Starting phenix.real_space_refine on Sat Aug 3 04:04:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9h_18281/08_2024/8q9h_18281.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9h_18281/08_2024/8q9h_18281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9h_18281/08_2024/8q9h_18281.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9h_18281/08_2024/8q9h_18281.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9h_18281/08_2024/8q9h_18281.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9h_18281/08_2024/8q9h_18281.cif" } resolution = 2.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2106 2.51 5 N 606 2.21 5 O 624 1.98 5 H 3480 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 338": "OE1" <-> "OE2" Residue "A ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 372": "OE1" <-> "OE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 372": "OE1" <-> "OE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 372": "OE1" <-> "OE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 372": "OE1" <-> "OE2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 372": "OE1" <-> "OE2" Residue "G GLU 338": "OE1" <-> "OE2" Residue "G ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 372": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6822 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "B" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "C" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "D" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "E" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "G" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 3.85, per 1000 atoms: 0.56 Number of scatterers: 6822 At special positions: 0 Unit cell: (98.872, 137.403, 35.623, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 624 8.00 N 606 7.00 C 2106 6.00 H 3480 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 4.58 Conformation dependent library (CDL) restraints added in 794.2 milliseconds 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 49.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 307 through 310 removed outlier: 6.515A pdb=" N GLN A 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N TYR E 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL A 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.663A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 321 removed outlier: 6.345A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 325 through 330 removed outlier: 5.840A pdb=" N GLY A 326 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N HIS C 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY E 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN A 327 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 342 Processing sheet with id=AA6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.439A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 350 through 357 removed outlier: 6.567A pdb=" N GLN A 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ILE E 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LYS A 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N SER E 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLY A 355 " --> pdb=" O SER E 356 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.457A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 369 through 377 removed outlier: 6.365A pdb=" N LYS A 370 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N THR C 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLU A 372 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N LYS C 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N HIS A 374 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N THR C 377 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU A 376 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LYS A 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLU E 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE A 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N HIS E 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N THR A 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LEU E 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LYS A 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 307 through 310 removed outlier: 6.557A pdb=" N GLN B 307 " --> pdb=" O ILE G 308 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N TYR G 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL B 309 " --> pdb=" O TYR G 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.642A pdb=" N VAL B 313 " --> pdb=" O ASP G 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 317 through 321 removed outlier: 6.327A pdb=" N VAL D 318 " --> pdb=" O THR G 319 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N LYS G 321 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N SER D 320 " --> pdb=" O LYS G 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 325 through 330 removed outlier: 8.808A pdb=" N LEU B 325 " --> pdb=" O GLY G 326 " (cutoff:3.500A) removed outlier: 9.778A pdb=" N ILE G 328 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASN B 327 " --> pdb=" O ILE G 328 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N HIS G 330 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N HIS B 329 " --> pdb=" O HIS G 330 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N GLY D 326 " --> pdb=" O ASN G 327 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N HIS G 329 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE D 328 " --> pdb=" O HIS G 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 337 through 342 removed outlier: 6.532A pdb=" N GLU B 338 " --> pdb=" O VAL G 339 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N SER G 341 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LYS B 340 " --> pdb=" O SER G 341 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL D 337 " --> pdb=" O GLU G 338 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LYS G 340 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL D 339 " --> pdb=" O LYS G 340 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLU G 342 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N SER D 341 " --> pdb=" O GLU G 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 345 through 346 removed outlier: 6.422A pdb=" N ASP B 345 " --> pdb=" O PHE G 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 350 through 357 removed outlier: 6.574A pdb=" N GLN B 351 " --> pdb=" O SER G 352 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ILE G 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LYS B 353 " --> pdb=" O ILE G 354 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N SER G 356 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLY B 355 " --> pdb=" O SER G 356 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 360 through 362 removed outlier: 6.412A pdb=" N THR D 361 " --> pdb=" O HIS G 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 369 through 377 65 hydrogen bonds defined for protein. 195 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: 2.05 Time building geometry restraints manager: 4.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 3474 1.12 - 1.29: 558 1.29 - 1.46: 992 1.46 - 1.64: 1846 1.64 - 1.81: 6 Bond restraints: 6876 Sorted by residual: bond pdb=" CE1 HIS A 330 " pdb=" HE1 HIS A 330 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N ASN E 359 " pdb=" H ASN E 359 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N LEU C 325 " pdb=" H LEU C 325 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" ND2 ASN B 359 " pdb="HD22 ASN B 359 " 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 C 306 " pdb=" H VAL C 306 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 6871 not shown) Histogram of bond angle deviations from ideal: 96.88 - 103.25: 25 103.25 - 109.62: 5504 109.62 - 115.99: 3481 115.99 - 122.35: 2774 122.35 - 128.72: 762 Bond angle restraints: 12546 Sorted by residual: angle pdb=" CB HIS G 329 " pdb=" CG HIS G 329 " pdb=" CD2 HIS G 329 " ideal model delta sigma weight residual 131.20 125.24 5.96 1.30e+00 5.92e-01 2.10e+01 angle pdb=" CB HIS A 329 " pdb=" CG HIS A 329 " pdb=" CD2 HIS A 329 " ideal model delta sigma weight residual 131.20 125.29 5.91 1.30e+00 5.92e-01 2.07e+01 angle pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " pdb=" CD2 HIS E 374 " ideal model delta sigma weight residual 131.20 125.44 5.76 1.30e+00 5.92e-01 1.97e+01 angle pdb=" N GLY G 326 " pdb=" CA GLY G 326 " pdb=" C GLY G 326 " ideal model delta sigma weight residual 110.69 116.56 -5.87 1.33e+00 5.65e-01 1.95e+01 angle pdb=" CB HIS D 329 " pdb=" CG HIS D 329 " pdb=" CD2 HIS D 329 " ideal model delta sigma weight residual 131.20 125.49 5.71 1.30e+00 5.92e-01 1.93e+01 ... (remaining 12541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.36: 2753 13.36 - 26.73: 203 26.73 - 40.09: 86 40.09 - 53.45: 40 53.45 - 66.81: 86 Dihedral angle restraints: 3168 sinusoidal: 1806 harmonic: 1362 Sorted by residual: dihedral pdb=" CA THR C 319 " pdb=" C THR C 319 " pdb=" N SER C 320 " pdb=" CA SER C 320 " ideal model delta harmonic sigma weight residual 180.00 157.49 22.51 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA THR A 319 " pdb=" C THR A 319 " pdb=" N SER A 320 " pdb=" CA SER A 320 " ideal model delta harmonic sigma weight residual 180.00 158.95 21.05 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA THR G 319 " pdb=" C THR G 319 " pdb=" N SER G 320 " pdb=" CA SER G 320 " ideal model delta harmonic sigma weight residual 180.00 160.23 19.77 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 3165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 198 0.046 - 0.093: 190 0.093 - 0.139: 79 0.139 - 0.185: 36 0.185 - 0.231: 13 Chirality restraints: 516 Sorted by residual: chirality pdb=" CA LYS C 347 " pdb=" N LYS C 347 " pdb=" C LYS C 347 " pdb=" CB LYS C 347 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA LYS B 331 " pdb=" N LYS B 331 " pdb=" C LYS B 331 " pdb=" CB LYS B 331 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA LYS C 331 " pdb=" N LYS C 331 " pdb=" C LYS C 331 " pdb=" CB LYS C 331 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 513 not shown) Planarity restraints: 990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 310 " 0.102 2.00e-02 2.50e+03 4.08e-02 5.01e+01 pdb=" CG TYR B 310 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR B 310 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR B 310 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR B 310 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR B 310 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR B 310 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 310 " 0.053 2.00e-02 2.50e+03 pdb=" HD1 TYR B 310 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR B 310 " -0.017 2.00e-02 2.50e+03 pdb=" HE1 TYR B 310 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 TYR B 310 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " -0.095 2.00e-02 2.50e+03 3.82e-02 4.38e+01 pdb=" CG TYR C 310 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " -0.050 2.00e-02 2.50e+03 pdb=" HD1 TYR C 310 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 TYR C 310 " 0.015 2.00e-02 2.50e+03 pdb=" HE1 TYR C 310 " -0.004 2.00e-02 2.50e+03 pdb=" HE2 TYR C 310 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " -0.091 2.00e-02 2.50e+03 3.75e-02 4.21e+01 pdb=" CG TYR A 310 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.063 2.00e-02 2.50e+03 pdb=" HD1 TYR A 310 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 TYR A 310 " 0.015 2.00e-02 2.50e+03 pdb=" HE1 TYR A 310 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR A 310 " -0.005 2.00e-02 2.50e+03 ... (remaining 987 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 542 2.18 - 2.79: 12035 2.79 - 3.39: 17518 3.39 - 4.00: 24456 4.00 - 4.60: 33284 Nonbonded interactions: 87835 Sorted by model distance: nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.580 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.587 2.450 nonbonded pdb=" OD1 ASP G 314 " pdb=" HG SER G 316 " model vdw 1.610 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.613 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.616 2.450 ... (remaining 87830 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'G' } 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: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 23.820 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 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 3396 Z= 0.725 Angle : 1.727 5.962 4548 Z= 1.150 Chirality : 0.083 0.231 516 Planarity : 0.010 0.049 576 Dihedral : 10.930 59.436 1296 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.32), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.90 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.004 HIS G 330 PHE 0.033 0.010 PHE C 378 TYR 0.096 0.031 TYR B 310 ARG 0.004 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 SER cc_start: 0.8009 (t) cc_final: 0.7790 (p) REVERT: A 340 LYS cc_start: 0.7620 (mtpt) cc_final: 0.7093 (mttt) REVERT: A 369 LYS cc_start: 0.7334 (mttt) cc_final: 0.6724 (mtpm) REVERT: A 372 GLU cc_start: 0.7210 (tt0) cc_final: 0.6830 (tt0) REVERT: B 311 LYS cc_start: 0.5947 (ttpt) cc_final: 0.5522 (mttm) REVERT: B 321 LYS cc_start: 0.7499 (ttpt) cc_final: 0.7117 (mtpm) REVERT: B 340 LYS cc_start: 0.7691 (mtpt) cc_final: 0.7208 (mttm) REVERT: B 343 LYS cc_start: 0.8258 (mttt) cc_final: 0.7770 (mtpt) REVERT: B 349 ARG cc_start: 0.7189 (mtt180) cc_final: 0.5521 (mmp-170) REVERT: B 369 LYS cc_start: 0.7307 (mttt) cc_final: 0.6725 (mtpm) REVERT: B 372 GLU cc_start: 0.7526 (tt0) cc_final: 0.7214 (tt0) REVERT: C 311 LYS cc_start: 0.5871 (ttpt) cc_final: 0.5476 (tptt) REVERT: C 340 LYS cc_start: 0.7646 (mtpt) cc_final: 0.7330 (mttm) REVERT: C 343 LYS cc_start: 0.8247 (mttt) cc_final: 0.7994 (mttm) REVERT: C 349 ARG cc_start: 0.7211 (mtt180) cc_final: 0.5500 (mmp-170) REVERT: C 372 GLU cc_start: 0.7646 (tt0) cc_final: 0.7124 (tp30) REVERT: D 311 LYS cc_start: 0.6851 (ttpt) cc_final: 0.6101 (ttpp) REVERT: D 316 SER cc_start: 0.6513 (m) cc_final: 0.6258 (p) REVERT: D 321 LYS cc_start: 0.8006 (ttpt) cc_final: 0.7806 (ttmm) REVERT: D 340 LYS cc_start: 0.7851 (mtpt) cc_final: 0.7480 (mttm) REVERT: D 349 ARG cc_start: 0.7353 (mtt180) cc_final: 0.5359 (pmt-80) REVERT: D 369 LYS cc_start: 0.7887 (mttt) cc_final: 0.7258 (mtpm) REVERT: D 375 LYS cc_start: 0.6772 (tttt) cc_final: 0.6371 (tttm) REVERT: E 311 LYS cc_start: 0.7090 (ttpt) cc_final: 0.6297 (ttpp) REVERT: E 340 LYS cc_start: 0.7809 (mtpt) cc_final: 0.7415 (mttp) REVERT: E 349 ARG cc_start: 0.7391 (mtt180) cc_final: 0.5307 (pmt-80) REVERT: G 340 LYS cc_start: 0.7460 (mtpt) cc_final: 0.7214 (mttm) REVERT: G 369 LYS cc_start: 0.7225 (mttt) cc_final: 0.6750 (mptt) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 3.0419 time to fit residues: 453.4738 Evaluate side-chains 126 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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: 6.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS D 351 GLN D 362 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3396 Z= 0.223 Angle : 0.601 4.520 4548 Z= 0.319 Chirality : 0.052 0.142 516 Planarity : 0.003 0.019 576 Dihedral : 5.851 15.350 444 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.56 % Allowed : 11.72 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.34), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.91 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 362 PHE 0.007 0.001 PHE G 346 TYR 0.018 0.004 TYR D 310 ARG 0.002 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 133 time to evaluate : 0.577 Fit side-chains REVERT: A 340 LYS cc_start: 0.7771 (mtpt) cc_final: 0.7307 (mttt) REVERT: A 343 LYS cc_start: 0.8178 (mtmt) cc_final: 0.7810 (mttm) REVERT: A 349 ARG cc_start: 0.7124 (mtt180) cc_final: 0.6603 (mtp85) REVERT: A 369 LYS cc_start: 0.7345 (mttt) cc_final: 0.6735 (mtpm) REVERT: A 372 GLU cc_start: 0.7235 (tt0) cc_final: 0.6968 (tp30) REVERT: B 311 LYS cc_start: 0.6601 (ttpt) cc_final: 0.6036 (mttm) REVERT: B 321 LYS cc_start: 0.7635 (ttpt) cc_final: 0.7432 (ttmm) REVERT: B 349 ARG cc_start: 0.7321 (mtt180) cc_final: 0.5463 (mmp-170) REVERT: B 369 LYS cc_start: 0.7339 (mttt) cc_final: 0.6711 (mtpm) REVERT: B 372 GLU cc_start: 0.7745 (tt0) cc_final: 0.7306 (tt0) REVERT: C 311 LYS cc_start: 0.6360 (ttpt) cc_final: 0.5829 (tptt) REVERT: C 340 LYS cc_start: 0.7797 (mtpt) cc_final: 0.7501 (mttm) REVERT: C 343 LYS cc_start: 0.8345 (mttt) cc_final: 0.8080 (mttm) REVERT: C 349 ARG cc_start: 0.7409 (mtt180) cc_final: 0.5634 (mmp-170) REVERT: C 369 LYS cc_start: 0.7703 (mttt) cc_final: 0.7029 (mtpm) REVERT: C 372 GLU cc_start: 0.7811 (tt0) cc_final: 0.7373 (tt0) REVERT: D 311 LYS cc_start: 0.6751 (ttpt) cc_final: 0.6185 (ttpp) REVERT: D 316 SER cc_start: 0.6358 (m) cc_final: 0.6152 (p) REVERT: D 340 LYS cc_start: 0.7977 (mtpt) cc_final: 0.7621 (mttm) REVERT: D 349 ARG cc_start: 0.7200 (mtt180) cc_final: 0.5330 (pmt-80) REVERT: D 369 LYS cc_start: 0.7846 (mttt) cc_final: 0.7247 (mtpm) REVERT: D 375 LYS cc_start: 0.6880 (tttt) cc_final: 0.6389 (mtpm) REVERT: E 311 LYS cc_start: 0.7143 (ttpt) cc_final: 0.6320 (ttpp) REVERT: E 314 ASP cc_start: 0.6507 (t0) cc_final: 0.5902 (t0) REVERT: E 340 LYS cc_start: 0.8029 (mtpt) cc_final: 0.7779 (mttm) REVERT: E 349 ARG cc_start: 0.7456 (mtt180) cc_final: 0.5321 (pmt-80) REVERT: E 372 GLU cc_start: 0.7379 (tt0) cc_final: 0.7159 (tt0) REVERT: G 314 ASP cc_start: 0.6185 (t0) cc_final: 0.5749 (t0) REVERT: G 340 LYS cc_start: 0.7720 (mtpt) cc_final: 0.7444 (mttm) REVERT: G 369 LYS cc_start: 0.7251 (mttt) cc_final: 0.6740 (mtpm) REVERT: G 370 LYS cc_start: 0.6792 (tttp) cc_final: 0.6570 (tttt) outliers start: 6 outliers final: 1 residues processed: 136 average time/residue: 2.9095 time to fit residues: 403.9608 Evaluate side-chains 124 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 331 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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: 0.7770 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3396 Z= 0.171 Angle : 0.551 4.587 4548 Z= 0.287 Chirality : 0.051 0.143 516 Planarity : 0.002 0.014 576 Dihedral : 4.997 13.726 444 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.04 % Allowed : 15.89 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.34), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.06 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 362 PHE 0.004 0.001 PHE G 346 TYR 0.013 0.003 TYR D 310 ARG 0.000 0.000 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 132 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7787 (mtpt) cc_final: 0.7333 (mttt) REVERT: A 343 LYS cc_start: 0.8170 (mtmt) cc_final: 0.7874 (mttm) REVERT: A 349 ARG cc_start: 0.7153 (mtt180) cc_final: 0.6792 (mtp85) REVERT: A 369 LYS cc_start: 0.7359 (mttt) cc_final: 0.6783 (mtpm) REVERT: A 372 GLU cc_start: 0.7274 (tt0) cc_final: 0.6971 (tt0) REVERT: B 311 LYS cc_start: 0.6464 (ttpt) cc_final: 0.6076 (mtpp) REVERT: B 319 THR cc_start: 0.7241 (m) cc_final: 0.6571 (p) REVERT: B 340 LYS cc_start: 0.7906 (mtpp) cc_final: 0.7282 (mttm) REVERT: B 343 LYS cc_start: 0.8407 (mttt) cc_final: 0.7906 (mtpt) REVERT: B 349 ARG cc_start: 0.7309 (mtt180) cc_final: 0.5421 (mmp-170) REVERT: B 369 LYS cc_start: 0.7347 (mttt) cc_final: 0.6705 (mtpm) REVERT: B 372 GLU cc_start: 0.7748 (tt0) cc_final: 0.7522 (tt0) REVERT: C 311 LYS cc_start: 0.6331 (ttpt) cc_final: 0.5798 (mmtt) REVERT: C 340 LYS cc_start: 0.7802 (mtpt) cc_final: 0.7544 (mttm) REVERT: C 349 ARG cc_start: 0.7447 (mtt180) cc_final: 0.5652 (mmp-170) REVERT: C 369 LYS cc_start: 0.7697 (mttt) cc_final: 0.7042 (mtpm) REVERT: C 372 GLU cc_start: 0.7874 (tt0) cc_final: 0.7448 (tt0) REVERT: D 311 LYS cc_start: 0.6790 (ttpt) cc_final: 0.6312 (ttpp) REVERT: D 316 SER cc_start: 0.6471 (m) cc_final: 0.6192 (p) REVERT: D 349 ARG cc_start: 0.7290 (mtt180) cc_final: 0.5325 (pmt-80) REVERT: D 369 LYS cc_start: 0.7926 (mttt) cc_final: 0.7261 (mtpm) REVERT: E 311 LYS cc_start: 0.7136 (ttpt) cc_final: 0.6338 (ttpp) REVERT: E 314 ASP cc_start: 0.6653 (t0) cc_final: 0.6073 (t0) REVERT: E 340 LYS cc_start: 0.8070 (mtpt) cc_final: 0.7827 (mttm) REVERT: E 349 ARG cc_start: 0.7494 (mtt180) cc_final: 0.5360 (pmt-80) REVERT: G 314 ASP cc_start: 0.6195 (t0) cc_final: 0.5692 (t0) REVERT: G 340 LYS cc_start: 0.7716 (mtpt) cc_final: 0.7484 (mttm) REVERT: G 369 LYS cc_start: 0.7301 (mttt) cc_final: 0.6691 (mtpm) outliers start: 4 outliers final: 1 residues processed: 135 average time/residue: 3.0371 time to fit residues: 418.6922 Evaluate side-chains 123 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 331 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3396 Z= 0.323 Angle : 0.636 4.992 4548 Z= 0.337 Chirality : 0.052 0.151 516 Planarity : 0.003 0.018 576 Dihedral : 5.228 14.532 444 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.04 % Allowed : 19.53 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 329 PHE 0.007 0.001 PHE G 346 TYR 0.019 0.005 TYR D 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 117 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.5934 (t0) cc_final: 0.5671 (t70) REVERT: A 340 LYS cc_start: 0.7805 (mtpt) cc_final: 0.7247 (mttt) REVERT: A 349 ARG cc_start: 0.7147 (mtt180) cc_final: 0.6683 (mtp85) REVERT: A 369 LYS cc_start: 0.7347 (mttt) cc_final: 0.6761 (mtpm) REVERT: A 372 GLU cc_start: 0.7240 (tt0) cc_final: 0.6796 (tt0) REVERT: B 311 LYS cc_start: 0.6365 (ttpt) cc_final: 0.5940 (mttm) REVERT: B 319 THR cc_start: 0.7239 (m) cc_final: 0.6564 (p) REVERT: B 349 ARG cc_start: 0.7215 (mtt180) cc_final: 0.5287 (mmp-170) REVERT: B 369 LYS cc_start: 0.7343 (mttt) cc_final: 0.6665 (mtpm) REVERT: B 372 GLU cc_start: 0.7738 (tt0) cc_final: 0.7310 (tt0) REVERT: C 311 LYS cc_start: 0.6271 (ttpt) cc_final: 0.5756 (mmtt) REVERT: C 319 THR cc_start: 0.7386 (m) cc_final: 0.6712 (p) REVERT: C 340 LYS cc_start: 0.7859 (mtpt) cc_final: 0.7624 (mttm) REVERT: C 349 ARG cc_start: 0.7402 (mtt180) cc_final: 0.5550 (mmp-170) REVERT: C 372 GLU cc_start: 0.7763 (tt0) cc_final: 0.7340 (tt0) REVERT: C 373 THR cc_start: 0.6236 (m) cc_final: 0.5793 (p) REVERT: D 311 LYS cc_start: 0.6839 (ttpt) cc_final: 0.6314 (pttp) REVERT: D 316 SER cc_start: 0.6570 (m) cc_final: 0.6231 (p) REVERT: D 343 LYS cc_start: 0.8304 (mttt) cc_final: 0.7953 (mttm) REVERT: D 349 ARG cc_start: 0.7305 (mtt180) cc_final: 0.5230 (pmt-80) REVERT: D 369 LYS cc_start: 0.7982 (mttt) cc_final: 0.7314 (mtpm) REVERT: E 311 LYS cc_start: 0.6965 (ttpt) cc_final: 0.6319 (ttpp) REVERT: E 314 ASP cc_start: 0.6430 (t0) cc_final: 0.5929 (t0) REVERT: E 340 LYS cc_start: 0.8070 (mtpt) cc_final: 0.7518 (mttp) REVERT: E 349 ARG cc_start: 0.7537 (mtt180) cc_final: 0.5364 (pmt-80) REVERT: G 314 ASP cc_start: 0.5712 (t0) cc_final: 0.5461 (t0) outliers start: 4 outliers final: 1 residues processed: 120 average time/residue: 2.7686 time to fit residues: 340.0491 Evaluate side-chains 116 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 324 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: 0.8980 chunk 34 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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: 0.7775 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3396 Z= 0.206 Angle : 0.561 4.122 4548 Z= 0.290 Chirality : 0.051 0.144 516 Planarity : 0.002 0.020 576 Dihedral : 4.952 13.489 444 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 0.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.78 % Allowed : 21.35 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 362 PHE 0.004 0.001 PHE G 346 TYR 0.012 0.003 TYR D 310 ARG 0.001 0.000 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 0.553 Fit side-chains REVERT: A 314 ASP cc_start: 0.5750 (t0) cc_final: 0.5083 (t70) REVERT: A 340 LYS cc_start: 0.7829 (mtpt) cc_final: 0.7320 (mttt) REVERT: A 349 ARG cc_start: 0.7179 (mtt180) cc_final: 0.6766 (mtp85) REVERT: A 369 LYS cc_start: 0.7407 (mttt) cc_final: 0.6804 (mtpm) REVERT: A 372 GLU cc_start: 0.7312 (tt0) cc_final: 0.6817 (tt0) REVERT: B 311 LYS cc_start: 0.6457 (ttpt) cc_final: 0.6099 (mttm) REVERT: B 314 ASP cc_start: 0.7539 (t70) cc_final: 0.7128 (t70) REVERT: B 319 THR cc_start: 0.7248 (m) cc_final: 0.6572 (p) REVERT: B 340 LYS cc_start: 0.7927 (mtpp) cc_final: 0.7331 (mttm) REVERT: B 349 ARG cc_start: 0.7310 (mtt180) cc_final: 0.5399 (mmp-170) REVERT: B 372 GLU cc_start: 0.7731 (tt0) cc_final: 0.7487 (tt0) REVERT: C 319 THR cc_start: 0.7398 (m) cc_final: 0.6778 (p) REVERT: C 349 ARG cc_start: 0.7431 (mtt180) cc_final: 0.5588 (mmp-170) REVERT: C 372 GLU cc_start: 0.7698 (tt0) cc_final: 0.7312 (tt0) REVERT: C 373 THR cc_start: 0.6293 (m) cc_final: 0.5890 (p) REVERT: D 311 LYS cc_start: 0.6787 (ttpt) cc_final: 0.6227 (pttp) REVERT: D 316 SER cc_start: 0.6484 (m) cc_final: 0.6165 (p) REVERT: D 349 ARG cc_start: 0.7252 (mtt180) cc_final: 0.5210 (pmt-80) REVERT: E 311 LYS cc_start: 0.6973 (ttpt) cc_final: 0.6291 (ttpp) REVERT: E 314 ASP cc_start: 0.6499 (t0) cc_final: 0.5995 (t0) REVERT: E 319 THR cc_start: 0.8051 (m) cc_final: 0.7523 (p) REVERT: E 349 ARG cc_start: 0.7532 (mtt180) cc_final: 0.5369 (pmt-80) REVERT: G 311 LYS cc_start: 0.6119 (mtmt) cc_final: 0.5770 (mttm) REVERT: G 314 ASP cc_start: 0.5966 (t0) cc_final: 0.5229 (t70) outliers start: 3 outliers final: 1 residues processed: 99 average time/residue: 2.3875 time to fit residues: 243.4137 Evaluate side-chains 98 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 331 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3396 Z= 0.303 Angle : 0.608 4.538 4548 Z= 0.321 Chirality : 0.051 0.151 516 Planarity : 0.002 0.022 576 Dihedral : 5.109 13.995 444 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.26 % Allowed : 22.40 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 329 PHE 0.006 0.001 PHE G 346 TYR 0.017 0.004 TYR C 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.5626 (t0) cc_final: 0.4974 (t70) REVERT: A 349 ARG cc_start: 0.7191 (mtt180) cc_final: 0.6721 (mtp85) REVERT: A 369 LYS cc_start: 0.7440 (mttt) cc_final: 0.6838 (mtpm) REVERT: A 372 GLU cc_start: 0.7326 (tt0) cc_final: 0.6767 (tt0) REVERT: B 311 LYS cc_start: 0.6229 (ttpt) cc_final: 0.5810 (mttm) REVERT: B 314 ASP cc_start: 0.7322 (t70) cc_final: 0.6988 (t70) REVERT: B 319 THR cc_start: 0.7257 (m) cc_final: 0.6581 (p) REVERT: B 349 ARG cc_start: 0.7254 (mtt180) cc_final: 0.5340 (mmp-170) REVERT: C 319 THR cc_start: 0.7389 (m) cc_final: 0.6764 (p) REVERT: C 349 ARG cc_start: 0.7459 (mtt180) cc_final: 0.5628 (mmp-170) REVERT: C 372 GLU cc_start: 0.7678 (tt0) cc_final: 0.7281 (tt0) REVERT: C 373 THR cc_start: 0.6260 (m) cc_final: 0.5865 (p) REVERT: D 316 SER cc_start: 0.6525 (m) cc_final: 0.6175 (p) REVERT: D 349 ARG cc_start: 0.7293 (mtt180) cc_final: 0.5236 (pmt-80) REVERT: E 314 ASP cc_start: 0.6324 (t0) cc_final: 0.5801 (t0) REVERT: E 319 THR cc_start: 0.8071 (m) cc_final: 0.7556 (p) REVERT: E 349 ARG cc_start: 0.7515 (mtt180) cc_final: 0.5336 (pmt-80) REVERT: G 314 ASP cc_start: 0.5833 (t0) cc_final: 0.5196 (t70) outliers start: 1 outliers final: 1 residues processed: 92 average time/residue: 2.1392 time to fit residues: 203.0468 Evaluate side-chains 91 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 331 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.0010 chunk 34 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3396 Z= 0.124 Angle : 0.488 3.771 4548 Z= 0.249 Chirality : 0.051 0.141 516 Planarity : 0.002 0.021 576 Dihedral : 4.606 12.175 444 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.26 % Allowed : 21.88 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 362 PHE 0.001 0.000 PHE G 346 TYR 0.006 0.002 TYR D 310 ARG 0.001 0.000 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 1.675 Fit side-chains revert: symmetry clash REVERT: A 314 ASP cc_start: 0.5716 (t0) cc_final: 0.5123 (t70) REVERT: A 324 SER cc_start: 0.8212 (p) cc_final: 0.7993 (t) REVERT: A 349 ARG cc_start: 0.7211 (mtt180) cc_final: 0.6776 (mtp85) REVERT: A 369 LYS cc_start: 0.7442 (mttt) cc_final: 0.6866 (mtpm) REVERT: A 372 GLU cc_start: 0.7388 (tt0) cc_final: 0.6850 (tt0) REVERT: B 311 LYS cc_start: 0.6421 (ttpt) cc_final: 0.5961 (mttm) REVERT: B 314 ASP cc_start: 0.7419 (t70) cc_final: 0.6848 (t70) REVERT: B 319 THR cc_start: 0.7226 (m) cc_final: 0.6561 (p) REVERT: B 340 LYS cc_start: 0.7881 (mtpp) cc_final: 0.7308 (mttm) REVERT: B 349 ARG cc_start: 0.7365 (mtt180) cc_final: 0.5479 (mmp-170) REVERT: C 314 ASP cc_start: 0.7271 (t0) cc_final: 0.7015 (t0) REVERT: C 319 THR cc_start: 0.7413 (m) cc_final: 0.6894 (p) REVERT: C 349 ARG cc_start: 0.7506 (mtt180) cc_final: 0.5545 (mmp-170) REVERT: C 372 GLU cc_start: 0.7728 (tt0) cc_final: 0.7290 (tt0) REVERT: C 373 THR cc_start: 0.6315 (m) cc_final: 0.5953 (p) REVERT: D 314 ASP cc_start: 0.5662 (t0) cc_final: 0.5332 (t0) REVERT: D 316 SER cc_start: 0.6433 (m) cc_final: 0.6135 (p) REVERT: D 349 ARG cc_start: 0.7284 (mtt180) cc_final: 0.5232 (pmt-80) REVERT: E 314 ASP cc_start: 0.6656 (t0) cc_final: 0.6030 (t0) REVERT: E 319 THR cc_start: 0.8004 (m) cc_final: 0.7497 (p) REVERT: E 349 ARG cc_start: 0.7482 (mtt180) cc_final: 0.5319 (pmt-80) REVERT: E 372 GLU cc_start: 0.7434 (tt0) cc_final: 0.7071 (tt0) REVERT: G 314 ASP cc_start: 0.5931 (t0) cc_final: 0.4799 (t70) outliers start: 1 outliers final: 1 residues processed: 96 average time/residue: 2.2222 time to fit residues: 220.7214 Evaluate side-chains 94 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 331 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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: 0.7766 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3396 Z= 0.192 Angle : 0.524 3.791 4548 Z= 0.271 Chirality : 0.051 0.143 516 Planarity : 0.002 0.021 576 Dihedral : 4.650 12.833 444 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 0.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.26 % Allowed : 22.92 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.004 0.001 PHE G 346 TYR 0.011 0.003 TYR B 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: A 314 ASP cc_start: 0.5668 (t0) cc_final: 0.5028 (t70) REVERT: A 349 ARG cc_start: 0.7218 (mtt180) cc_final: 0.6780 (mtp85) REVERT: A 369 LYS cc_start: 0.7449 (mttt) cc_final: 0.6823 (mtpm) REVERT: A 372 GLU cc_start: 0.7372 (tt0) cc_final: 0.6807 (tt0) REVERT: B 311 LYS cc_start: 0.6255 (ttpt) cc_final: 0.5834 (mttm) REVERT: B 314 ASP cc_start: 0.7356 (t70) cc_final: 0.6830 (t70) REVERT: B 319 THR cc_start: 0.7251 (m) cc_final: 0.6583 (p) REVERT: B 340 LYS cc_start: 0.7914 (mtpp) cc_final: 0.7350 (mttm) REVERT: B 349 ARG cc_start: 0.7313 (mtt180) cc_final: 0.5411 (mmp-170) REVERT: C 319 THR cc_start: 0.7434 (m) cc_final: 0.6880 (p) REVERT: C 349 ARG cc_start: 0.7455 (mtt180) cc_final: 0.5630 (mmp-170) REVERT: C 372 GLU cc_start: 0.7705 (tt0) cc_final: 0.7266 (tt0) REVERT: C 373 THR cc_start: 0.6297 (m) cc_final: 0.5930 (p) REVERT: D 316 SER cc_start: 0.6375 (m) cc_final: 0.6074 (p) REVERT: D 349 ARG cc_start: 0.7308 (mtt180) cc_final: 0.5252 (pmt-80) REVERT: E 314 ASP cc_start: 0.6486 (t0) cc_final: 0.5941 (t0) REVERT: E 319 THR cc_start: 0.8043 (m) cc_final: 0.7532 (p) REVERT: E 349 ARG cc_start: 0.7507 (mtt180) cc_final: 0.5314 (pmt-80) REVERT: E 372 GLU cc_start: 0.7444 (tt0) cc_final: 0.7021 (tt0) REVERT: G 314 ASP cc_start: 0.5844 (t0) cc_final: 0.4833 (t70) outliers start: 1 outliers final: 1 residues processed: 93 average time/residue: 2.0810 time to fit residues: 199.5990 Evaluate side-chains 92 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 331 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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: 0.7769 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3396 Z= 0.206 Angle : 0.545 4.079 4548 Z= 0.283 Chirality : 0.051 0.143 516 Planarity : 0.002 0.021 576 Dihedral : 4.775 13.356 444 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 0.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.26 % Allowed : 22.92 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.004 0.001 PHE G 346 TYR 0.013 0.003 TYR D 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 314 ASP cc_start: 0.5562 (t0) cc_final: 0.4853 (t70) REVERT: A 349 ARG cc_start: 0.7215 (mtt180) cc_final: 0.6757 (mtp85) REVERT: A 372 GLU cc_start: 0.7366 (tt0) cc_final: 0.6794 (tt0) REVERT: B 311 LYS cc_start: 0.6270 (ttpt) cc_final: 0.5845 (mttm) REVERT: B 314 ASP cc_start: 0.7341 (t70) cc_final: 0.6813 (t70) REVERT: B 319 THR cc_start: 0.7259 (m) cc_final: 0.6593 (p) REVERT: B 340 LYS cc_start: 0.7922 (mtpp) cc_final: 0.7356 (mttm) REVERT: B 349 ARG cc_start: 0.7323 (mtt180) cc_final: 0.5401 (mmp-170) REVERT: C 319 THR cc_start: 0.7416 (m) cc_final: 0.6835 (p) REVERT: C 349 ARG cc_start: 0.7415 (mtt180) cc_final: 0.5615 (mmp-170) REVERT: C 372 GLU cc_start: 0.7721 (tt0) cc_final: 0.7277 (tt0) REVERT: C 373 THR cc_start: 0.6277 (m) cc_final: 0.5903 (p) REVERT: D 316 SER cc_start: 0.6423 (m) cc_final: 0.6116 (p) REVERT: D 349 ARG cc_start: 0.7331 (mtt180) cc_final: 0.5263 (pmt-80) REVERT: E 314 ASP cc_start: 0.6450 (t0) cc_final: 0.5946 (t0) REVERT: E 319 THR cc_start: 0.8045 (m) cc_final: 0.7535 (p) REVERT: E 349 ARG cc_start: 0.7534 (mtt180) cc_final: 0.5336 (pmt-80) REVERT: G 314 ASP cc_start: 0.5786 (t0) cc_final: 0.4790 (t70) outliers start: 1 outliers final: 1 residues processed: 92 average time/residue: 2.1046 time to fit residues: 199.9963 Evaluate side-chains 92 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 331 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 8.9990 chunk 26 optimal weight: 0.0270 chunk 35 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.7844 ------------------------------------------------------------------------------- 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: 0.7764 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3396 Z= 0.170 Angle : 0.515 3.793 4548 Z= 0.266 Chirality : 0.051 0.141 516 Planarity : 0.002 0.021 576 Dihedral : 4.656 12.710 444 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 0.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.26 % Allowed : 23.18 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.003 0.001 PHE G 346 TYR 0.010 0.003 TYR D 310 ARG 0.001 0.000 ARG A 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.558 Fit side-chains REVERT: A 314 ASP cc_start: 0.5619 (t0) cc_final: 0.4977 (t70) REVERT: A 349 ARG cc_start: 0.7230 (mtt180) cc_final: 0.6789 (mtp85) REVERT: A 372 GLU cc_start: 0.7393 (tt0) cc_final: 0.6838 (tt0) REVERT: B 311 LYS cc_start: 0.6272 (ttpt) cc_final: 0.5843 (mttm) REVERT: B 314 ASP cc_start: 0.7339 (t70) cc_final: 0.6812 (t70) REVERT: B 319 THR cc_start: 0.7284 (m) cc_final: 0.6613 (p) REVERT: B 340 LYS cc_start: 0.7907 (mtpp) cc_final: 0.7344 (mttm) REVERT: B 343 LYS cc_start: 0.8448 (mttt) cc_final: 0.8197 (mttm) REVERT: B 349 ARG cc_start: 0.7328 (mtt180) cc_final: 0.5424 (mmp-170) REVERT: C 319 THR cc_start: 0.7434 (m) cc_final: 0.6871 (p) REVERT: C 349 ARG cc_start: 0.7428 (mtt180) cc_final: 0.5514 (mmp-170) REVERT: C 372 GLU cc_start: 0.7701 (tt0) cc_final: 0.7260 (tt0) REVERT: C 373 THR cc_start: 0.6291 (m) cc_final: 0.5927 (p) REVERT: D 316 SER cc_start: 0.6386 (m) cc_final: 0.6083 (p) REVERT: D 349 ARG cc_start: 0.7353 (mtt180) cc_final: 0.5240 (pmt-80) REVERT: E 314 ASP cc_start: 0.6558 (t0) cc_final: 0.6003 (t0) REVERT: E 319 THR cc_start: 0.8018 (m) cc_final: 0.7506 (p) REVERT: E 349 ARG cc_start: 0.7511 (mtt180) cc_final: 0.5333 (pmt-80) REVERT: E 372 GLU cc_start: 0.7474 (tt0) cc_final: 0.7108 (tt0) REVERT: G 314 ASP cc_start: 0.5680 (t0) cc_final: 0.4718 (t70) outliers start: 1 outliers final: 1 residues processed: 92 average time/residue: 2.0893 time to fit residues: 198.4539 Evaluate side-chains 92 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 331 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.1980 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.4427 r_free = 0.4427 target = 0.168840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.143634 restraints weight = 9949.544| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 1.39 r_work: 0.4070 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.4004 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3396 Z= 0.164 Angle : 0.519 5.398 4548 Z= 0.266 Chirality : 0.051 0.140 516 Planarity : 0.002 0.020 576 Dihedral : 4.598 12.590 444 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 0.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.26 % Allowed : 23.18 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.33), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.003 0.001 PHE G 346 TYR 0.009 0.002 TYR A 310 ARG 0.001 0.000 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5217.10 seconds wall clock time: 91 minutes 55.91 seconds (5515.91 seconds total)