Starting phenix.real_space_refine on Wed Jan 17 23:11:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9h_18281/01_2024/8q9h_18281.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9h_18281/01_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_18281/01_2024/8q9h_18281.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9h_18281/01_2024/8q9h_18281.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9h_18281/01_2024/8q9h_18281.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9h_18281/01_2024/8q9h_18281.pdb" } 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-1.21-5211/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: 3.81, 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: 5.40 Conformation dependent library (CDL) restraints added in 676.6 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: 0.77 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: 2.25 Time building geometry restraints manager: 5.62 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: 2735 13.36 - 26.73: 191 26.73 - 40.09: 50 40.09 - 53.45: 13 53.45 - 66.81: 71 Dihedral angle restraints: 3060 sinusoidal: 1698 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 3057 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 1.850 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.587 1.850 nonbonded pdb=" OD1 ASP G 314 " pdb=" HG SER G 316 " model vdw 1.610 1.850 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.613 1.850 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.616 1.850 ... (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 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 11.510 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 26.670 Find NCS groups from input model: 0.320 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: 0.010 Load rotamer database and sin/cos tables:12.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.850 ------------------------------------------------------------------------------- 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 : 0.595 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: 3.0404 time to fit residues: 453.1781 Evaluate side-chains 126 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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: 5.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3396 Z= 0.222 Angle : 0.621 4.568 4548 Z= 0.331 Chirality : 0.053 0.149 516 Planarity : 0.003 0.017 576 Dihedral : 5.791 14.903 444 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.56 % Allowed : 12.24 % Favored : 86.20 % 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: -1.10 (0.34), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.83 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 362 PHE 0.008 0.001 PHE A 346 TYR 0.019 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 143 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 137 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7762 (mtpt) cc_final: 0.7295 (mttt) REVERT: A 343 LYS cc_start: 0.8161 (mtmt) cc_final: 0.7793 (mttm) REVERT: A 349 ARG cc_start: 0.7082 (mtt180) cc_final: 0.6565 (mtp85) REVERT: A 369 LYS cc_start: 0.7267 (mttt) cc_final: 0.6670 (mtpm) REVERT: A 372 GLU cc_start: 0.7155 (tt0) cc_final: 0.6862 (tt0) REVERT: B 311 LYS cc_start: 0.6530 (ttpt) cc_final: 0.5958 (mttm) REVERT: B 321 LYS cc_start: 0.7578 (ttpt) cc_final: 0.7378 (ttmm) REVERT: B 349 ARG cc_start: 0.7196 (mtt180) cc_final: 0.5377 (mmp-170) REVERT: B 369 LYS cc_start: 0.7227 (mttt) cc_final: 0.6600 (mtpm) REVERT: B 372 GLU cc_start: 0.7698 (tt0) cc_final: 0.7329 (tt0) REVERT: C 311 LYS cc_start: 0.6190 (ttpt) cc_final: 0.5726 (tptt) REVERT: C 340 LYS cc_start: 0.7801 (mtpt) cc_final: 0.7499 (mttm) REVERT: C 343 LYS cc_start: 0.8345 (mttt) cc_final: 0.8085 (mttm) REVERT: C 349 ARG cc_start: 0.7354 (mtt180) cc_final: 0.5578 (mmp-170) REVERT: C 369 LYS cc_start: 0.7551 (mttt) cc_final: 0.6895 (mtpm) REVERT: C 372 GLU cc_start: 0.7710 (tt0) cc_final: 0.7292 (tt0) REVERT: D 311 LYS cc_start: 0.6757 (ttpt) cc_final: 0.6260 (ttpp) REVERT: D 316 SER cc_start: 0.6554 (m) cc_final: 0.6275 (p) REVERT: D 340 LYS cc_start: 0.8034 (mtpt) cc_final: 0.7621 (mttm) REVERT: D 349 ARG cc_start: 0.7168 (mtt180) cc_final: 0.5344 (pmt-80) REVERT: D 369 LYS cc_start: 0.7839 (mttt) cc_final: 0.7236 (mtpm) REVERT: E 311 LYS cc_start: 0.7172 (ttpt) cc_final: 0.6379 (ttpp) REVERT: E 314 ASP cc_start: 0.5872 (t0) cc_final: 0.5355 (t0) REVERT: E 340 LYS cc_start: 0.8010 (mtpt) cc_final: 0.7757 (mttm) REVERT: E 349 ARG cc_start: 0.7415 (mtt180) cc_final: 0.5441 (pmt-80) REVERT: G 340 LYS cc_start: 0.7641 (mtpt) cc_final: 0.7366 (mttm) REVERT: G 369 LYS cc_start: 0.7216 (mttt) cc_final: 0.6703 (mtpm) outliers start: 6 outliers final: 2 residues processed: 140 average time/residue: 3.1013 time to fit residues: 443.2965 Evaluate side-chains 125 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 123 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 331 LYS 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: 8.9990 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3396 Z= 0.262 Angle : 0.631 5.749 4548 Z= 0.330 Chirality : 0.051 0.164 516 Planarity : 0.002 0.017 576 Dihedral : 5.276 13.957 444 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.30 % Allowed : 14.58 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.34), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 329 PHE 0.006 0.001 PHE A 346 TYR 0.018 0.004 TYR D 310 ARG 0.001 0.000 ARG A 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 133 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 128 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 314 ASP cc_start: 0.5320 (t0) cc_final: 0.5102 (t0) REVERT: A 340 LYS cc_start: 0.7784 (mtpt) cc_final: 0.7227 (mttt) REVERT: A 349 ARG cc_start: 0.7105 (mtt180) cc_final: 0.6671 (mtp85) REVERT: A 369 LYS cc_start: 0.7275 (mttt) cc_final: 0.6685 (mtpm) REVERT: A 372 GLU cc_start: 0.7181 (tt0) cc_final: 0.6673 (tt0) REVERT: B 311 LYS cc_start: 0.6457 (ttpt) cc_final: 0.6074 (mttm) REVERT: B 319 THR cc_start: 0.7227 (m) cc_final: 0.6572 (p) REVERT: B 321 LYS cc_start: 0.7571 (ttpt) cc_final: 0.7361 (ttmm) REVERT: B 340 LYS cc_start: 0.7991 (mtpp) cc_final: 0.7347 (mttm) REVERT: B 349 ARG cc_start: 0.7218 (mtt180) cc_final: 0.5312 (mmp-170) REVERT: B 369 LYS cc_start: 0.7300 (mttt) cc_final: 0.6664 (mtpm) REVERT: C 311 LYS cc_start: 0.6274 (ttpt) cc_final: 0.5756 (tptt) REVERT: C 340 LYS cc_start: 0.7871 (mtpt) cc_final: 0.7621 (mttm) REVERT: C 343 LYS cc_start: 0.8365 (mttt) cc_final: 0.8107 (mttm) REVERT: C 349 ARG cc_start: 0.7338 (mtt180) cc_final: 0.5506 (mmp-170) REVERT: C 369 LYS cc_start: 0.7520 (mttt) cc_final: 0.6895 (mtpm) REVERT: C 372 GLU cc_start: 0.7738 (tt0) cc_final: 0.7321 (tt0) REVERT: C 373 THR cc_start: 0.6109 (m) cc_final: 0.5669 (p) REVERT: D 311 LYS cc_start: 0.6764 (ttpt) cc_final: 0.6344 (ttpp) REVERT: D 314 ASP cc_start: 0.5458 (t70) cc_final: 0.4946 (t70) REVERT: D 316 SER cc_start: 0.6608 (m) cc_final: 0.6251 (p) REVERT: D 340 LYS cc_start: 0.8113 (mtpt) cc_final: 0.7680 (mttm) REVERT: D 343 LYS cc_start: 0.8329 (mtmt) cc_final: 0.8010 (mttm) REVERT: D 349 ARG cc_start: 0.7216 (mtt180) cc_final: 0.5223 (pmt-80) REVERT: D 369 LYS cc_start: 0.7969 (mttt) cc_final: 0.7292 (mtpm) REVERT: E 311 LYS cc_start: 0.6942 (ttpt) cc_final: 0.6343 (ttpp) REVERT: E 314 ASP cc_start: 0.5758 (t0) cc_final: 0.5443 (t0) REVERT: E 340 LYS cc_start: 0.8086 (mtpt) cc_final: 0.7573 (mttp) REVERT: E 349 ARG cc_start: 0.7499 (mtt180) cc_final: 0.5358 (pmt-80) REVERT: G 311 LYS cc_start: 0.6050 (mtpt) cc_final: 0.5647 (mttm) outliers start: 5 outliers final: 2 residues processed: 131 average time/residue: 3.0222 time to fit residues: 404.5092 Evaluate side-chains 125 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 123 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain G 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: 6.9990 chunk 18 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3396 Z= 0.371 Angle : 0.667 5.257 4548 Z= 0.355 Chirality : 0.051 0.160 516 Planarity : 0.003 0.021 576 Dihedral : 5.407 13.717 444 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.56 % Allowed : 17.19 % Favored : 81.25 % 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: -1.48 (0.34), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 329 PHE 0.008 0.002 PHE G 346 TYR 0.021 0.005 TYR D 310 ARG 0.002 0.001 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 107 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 101 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: A 314 ASP cc_start: 0.5020 (t0) cc_final: 0.4775 (t0) REVERT: A 340 LYS cc_start: 0.7839 (mtpt) cc_final: 0.7319 (mttt) REVERT: A 349 ARG cc_start: 0.7106 (mtt180) cc_final: 0.6650 (mtp85) REVERT: A 369 LYS cc_start: 0.7348 (mttt) cc_final: 0.6765 (mtpm) REVERT: A 372 GLU cc_start: 0.7157 (tt0) cc_final: 0.6661 (tt0) REVERT: B 311 LYS cc_start: 0.6309 (ttpt) cc_final: 0.6016 (mttm) REVERT: B 319 THR cc_start: 0.7245 (m) cc_final: 0.6577 (p) REVERT: B 321 LYS cc_start: 0.7593 (ttpt) cc_final: 0.7335 (ttmm) REVERT: B 340 LYS cc_start: 0.7872 (mtpp) cc_final: 0.7243 (mttm) REVERT: B 349 ARG cc_start: 0.7212 (mtt180) cc_final: 0.5363 (mmp-170) REVERT: B 369 LYS cc_start: 0.7342 (mttt) cc_final: 0.6681 (mtpm) REVERT: C 319 THR cc_start: 0.7297 (m) cc_final: 0.6566 (p) REVERT: C 349 ARG cc_start: 0.7365 (mtt180) cc_final: 0.5520 (mmp-170) REVERT: C 372 GLU cc_start: 0.7772 (tt0) cc_final: 0.7401 (tt0) REVERT: C 373 THR cc_start: 0.6009 (m) cc_final: 0.5589 (p) REVERT: D 311 LYS cc_start: 0.6773 (ttpt) cc_final: 0.6232 (pttp) REVERT: D 314 ASP cc_start: 0.5357 (t70) cc_final: 0.4919 (t0) REVERT: D 316 SER cc_start: 0.6670 (m) cc_final: 0.6155 (p) REVERT: D 319 THR cc_start: 0.7990 (m) cc_final: 0.7555 (p) REVERT: D 349 ARG cc_start: 0.7269 (mtt180) cc_final: 0.5229 (pmt-80) REVERT: D 370 LYS cc_start: 0.7091 (OUTLIER) cc_final: 0.6739 (tttt) REVERT: E 314 ASP cc_start: 0.5499 (t0) cc_final: 0.5218 (t0) REVERT: E 349 ARG cc_start: 0.7525 (mtt180) cc_final: 0.5387 (pmt-80) REVERT: G 311 LYS cc_start: 0.6093 (mtpt) cc_final: 0.5654 (mttt) REVERT: G 349 ARG cc_start: 0.7060 (mtp85) cc_final: 0.6792 (mtt180) outliers start: 6 outliers final: 4 residues processed: 106 average time/residue: 2.7810 time to fit residues: 302.8098 Evaluate side-chains 103 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain G residue 331 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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: 0.7769 moved from start: 0.4735 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= 0.215 Angle : 0.564 4.335 4548 Z= 0.295 Chirality : 0.050 0.150 516 Planarity : 0.002 0.020 576 Dihedral : 5.087 13.175 444 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.04 % Allowed : 20.05 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.34), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.13 (0.26), 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 C 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 102 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 0.634 Fit side-chains REVERT: A 349 ARG cc_start: 0.7147 (mtt180) cc_final: 0.6685 (mtp85) REVERT: A 369 LYS cc_start: 0.7404 (mttt) cc_final: 0.6773 (mtpm) REVERT: A 372 GLU cc_start: 0.7205 (tt0) cc_final: 0.6631 (tt0) REVERT: B 311 LYS cc_start: 0.6299 (ttpt) cc_final: 0.6008 (mttm) REVERT: B 319 THR cc_start: 0.7231 (m) cc_final: 0.6571 (p) REVERT: B 321 LYS cc_start: 0.7521 (ttpt) cc_final: 0.7260 (ttmm) REVERT: B 340 LYS cc_start: 0.7860 (mtpp) cc_final: 0.7242 (mttm) REVERT: B 349 ARG cc_start: 0.7241 (mtt180) cc_final: 0.5382 (mmp-170) REVERT: B 369 LYS cc_start: 0.7366 (mttt) cc_final: 0.6689 (mtpm) REVERT: C 319 THR cc_start: 0.7343 (m) cc_final: 0.6679 (p) REVERT: C 349 ARG cc_start: 0.7384 (mtt180) cc_final: 0.5530 (mmp-170) REVERT: C 372 GLU cc_start: 0.7718 (tt0) cc_final: 0.7322 (tt0) REVERT: C 373 THR cc_start: 0.6127 (m) cc_final: 0.5729 (p) REVERT: D 314 ASP cc_start: 0.5484 (t70) cc_final: 0.5178 (t0) REVERT: D 316 SER cc_start: 0.6605 (m) cc_final: 0.6109 (p) REVERT: D 349 ARG cc_start: 0.7223 (mtt180) cc_final: 0.5216 (pmt-80) REVERT: D 370 LYS cc_start: 0.7035 (OUTLIER) cc_final: 0.6722 (tttt) REVERT: E 314 ASP cc_start: 0.5726 (t0) cc_final: 0.5471 (t0) REVERT: E 319 THR cc_start: 0.8035 (m) cc_final: 0.7518 (p) REVERT: E 349 ARG cc_start: 0.7500 (mtt180) cc_final: 0.5393 (pmt-80) REVERT: G 311 LYS cc_start: 0.5912 (mtpt) cc_final: 0.5458 (mttt) REVERT: G 349 ARG cc_start: 0.7124 (mtp85) cc_final: 0.6722 (mtt180) outliers start: 4 outliers final: 2 residues processed: 102 average time/residue: 2.3359 time to fit residues: 245.3399 Evaluate side-chains 98 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain G 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: 7.9990 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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: 0.7775 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3396 Z= 0.357 Angle : 0.635 4.776 4548 Z= 0.339 Chirality : 0.051 0.159 516 Planarity : 0.003 0.021 576 Dihedral : 5.333 13.684 444 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.04 % Allowed : 21.61 % 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: -1.59 (0.34), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.007 0.001 PHE G 346 TYR 0.019 0.005 TYR C 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.7145 (mtt180) cc_final: 0.6689 (mtp85) REVERT: A 372 GLU cc_start: 0.7183 (tt0) cc_final: 0.6693 (tt0) REVERT: B 311 LYS cc_start: 0.6363 (ttpt) cc_final: 0.5863 (mmtm) REVERT: B 319 THR cc_start: 0.7179 (m) cc_final: 0.6525 (p) REVERT: B 340 LYS cc_start: 0.7879 (mtpp) cc_final: 0.7276 (mttm) REVERT: B 349 ARG cc_start: 0.7212 (mtt180) cc_final: 0.5343 (mmp-170) REVERT: B 369 LYS cc_start: 0.7378 (mttt) cc_final: 0.6682 (mtpm) REVERT: C 319 THR cc_start: 0.7308 (m) cc_final: 0.6622 (p) REVERT: C 349 ARG cc_start: 0.7302 (mtt180) cc_final: 0.5473 (mmp-170) REVERT: C 372 GLU cc_start: 0.7744 (tt0) cc_final: 0.7349 (tt0) REVERT: C 373 THR cc_start: 0.6134 (m) cc_final: 0.5735 (p) REVERT: D 314 ASP cc_start: 0.5358 (t70) cc_final: 0.5058 (t0) REVERT: D 316 SER cc_start: 0.6553 (m) cc_final: 0.6061 (p) REVERT: D 319 THR cc_start: 0.7989 (m) cc_final: 0.7562 (p) REVERT: D 349 ARG cc_start: 0.7311 (mtt180) cc_final: 0.5213 (pmt-80) REVERT: D 370 LYS cc_start: 0.7068 (OUTLIER) cc_final: 0.6737 (tttt) REVERT: E 314 ASP cc_start: 0.5582 (t0) cc_final: 0.5143 (t0) REVERT: E 349 ARG cc_start: 0.7462 (mtt180) cc_final: 0.5332 (pmt-80) outliers start: 4 outliers final: 3 residues processed: 99 average time/residue: 2.3838 time to fit residues: 242.7944 Evaluate side-chains 98 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain G 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: 0.5980 chunk 34 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4885 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= 0.186 Angle : 0.540 4.162 4548 Z= 0.281 Chirality : 0.050 0.147 516 Planarity : 0.002 0.019 576 Dihedral : 4.974 12.684 444 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.78 % Allowed : 22.40 % 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: -1.58 (0.34), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 362 PHE 0.003 0.001 PHE G 346 TYR 0.010 0.003 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 98 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 349 ARG cc_start: 0.7173 (mtt180) cc_final: 0.6710 (mtp85) REVERT: A 372 GLU cc_start: 0.7198 (tt0) cc_final: 0.6644 (tt0) REVERT: B 311 LYS cc_start: 0.6395 (ttpt) cc_final: 0.5895 (mmtm) REVERT: B 319 THR cc_start: 0.7227 (m) cc_final: 0.6550 (p) REVERT: B 340 LYS cc_start: 0.7859 (mtpp) cc_final: 0.7264 (mttm) REVERT: B 349 ARG cc_start: 0.7296 (mtt180) cc_final: 0.5447 (mmp-170) REVERT: C 319 THR cc_start: 0.7305 (m) cc_final: 0.6665 (p) REVERT: C 349 ARG cc_start: 0.7382 (mtt180) cc_final: 0.5571 (mmp-170) REVERT: C 372 GLU cc_start: 0.7602 (tt0) cc_final: 0.7194 (tt0) REVERT: C 373 THR cc_start: 0.6092 (m) cc_final: 0.5698 (p) REVERT: D 316 SER cc_start: 0.6528 (m) cc_final: 0.6018 (p) REVERT: D 349 ARG cc_start: 0.7243 (mtt180) cc_final: 0.5235 (pmt-80) REVERT: D 370 LYS cc_start: 0.7033 (OUTLIER) cc_final: 0.6727 (tttt) REVERT: E 314 ASP cc_start: 0.5769 (t0) cc_final: 0.5322 (t0) REVERT: E 319 THR cc_start: 0.8043 (m) cc_final: 0.7533 (p) REVERT: E 349 ARG cc_start: 0.7495 (mtt180) cc_final: 0.5366 (pmt-80) REVERT: G 349 ARG cc_start: 0.7099 (mtp85) cc_final: 0.6717 (mtt180) outliers start: 3 outliers final: 2 residues processed: 98 average time/residue: 2.2780 time to fit residues: 229.8796 Evaluate side-chains 98 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain G 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: 8.9990 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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: 0.7770 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3396 Z= 0.269 Angle : 0.583 4.450 4548 Z= 0.307 Chirality : 0.050 0.151 516 Planarity : 0.002 0.021 576 Dihedral : 5.102 13.117 444 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.78 % Allowed : 22.14 % Favored : 77.08 % 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: -1.61 (0.34), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.005 0.001 PHE G 346 TYR 0.016 0.004 TYR C 310 ARG 0.001 0.000 ARG A 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 99 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 96 time to evaluate : 0.649 Fit side-chains REVERT: A 349 ARG cc_start: 0.7180 (mtt180) cc_final: 0.6706 (mtp85) REVERT: A 372 GLU cc_start: 0.7202 (tt0) cc_final: 0.6663 (tt0) REVERT: B 311 LYS cc_start: 0.6376 (ttpt) cc_final: 0.6015 (mmtm) REVERT: B 319 THR cc_start: 0.7248 (m) cc_final: 0.6573 (p) REVERT: B 340 LYS cc_start: 0.7871 (mtpp) cc_final: 0.7280 (mttm) REVERT: B 349 ARG cc_start: 0.7255 (mtt180) cc_final: 0.5342 (mmp-170) REVERT: C 319 THR cc_start: 0.7305 (m) cc_final: 0.6664 (p) REVERT: C 349 ARG cc_start: 0.7365 (mtt180) cc_final: 0.5545 (mmp-170) REVERT: C 372 GLU cc_start: 0.7632 (tt0) cc_final: 0.7269 (tt0) REVERT: C 373 THR cc_start: 0.6087 (m) cc_final: 0.5689 (p) REVERT: D 316 SER cc_start: 0.6597 (m) cc_final: 0.6081 (p) REVERT: D 349 ARG cc_start: 0.7287 (mtt180) cc_final: 0.5254 (pmt-80) REVERT: D 370 LYS cc_start: 0.7073 (OUTLIER) cc_final: 0.6754 (tttt) REVERT: E 314 ASP cc_start: 0.5601 (t0) cc_final: 0.5149 (t0) REVERT: E 319 THR cc_start: 0.8040 (m) cc_final: 0.7527 (p) REVERT: E 349 ARG cc_start: 0.7522 (mtt180) cc_final: 0.5376 (pmt-80) REVERT: G 311 LYS cc_start: 0.5853 (mtpt) cc_final: 0.5426 (mttp) outliers start: 3 outliers final: 2 residues processed: 99 average time/residue: 2.2573 time to fit residues: 230.0664 Evaluate side-chains 98 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain G 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: 9.9990 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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: 0.7766 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3396 Z= 0.245 Angle : 0.568 4.421 4548 Z= 0.298 Chirality : 0.050 0.152 516 Planarity : 0.002 0.021 576 Dihedral : 5.043 12.817 444 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.78 % Allowed : 22.66 % 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: -1.60 (0.34), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.005 0.001 PHE G 346 TYR 0.014 0.003 TYR C 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 98 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 0.616 Fit side-chains REVERT: A 349 ARG cc_start: 0.7190 (mtt180) cc_final: 0.6819 (mtp85) REVERT: A 372 GLU cc_start: 0.7199 (tt0) cc_final: 0.6666 (tt0) REVERT: B 311 LYS cc_start: 0.6417 (ttpt) cc_final: 0.6072 (mmtm) REVERT: B 319 THR cc_start: 0.7252 (m) cc_final: 0.6596 (p) REVERT: B 340 LYS cc_start: 0.7870 (mtpp) cc_final: 0.7282 (mttm) REVERT: B 343 LYS cc_start: 0.8364 (mttt) cc_final: 0.8108 (mttm) REVERT: B 349 ARG cc_start: 0.7276 (mtt180) cc_final: 0.5378 (mmp-170) REVERT: C 319 THR cc_start: 0.7309 (m) cc_final: 0.6672 (p) REVERT: C 349 ARG cc_start: 0.7402 (mtt180) cc_final: 0.5581 (mmp-170) REVERT: C 372 GLU cc_start: 0.7638 (tt0) cc_final: 0.7274 (tt0) REVERT: C 373 THR cc_start: 0.6090 (m) cc_final: 0.5694 (p) REVERT: D 316 SER cc_start: 0.6616 (m) cc_final: 0.6093 (p) REVERT: D 349 ARG cc_start: 0.7315 (mtt180) cc_final: 0.5263 (pmt-80) REVERT: D 370 LYS cc_start: 0.7055 (OUTLIER) cc_final: 0.6740 (tttt) REVERT: E 314 ASP cc_start: 0.5554 (t0) cc_final: 0.5109 (t0) REVERT: E 319 THR cc_start: 0.8037 (m) cc_final: 0.7526 (p) REVERT: E 349 ARG cc_start: 0.7513 (mtt180) cc_final: 0.5408 (pmt-80) REVERT: G 311 LYS cc_start: 0.5830 (mtpt) cc_final: 0.5405 (mttp) outliers start: 3 outliers final: 2 residues processed: 98 average time/residue: 2.2489 time to fit residues: 226.9362 Evaluate side-chains 98 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain G 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: 6.9990 chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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: 0.7764 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3396 Z= 0.236 Angle : 0.564 4.355 4548 Z= 0.296 Chirality : 0.050 0.150 516 Planarity : 0.002 0.020 576 Dihedral : 5.010 12.845 444 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.78 % Allowed : 22.66 % 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: -1.58 (0.34), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.005 0.001 PHE G 346 TYR 0.014 0.003 TYR C 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 98 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 0.667 Fit side-chains REVERT: A 349 ARG cc_start: 0.7190 (mtt180) cc_final: 0.6819 (mtp85) REVERT: A 372 GLU cc_start: 0.7205 (tt0) cc_final: 0.6672 (tt0) REVERT: B 311 LYS cc_start: 0.6408 (ttpt) cc_final: 0.6064 (mmtm) REVERT: B 319 THR cc_start: 0.7264 (m) cc_final: 0.6589 (p) REVERT: B 340 LYS cc_start: 0.7865 (mtpp) cc_final: 0.7278 (mttm) REVERT: B 343 LYS cc_start: 0.8365 (mttt) cc_final: 0.8106 (mttm) REVERT: B 349 ARG cc_start: 0.7282 (mtt180) cc_final: 0.5446 (mmp-170) REVERT: C 319 THR cc_start: 0.7312 (m) cc_final: 0.6680 (p) REVERT: C 349 ARG cc_start: 0.7378 (mtt180) cc_final: 0.5539 (mmp-170) REVERT: C 372 GLU cc_start: 0.7618 (tt0) cc_final: 0.7261 (tt0) REVERT: C 373 THR cc_start: 0.6088 (m) cc_final: 0.5693 (p) REVERT: D 316 SER cc_start: 0.6404 (m) cc_final: 0.5891 (p) REVERT: D 349 ARG cc_start: 0.7357 (mtt180) cc_final: 0.5296 (pmt-80) REVERT: D 370 LYS cc_start: 0.7055 (OUTLIER) cc_final: 0.6742 (tttt) REVERT: E 314 ASP cc_start: 0.5571 (t0) cc_final: 0.5108 (t0) REVERT: E 319 THR cc_start: 0.8033 (m) cc_final: 0.7529 (p) REVERT: E 349 ARG cc_start: 0.7524 (mtt180) cc_final: 0.5388 (pmt-80) REVERT: G 311 LYS cc_start: 0.5825 (mtpt) cc_final: 0.5399 (mttp) REVERT: G 349 ARG cc_start: 0.7102 (mtp85) cc_final: 0.6714 (mtt180) outliers start: 3 outliers final: 2 residues processed: 98 average time/residue: 2.3211 time to fit residues: 234.1000 Evaluate side-chains 98 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain G 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: 1.9990 chunk 1 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.166106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.140757 restraints weight = 10010.276| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 1.37 r_work: 0.4022 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3957 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.5050 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= 0.140 Angle : 0.509 3.765 4548 Z= 0.260 Chirality : 0.050 0.141 516 Planarity : 0.002 0.018 576 Dihedral : 4.712 12.110 444 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.78 % Allowed : 22.92 % Favored : 76.30 % 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: -1.52 (0.35), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 362 PHE 0.002 0.000 PHE G 346 TYR 0.007 0.002 TYR A 310 ARG 0.000 0.000 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5432.79 seconds wall clock time: 95 minutes 20.02 seconds (5720.02 seconds total)