Starting phenix.real_space_refine on Mon Mar 11 04:41:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q98_18271/03_2024/8q98_18271.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q98_18271/03_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_18271/03_2024/8q98_18271.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q98_18271/03_2024/8q98_18271.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q98_18271/03_2024/8q98_18271.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q98_18271/03_2024/8q98_18271.pdb" } 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-5265/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: 3.74, per 1000 atoms: 0.53 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: 5.01 Conformation dependent library (CDL) restraints added in 771.0 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: 0.62 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: 2.40 Time building geometry restraints manager: 5.23 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 1.850 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.585 1.850 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.603 1.850 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.605 1.850 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.611 1.850 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.670 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: 0.120 Extract box with map and model: 11.690 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 26.360 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 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:11.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.070 ------------------------------------------------------------------------------- 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 : 0.656 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: 3.3480 time to fit residues: 525.8345 Evaluate side-chains 126 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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: 1.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.2601 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= 0.268 Angle : 0.597 4.130 4680 Z= 0.309 Chirality : 0.050 0.138 528 Planarity : 0.004 0.032 594 Dihedral : 5.505 13.256 462 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: -0.48 (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 HIS 0.004 0.001 HIS C 330 PHE 0.006 0.002 PHE E 346 TYR 0.006 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 129 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 126 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.5856 (mttt) cc_final: 0.5576 (mttm) REVERT: A 331 LYS cc_start: 0.6374 (mttt) cc_final: 0.5889 (mtpp) REVERT: A 338 GLU cc_start: 0.6407 (tt0) cc_final: 0.5845 (mt-10) REVERT: A 340 LYS cc_start: 0.6230 (tttt) cc_final: 0.5557 (mttm) REVERT: A 351 GLN cc_start: 0.6124 (tt0) cc_final: 0.5799 (mt0) REVERT: A 353 LYS cc_start: 0.5852 (mttt) cc_final: 0.5572 (tttm) REVERT: A 369 LYS cc_start: 0.6230 (tttt) cc_final: 0.5879 (tttp) REVERT: A 372 GLU cc_start: 0.6354 (tt0) cc_final: 0.5848 (mt-10) REVERT: A 373 THR cc_start: 0.6600 (m) cc_final: 0.6106 (p) REVERT: A 375 LYS cc_start: 0.6430 (tttt) cc_final: 0.5858 (ttpt) REVERT: B 307 GLN cc_start: 0.6808 (tt0) cc_final: 0.6567 (tt0) REVERT: B 317 LYS cc_start: 0.6070 (mttt) cc_final: 0.5813 (mttm) REVERT: B 331 LYS cc_start: 0.6649 (mttt) cc_final: 0.6207 (mtpt) REVERT: B 338 GLU cc_start: 0.6178 (tt0) cc_final: 0.5790 (mt-10) REVERT: B 340 LYS cc_start: 0.6279 (tttt) cc_final: 0.5591 (mttt) REVERT: B 343 LYS cc_start: 0.7089 (mtmt) cc_final: 0.6792 (mttp) REVERT: B 351 GLN cc_start: 0.6168 (tt0) cc_final: 0.5902 (mt0) REVERT: B 353 LYS cc_start: 0.5684 (mttt) cc_final: 0.5468 (tttp) REVERT: B 369 LYS cc_start: 0.6223 (tttt) cc_final: 0.5944 (tttp) REVERT: B 373 THR cc_start: 0.6751 (m) cc_final: 0.6194 (p) REVERT: C 307 GLN cc_start: 0.7360 (tt0) cc_final: 0.7022 (tt0) REVERT: C 331 LYS cc_start: 0.6557 (mttt) cc_final: 0.6048 (mtpt) REVERT: C 338 GLU cc_start: 0.6545 (tt0) cc_final: 0.6173 (mt-10) REVERT: C 340 LYS cc_start: 0.6927 (tttt) cc_final: 0.6189 (mttt) REVERT: C 342 GLU cc_start: 0.6479 (tt0) cc_final: 0.6275 (tt0) REVERT: C 347 LYS cc_start: 0.6715 (mttt) cc_final: 0.5654 (mppt) REVERT: C 349 ARG cc_start: 0.6430 (mtp180) cc_final: 0.6031 (mtt180) REVERT: C 351 GLN cc_start: 0.6792 (tt0) cc_final: 0.6535 (mt0) REVERT: C 369 LYS cc_start: 0.6777 (tttt) cc_final: 0.6485 (tttp) REVERT: C 373 THR cc_start: 0.7305 (m) cc_final: 0.6958 (p) REVERT: C 375 LYS cc_start: 0.7083 (tttt) cc_final: 0.6613 (tttp) REVERT: D 317 LYS cc_start: 0.6447 (mttt) cc_final: 0.6196 (mttm) REVERT: D 331 LYS cc_start: 0.6667 (mttt) cc_final: 0.6211 (mtpt) REVERT: D 343 LYS cc_start: 0.7394 (mttp) cc_final: 0.7175 (mtmm) REVERT: D 345 ASP cc_start: 0.7226 (t0) cc_final: 0.6938 (t0) REVERT: D 369 LYS cc_start: 0.6715 (tttt) cc_final: 0.6359 (tttt) REVERT: D 372 GLU cc_start: 0.6490 (tt0) cc_final: 0.6027 (mt-10) REVERT: D 373 THR cc_start: 0.7174 (m) cc_final: 0.6823 (p) REVERT: D 375 LYS cc_start: 0.6917 (tttt) cc_final: 0.6341 (ttpt) REVERT: E 331 LYS cc_start: 0.6751 (mttt) cc_final: 0.6296 (mtpt) REVERT: E 338 GLU cc_start: 0.6245 (tt0) cc_final: 0.5779 (mt-10) REVERT: E 340 LYS cc_start: 0.6392 (tttt) cc_final: 0.5707 (mttt) REVERT: E 351 GLN cc_start: 0.6278 (tt0) cc_final: 0.5993 (mt0) REVERT: E 353 LYS cc_start: 0.5782 (mttt) cc_final: 0.5573 (tttp) REVERT: E 369 LYS cc_start: 0.6361 (tttt) cc_final: 0.6052 (tttp) REVERT: E 373 THR cc_start: 0.6954 (m) cc_final: 0.6328 (p) REVERT: E 375 LYS cc_start: 0.6561 (tttt) cc_final: 0.6106 (ttpt) REVERT: F 331 LYS cc_start: 0.6543 (mttt) cc_final: 0.6311 (mtpp) REVERT: F 338 GLU cc_start: 0.6378 (tt0) cc_final: 0.5871 (mt-10) REVERT: F 340 LYS cc_start: 0.6299 (tttt) cc_final: 0.5597 (mttt) REVERT: F 345 ASP cc_start: 0.6780 (t0) cc_final: 0.6291 (m-30) REVERT: F 351 GLN cc_start: 0.6171 (tt0) cc_final: 0.5906 (mt0) REVERT: F 372 GLU cc_start: 0.6634 (tt0) cc_final: 0.6325 (tt0) REVERT: F 373 THR cc_start: 0.6800 (m) cc_final: 0.6222 (p) REVERT: F 375 LYS cc_start: 0.6586 (tttt) cc_final: 0.6220 (tttp) outliers start: 3 outliers final: 1 residues processed: 126 average time/residue: 3.7755 time to fit residues: 484.2084 Evaluate side-chains 123 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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: 5.9990 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 37 optimal weight: 0.0040 chunk 13 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 overall best weight: 1.6396 ------------------------------------------------------------------------------- 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: 0.6522 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3498 Z= 0.146 Angle : 0.486 3.905 4680 Z= 0.249 Chirality : 0.052 0.141 528 Planarity : 0.003 0.020 594 Dihedral : 5.061 12.031 462 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 4.80 % Favored : 94.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.38), 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 HIS 0.002 0.001 HIS C 330 PHE 0.007 0.001 PHE E 346 TYR 0.007 0.001 TYR B 310 ARG 0.002 0.000 ARG C 349 *********************** 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 134 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 130 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.5839 (mttt) cc_final: 0.5600 (mttm) REVERT: A 331 LYS cc_start: 0.6326 (mttt) cc_final: 0.5851 (mtpp) REVERT: A 345 ASP cc_start: 0.7192 (OUTLIER) cc_final: 0.6077 (t70) REVERT: A 351 GLN cc_start: 0.6104 (tt0) cc_final: 0.5792 (mt0) REVERT: A 353 LYS cc_start: 0.5796 (mttt) cc_final: 0.5533 (tttm) REVERT: A 369 LYS cc_start: 0.6230 (tttt) cc_final: 0.5834 (tttp) REVERT: A 372 GLU cc_start: 0.6359 (tt0) cc_final: 0.5907 (mt-10) REVERT: A 373 THR cc_start: 0.6605 (m) cc_final: 0.6122 (p) REVERT: A 375 LYS cc_start: 0.6448 (tttt) cc_final: 0.5878 (ttpt) REVERT: B 307 GLN cc_start: 0.6775 (tt0) cc_final: 0.6509 (tt0) REVERT: B 317 LYS cc_start: 0.6051 (mttt) cc_final: 0.5804 (mttm) REVERT: B 331 LYS cc_start: 0.6644 (mttt) cc_final: 0.6197 (mtpt) REVERT: B 338 GLU cc_start: 0.6210 (tt0) cc_final: 0.5773 (mt-10) REVERT: B 340 LYS cc_start: 0.6313 (tttt) cc_final: 0.5622 (mttt) REVERT: B 343 LYS cc_start: 0.7114 (mtmt) cc_final: 0.6842 (mttp) REVERT: B 351 GLN cc_start: 0.6185 (tt0) cc_final: 0.5918 (mt0) REVERT: B 369 LYS cc_start: 0.6277 (tttt) cc_final: 0.6000 (tttp) REVERT: B 373 THR cc_start: 0.6698 (m) cc_final: 0.6200 (p) REVERT: C 307 GLN cc_start: 0.7292 (tt0) cc_final: 0.6976 (tt0) REVERT: C 331 LYS cc_start: 0.6480 (mttt) cc_final: 0.6008 (mtpt) REVERT: C 338 GLU cc_start: 0.6508 (tt0) cc_final: 0.6173 (mt-10) REVERT: C 340 LYS cc_start: 0.6936 (tttt) cc_final: 0.6211 (mttm) REVERT: C 342 GLU cc_start: 0.6386 (tt0) cc_final: 0.6161 (tt0) REVERT: C 347 LYS cc_start: 0.6703 (mttt) cc_final: 0.5703 (mppt) REVERT: C 349 ARG cc_start: 0.6189 (mtp180) cc_final: 0.5970 (mtt180) REVERT: C 351 GLN cc_start: 0.6763 (tt0) cc_final: 0.6523 (mt0) REVERT: C 369 LYS cc_start: 0.6749 (tttt) cc_final: 0.6455 (tttp) REVERT: C 373 THR cc_start: 0.7273 (m) cc_final: 0.6940 (p) REVERT: C 375 LYS cc_start: 0.7040 (tttt) cc_final: 0.6574 (tttp) REVERT: D 317 LYS cc_start: 0.6426 (mttt) cc_final: 0.6225 (mttm) REVERT: D 331 LYS cc_start: 0.6611 (mttt) cc_final: 0.6158 (mtpt) REVERT: D 338 GLU cc_start: 0.6725 (tt0) cc_final: 0.6318 (mt-10) REVERT: D 340 LYS cc_start: 0.6928 (tttt) cc_final: 0.6270 (mttt) REVERT: D 369 LYS cc_start: 0.6706 (tttt) cc_final: 0.6289 (tttp) REVERT: D 372 GLU cc_start: 0.6491 (tt0) cc_final: 0.6047 (mt-10) REVERT: D 373 THR cc_start: 0.7153 (m) cc_final: 0.6779 (p) REVERT: D 375 LYS cc_start: 0.6909 (tttt) cc_final: 0.6318 (ttpt) REVERT: E 331 LYS cc_start: 0.6749 (mttt) cc_final: 0.6238 (mtpp) REVERT: E 338 GLU cc_start: 0.6312 (tt0) cc_final: 0.5813 (mt-10) REVERT: E 340 LYS cc_start: 0.6444 (tttt) cc_final: 0.5750 (mttt) REVERT: E 351 GLN cc_start: 0.6243 (tt0) cc_final: 0.5977 (mt0) REVERT: E 369 LYS cc_start: 0.6386 (tttt) cc_final: 0.6073 (tttp) REVERT: E 373 THR cc_start: 0.6954 (m) cc_final: 0.6327 (p) REVERT: E 375 LYS cc_start: 0.6579 (tttt) cc_final: 0.6155 (ttpt) REVERT: F 331 LYS cc_start: 0.6592 (mttt) cc_final: 0.6320 (mtpp) REVERT: F 338 GLU cc_start: 0.6386 (tt0) cc_final: 0.5900 (mt-10) REVERT: F 340 LYS cc_start: 0.6291 (tttt) cc_final: 0.5576 (mttt) REVERT: F 345 ASP cc_start: 0.6783 (t0) cc_final: 0.6281 (m-30) REVERT: F 351 GLN cc_start: 0.6159 (tt0) cc_final: 0.5927 (mt0) REVERT: F 372 GLU cc_start: 0.6669 (tt0) cc_final: 0.6412 (tt0) REVERT: F 373 THR cc_start: 0.6829 (m) cc_final: 0.6251 (p) REVERT: F 375 LYS cc_start: 0.6569 (tttt) cc_final: 0.6205 (tttp) outliers start: 4 outliers final: 1 residues processed: 130 average time/residue: 3.8323 time to fit residues: 507.0382 Evaluate side-chains 125 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 123 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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: 10.0000 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 36 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- 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: 0.6541 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3498 Z= 0.294 Angle : 0.567 4.430 4680 Z= 0.295 Chirality : 0.051 0.129 528 Planarity : 0.004 0.027 594 Dihedral : 5.190 11.733 462 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: -0.59 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.44 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 330 PHE 0.010 0.002 PHE E 346 TYR 0.009 0.002 TYR E 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 121 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 118 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.5885 (mttt) cc_final: 0.5619 (mttm) REVERT: A 331 LYS cc_start: 0.6306 (mttt) cc_final: 0.5815 (mtpp) REVERT: A 345 ASP cc_start: 0.7056 (OUTLIER) cc_final: 0.6347 (t70) REVERT: A 351 GLN cc_start: 0.6188 (tt0) cc_final: 0.5858 (mt0) REVERT: A 353 LYS cc_start: 0.5861 (mttt) cc_final: 0.5575 (tttm) REVERT: A 369 LYS cc_start: 0.6210 (tttt) cc_final: 0.5801 (tttp) REVERT: A 372 GLU cc_start: 0.6337 (tt0) cc_final: 0.5885 (mt-10) REVERT: A 373 THR cc_start: 0.6644 (m) cc_final: 0.6179 (p) REVERT: A 375 LYS cc_start: 0.6466 (tttt) cc_final: 0.5891 (ttpt) REVERT: B 307 GLN cc_start: 0.6782 (tt0) cc_final: 0.6532 (tt0) REVERT: B 317 LYS cc_start: 0.6060 (mttt) cc_final: 0.5808 (mttm) REVERT: B 331 LYS cc_start: 0.6589 (mttt) cc_final: 0.6113 (mtpt) REVERT: B 342 GLU cc_start: 0.6256 (tt0) cc_final: 0.5971 (tt0) REVERT: B 351 GLN cc_start: 0.6166 (tt0) cc_final: 0.5951 (mt0) REVERT: B 369 LYS cc_start: 0.6242 (tttt) cc_final: 0.5996 (tttp) REVERT: B 373 THR cc_start: 0.6773 (m) cc_final: 0.6271 (p) REVERT: C 307 GLN cc_start: 0.7338 (tt0) cc_final: 0.7017 (tt0) REVERT: C 331 LYS cc_start: 0.6491 (mttt) cc_final: 0.6021 (mtpt) REVERT: C 338 GLU cc_start: 0.6541 (tt0) cc_final: 0.6198 (mt-10) REVERT: C 340 LYS cc_start: 0.6891 (tttt) cc_final: 0.6202 (mttt) REVERT: C 347 LYS cc_start: 0.6670 (mttt) cc_final: 0.5705 (mppt) REVERT: C 349 ARG cc_start: 0.6253 (mtp180) cc_final: 0.5974 (mtt180) REVERT: C 351 GLN cc_start: 0.6772 (tt0) cc_final: 0.6532 (mt0) REVERT: C 369 LYS cc_start: 0.6709 (tttt) cc_final: 0.6401 (tttp) REVERT: C 373 THR cc_start: 0.7294 (m) cc_final: 0.6952 (p) REVERT: C 375 LYS cc_start: 0.7053 (tttt) cc_final: 0.6582 (tttp) REVERT: D 317 LYS cc_start: 0.6478 (mttt) cc_final: 0.6257 (mttm) REVERT: D 331 LYS cc_start: 0.6601 (mttt) cc_final: 0.6110 (mtpp) REVERT: D 338 GLU cc_start: 0.6710 (tt0) cc_final: 0.6349 (mt-10) REVERT: D 340 LYS cc_start: 0.6937 (tttt) cc_final: 0.6270 (mttt) REVERT: D 345 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.6875 (t70) REVERT: D 369 LYS cc_start: 0.6721 (tttt) cc_final: 0.6367 (tttp) REVERT: D 372 GLU cc_start: 0.6468 (tt0) cc_final: 0.6024 (mt-10) REVERT: D 373 THR cc_start: 0.7166 (m) cc_final: 0.6812 (p) REVERT: D 375 LYS cc_start: 0.6880 (tttt) cc_final: 0.6300 (ttpt) REVERT: E 331 LYS cc_start: 0.6816 (mttt) cc_final: 0.6336 (mtpt) REVERT: E 338 GLU cc_start: 0.6347 (tt0) cc_final: 0.5472 (mt-10) REVERT: E 340 LYS cc_start: 0.6500 (tttt) cc_final: 0.5677 (mmpt) REVERT: E 351 GLN cc_start: 0.6224 (tt0) cc_final: 0.6000 (mt0) REVERT: E 369 LYS cc_start: 0.6393 (tttt) cc_final: 0.6075 (tttp) REVERT: E 373 THR cc_start: 0.6955 (m) cc_final: 0.6357 (p) REVERT: E 375 LYS cc_start: 0.6583 (tttt) cc_final: 0.6151 (ttpt) REVERT: F 331 LYS cc_start: 0.6623 (mttt) cc_final: 0.6314 (mtpp) REVERT: F 338 GLU cc_start: 0.6408 (tt0) cc_final: 0.5924 (mt-10) REVERT: F 340 LYS cc_start: 0.6354 (tttt) cc_final: 0.5638 (mttt) REVERT: F 345 ASP cc_start: 0.6763 (t0) cc_final: 0.6272 (m-30) REVERT: F 351 GLN cc_start: 0.6332 (tt0) cc_final: 0.6064 (mt0) REVERT: F 372 GLU cc_start: 0.6640 (tt0) cc_final: 0.6225 (mt-10) REVERT: F 373 THR cc_start: 0.6782 (m) cc_final: 0.6237 (p) REVERT: F 375 LYS cc_start: 0.6595 (tttt) cc_final: 0.6230 (tttp) outliers start: 3 outliers final: 1 residues processed: 118 average time/residue: 3.6364 time to fit residues: 437.0526 Evaluate side-chains 121 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 118 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 30 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 36 optimal weight: 0.0670 chunk 10 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 overall best weight: 2.4124 ------------------------------------------------------------------------------- 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: 0.6539 moved from start: 0.3595 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= 0.180 Angle : 0.500 4.002 4680 Z= 0.258 Chirality : 0.051 0.131 528 Planarity : 0.003 0.025 594 Dihedral : 4.991 11.767 462 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: -0.57 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.42 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 374 PHE 0.008 0.002 PHE B 346 TYR 0.008 0.002 TYR B 310 ARG 0.002 0.000 ARG C 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 124 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 121 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.5919 (mttt) cc_final: 0.5690 (mttm) REVERT: A 331 LYS cc_start: 0.6308 (mttt) cc_final: 0.5827 (mtpp) REVERT: A 345 ASP cc_start: 0.7057 (OUTLIER) cc_final: 0.5997 (t70) REVERT: A 347 LYS cc_start: 0.6940 (mttt) cc_final: 0.6678 (mmtp) REVERT: A 351 GLN cc_start: 0.6136 (tt0) cc_final: 0.5816 (mt0) REVERT: A 353 LYS cc_start: 0.5831 (mttt) cc_final: 0.5561 (tttm) REVERT: A 369 LYS cc_start: 0.6215 (tttt) cc_final: 0.5815 (tttp) REVERT: A 372 GLU cc_start: 0.6335 (tt0) cc_final: 0.5886 (mt-10) REVERT: A 373 THR cc_start: 0.6640 (m) cc_final: 0.6178 (p) REVERT: A 375 LYS cc_start: 0.6477 (tttt) cc_final: 0.5907 (ttpt) REVERT: B 307 GLN cc_start: 0.6820 (tt0) cc_final: 0.6512 (tt0) REVERT: B 317 LYS cc_start: 0.6036 (mttt) cc_final: 0.5790 (mttm) REVERT: B 331 LYS cc_start: 0.6596 (mttt) cc_final: 0.6118 (mtpt) REVERT: B 351 GLN cc_start: 0.6133 (tt0) cc_final: 0.5927 (mt0) REVERT: B 369 LYS cc_start: 0.6284 (tttt) cc_final: 0.6039 (tttp) REVERT: B 373 THR cc_start: 0.6716 (m) cc_final: 0.6229 (p) REVERT: C 307 GLN cc_start: 0.7313 (tt0) cc_final: 0.7014 (tt0) REVERT: C 331 LYS cc_start: 0.6490 (mttt) cc_final: 0.6013 (mtpt) REVERT: C 338 GLU cc_start: 0.6530 (tt0) cc_final: 0.6189 (mt-10) REVERT: C 340 LYS cc_start: 0.6934 (tttt) cc_final: 0.6220 (mttm) REVERT: C 342 GLU cc_start: 0.6457 (tt0) cc_final: 0.6231 (tt0) REVERT: C 347 LYS cc_start: 0.6654 (mttt) cc_final: 0.5705 (mppt) REVERT: C 349 ARG cc_start: 0.6280 (mtp180) cc_final: 0.6019 (mtt180) REVERT: C 351 GLN cc_start: 0.6762 (tt0) cc_final: 0.6537 (mt0) REVERT: C 369 LYS cc_start: 0.6721 (tttt) cc_final: 0.6413 (tttp) REVERT: C 373 THR cc_start: 0.7274 (m) cc_final: 0.6956 (p) REVERT: C 375 LYS cc_start: 0.7036 (tttt) cc_final: 0.6575 (tttp) REVERT: D 331 LYS cc_start: 0.6651 (mttt) cc_final: 0.6167 (mtpp) REVERT: D 338 GLU cc_start: 0.6702 (tt0) cc_final: 0.6286 (mt-10) REVERT: D 340 LYS cc_start: 0.6941 (tttt) cc_final: 0.6279 (mttt) REVERT: D 345 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.6784 (t70) REVERT: D 369 LYS cc_start: 0.6696 (tttt) cc_final: 0.6251 (tttp) REVERT: D 372 GLU cc_start: 0.6492 (tt0) cc_final: 0.6031 (mt-10) REVERT: D 373 THR cc_start: 0.7157 (m) cc_final: 0.6787 (p) REVERT: D 375 LYS cc_start: 0.6923 (tttt) cc_final: 0.6322 (ttpt) REVERT: E 331 LYS cc_start: 0.6806 (mttt) cc_final: 0.6320 (mtpt) REVERT: E 340 LYS cc_start: 0.6461 (tttt) cc_final: 0.5629 (mmpt) REVERT: E 351 GLN cc_start: 0.6217 (tt0) cc_final: 0.6000 (mt0) REVERT: E 369 LYS cc_start: 0.6388 (tttt) cc_final: 0.6079 (tttp) REVERT: E 373 THR cc_start: 0.6965 (m) cc_final: 0.6356 (p) REVERT: E 375 LYS cc_start: 0.6609 (tttt) cc_final: 0.6160 (ttpt) REVERT: F 331 LYS cc_start: 0.6684 (mttt) cc_final: 0.6369 (mtpp) REVERT: F 338 GLU cc_start: 0.6408 (tt0) cc_final: 0.5933 (mt-10) REVERT: F 340 LYS cc_start: 0.6324 (tttt) cc_final: 0.5607 (mttt) REVERT: F 345 ASP cc_start: 0.6688 (t0) cc_final: 0.6261 (m-30) REVERT: F 351 GLN cc_start: 0.6288 (tt0) cc_final: 0.6054 (mt0) REVERT: F 372 GLU cc_start: 0.6689 (tt0) cc_final: 0.6241 (mt-10) REVERT: F 373 THR cc_start: 0.6875 (m) cc_final: 0.6308 (p) REVERT: F 375 LYS cc_start: 0.6575 (tttt) cc_final: 0.6211 (tttp) outliers start: 3 outliers final: 0 residues processed: 121 average time/residue: 3.7233 time to fit residues: 458.6807 Evaluate side-chains 121 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain D 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: 6.9990 chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3498 Z= 0.296 Angle : 0.562 4.415 4680 Z= 0.294 Chirality : 0.050 0.126 528 Planarity : 0.004 0.029 594 Dihedral : 5.129 11.754 462 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 1.99 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: -0.67 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.50 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 330 PHE 0.009 0.002 PHE E 346 TYR 0.010 0.002 TYR E 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 119 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 117 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.5941 (mttt) cc_final: 0.5685 (mttm) REVERT: A 331 LYS cc_start: 0.6324 (mttt) cc_final: 0.5817 (mtpp) REVERT: A 345 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6375 (t70) REVERT: A 351 GLN cc_start: 0.6132 (tt0) cc_final: 0.5793 (mt0) REVERT: A 353 LYS cc_start: 0.5823 (mttt) cc_final: 0.5554 (tttm) REVERT: A 369 LYS cc_start: 0.6220 (tttt) cc_final: 0.5811 (tttp) REVERT: A 372 GLU cc_start: 0.6341 (tt0) cc_final: 0.5855 (mt-10) REVERT: A 373 THR cc_start: 0.6660 (m) cc_final: 0.6189 (p) REVERT: A 375 LYS cc_start: 0.6500 (tttt) cc_final: 0.5925 (ttpt) REVERT: B 307 GLN cc_start: 0.6784 (tt0) cc_final: 0.6461 (tt0) REVERT: B 317 LYS cc_start: 0.6066 (mttt) cc_final: 0.5793 (mttm) REVERT: B 331 LYS cc_start: 0.6590 (mttt) cc_final: 0.6082 (mtpm) REVERT: B 347 LYS cc_start: 0.7339 (mptm) cc_final: 0.6976 (mptp) REVERT: B 369 LYS cc_start: 0.6259 (tttt) cc_final: 0.6007 (tttp) REVERT: B 373 THR cc_start: 0.6775 (m) cc_final: 0.6272 (p) REVERT: C 307 GLN cc_start: 0.7359 (tt0) cc_final: 0.7071 (tt0) REVERT: C 331 LYS cc_start: 0.6464 (mttt) cc_final: 0.5999 (mtpt) REVERT: C 338 GLU cc_start: 0.6506 (tt0) cc_final: 0.6149 (mt-10) REVERT: C 340 LYS cc_start: 0.6885 (tttt) cc_final: 0.6205 (mttt) REVERT: C 342 GLU cc_start: 0.6488 (tt0) cc_final: 0.6257 (tt0) REVERT: C 347 LYS cc_start: 0.6671 (mttt) cc_final: 0.5760 (mppt) REVERT: C 349 ARG cc_start: 0.6306 (mtp180) cc_final: 0.6026 (mtt180) REVERT: C 351 GLN cc_start: 0.6770 (tt0) cc_final: 0.6520 (mt0) REVERT: C 369 LYS cc_start: 0.6691 (tttt) cc_final: 0.6372 (tttp) REVERT: C 373 THR cc_start: 0.7284 (m) cc_final: 0.6950 (p) REVERT: C 375 LYS cc_start: 0.7061 (tttt) cc_final: 0.6593 (tttp) REVERT: D 331 LYS cc_start: 0.6655 (mttt) cc_final: 0.6171 (mtpp) REVERT: D 345 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.6773 (t70) REVERT: D 369 LYS cc_start: 0.6729 (tttt) cc_final: 0.6337 (tttp) REVERT: D 372 GLU cc_start: 0.6479 (tt0) cc_final: 0.6049 (mt-10) REVERT: D 373 THR cc_start: 0.7165 (m) cc_final: 0.6801 (p) REVERT: D 375 LYS cc_start: 0.6875 (tttt) cc_final: 0.6290 (ttpt) REVERT: E 331 LYS cc_start: 0.6787 (mttt) cc_final: 0.6284 (mtpt) REVERT: E 340 LYS cc_start: 0.6497 (tttt) cc_final: 0.5685 (mmpt) REVERT: E 351 GLN cc_start: 0.6220 (tt0) cc_final: 0.6006 (mt0) REVERT: E 369 LYS cc_start: 0.6364 (tttt) cc_final: 0.6056 (tttp) REVERT: E 373 THR cc_start: 0.6928 (m) cc_final: 0.6330 (p) REVERT: E 375 LYS cc_start: 0.6605 (tttt) cc_final: 0.6155 (ttpt) REVERT: F 331 LYS cc_start: 0.6820 (mttt) cc_final: 0.6438 (mtpp) REVERT: F 338 GLU cc_start: 0.6407 (tt0) cc_final: 0.5931 (mt-10) REVERT: F 340 LYS cc_start: 0.6343 (tttt) cc_final: 0.5645 (mttt) REVERT: F 345 ASP cc_start: 0.6703 (t0) cc_final: 0.6351 (t0) REVERT: F 351 GLN cc_start: 0.6296 (tt0) cc_final: 0.6063 (mt0) REVERT: F 372 GLU cc_start: 0.6663 (tt0) cc_final: 0.6180 (mt-10) REVERT: F 373 THR cc_start: 0.6839 (m) cc_final: 0.6293 (p) REVERT: F 375 LYS cc_start: 0.6588 (tttt) cc_final: 0.6221 (tttp) outliers start: 2 outliers final: 0 residues processed: 117 average time/residue: 3.8799 time to fit residues: 462.2216 Evaluate side-chains 117 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 22 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.3772 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= 0.271 Angle : 0.546 4.211 4680 Z= 0.286 Chirality : 0.051 0.130 528 Planarity : 0.004 0.028 594 Dihedral : 5.088 11.732 462 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.01 % Allowed : 7.07 % 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 0.004 0.001 HIS C 330 PHE 0.009 0.002 PHE F 346 TYR 0.010 0.002 TYR B 310 ARG 0.003 0.000 ARG C 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 119 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 115 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.5987 (mttt) cc_final: 0.5758 (mttm) REVERT: A 331 LYS cc_start: 0.6344 (mttt) cc_final: 0.5838 (mtpp) REVERT: A 345 ASP cc_start: 0.7086 (OUTLIER) cc_final: 0.6370 (t70) REVERT: A 351 GLN cc_start: 0.6136 (tt0) cc_final: 0.5796 (mt0) REVERT: A 353 LYS cc_start: 0.5785 (mttt) cc_final: 0.5535 (tttm) REVERT: A 369 LYS cc_start: 0.6231 (tttt) cc_final: 0.5821 (tttp) REVERT: A 372 GLU cc_start: 0.6349 (tt0) cc_final: 0.5859 (mt-10) REVERT: A 373 THR cc_start: 0.6661 (m) cc_final: 0.6190 (p) REVERT: A 375 LYS cc_start: 0.6478 (tttt) cc_final: 0.5905 (ttpt) REVERT: B 307 GLN cc_start: 0.6795 (tt0) cc_final: 0.6479 (tt0) REVERT: B 317 LYS cc_start: 0.6034 (mttt) cc_final: 0.5768 (mttm) REVERT: B 331 LYS cc_start: 0.6606 (mttt) cc_final: 0.6104 (mtpm) REVERT: B 347 LYS cc_start: 0.7335 (mptm) cc_final: 0.7090 (mptp) REVERT: B 369 LYS cc_start: 0.6272 (tttt) cc_final: 0.5973 (tttp) REVERT: B 373 THR cc_start: 0.6757 (m) cc_final: 0.6256 (p) REVERT: C 307 GLN cc_start: 0.7352 (tt0) cc_final: 0.7081 (tt0) REVERT: C 331 LYS cc_start: 0.6453 (mttt) cc_final: 0.5986 (mtpt) REVERT: C 338 GLU cc_start: 0.6500 (tt0) cc_final: 0.6144 (mt-10) REVERT: C 340 LYS cc_start: 0.6881 (tttt) cc_final: 0.6195 (mttt) REVERT: C 342 GLU cc_start: 0.6498 (tt0) cc_final: 0.6245 (tt0) REVERT: C 347 LYS cc_start: 0.6693 (mttt) cc_final: 0.5740 (mppt) REVERT: C 349 ARG cc_start: 0.6334 (mtp180) cc_final: 0.6044 (mtt180) REVERT: C 351 GLN cc_start: 0.6787 (tt0) cc_final: 0.6529 (mt0) REVERT: C 369 LYS cc_start: 0.6673 (tttt) cc_final: 0.6351 (tttp) REVERT: C 373 THR cc_start: 0.7290 (m) cc_final: 0.6953 (p) REVERT: C 375 LYS cc_start: 0.7050 (tttt) cc_final: 0.6581 (tttp) REVERT: D 331 LYS cc_start: 0.6668 (mttt) cc_final: 0.6198 (mtpp) REVERT: D 345 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.6818 (m-30) REVERT: D 347 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.6182 (tppt) REVERT: D 369 LYS cc_start: 0.6711 (tttt) cc_final: 0.6248 (tttp) REVERT: D 372 GLU cc_start: 0.6468 (tt0) cc_final: 0.6068 (mt-10) REVERT: D 373 THR cc_start: 0.7151 (m) cc_final: 0.6785 (p) REVERT: D 375 LYS cc_start: 0.6913 (tttt) cc_final: 0.6312 (ttpt) REVERT: E 331 LYS cc_start: 0.6743 (mttt) cc_final: 0.6244 (mtpt) REVERT: E 340 LYS cc_start: 0.6483 (tttt) cc_final: 0.5660 (mmpt) REVERT: E 351 GLN cc_start: 0.6191 (tt0) cc_final: 0.5976 (mt0) REVERT: E 369 LYS cc_start: 0.6368 (tttt) cc_final: 0.6062 (tttp) REVERT: E 373 THR cc_start: 0.6929 (m) cc_final: 0.6329 (p) REVERT: E 375 LYS cc_start: 0.6603 (tttt) cc_final: 0.6150 (ttpt) REVERT: F 331 LYS cc_start: 0.6814 (mttt) cc_final: 0.6413 (mtpp) REVERT: F 338 GLU cc_start: 0.6404 (tt0) cc_final: 0.5926 (mt-10) REVERT: F 340 LYS cc_start: 0.6377 (tttt) cc_final: 0.5656 (mttt) REVERT: F 345 ASP cc_start: 0.6700 (t0) cc_final: 0.6333 (t0) REVERT: F 351 GLN cc_start: 0.6307 (tt0) cc_final: 0.6029 (mt0) REVERT: F 372 GLU cc_start: 0.6665 (tt0) cc_final: 0.6242 (mt-10) REVERT: F 373 THR cc_start: 0.6841 (m) cc_final: 0.6291 (p) REVERT: F 375 LYS cc_start: 0.6590 (tttt) cc_final: 0.6217 (tttp) outliers start: 4 outliers final: 1 residues processed: 116 average time/residue: 3.6907 time to fit residues: 435.9838 Evaluate side-chains 119 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 115 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 347 LYS Chi-restraints excluded: chain E residue 305 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.3789 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= 0.134 Angle : 0.465 3.890 4680 Z= 0.238 Chirality : 0.051 0.130 528 Planarity : 0.003 0.021 594 Dihedral : 4.807 11.690 462 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 0.76 % Allowed : 7.58 % Favored : 91.67 % 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: -0.55 (0.38), 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 HIS 0.002 0.001 HIS F 374 PHE 0.006 0.001 PHE F 346 TYR 0.008 0.001 TYR B 310 ARG 0.002 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 125 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 122 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.6044 (mttt) cc_final: 0.5808 (mttm) REVERT: A 331 LYS cc_start: 0.6333 (mttt) cc_final: 0.5830 (mtpp) REVERT: A 345 ASP cc_start: 0.7021 (OUTLIER) cc_final: 0.5982 (t70) REVERT: A 347 LYS cc_start: 0.6951 (mttt) cc_final: 0.6680 (mmtp) REVERT: A 351 GLN cc_start: 0.6102 (tt0) cc_final: 0.5801 (mt0) REVERT: A 353 LYS cc_start: 0.5844 (mttt) cc_final: 0.5531 (tttm) REVERT: A 369 LYS cc_start: 0.6243 (tttt) cc_final: 0.5842 (tttp) REVERT: A 372 GLU cc_start: 0.6367 (tt0) cc_final: 0.5886 (mt-10) REVERT: A 373 THR cc_start: 0.6639 (m) cc_final: 0.6172 (p) REVERT: A 375 LYS cc_start: 0.6481 (tttt) cc_final: 0.5887 (ttpt) REVERT: B 307 GLN cc_start: 0.6780 (tt0) cc_final: 0.6458 (tt0) REVERT: B 317 LYS cc_start: 0.6024 (mttt) cc_final: 0.5761 (mttm) REVERT: B 331 LYS cc_start: 0.6591 (mttt) cc_final: 0.6095 (mtpm) REVERT: B 347 LYS cc_start: 0.7399 (mptm) cc_final: 0.7105 (mptp) REVERT: B 369 LYS cc_start: 0.6266 (tttt) cc_final: 0.6006 (tttp) REVERT: B 373 THR cc_start: 0.6697 (m) cc_final: 0.6205 (p) REVERT: C 331 LYS cc_start: 0.6501 (mttt) cc_final: 0.6027 (mtpt) REVERT: C 338 GLU cc_start: 0.6500 (tt0) cc_final: 0.6179 (mt-10) REVERT: C 340 LYS cc_start: 0.6839 (tttt) cc_final: 0.6168 (mttt) REVERT: C 342 GLU cc_start: 0.6496 (tt0) cc_final: 0.6258 (tt0) REVERT: C 347 LYS cc_start: 0.6737 (mttt) cc_final: 0.5764 (mppt) REVERT: C 349 ARG cc_start: 0.6327 (mtp180) cc_final: 0.6011 (mtt180) REVERT: C 351 GLN cc_start: 0.6771 (tt0) cc_final: 0.6522 (mt0) REVERT: C 369 LYS cc_start: 0.6672 (tttt) cc_final: 0.6373 (tttp) REVERT: C 373 THR cc_start: 0.7289 (m) cc_final: 0.6968 (p) REVERT: C 375 LYS cc_start: 0.7047 (tttt) cc_final: 0.6575 (tttp) REVERT: D 331 LYS cc_start: 0.6643 (mttt) cc_final: 0.6179 (mtpp) REVERT: D 345 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.7081 (m-30) REVERT: D 369 LYS cc_start: 0.6698 (tttt) cc_final: 0.6240 (tttp) REVERT: D 372 GLU cc_start: 0.6504 (tt0) cc_final: 0.6040 (mt-10) REVERT: D 373 THR cc_start: 0.7147 (m) cc_final: 0.6787 (p) REVERT: D 375 LYS cc_start: 0.6945 (tttt) cc_final: 0.6332 (ttpt) REVERT: E 331 LYS cc_start: 0.6738 (mttt) cc_final: 0.6249 (mtpt) REVERT: E 338 GLU cc_start: 0.6352 (tt0) cc_final: 0.5483 (mt-10) REVERT: E 340 LYS cc_start: 0.6450 (tttt) cc_final: 0.5616 (mmpt) REVERT: E 351 GLN cc_start: 0.6218 (tt0) cc_final: 0.6009 (mt0) REVERT: E 369 LYS cc_start: 0.6362 (tttt) cc_final: 0.6062 (tttp) REVERT: E 373 THR cc_start: 0.6934 (m) cc_final: 0.6328 (p) REVERT: E 375 LYS cc_start: 0.6598 (tttt) cc_final: 0.6186 (ttpt) REVERT: F 331 LYS cc_start: 0.6798 (mttt) cc_final: 0.6360 (mtpp) REVERT: F 338 GLU cc_start: 0.6404 (tt0) cc_final: 0.5940 (mt-10) REVERT: F 340 LYS cc_start: 0.6367 (tttt) cc_final: 0.5606 (mttt) REVERT: F 345 ASP cc_start: 0.6720 (t0) cc_final: 0.6323 (m-30) REVERT: F 351 GLN cc_start: 0.6280 (tt0) cc_final: 0.6033 (mt0) REVERT: F 372 GLU cc_start: 0.6687 (tt0) cc_final: 0.6247 (mt-10) REVERT: F 373 THR cc_start: 0.6893 (m) cc_final: 0.6327 (p) REVERT: F 375 LYS cc_start: 0.6549 (tttt) cc_final: 0.6180 (tttp) outliers start: 3 outliers final: 1 residues processed: 123 average time/residue: 3.7822 time to fit residues: 473.7702 Evaluate side-chains 125 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 122 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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=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: 4.9990 chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3498 Z= 0.159 Angle : 0.473 3.949 4680 Z= 0.242 Chirality : 0.051 0.129 528 Planarity : 0.003 0.023 594 Dihedral : 4.769 11.589 462 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 0.51 % Allowed : 8.08 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 0.002 0.001 HIS C 330 PHE 0.006 0.001 PHE B 346 TYR 0.008 0.001 TYR B 310 ARG 0.001 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 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: A 317 LYS cc_start: 0.6023 (mttt) cc_final: 0.5794 (mttm) REVERT: A 331 LYS cc_start: 0.6341 (mttt) cc_final: 0.5835 (mtpp) REVERT: A 345 ASP cc_start: 0.7045 (OUTLIER) cc_final: 0.6034 (t70) REVERT: A 347 LYS cc_start: 0.6941 (mttt) cc_final: 0.6678 (mmtp) REVERT: A 351 GLN cc_start: 0.6098 (tt0) cc_final: 0.5810 (mt0) REVERT: A 353 LYS cc_start: 0.5872 (mttt) cc_final: 0.5547 (tttm) REVERT: A 369 LYS cc_start: 0.6243 (tttt) cc_final: 0.5845 (tttp) REVERT: A 372 GLU cc_start: 0.6382 (tt0) cc_final: 0.5868 (mt-10) REVERT: A 373 THR cc_start: 0.6629 (m) cc_final: 0.6165 (p) REVERT: A 375 LYS cc_start: 0.6474 (tttt) cc_final: 0.5894 (ttpt) REVERT: B 307 GLN cc_start: 0.6775 (tt0) cc_final: 0.6455 (tt0) REVERT: B 317 LYS cc_start: 0.6024 (mttt) cc_final: 0.5756 (mttm) REVERT: B 331 LYS cc_start: 0.6593 (mttt) cc_final: 0.6093 (mtpm) REVERT: B 338 GLU cc_start: 0.6275 (tt0) cc_final: 0.5731 (mt-10) REVERT: B 340 LYS cc_start: 0.6417 (tttt) cc_final: 0.5688 (mttt) REVERT: B 347 LYS cc_start: 0.7417 (mptm) cc_final: 0.7135 (mptp) REVERT: B 369 LYS cc_start: 0.6234 (tttt) cc_final: 0.5977 (tttp) REVERT: B 373 THR cc_start: 0.6714 (m) cc_final: 0.6219 (p) REVERT: C 331 LYS cc_start: 0.6515 (mttt) cc_final: 0.6034 (mtpt) REVERT: C 338 GLU cc_start: 0.6506 (tt0) cc_final: 0.6177 (mt-10) REVERT: C 340 LYS cc_start: 0.6883 (tttt) cc_final: 0.6174 (mttt) REVERT: C 342 GLU cc_start: 0.6494 (tt0) cc_final: 0.6257 (tt0) REVERT: C 347 LYS cc_start: 0.6726 (mttt) cc_final: 0.5757 (mppt) REVERT: C 349 ARG cc_start: 0.6292 (mtp180) cc_final: 0.6051 (mtt180) REVERT: C 351 GLN cc_start: 0.6742 (tt0) cc_final: 0.6497 (mt0) REVERT: C 369 LYS cc_start: 0.6671 (tttt) cc_final: 0.6367 (tttp) REVERT: C 373 THR cc_start: 0.7294 (m) cc_final: 0.6968 (p) REVERT: C 375 LYS cc_start: 0.7042 (tttt) cc_final: 0.6576 (tttp) REVERT: D 331 LYS cc_start: 0.6556 (mttt) cc_final: 0.6094 (mtpp) REVERT: D 345 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.7079 (m-30) REVERT: D 369 LYS cc_start: 0.6707 (tttt) cc_final: 0.6247 (tttp) REVERT: D 372 GLU cc_start: 0.6546 (tt0) cc_final: 0.6059 (mt-10) REVERT: D 373 THR cc_start: 0.7144 (m) cc_final: 0.6783 (p) REVERT: D 375 LYS cc_start: 0.6915 (tttt) cc_final: 0.6306 (ttpt) REVERT: E 331 LYS cc_start: 0.6749 (mttt) cc_final: 0.6262 (mtpt) REVERT: E 340 LYS cc_start: 0.6444 (tttt) cc_final: 0.5630 (mmpt) REVERT: E 351 GLN cc_start: 0.6172 (tt0) cc_final: 0.5966 (mt0) REVERT: E 369 LYS cc_start: 0.6364 (tttt) cc_final: 0.6101 (tttp) REVERT: E 373 THR cc_start: 0.6933 (m) cc_final: 0.6321 (p) REVERT: E 375 LYS cc_start: 0.6554 (tttt) cc_final: 0.6149 (ttpt) REVERT: F 331 LYS cc_start: 0.6809 (mttt) cc_final: 0.6392 (mtpp) REVERT: F 338 GLU cc_start: 0.6395 (tt0) cc_final: 0.5927 (mt-10) REVERT: F 340 LYS cc_start: 0.6357 (tttt) cc_final: 0.5593 (mttt) REVERT: F 345 ASP cc_start: 0.6742 (t0) cc_final: 0.6319 (m-30) REVERT: F 351 GLN cc_start: 0.6276 (tt0) cc_final: 0.6038 (mt0) REVERT: F 372 GLU cc_start: 0.6688 (tt0) cc_final: 0.6246 (mt-10) REVERT: F 373 THR cc_start: 0.6903 (m) cc_final: 0.6331 (p) REVERT: F 375 LYS cc_start: 0.6554 (tttt) cc_final: 0.6189 (tttp) outliers start: 2 outliers final: 0 residues processed: 119 average time/residue: 3.7082 time to fit residues: 449.4249 Evaluate side-chains 121 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain D 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: 2.9990 chunk 26 optimal weight: 8.9990 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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: 0.6546 moved from start: 0.3847 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= 0.168 Angle : 0.479 3.926 4680 Z= 0.247 Chirality : 0.050 0.124 528 Planarity : 0.003 0.026 594 Dihedral : 4.811 11.520 462 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 0.51 % Allowed : 8.08 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.53 (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 HIS 0.003 0.001 HIS C 330 PHE 0.007 0.002 PHE F 346 TYR 0.008 0.002 TYR B 310 ARG 0.002 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 123 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 121 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.6351 (mttt) cc_final: 0.5845 (mtpp) REVERT: A 345 ASP cc_start: 0.6971 (OUTLIER) cc_final: 0.6038 (t70) REVERT: A 347 LYS cc_start: 0.6959 (mttt) cc_final: 0.6615 (mmtp) REVERT: A 351 GLN cc_start: 0.6096 (tt0) cc_final: 0.5810 (mt0) REVERT: A 353 LYS cc_start: 0.5846 (mttt) cc_final: 0.5524 (tttm) REVERT: A 369 LYS cc_start: 0.6212 (tttt) cc_final: 0.5815 (tttp) REVERT: A 372 GLU cc_start: 0.6358 (tt0) cc_final: 0.5868 (mt-10) REVERT: A 373 THR cc_start: 0.6646 (m) cc_final: 0.6181 (p) REVERT: A 375 LYS cc_start: 0.6473 (tttt) cc_final: 0.5892 (ttpt) REVERT: B 307 GLN cc_start: 0.6765 (tt0) cc_final: 0.6435 (tt0) REVERT: B 317 LYS cc_start: 0.6014 (mttt) cc_final: 0.5750 (mttm) REVERT: B 331 LYS cc_start: 0.6602 (mttt) cc_final: 0.6099 (mtpm) REVERT: B 347 LYS cc_start: 0.7441 (mptm) cc_final: 0.7147 (mptp) REVERT: B 369 LYS cc_start: 0.6226 (tttt) cc_final: 0.5968 (tttp) REVERT: B 373 THR cc_start: 0.6730 (m) cc_final: 0.6226 (p) REVERT: C 331 LYS cc_start: 0.6506 (mttt) cc_final: 0.6031 (mtpt) REVERT: C 338 GLU cc_start: 0.6512 (tt0) cc_final: 0.6180 (mt-10) REVERT: C 340 LYS cc_start: 0.6895 (tttt) cc_final: 0.6193 (mttm) REVERT: C 342 GLU cc_start: 0.6491 (tt0) cc_final: 0.6269 (tt0) REVERT: C 345 ASP cc_start: 0.7540 (t70) cc_final: 0.6744 (m-30) REVERT: C 347 LYS cc_start: 0.6736 (mttt) cc_final: 0.5770 (mppt) REVERT: C 349 ARG cc_start: 0.6300 (mtp180) cc_final: 0.6048 (mtt180) REVERT: C 351 GLN cc_start: 0.6749 (tt0) cc_final: 0.6504 (mt0) REVERT: C 369 LYS cc_start: 0.6674 (tttt) cc_final: 0.6370 (tttp) REVERT: C 373 THR cc_start: 0.7283 (m) cc_final: 0.6954 (p) REVERT: C 375 LYS cc_start: 0.7049 (tttt) cc_final: 0.6583 (tttp) REVERT: D 331 LYS cc_start: 0.6656 (mttt) cc_final: 0.6199 (mtpp) REVERT: D 345 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.7060 (m-30) REVERT: D 369 LYS cc_start: 0.6727 (tttt) cc_final: 0.6268 (tttp) REVERT: D 372 GLU cc_start: 0.6538 (tt0) cc_final: 0.6052 (mt-10) REVERT: D 373 THR cc_start: 0.7139 (m) cc_final: 0.6786 (p) REVERT: D 375 LYS cc_start: 0.6920 (tttt) cc_final: 0.6309 (ttpt) REVERT: E 331 LYS cc_start: 0.6768 (mttt) cc_final: 0.6274 (mtpt) REVERT: E 340 LYS cc_start: 0.6451 (tttt) cc_final: 0.5627 (mmpt) REVERT: E 351 GLN cc_start: 0.6173 (tt0) cc_final: 0.5968 (mt0) REVERT: E 369 LYS cc_start: 0.6368 (tttt) cc_final: 0.6103 (tttp) REVERT: E 373 THR cc_start: 0.6960 (m) cc_final: 0.6337 (p) REVERT: E 375 LYS cc_start: 0.6567 (tttt) cc_final: 0.6090 (ttpt) REVERT: F 331 LYS cc_start: 0.6844 (mttt) cc_final: 0.6414 (mtpp) REVERT: F 338 GLU cc_start: 0.6396 (tt0) cc_final: 0.5931 (mt-10) REVERT: F 340 LYS cc_start: 0.6364 (tttt) cc_final: 0.5616 (mttt) REVERT: F 345 ASP cc_start: 0.6721 (t0) cc_final: 0.6268 (m-30) REVERT: F 351 GLN cc_start: 0.6287 (tt0) cc_final: 0.6043 (mt0) REVERT: F 372 GLU cc_start: 0.6716 (tt0) cc_final: 0.6299 (mt-10) REVERT: F 373 THR cc_start: 0.6900 (m) cc_final: 0.6330 (p) REVERT: F 375 LYS cc_start: 0.6554 (tttt) cc_final: 0.6183 (tttp) outliers start: 2 outliers final: 0 residues processed: 121 average time/residue: 3.6708 time to fit residues: 452.3157 Evaluate side-chains 122 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 120 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain D residue 345 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 28 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 41 optimal weight: 0.4980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4118 r_free = 0.4118 target = 0.152969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.139613 restraints weight = 7755.475| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 0.72 r_work: 0.3893 rms_B_bonded: 0.68 restraints_weight: 0.5000 r_work: 0.3833 rms_B_bonded: 1.19 restraints_weight: 0.2500 r_work: 0.3672 rms_B_bonded: 3.42 restraints_weight: 0.1250 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 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 : 0.002 0.016 3498 Z= 0.120 Angle : 0.448 3.875 4680 Z= 0.227 Chirality : 0.051 0.129 528 Planarity : 0.002 0.021 594 Dihedral : 4.608 11.501 462 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 0.51 % Allowed : 8.08 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.44 (0.39), 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 0.002 0.001 HIS F 374 PHE 0.005 0.001 PHE F 346 TYR 0.007 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: 7267.42 seconds wall clock time: 126 minutes 36.43 seconds (7596.43 seconds total)