.003 0.001 ARG C 349 *********************** 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 128 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.5905 (mttt) cc_final: 0.5565 (mttm) REVERT: A 331 LYS cc_start: 0.6430 (mttt) cc_final: 0.5952 (mtpp) REVERT: A 338 GLU cc_start: 0.6402 (tt0) cc_final: 0.5835 (mt-10) REVERT: A 340 LYS cc_start: 0.6200 (tttt) cc_final: 0.5507 (mttm) REVERT: A 351 GLN cc_start: 0.6130 (tt0) cc_final: 0.5815 (mt0) REVERT: A 353 LYS cc_start: 0.5853 (mttt) cc_final: 0.5579 (tttm) REVERT: A 369 LYS cc_start: 0.6268 (tttt) cc_final: 0.5866 (tttp) REVERT: A 372 GLU cc_start: 0.6378 (tt0) cc_final: 0.5873 (mt-10) REVERT: A 373 THR cc_start: 0.6701 (m) cc_final: 0.6217 (p) REVERT: A 375 LYS cc_start: 0.6514 (tttt) cc_final: 0.5948 (ttpt) REVERT: B 307 GLN cc_start: 0.6861 (tt0) cc_final: 0.6561 (tt0) REVERT: B 317 LYS cc_start: 0.6116 (mttt) cc_final: 0.5858 (mttm) REVERT: B 331 LYS cc_start: 0.6678 (mttt) cc_final: 0.6237 (mtpt) REVERT: B 343 LYS cc_start: 0.7092 (mtmt) cc_final: 0.6846 (mttp) REVERT: B 351 GLN cc_start: 0.6168 (tt0) cc_final: 0.5907 (mt0) REVERT: B 353 LYS cc_start: 0.5682 (mttt) cc_final: 0.5464 (tttp) REVERT: B 369 LYS cc_start: 0.6249 (tttt) cc_final: 0.5972 (tttp) REVERT: B 373 THR cc_start: 0.6822 (m) cc_final: 0.6340 (p) REVERT: C 307 GLN cc_start: 0.7404 (tt0) cc_final: 0.7063 (tt0) REVERT: C 331 LYS cc_start: 0.6578 (mttt) cc_final: 0.6074 (mtpt) REVERT: C 338 GLU cc_start: 0.6554 (tt0) cc_final: 0.6181 (mt-10) REVERT: C 340 LYS cc_start: 0.6917 (tttt) cc_final: 0.6166 (mttt) REVERT: C 342 GLU cc_start: 0.6447 (tt0) cc_final: 0.6190 (tt0) REVERT: C 347 LYS cc_start: 0.6684 (mttt) cc_final: 0.5658 (mppt) REVERT: C 349 ARG cc_start: 0.6449 (mtp180) cc_final: 0.6024 (mtt180) REVERT: C 351 GLN cc_start: 0.6776 (tt0) cc_final: 0.6509 (mt0) REVERT: C 369 LYS cc_start: 0.6764 (tttt) cc_final: 0.6466 (tttp) REVERT: C 373 THR cc_start: 0.7277 (m) cc_final: 0.6930 (p) REVERT: C 375 LYS cc_start: 0.7083 (tttt) cc_final: 0.6611 (tttp) REVERT: D 317 LYS cc_start: 0.6416 (mttt) cc_final: 0.6102 (mttm) REVERT: D 331 LYS cc_start: 0.6698 (mttt) cc_final: 0.6263 (mtpt) REVERT: D 342 GLU cc_start: 0.6671 (tt0) cc_final: 0.6468 (tt0) REVERT: D 343 LYS cc_start: 0.7366 (mttp) cc_final: 0.7159 (mtmm) REVERT: D 345 ASP cc_start: 0.7229 (t0) cc_final: 0.6895 (t0) REVERT: D 349 ARG cc_start: 0.5502 (mtm180) cc_final: 0.5164 (mtt180) REVERT: D 369 LYS cc_start: 0.6715 (tttt) cc_final: 0.6355 (tttt) REVERT: D 372 GLU cc_start: 0.6488 (tt0) cc_final: 0.6031 (mt-10) REVERT: D 373 THR cc_start: 0.7222 (m) cc_final: 0.6854 (p) REVERT: D 375 LYS cc_start: 0.6953 (tttt) cc_final: 0.6375 (ttpt) REVERT: E 331 LYS cc_start: 0.6753 (mttt) cc_final: 0.6301 (mtpt) REVERT: E 338 GLU cc_start: 0.6323 (tt0) cc_final: 0.5862 (mt-10) REVERT: E 340 LYS cc_start: 0.6522 (tttt) cc_final: 0.5817 (mttt) REVERT: E 351 GLN cc_start: 0.6280 (tt0) cc_final: 0.5995 (mt0) REVERT: E 369 LYS cc_start: 0.6349 (tttt) cc_final: 0.6032 (tttp) REVERT: E 373 THR cc_start: 0.6947 (m) cc_final: 0.6335 (p) REVERT: E 375 LYS cc_start: 0.6544 (tttt) cc_final: 0.6092 (ttpt) REVERT: F 331 LYS cc_start: 0.6564 (mttt) cc_final: 0.6323 (mtpp) REVERT: F 338 GLU cc_start: 0.6427 (tt0) cc_final: 0.5932 (mt-10) REVERT: F 340 LYS cc_start: 0.6408 (tttt) cc_final: 0.5701 (mttt) REVERT: F 345 ASP cc_start: 0.6767 (t0) cc_final: 0.6284 (m-30) REVERT: F 351 GLN cc_start: 0.6314 (tt0) cc_final: 0.6039 (mt0) REVERT: F 372 GLU cc_start: 0.6686 (tt0) cc_final: 0.6418 (tt0) REVERT: F 373 THR cc_start: 0.6789 (m) cc_final: 0.6217 (p) REVERT: F 375 LYS cc_start: 0.6575 (tttt) cc_final: 0.6213 (tttp) outliers start: 3 outliers final: 1 residues processed: 125 average time/residue: 3.9565 time to fit residues: 503.1029 Evaluate side-chains 124 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 305 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.3350 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= 0.304 Angle : 0.609 4.717 4680 Z= 0.320 Chirality : 0.053 0.133 528 Planarity : 0.004 0.032 594 Dihedral : 5.319 12.217 462 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 0.51 % Allowed : 6.06 % Favored : 93.43 % 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: -0.60 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.45 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 330 PHE 0.010 0.002 PHE E 346 TYR 0.011 0.002 TYR B 310 ARG 0.003 0.001 ARG E 379 *********************** 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 125 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 123 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.5858 (mttt) cc_final: 0.5570 (mttm) REVERT: A 331 LYS cc_start: 0.6385 (mttt) cc_final: 0.5901 (mtpp) REVERT: A 338 GLU cc_start: 0.6389 (tt0) cc_final: 0.5790 (mt-10) REVERT: A 340 LYS cc_start: 0.6233 (tttt) cc_final: 0.5553 (mttt) REVERT: A 345 ASP cc_start: 0.7265 (OUTLIER) cc_final: 0.6246 (t70) REVERT: A 347 LYS cc_start: 0.7059 (mttt) cc_final: 0.6702 (mptm) REVERT: A 351 GLN cc_start: 0.6152 (tt0) cc_final: 0.5797 (mt0) REVERT: A 353 LYS cc_start: 0.5853 (mttt) cc_final: 0.5569 (tttm) REVERT: A 369 LYS cc_start: 0.6279 (tttt) cc_final: 0.5874 (tttp) REVERT: A 372 GLU cc_start: 0.6359 (tt0) cc_final: 0.5960 (mt-10) REVERT: A 373 THR cc_start: 0.6711 (m) cc_final: 0.6253 (p) REVERT: A 375 LYS cc_start: 0.6511 (tttt) cc_final: 0.5941 (ttpt) REVERT: B 307 GLN cc_start: 0.6851 (tt0) cc_final: 0.6599 (tt0) REVERT: B 317 LYS cc_start: 0.6070 (mttt) cc_final: 0.5813 (mttm) REVERT: B 331 LYS cc_start: 0.6651 (mttt) cc_final: 0.6214 (mtpt) REVERT: B 343 LYS cc_start: 0.6948 (mtmt) cc_final: 0.6736 (mttp) REVERT: B 351 GLN cc_start: 0.6136 (tt0) cc_final: 0.5928 (mt0) REVERT: B 369 LYS cc_start: 0.6259 (tttt) cc_final: 0.6020 (tttp) REVERT: B 373 THR cc_start: 0.6789 (m) cc_final: 0.6334 (p) REVERT: C 307 GLN cc_start: 0.7371 (tt0) cc_final: 0.7052 (tt0) REVERT: C 331 LYS cc_start: 0.6535 (mttt) cc_final: 0.6093 (mtpt) REVERT: C 338 GLU cc_start: 0.6518 (tt0) cc_final: 0.6163 (mt-10) REVERT: C 340 LYS cc_start: 0.6900 (tttt) cc_final: 0.6210 (mttt) REVERT: C 347 LYS cc_start: 0.6634 (mttt) cc_final: 0.5642 (mppt) REVERT: C 349 ARG cc_start: 0.6248 (mtp180) cc_final: 0.6034 (mtt180) REVERT: C 351 GLN cc_start: 0.6746 (tt0) cc_final: 0.6518 (mt0) REVERT: C 369 LYS cc_start: 0.6716 (tttt) cc_final: 0.6392 (tttp) REVERT: C 373 THR cc_start: 0.7277 (m) cc_final: 0.6944 (p) REVERT: C 375 LYS cc_start: 0.7058 (tttt) cc_final: 0.6586 (tttp) REVERT: D 314 ASP cc_start: 0.6909 (t0) cc_final: 0.6681 (t0) REVERT: D 317 LYS cc_start: 0.6416 (mttt) cc_final: 0.6156 (mttm) REVERT: D 331 LYS cc_start: 0.6684 (mttt) cc_final: 0.6229 (mtpt) REVERT: D 338 GLU cc_start: 0.6730 (tt0) cc_final: 0.6344 (mt-10) REVERT: D 340 LYS cc_start: 0.6910 (tttt) cc_final: 0.6252 (mttt) REVERT: D 349 ARG cc_start: 0.5384 (mtm180) cc_final: 0.5174 (mtt180) REVERT: D 369 LYS cc_start: 0.6714 (tttt) cc_final: 0.6344 (tttp) REVERT: D 372 GLU cc_start: 0.6497 (tt0) cc_final: 0.6069 (mt-10) REVERT: D 373 THR cc_start: 0.7177 (m) cc_final: 0.6819 (p) REVERT: D 375 LYS cc_start: 0.6944 (tttt) cc_final: 0.6359 (ttpt) REVERT: E 331 LYS cc_start: 0.6783 (mttt) cc_final: 0.6338 (mtpt) REVERT: E 351 GLN cc_start: 0.6231 (tt0) cc_final: 0.6014 (mt0) REVERT: E 369 LYS cc_start: 0.6360 (tttt) cc_final: 0.6124 (tttp) REVERT: E 373 THR cc_start: 0.6945 (m) cc_final: 0.6357 (p) REVERT: E 375 LYS cc_start: 0.6584 (tttt) cc_final: 0.6153 (ttpt) REVERT: F 331 LYS cc_start: 0.6598 (mttt) cc_final: 0.6322 (mtpp) REVERT: F 338 GLU cc_start: 0.6435 (tt0) cc_final: 0.5976 (mt-10) REVERT: F 340 LYS cc_start: 0.6444 (tttt) cc_final: 0.5695 (mttt) REVERT: F 345 ASP cc_start: 0.6784 (t0) cc_final: 0.6253 (m-30) REVERT: F 351 GLN cc_start: 0.6358 (tt0) cc_final: 0.6134 (mt0) REVERT: F 372 GLU cc_start: 0.6658 (tt0) cc_final: 0.6421 (tt0) REVERT: F 373 THR cc_start: 0.6779 (m) cc_final: 0.6228 (p) REVERT: F 375 LYS cc_start: 0.6586 (tttt) cc_final: 0.6225 (tttp) outliers start: 2 outliers final: 1 residues processed: 123 average time/residue: 3.9206 time to fit residues: 490.8326 Evaluate side-chains 119 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 117 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain E residue 305 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3498 Z= 0.332 Angle : 0.606 4.569 4680 Z= 0.317 Chirality : 0.052 0.133 528 Planarity : 0.004 0.034 594 Dihedral : 5.255 12.149 462 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.76 % Allowed : 7.32 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.68 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.51 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 330 PHE 0.010 0.002 PHE B 346 TYR 0.010 0.002 TYR B 310 ARG 0.003 0.001 ARG C 349 *********************** 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 122 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 119 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.6964 (t0) cc_final: 0.6752 (t0) REVERT: A 317 LYS cc_start: 0.5869 (mttt) cc_final: 0.5561 (mttm) REVERT: A 331 LYS cc_start: 0.6377 (mttt) cc_final: 0.5899 (mtpp) REVERT: A 345 ASP cc_start: 0.7128 (OUTLIER) cc_final: 0.6495 (t70) REVERT: A 351 GLN cc_start: 0.6168 (tt0) cc_final: 0.5809 (mt0) REVERT: A 353 LYS cc_start: 0.5819 (mttt) cc_final: 0.5555 (tttm) REVERT: A 369 LYS cc_start: 0.6270 (tttt) cc_final: 0.5868 (tttp) REVERT: A 372 GLU cc_start: 0.6344 (tt0) cc_final: 0.5881 (mt-10) REVERT: A 373 THR cc_start: 0.6717 (m) cc_final: 0.6253 (p) REVERT: A 375 LYS cc_start: 0.6497 (tttt) cc_final: 0.5923 (ttpt) REVERT: B 307 GLN cc_start: 0.6785 (tt0) cc_final: 0.6458 (tt0) REVERT: B 317 LYS cc_start: 0.6057 (mttt) cc_final: 0.5805 (mttm) REVERT: B 331 LYS cc_start: 0.6611 (mttt) cc_final: 0.6148 (mtpt) REVERT: B 351 GLN cc_start: 0.6158 (tt0) cc_final: 0.5953 (mt0) REVERT: B 369 LYS cc_start: 0.6253 (tttt) cc_final: 0.6001 (tttp) REVERT: B 373 THR cc_start: 0.6811 (m) cc_final: 0.6338 (p) REVERT: C 307 GLN cc_start: 0.7399 (tt0) cc_final: 0.7115 (tt0) REVERT: C 331 LYS cc_start: 0.6445 (mttt) cc_final: 0.5984 (mtpt) REVERT: C 338 GLU cc_start: 0.6515 (tt0) cc_final: 0.6165 (mt-10) REVERT: C 340 LYS cc_start: 0.6891 (tttt) cc_final: 0.6186 (mttt) REVERT: C 347 LYS cc_start: 0.6644 (mttt) cc_final: 0.5722 (mppt) REVERT: C 349 ARG cc_start: 0.6290 (mtp180) cc_final: 0.6030 (mtt180) REVERT: C 351 GLN cc_start: 0.6771 (tt0) cc_final: 0.6526 (mt0) REVERT: C 369 LYS cc_start: 0.6672 (tttt) cc_final: 0.6380 (tttp) REVERT: C 373 THR cc_start: 0.7267 (m) cc_final: 0.6942 (p) REVERT: C 375 LYS cc_start: 0.7067 (tttt) cc_final: 0.6601 (tttp) REVERT: D 317 LYS cc_start: 0.6449 (mttt) cc_final: 0.6189 (mttm) REVERT: D 331 LYS cc_start: 0.6739 (mttt) cc_final: 0.6259 (mtpp) REVERT: D 338 GLU cc_start: 0.6700 (tt0) cc_final: 0.6308 (mt-10) REVERT: D 340 LYS cc_start: 0.6952 (tttt) cc_final: 0.6251 (mttt) REVERT: D 349 ARG cc_start: 0.5428 (mtm180) cc_final: 0.5142 (mtt180) REVERT: D 369 LYS cc_start: 0.6725 (tttt) cc_final: 0.6334 (tttp) REVERT: D 372 GLU cc_start: 0.6494 (tt0) cc_final: 0.6075 (mt-10) REVERT: D 373 THR cc_start: 0.7175 (m) cc_final: 0.6812 (p) REVERT: D 375 LYS cc_start: 0.6946 (tttt) cc_final: 0.6347 (ttpt) REVERT: E 331 LYS cc_start: 0.6834 (mttt) cc_final: 0.6339 (mtpt) REVERT: E 340 LYS cc_start: 0.6532 (tttt) cc_final: 0.5690 (mmpt) REVERT: E 345 ASP cc_start: 0.7030 (OUTLIER) cc_final: 0.6260 (t70) REVERT: E 351 GLN cc_start: 0.6171 (tt0) cc_final: 0.5963 (mt0) REVERT: E 369 LYS cc_start: 0.6384 (tttt) cc_final: 0.6157 (tttp) REVERT: E 373 THR cc_start: 0.6917 (m) cc_final: 0.6322 (p) REVERT: E 375 LYS cc_start: 0.6608 (tttt) cc_final: 0.6172 (ttpt) REVERT: F 331 LYS cc_start: 0.6697 (mttt) cc_final: 0.6370 (mtpp) REVERT: F 338 GLU cc_start: 0.6428 (tt0) cc_final: 0.5945 (mt-10) REVERT: F 340 LYS cc_start: 0.6473 (tttt) cc_final: 0.5742 (mttt) REVERT: F 345 ASP cc_start: 0.6745 (t0) cc_final: 0.6358 (t0) REVERT: F 351 GLN cc_start: 0.6400 (tt0) cc_final: 0.6128 (mt0) REVERT: F 372 GLU cc_start: 0.6642 (tt0) cc_final: 0.6261 (mt-10) REVERT: F 373 THR cc_start: 0.6795 (m) cc_final: 0.6265 (p) REVERT: F 375 LYS cc_start: 0.6579 (tttt) cc_final: 0.6213 (tttp) outliers start: 3 outliers final: 1 residues processed: 120 average time/residue: 3.6956 time to fit residues: 451.7395 Evaluate side-chains 120 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 117 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 345 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.0040 chunk 16 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 0.0000 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.3680 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= 0.118 Angle : 0.473 3.984 4680 Z= 0.242 Chirality : 0.053 0.139 528 Planarity : 0.002 0.019 594 Dihedral : 4.822 12.357 462 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 0.25 % Allowed : 7.58 % Favored : 92.17 % 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: -0.46 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.34 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.005 0.001 PHE E 378 TYR 0.007 0.001 TYR B 310 ARG 0.001 0.000 ARG D 349 *********************** 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 123 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.5924 (mttt) cc_final: 0.5604 (mttm) REVERT: A 331 LYS cc_start: 0.6488 (mttt) cc_final: 0.6010 (mtpp) REVERT: A 345 ASP cc_start: 0.7104 (OUTLIER) cc_final: 0.6465 (t70) REVERT: A 351 GLN cc_start: 0.6107 (tt0) cc_final: 0.5806 (mt0) REVERT: A 353 LYS cc_start: 0.5843 (mttt) cc_final: 0.5504 (tttm) REVERT: A 369 LYS cc_start: 0.6330 (tttt) cc_final: 0.5935 (tttp) REVERT: A 372 GLU cc_start: 0.6364 (tt0) cc_final: 0.5905 (mt-10) REVERT: A 373 THR cc_start: 0.6715 (m) cc_final: 0.6272 (p) REVERT: A 375 LYS cc_start: 0.6526 (tttt) cc_final: 0.5924 (ttpt) REVERT: B 307 GLN cc_start: 0.6821 (tt0) cc_final: 0.6420 (tt0) REVERT: B 317 LYS cc_start: 0.6108 (mttt) cc_final: 0.5863 (mttm) REVERT: B 331 LYS cc_start: 0.6633 (mttt) cc_final: 0.6165 (mtpt) REVERT: B 369 LYS cc_start: 0.6272 (tttt) cc_final: 0.5989 (tttp) REVERT: B 373 THR cc_start: 0.6764 (m) cc_final: 0.6336 (p) REVERT: C 331 LYS cc_start: 0.6502 (mttt) cc_final: 0.6035 (mtpt) REVERT: C 338 GLU cc_start: 0.6519 (tt0) cc_final: 0.6191 (mt-10) REVERT: C 340 LYS cc_start: 0.6901 (tttt) cc_final: 0.6131 (mttt) REVERT: C 347 LYS cc_start: 0.6682 (mttt) cc_final: 0.5753 (mppt) REVERT: C 349 ARG cc_start: 0.6313 (mtp180) cc_final: 0.6013 (mtt180) REVERT: C 351 GLN cc_start: 0.6714 (tt0) cc_final: 0.6504 (mt0) REVERT: C 369 LYS cc_start: 0.6719 (tttt) cc_final: 0.6412 (tttp) REVERT: C 373 THR cc_start: 0.7243 (m) cc_final: 0.6900 (p) REVERT: C 375 LYS cc_start: 0.6991 (tttt) cc_final: 0.6536 (tttp) REVERT: D 317 LYS cc_start: 0.6418 (mttt) cc_final: 0.6172 (mttm) REVERT: D 331 LYS cc_start: 0.6775 (mttt) cc_final: 0.6270 (mtpp) REVERT: D 349 ARG cc_start: 0.5378 (mtm180) cc_final: 0.5148 (mtt180) REVERT: D 369 LYS cc_start: 0.6683 (tttt) cc_final: 0.6232 (tttp) REVERT: D 372 GLU cc_start: 0.6586 (tt0) cc_final: 0.6069 (mt-10) REVERT: D 373 THR cc_start: 0.7195 (m) cc_final: 0.6814 (p) REVERT: D 375 LYS cc_start: 0.6977 (tttt) cc_final: 0.6369 (ttpt) REVERT: E 331 LYS cc_start: 0.6806 (mttt) cc_final: 0.6348 (mtpt) REVERT: E 340 LYS cc_start: 0.6562 (tttt) cc_final: 0.5709 (mmpt) REVERT: E 351 GLN cc_start: 0.6163 (tt0) cc_final: 0.5961 (mt0) REVERT: E 369 LYS cc_start: 0.6397 (tttt) cc_final: 0.6095 (tttp) REVERT: E 373 THR cc_start: 0.6926 (m) cc_final: 0.6319 (p) REVERT: E 375 LYS cc_start: 0.6599 (tttt) cc_final: 0.6201 (ttpt) REVERT: F 331 LYS cc_start: 0.6653 (mttt) cc_final: 0.6330 (mtpp) REVERT: F 345 ASP cc_start: 0.6761 (t0) cc_final: 0.6308 (m-30) REVERT: F 351 GLN cc_start: 0.6379 (tt0) cc_final: 0.6138 (mt0) REVERT: F 372 GLU cc_start: 0.6715 (tt0) cc_final: 0.6262 (mt-10) REVERT: F 373 THR cc_start: 0.6890 (m) cc_final: 0.6321 (p) REVERT: F 375 LYS cc_start: 0.6527 (tttt) cc_final: 0.6162 (tttp) outliers start: 1 outliers final: 0 residues processed: 122 average time/residue: 3.7488 time to fit residues: 466.0376 Evaluate side-chains 120 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3498 Z= 0.225 Angle : 0.521 4.103 4680 Z= 0.270 Chirality : 0.052 0.129 528 Planarity : 0.003 0.024 594 Dihedral : 4.958 12.143 462 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.25 % Allowed : 8.84 % Favored : 90.91 % 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: -0.54 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.40 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 330 PHE 0.007 0.002 PHE E 346 TYR 0.008 0.002 TYR B 310 ARG 0.002 0.000 ARG C 349 *********************** 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 118 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.5902 (mttt) cc_final: 0.5636 (mttm) REVERT: A 331 LYS cc_start: 0.6393 (mttt) cc_final: 0.5911 (mtpp) REVERT: A 345 ASP cc_start: 0.7057 (OUTLIER) cc_final: 0.6448 (t70) REVERT: A 351 GLN cc_start: 0.6134 (tt0) cc_final: 0.5808 (mt0) REVERT: A 353 LYS cc_start: 0.5885 (mttt) cc_final: 0.5544 (tttm) REVERT: A 369 LYS cc_start: 0.6296 (tttt) cc_final: 0.5903 (tttp) REVERT: A 372 GLU cc_start: 0.6392 (tt0) cc_final: 0.5879 (mt-10) REVERT: A 373 THR cc_start: 0.6707 (m) cc_final: 0.6263 (p) REVERT: A 375 LYS cc_start: 0.6502 (tttt) cc_final: 0.5935 (ttpt) REVERT: B 307 GLN cc_start: 0.6818 (tt0) cc_final: 0.6414 (tt0) REVERT: B 317 LYS cc_start: 0.6082 (mttt) cc_final: 0.5837 (mttm) REVERT: B 331 LYS cc_start: 0.6631 (mttt) cc_final: 0.6147 (mtpt) REVERT: B 369 LYS cc_start: 0.6266 (tttt) cc_final: 0.5923 (tttp) REVERT: B 373 THR cc_start: 0.6811 (m) cc_final: 0.6357 (p) REVERT: C 331 LYS cc_start: 0.6533 (mttt) cc_final: 0.6065 (mtpt) REVERT: C 338 GLU cc_start: 0.6548 (tt0) cc_final: 0.6194 (mt-10) REVERT: C 340 LYS cc_start: 0.6918 (tttt) cc_final: 0.6166 (mttt) REVERT: C 347 LYS cc_start: 0.6648 (mttt) cc_final: 0.5725 (mppt) REVERT: C 349 ARG cc_start: 0.6333 (mtp180) cc_final: 0.6076 (mtt180) REVERT: C 351 GLN cc_start: 0.6748 (tt0) cc_final: 0.6511 (mt0) REVERT: C 369 LYS cc_start: 0.6670 (tttt) cc_final: 0.6364 (tttp) REVERT: C 373 THR cc_start: 0.7288 (m) cc_final: 0.6940 (p) REVERT: C 375 LYS cc_start: 0.7007 (tttt) cc_final: 0.6555 (tttp) REVERT: D 317 LYS cc_start: 0.6416 (mttt) cc_final: 0.6144 (mttm) REVERT: D 331 LYS cc_start: 0.6781 (mttt) cc_final: 0.6277 (mtpp) REVERT: D 349 ARG cc_start: 0.5418 (mtm180) cc_final: 0.5156 (mtt180) REVERT: D 369 LYS cc_start: 0.6714 (tttt) cc_final: 0.6252 (tttp) REVERT: D 372 GLU cc_start: 0.6529 (tt0) cc_final: 0.6063 (mt-10) REVERT: D 373 THR cc_start: 0.7169 (m) cc_final: 0.6799 (p) REVERT: D 375 LYS cc_start: 0.6929 (tttt) cc_final: 0.6345 (ttpt) REVERT: E 331 LYS cc_start: 0.6792 (mttt) cc_final: 0.6295 (mtpt) REVERT: E 340 LYS cc_start: 0.6558 (tttt) cc_final: 0.5709 (mmpt) REVERT: E 351 GLN cc_start: 0.6189 (tt0) cc_final: 0.5987 (mt0) REVERT: E 369 LYS cc_start: 0.6389 (tttt) cc_final: 0.6094 (tttp) REVERT: E 373 THR cc_start: 0.6918 (m) cc_final: 0.6315 (p) REVERT: E 375 LYS cc_start: 0.6586 (tttt) cc_final: 0.6153 (ttpt) REVERT: F 331 LYS cc_start: 0.6725 (mttt) cc_final: 0.6360 (mtpp) REVERT: F 345 ASP cc_start: 0.6750 (t0) cc_final: 0.6288 (m-30) REVERT: F 351 GLN cc_start: 0.6390 (tt0) cc_final: 0.6129 (mt0) REVERT: F 372 GLU cc_start: 0.6687 (tt0) cc_final: 0.6202 (mt-10) REVERT: F 373 THR cc_start: 0.6885 (m) cc_final: 0.6329 (p) REVERT: F 375 LYS cc_start: 0.6588 (tttt) cc_final: 0.6218 (tttp) outliers start: 1 outliers final: 0 residues processed: 117 average time/residue: 3.8003 time to fit residues: 452.7267 Evaluate side-chains 118 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 16 optimal weight: 0.0980 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 0.0570 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3498 Z= 0.107 Angle : 0.454 3.975 4680 Z= 0.232 Chirality : 0.052 0.137 528 Planarity : 0.002 0.015 594 Dihedral : 4.603 12.312 462 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 0.51 % Allowed : 7.32 % Favored : 92.17 % 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: -0.42 (0.39), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.31 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.004 0.001 PHE B 378 TYR 0.006 0.001 TYR B 310 ARG 0.001 0.000 ARG D 349 *********************** 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 123 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 121 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.5975 (mttt) cc_final: 0.5716 (mttm) REVERT: A 331 LYS cc_start: 0.6497 (mttt) cc_final: 0.6027 (mtpp) REVERT: A 345 ASP cc_start: 0.7016 (OUTLIER) cc_final: 0.6409 (t70) REVERT: A 351 GLN cc_start: 0.6050 (tt0) cc_final: 0.5760 (mt0) REVERT: A 353 LYS cc_start: 0.5802 (mttt) cc_final: 0.5473 (tttm) REVERT: A 369 LYS cc_start: 0.6320 (tttt) cc_final: 0.5859 (tttp) REVERT: A 372 GLU cc_start: 0.6382 (tt0) cc_final: 0.5861 (mt-10) REVERT: A 373 THR cc_start: 0.6716 (m) cc_final: 0.6291 (p) REVERT: A 375 LYS cc_start: 0.6511 (tttt) cc_final: 0.5911 (ttpt) REVERT: B 307 GLN cc_start: 0.6863 (tt0) cc_final: 0.6466 (tt0) REVERT: B 317 LYS cc_start: 0.6129 (mttt) cc_final: 0.5881 (mttm) REVERT: B 331 LYS cc_start: 0.6654 (mttt) cc_final: 0.6181 (mtpt) REVERT: B 369 LYS cc_start: 0.6294 (tttt) cc_final: 0.6011 (tttp) REVERT: B 373 THR cc_start: 0.6741 (m) cc_final: 0.6317 (p) REVERT: C 331 LYS cc_start: 0.6545 (mttt) cc_final: 0.6088 (mtpt) REVERT: C 338 GLU cc_start: 0.6521 (tt0) cc_final: 0.6180 (mt-10) REVERT: C 340 LYS cc_start: 0.6921 (tttt) cc_final: 0.6155 (mttt) REVERT: C 347 LYS cc_start: 0.6675 (mttt) cc_final: 0.5740 (mppt) REVERT: C 349 ARG cc_start: 0.6352 (mtp180) cc_final: 0.6047 (mtt180) REVERT: C 369 LYS cc_start: 0.6709 (tttt) cc_final: 0.6395 (tttp) REVERT: C 373 THR cc_start: 0.7223 (m) cc_final: 0.6880 (p) REVERT: C 375 LYS cc_start: 0.6995 (tttt) cc_final: 0.6549 (tttp) REVERT: D 317 LYS cc_start: 0.6349 (mttt) cc_final: 0.6087 (mttm) REVERT: D 331 LYS cc_start: 0.6784 (mttt) cc_final: 0.6284 (mtpp) REVERT: D 349 ARG cc_start: 0.5402 (mtm180) cc_final: 0.5164 (mtt180) REVERT: D 369 LYS cc_start: 0.6696 (tttt) cc_final: 0.6243 (tttp) REVERT: D 372 GLU cc_start: 0.6659 (tt0) cc_final: 0.6137 (mt-10) REVERT: D 373 THR cc_start: 0.7178 (m) cc_final: 0.6790 (p) REVERT: D 375 LYS cc_start: 0.6972 (tttt) cc_final: 0.6358 (ttpt) REVERT: E 331 LYS cc_start: 0.6794 (mttt) cc_final: 0.6330 (mtpt) REVERT: E 340 LYS cc_start: 0.6584 (tttt) cc_final: 0.5730 (mmpt) REVERT: E 369 LYS cc_start: 0.6362 (tttt) cc_final: 0.6081 (tttp) REVERT: E 373 THR cc_start: 0.6936 (m) cc_final: 0.6324 (p) REVERT: E 375 LYS cc_start: 0.6594 (tttt) cc_final: 0.6189 (ttpt) REVERT: F 331 LYS cc_start: 0.6665 (mttt) cc_final: 0.6311 (mtpp) REVERT: F 345 ASP cc_start: 0.6750 (t0) cc_final: 0.6287 (m-30) REVERT: F 351 GLN cc_start: 0.6397 (tt0) cc_final: 0.6143 (mt0) REVERT: F 372 GLU cc_start: 0.6694 (tt0) cc_final: 0.6210 (mt-10) REVERT: F 373 THR cc_start: 0.6954 (m) cc_final: 0.6379 (p) REVERT: F 375 LYS cc_start: 0.6555 (tttt) cc_final: 0.6188 (tttp) outliers start: 2 outliers final: 1 residues processed: 121 average time/residue: 3.7901 time to fit residues: 467.2723 Evaluate side-chains 123 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 121 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP 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 3 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3498 Z= 0.207 Angle : 0.508 4.101 4680 Z= 0.263 Chirality : 0.052 0.128 528 Planarity : 0.003 0.020 594 Dihedral : 4.829 12.413 462 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.25 % Allowed : 7.83 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.51 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.38 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 330 PHE 0.007 0.002 PHE E 346 TYR 0.008 0.002 TYR B 310 ARG 0.001 0.000 ARG C 349 *********************** 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 119 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 118 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.6014 (mttt) cc_final: 0.5769 (mttm) REVERT: A 331 LYS cc_start: 0.6383 (mttt) cc_final: 0.5908 (mtpp) REVERT: A 345 ASP cc_start: 0.7012 (OUTLIER) cc_final: 0.6416 (t70) REVERT: A 351 GLN cc_start: 0.6137 (tt0) cc_final: 0.5806 (mt0) REVERT: A 353 LYS cc_start: 0.5877 (mttt) cc_final: 0.5547 (tttm) REVERT: A 369 LYS cc_start: 0.6296 (tttt) cc_final: 0.5832 (tttp) REVERT: A 372 GLU cc_start: 0.6361 (tt0) cc_final: 0.5818 (mt-10) REVERT: A 373 THR cc_start: 0.6715 (m) cc_final: 0.6274 (p) REVERT: A 375 LYS cc_start: 0.6514 (tttt) cc_final: 0.5929 (ttpt) REVERT: B 307 GLN cc_start: 0.6826 (tt0) cc_final: 0.6414 (tt0) REVERT: B 317 LYS cc_start: 0.6085 (mttt) cc_final: 0.5840 (mttm) REVERT: B 331 LYS cc_start: 0.6624 (mttt) cc_final: 0.6175 (mtpt) REVERT: B 369 LYS cc_start: 0.6272 (tttt) cc_final: 0.5924 (tttp) REVERT: B 373 THR cc_start: 0.6804 (m) cc_final: 0.6351 (p) REVERT: C 331 LYS cc_start: 0.6542 (mttt) cc_final: 0.6075 (mtpt) REVERT: C 338 GLU cc_start: 0.6527 (tt0) cc_final: 0.6190 (mt-10) REVERT: C 340 LYS cc_start: 0.6889 (tttt) cc_final: 0.6142 (mttt) REVERT: C 347 LYS cc_start: 0.6648 (mttt) cc_final: 0.5724 (mppt) REVERT: C 349 ARG cc_start: 0.6334 (mtp180) cc_final: 0.6088 (mtt180) REVERT: C 369 LYS cc_start: 0.6670 (tttt) cc_final: 0.6364 (tttp) REVERT: C 373 THR cc_start: 0.7287 (m) cc_final: 0.6930 (p) REVERT: C 375 LYS cc_start: 0.6980 (tttt) cc_final: 0.6530 (tttp) REVERT: D 317 LYS cc_start: 0.6443 (mttt) cc_final: 0.6171 (mttm) REVERT: D 331 LYS cc_start: 0.6779 (mttt) cc_final: 0.6280 (mtpp) REVERT: D 349 ARG cc_start: 0.5440 (mtm180) cc_final: 0.5153 (mtt180) REVERT: D 369 LYS cc_start: 0.6707 (tttt) cc_final: 0.6249 (tttp) REVERT: D 372 GLU cc_start: 0.6591 (tt0) cc_final: 0.6077 (mt-10) REVERT: D 373 THR cc_start: 0.7172 (m) cc_final: 0.6791 (p) REVERT: D 375 LYS cc_start: 0.6931 (tttt) cc_final: 0.6350 (ttpt) REVERT: E 331 LYS cc_start: 0.6747 (mttt) cc_final: 0.6253 (mtpt) REVERT: E 340 LYS cc_start: 0.6569 (tttt) cc_final: 0.5712 (mmpt) REVERT: E 369 LYS cc_start: 0.6360 (tttt) cc_final: 0.6104 (tttp) REVERT: E 373 THR cc_start: 0.6934 (m) cc_final: 0.6326 (p) REVERT: E 375 LYS cc_start: 0.6554 (tttt) cc_final: 0.6146 (ttpt) REVERT: F 331 LYS cc_start: 0.6722 (mttt) cc_final: 0.6337 (mtpp) REVERT: F 338 GLU cc_start: 0.6441 (tt0) cc_final: 0.5972 (mt-10) REVERT: F 340 LYS cc_start: 0.6591 (tttt) cc_final: 0.5830 (mttt) REVERT: F 345 ASP cc_start: 0.6745 (t0) cc_final: 0.6295 (m-30) REVERT: F 351 GLN cc_start: 0.6368 (tt0) cc_final: 0.6141 (mt0) REVERT: F 372 GLU cc_start: 0.6686 (tt0) cc_final: 0.6266 (mt-10) REVERT: F 373 THR cc_start: 0.6885 (m) cc_final: 0.6313 (p) REVERT: F 375 LYS cc_start: 0.6597 (tttt) cc_final: 0.6224 (tttp) outliers start: 1 outliers final: 0 residues processed: 118 average time/residue: 3.7491 time to fit residues: 450.5052 Evaluate side-chains 119 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 118 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.3891 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= 0.179 Angle : 0.500 3.991 4680 Z= 0.258 Chirality : 0.052 0.131 528 Planarity : 0.003 0.021 594 Dihedral : 4.814 12.368 462 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.25 % Allowed : 7.32 % Favored : 92.42 % 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: -0.52 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.38 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.007 0.002 PHE F 346 TYR 0.007 0.001 TYR B 310 ARG 0.002 0.000 ARG C 349 *********************** 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 120 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.6007 (mttt) cc_final: 0.5787 (mttm) REVERT: A 331 LYS cc_start: 0.6435 (mttt) cc_final: 0.5954 (mtpp) REVERT: A 345 ASP cc_start: 0.6995 (OUTLIER) cc_final: 0.6401 (t70) REVERT: A 351 GLN cc_start: 0.6140 (tt0) cc_final: 0.5805 (mt0) REVERT: A 353 LYS cc_start: 0.5849 (mttt) cc_final: 0.5524 (tttm) REVERT: A 369 LYS cc_start: 0.6304 (tttt) cc_final: 0.5839 (tttp) REVERT: A 372 GLU cc_start: 0.6390 (tt0) cc_final: 0.5947 (mt-10) REVERT: A 373 THR cc_start: 0.6723 (m) cc_final: 0.6285 (p) REVERT: A 375 LYS cc_start: 0.6522 (tttt) cc_final: 0.5931 (ttpt) REVERT: B 307 GLN cc_start: 0.6827 (tt0) cc_final: 0.6423 (tt0) REVERT: B 317 LYS cc_start: 0.6084 (mttt) cc_final: 0.5840 (mttm) REVERT: B 331 LYS cc_start: 0.6640 (mttt) cc_final: 0.6133 (mtpm) REVERT: B 340 LYS cc_start: 0.6470 (tttt) cc_final: 0.5697 (mttt) REVERT: B 369 LYS cc_start: 0.6272 (tttt) cc_final: 0.5917 (tttp) REVERT: B 373 THR cc_start: 0.6819 (m) cc_final: 0.6364 (p) REVERT: C 331 LYS cc_start: 0.6534 (mttt) cc_final: 0.6064 (mtpt) REVERT: C 338 GLU cc_start: 0.6525 (tt0) cc_final: 0.6181 (mt-10) REVERT: C 340 LYS cc_start: 0.6888 (tttt) cc_final: 0.6141 (mttt) REVERT: C 347 LYS cc_start: 0.6727 (mttt) cc_final: 0.5793 (mppt) REVERT: C 349 ARG cc_start: 0.6335 (mtp180) cc_final: 0.6080 (mtt180) REVERT: C 369 LYS cc_start: 0.6700 (tttt) cc_final: 0.6397 (tttp) REVERT: C 373 THR cc_start: 0.7270 (m) cc_final: 0.6912 (p) REVERT: C 375 LYS cc_start: 0.6973 (tttt) cc_final: 0.6521 (tttp) REVERT: D 317 LYS cc_start: 0.6466 (mttt) cc_final: 0.6216 (mttm) REVERT: D 331 LYS cc_start: 0.6747 (mttt) cc_final: 0.6257 (mtpp) REVERT: D 349 ARG cc_start: 0.5467 (mtm180) cc_final: 0.5159 (mtt180) REVERT: D 369 LYS cc_start: 0.6703 (tttt) cc_final: 0.6242 (tttp) REVERT: D 372 GLU cc_start: 0.6600 (tt0) cc_final: 0.6107 (mt-10) REVERT: D 373 THR cc_start: 0.7189 (m) cc_final: 0.6809 (p) REVERT: D 375 LYS cc_start: 0.6972 (tttt) cc_final: 0.6365 (ttpt) REVERT: E 331 LYS cc_start: 0.6750 (mttt) cc_final: 0.6253 (mtpt) REVERT: E 340 LYS cc_start: 0.6568 (tttt) cc_final: 0.5714 (mmpt) REVERT: E 369 LYS cc_start: 0.6362 (tttt) cc_final: 0.6104 (tttp) REVERT: E 372 GLU cc_start: 0.6718 (tt0) cc_final: 0.6371 (mt-10) REVERT: E 373 THR cc_start: 0.6965 (m) cc_final: 0.6358 (p) REVERT: E 375 LYS cc_start: 0.6544 (tttt) cc_final: 0.6140 (ttpt) REVERT: F 331 LYS cc_start: 0.6734 (mttt) cc_final: 0.6320 (mtpp) REVERT: F 345 ASP cc_start: 0.6773 (t0) cc_final: 0.6327 (m-30) REVERT: F 351 GLN cc_start: 0.6376 (tt0) cc_final: 0.6147 (mt0) REVERT: F 372 GLU cc_start: 0.6675 (tt0) cc_final: 0.6253 (mt-10) REVERT: F 373 THR cc_start: 0.6883 (m) cc_final: 0.6313 (p) REVERT: F 375 LYS cc_start: 0.6580 (tttt) cc_final: 0.6212 (tttp) outliers start: 1 outliers final: 0 residues processed: 119 average time/residue: 3.7220 time to fit residues: 451.1008 Evaluate side-chains 119 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 118 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.2980 chunk 26 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3498 Z= 0.206 Angle : 0.517 4.097 4680 Z= 0.268 Chirality : 0.052 0.129 528 Planarity : 0.003 0.022 594 Dihedral : 4.872 12.344 462 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.51 % Allowed : 7.07 % Favored : 92.42 % 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: -0.54 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.40 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 330 PHE 0.007 0.002 PHE F 346 TYR 0.008 0.001 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) ************************************************ 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 121 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.5968 (mttt) cc_final: 0.5738 (mttm) REVERT: A 331 LYS cc_start: 0.6396 (mttt) cc_final: 0.5912 (mtpp) REVERT: A 345 ASP cc_start: 0.7000 (OUTLIER) cc_final: 0.6402 (t70) REVERT: A 351 GLN cc_start: 0.6141 (tt0) cc_final: 0.5807 (mt0) REVERT: A 353 LYS cc_start: 0.5841 (mttt) cc_final: 0.5525 (tttm) REVERT: A 369 LYS cc_start: 0.6289 (tttt) cc_final: 0.5820 (tttp) REVERT: A 372 GLU cc_start: 0.6384 (tt0) cc_final: 0.5935 (mt-10) REVERT: A 373 THR cc_start: 0.6713 (m) cc_final: 0.6278 (p) REVERT: A 375 LYS cc_start: 0.6513 (tttt) cc_final: 0.5925 (ttpt) REVERT: B 307 GLN cc_start: 0.6820 (tt0) cc_final: 0.6408 (tt0) REVERT: B 317 LYS cc_start: 0.6059 (mttt) cc_final: 0.5814 (mttm) REVERT: B 331 LYS cc_start: 0.6656 (mttt) cc_final: 0.6149 (mtpm) REVERT: B 369 LYS cc_start: 0.6279 (tttt) cc_final: 0.5929 (tttp) REVERT: B 373 THR cc_start: 0.6814 (m) cc_final: 0.6359 (p) REVERT: C 331 LYS cc_start: 0.6528 (mttt) cc_final: 0.6064 (mtpt) REVERT: C 338 GLU cc_start: 0.6528 (tt0) cc_final: 0.6193 (mt-10) REVERT: C 340 LYS cc_start: 0.6897 (tttt) cc_final: 0.6156 (mttm) REVERT: C 347 LYS cc_start: 0.6690 (mttt) cc_final: 0.5755 (mppt) REVERT: C 349 ARG cc_start: 0.6340 (mtp180) cc_final: 0.6088 (mtt180) REVERT: C 369 LYS cc_start: 0.6677 (tttt) cc_final: 0.6376 (tttp) REVERT: C 373 THR cc_start: 0.7277 (m) cc_final: 0.6919 (p) REVERT: C 375 LYS cc_start: 0.6993 (tttt) cc_final: 0.6539 (tttp) REVERT: D 317 LYS cc_start: 0.6450 (mttt) cc_final: 0.6231 (mttm) REVERT: D 331 LYS cc_start: 0.6748 (mttt) cc_final: 0.6277 (mtpp) REVERT: D 349 ARG cc_start: 0.5505 (mtm180) cc_final: 0.5125 (mtt180) REVERT: D 369 LYS cc_start: 0.6708 (tttt) cc_final: 0.6236 (tttp) REVERT: D 372 GLU cc_start: 0.6576 (tt0) cc_final: 0.6084 (mt-10) REVERT: D 373 THR cc_start: 0.7166 (m) cc_final: 0.6796 (p) REVERT: D 375 LYS cc_start: 0.6960 (tttt) cc_final: 0.6362 (ttpt) REVERT: E 331 LYS cc_start: 0.6733 (mttt) cc_final: 0.6249 (mtpt) REVERT: E 340 LYS cc_start: 0.6562 (tttt) cc_final: 0.5724 (mmpt) REVERT: E 369 LYS cc_start: 0.6364 (tttt) cc_final: 0.6106 (tttp) REVERT: E 372 GLU cc_start: 0.6836 (tt0) cc_final: 0.6477 (mt-10) REVERT: E 373 THR cc_start: 0.6963 (m) cc_final: 0.6354 (p) REVERT: E 375 LYS cc_start: 0.6551 (tttt) cc_final: 0.6138 (ttpt) REVERT: F 331 LYS cc_start: 0.6753 (mttt) cc_final: 0.6318 (mtpp) REVERT: F 345 ASP cc_start: 0.6749 (t0) cc_final: 0.6307 (m-30) REVERT: F 351 GLN cc_start: 0.6359 (tt0) cc_final: 0.6133 (mt0) REVERT: F 372 GLU cc_start: 0.6683 (tt0) cc_final: 0.6210 (mt-10) REVERT: F 373 THR cc_start: 0.6888 (m) cc_final: 0.6321 (p) REVERT: F 375 LYS cc_start: 0.6598 (tttt) cc_final: 0.6224 (tttp) outliers start: 2 outliers final: 1 residues processed: 119 average time/residue: 3.7501 time to fit residues: 454.4725 Evaluate side-chains 121 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 0.0970 chunk 22 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.4159 r_free = 0.4159 target = 0.155352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.142293 restraints weight = 7756.712| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 0.73 r_work: 0.3942 rms_B_bonded: 0.68 restraints_weight: 0.5000 r_work: 0.3881 rms_B_bonded: 1.20 restraints_weight: 0.2500 r_work: 0.3718 rms_B_bonded: 3.43 restraints_weight: 0.1250 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.3945 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= 0.130 Angle : 0.473 3.976 4680 Z= 0.243 Chirality : 0.052 0.130 528 Planarity : 0.002 0.018 594 Dihedral : 4.660 12.446 462 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.51 % Allowed : 7.07 % Favored : 92.42 % 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: -0.45 (0.39), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.34 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.006 0.001 PHE F 346 TYR 0.006 0.001 TYR B 310 ARG 0.001 0.000 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7429.96 seconds wall clock time: 129 minutes 5.60 seconds (7745.60 seconds total)