Starting phenix.real_space_refine on Mon Mar 11 03:22:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9h_18281/03_2024/8q9h_18281.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9h_18281/03_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_18281/03_2024/8q9h_18281.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9h_18281/03_2024/8q9h_18281.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9h_18281/03_2024/8q9h_18281.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9h_18281/03_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-dev-5265/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: 3.53, per 1000 atoms: 0.52 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: 4.92 Conformation dependent library (CDL) restraints added in 789.8 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: 0.66 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: 2.19 Time building geometry restraints manager: 5.12 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 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: 2.920 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: 11.580 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.410 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.410 ------------------------------------------------------------------------------- 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 : 0.613 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: 3.0147 time to fit residues: 449.4127 Evaluate side-chains 126 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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: 1.9990 chunk 12 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN E 362 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3401 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= 0.199 Angle : 0.597 4.470 4548 Z= 0.318 Chirality : 0.052 0.145 516 Planarity : 0.003 0.018 576 Dihedral : 5.776 14.820 444 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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 0.003 0.001 HIS B 362 PHE 0.007 0.001 PHE A 346 TYR 0.017 0.003 TYR D 310 ARG 0.002 0.000 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 142 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 136 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7761 (mtpt) cc_final: 0.7302 (mttt) REVERT: A 343 LYS cc_start: 0.8160 (mtmt) cc_final: 0.7793 (mttm) REVERT: A 349 ARG cc_start: 0.7079 (mtt180) cc_final: 0.6565 (mtp85) REVERT: A 369 LYS cc_start: 0.7265 (mttt) cc_final: 0.6663 (mtpm) REVERT: A 372 GLU cc_start: 0.7148 (tt0) cc_final: 0.6882 (tt0) REVERT: B 311 LYS cc_start: 0.6527 (ttpt) cc_final: 0.5946 (mttm) REVERT: B 349 ARG cc_start: 0.7258 (mtt180) cc_final: 0.5438 (mmp-170) REVERT: B 369 LYS cc_start: 0.7244 (mttt) cc_final: 0.6616 (mtpm) REVERT: B 372 GLU cc_start: 0.7698 (tt0) cc_final: 0.7328 (tt0) REVERT: C 311 LYS cc_start: 0.6210 (ttpt) cc_final: 0.5750 (tptt) REVERT: C 340 LYS cc_start: 0.7781 (mtpt) cc_final: 0.7481 (mttm) REVERT: C 343 LYS cc_start: 0.8343 (mttt) cc_final: 0.8087 (mttm) REVERT: C 349 ARG cc_start: 0.7350 (mtt180) cc_final: 0.5585 (mmp-170) REVERT: C 369 LYS cc_start: 0.7530 (mttt) cc_final: 0.6858 (mtpm) REVERT: C 372 GLU cc_start: 0.7697 (tt0) cc_final: 0.7290 (tt0) REVERT: D 311 LYS cc_start: 0.6734 (ttpt) cc_final: 0.6237 (ttpp) REVERT: D 316 SER cc_start: 0.6545 (m) cc_final: 0.6303 (p) REVERT: D 321 LYS cc_start: 0.8010 (ttpt) cc_final: 0.7803 (ttmm) REVERT: D 340 LYS cc_start: 0.8014 (mtpt) cc_final: 0.7606 (mttm) REVERT: D 349 ARG cc_start: 0.7161 (mtt180) cc_final: 0.5367 (pmt-80) REVERT: D 369 LYS cc_start: 0.7849 (mttt) cc_final: 0.7247 (mtpm) REVERT: D 375 LYS cc_start: 0.6849 (tttt) cc_final: 0.6342 (mtpm) REVERT: E 311 LYS cc_start: 0.7173 (ttpt) cc_final: 0.6356 (ttpp) REVERT: E 314 ASP cc_start: 0.6001 (t0) cc_final: 0.5495 (t0) REVERT: E 340 LYS cc_start: 0.7987 (mtpt) cc_final: 0.7743 (mttm) REVERT: E 349 ARG cc_start: 0.7395 (mtt180) cc_final: 0.5453 (pmt-80) REVERT: G 340 LYS cc_start: 0.7629 (mtpt) cc_final: 0.7354 (mttm) REVERT: G 369 LYS cc_start: 0.7226 (mttt) cc_final: 0.6711 (mtpm) outliers start: 6 outliers final: 1 residues processed: 139 average time/residue: 3.0658 time to fit residues: 435.1663 Evaluate side-chains 125 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C 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: 0.0470 chunk 10 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 0.0980 chunk 28 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 overall best weight: 1.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3396 Z= 0.133 Angle : 0.520 4.788 4548 Z= 0.265 Chirality : 0.051 0.144 516 Planarity : 0.002 0.013 576 Dihedral : 4.890 12.723 444 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 16.15 % Favored : 83.85 % 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: -1.23 (0.34), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.93 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.004 0.001 PHE A 346 TYR 0.010 0.002 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 132 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.603 Fit side-chains REVERT: A 340 LYS cc_start: 0.7777 (mtpt) cc_final: 0.7335 (mttt) REVERT: A 343 LYS cc_start: 0.8160 (mtmt) cc_final: 0.7866 (mttm) REVERT: A 349 ARG cc_start: 0.7107 (mtt180) cc_final: 0.6770 (mtp85) REVERT: A 369 LYS cc_start: 0.7281 (mttt) cc_final: 0.6698 (mtpm) REVERT: A 372 GLU cc_start: 0.7202 (tt0) cc_final: 0.6876 (tt0) REVERT: B 311 LYS cc_start: 0.6568 (ttpt) cc_final: 0.6064 (mttm) REVERT: B 340 LYS cc_start: 0.7941 (mtpp) cc_final: 0.7294 (mttm) REVERT: B 343 LYS cc_start: 0.8391 (mttt) cc_final: 0.7910 (mtpt) REVERT: B 349 ARG cc_start: 0.7318 (mtt180) cc_final: 0.5398 (mmp-170) REVERT: B 369 LYS cc_start: 0.7265 (mttt) cc_final: 0.6634 (mtpm) REVERT: C 311 LYS cc_start: 0.6212 (ttpt) cc_final: 0.5723 (tptt) REVERT: C 340 LYS cc_start: 0.7780 (mtpt) cc_final: 0.7158 (mttp) REVERT: C 343 LYS cc_start: 0.8388 (mttt) cc_final: 0.8092 (mttm) REVERT: C 349 ARG cc_start: 0.7438 (mtt180) cc_final: 0.5568 (mmp-170) REVERT: C 369 LYS cc_start: 0.7578 (mttt) cc_final: 0.6933 (mtpm) REVERT: C 372 GLU cc_start: 0.7689 (tt0) cc_final: 0.7306 (tt0) REVERT: D 311 LYS cc_start: 0.6753 (ttpt) cc_final: 0.6235 (ttpp) REVERT: D 314 ASP cc_start: 0.5699 (t70) cc_final: 0.5293 (t70) REVERT: D 316 SER cc_start: 0.6426 (m) cc_final: 0.6133 (p) REVERT: D 321 LYS cc_start: 0.8017 (ttpt) cc_final: 0.7795 (ttmm) REVERT: D 340 LYS cc_start: 0.8040 (mtpt) cc_final: 0.7630 (mttm) REVERT: D 349 ARG cc_start: 0.7221 (mtt180) cc_final: 0.5361 (pmt-80) REVERT: D 369 LYS cc_start: 0.7848 (mttt) cc_final: 0.7200 (mtpm) REVERT: E 311 LYS cc_start: 0.7196 (ttpt) cc_final: 0.6381 (ttpp) REVERT: E 314 ASP cc_start: 0.6197 (t0) cc_final: 0.5707 (t0) REVERT: E 340 LYS cc_start: 0.8016 (mtpt) cc_final: 0.7797 (mttm) REVERT: E 349 ARG cc_start: 0.7417 (mtt180) cc_final: 0.5411 (pmt-80) REVERT: G 311 LYS cc_start: 0.5556 (mtpt) cc_final: 0.5259 (mttm) REVERT: G 369 LYS cc_start: 0.7262 (mttt) cc_final: 0.6668 (mtpm) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 2.9880 time to fit residues: 403.0885 Evaluate side-chains 125 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 20 optimal weight: 0.0670 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4406 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= 0.283 Angle : 0.617 4.888 4548 Z= 0.325 Chirality : 0.050 0.151 516 Planarity : 0.002 0.016 576 Dihedral : 5.115 13.861 444 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.78 % Allowed : 18.23 % Favored : 80.99 % 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: -1.39 (0.34), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.05 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 329 PHE 0.006 0.001 PHE G 346 TYR 0.018 0.004 TYR D 310 ARG 0.001 0.000 ARG E 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 126 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 123 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.5129 (t0) cc_final: 0.4891 (t0) REVERT: A 340 LYS cc_start: 0.7781 (mtpt) cc_final: 0.7228 (mttt) REVERT: A 349 ARG cc_start: 0.7091 (mtt180) cc_final: 0.6652 (mtp85) REVERT: A 369 LYS cc_start: 0.7279 (mttt) cc_final: 0.6715 (mtpm) REVERT: A 372 GLU cc_start: 0.7156 (tt0) cc_final: 0.6753 (tt0) REVERT: B 311 LYS cc_start: 0.6388 (ttpt) cc_final: 0.5894 (mttm) REVERT: B 319 THR cc_start: 0.7166 (m) cc_final: 0.6523 (p) REVERT: B 340 LYS cc_start: 0.7887 (mtpp) cc_final: 0.7265 (mttm) REVERT: B 349 ARG cc_start: 0.7208 (mtt180) cc_final: 0.5308 (mmp-170) REVERT: B 369 LYS cc_start: 0.7335 (mttt) cc_final: 0.6687 (mtpm) REVERT: C 311 LYS cc_start: 0.6233 (ttpt) cc_final: 0.5709 (tptt) REVERT: C 319 THR cc_start: 0.7314 (m) cc_final: 0.6598 (p) REVERT: C 340 LYS cc_start: 0.7869 (mtpt) cc_final: 0.7626 (mttm) REVERT: C 343 LYS cc_start: 0.8378 (mttt) cc_final: 0.8122 (mttm) REVERT: C 349 ARG cc_start: 0.7315 (mtt180) cc_final: 0.5463 (mmp-170) REVERT: C 369 LYS cc_start: 0.7532 (mttt) cc_final: 0.6915 (mtpm) REVERT: C 372 GLU cc_start: 0.7700 (tt0) cc_final: 0.7257 (tt0) REVERT: D 311 LYS cc_start: 0.6782 (ttpt) cc_final: 0.6390 (ttpp) REVERT: D 314 ASP cc_start: 0.5448 (t70) cc_final: 0.4981 (t0) REVERT: D 316 SER cc_start: 0.6478 (m) cc_final: 0.6035 (p) REVERT: D 343 LYS cc_start: 0.8305 (mttt) cc_final: 0.7966 (mttm) REVERT: D 349 ARG cc_start: 0.7232 (mtt180) cc_final: 0.5211 (pmt-80) REVERT: D 369 LYS cc_start: 0.7965 (mttt) cc_final: 0.7297 (mtpm) REVERT: D 370 LYS cc_start: 0.7117 (tttp) cc_final: 0.6880 (tttt) REVERT: E 311 LYS cc_start: 0.6945 (ttpt) cc_final: 0.6272 (ttpp) REVERT: E 314 ASP cc_start: 0.5719 (t0) cc_final: 0.5426 (t0) REVERT: E 340 LYS cc_start: 0.8101 (mtpt) cc_final: 0.7572 (mttp) REVERT: E 349 ARG cc_start: 0.7496 (mtt180) cc_final: 0.5358 (pmt-80) outliers start: 3 outliers final: 2 residues processed: 124 average time/residue: 3.1810 time to fit residues: 403.2687 Evaluate side-chains 121 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain E 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: 4.9990 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3396 Z= 0.352 Angle : 0.650 5.025 4548 Z= 0.344 Chirality : 0.051 0.153 516 Planarity : 0.003 0.019 576 Dihedral : 5.249 13.422 444 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.04 % Allowed : 20.31 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.51 (0.34), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (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 0.020 0.005 TYR D 310 ARG 0.002 0.001 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 : 0.597 Fit side-chains revert: symmetry clash REVERT: A 314 ASP cc_start: 0.5075 (t0) cc_final: 0.4863 (t0) REVERT: A 340 LYS cc_start: 0.7835 (mtpt) cc_final: 0.7324 (mttt) REVERT: A 349 ARG cc_start: 0.7144 (mtt180) cc_final: 0.6683 (mtp85) REVERT: A 369 LYS cc_start: 0.7395 (mttt) cc_final: 0.6785 (mtpm) REVERT: A 372 GLU cc_start: 0.7137 (tt0) cc_final: 0.6688 (tt0) REVERT: B 311 LYS cc_start: 0.6324 (ttpt) cc_final: 0.6029 (mttm) REVERT: B 319 THR cc_start: 0.7196 (m) cc_final: 0.6538 (p) REVERT: B 340 LYS cc_start: 0.7890 (mtpp) cc_final: 0.7265 (mttm) REVERT: B 349 ARG cc_start: 0.7255 (mtt180) cc_final: 0.5365 (mmp-170) REVERT: B 369 LYS cc_start: 0.7374 (mttt) cc_final: 0.6721 (mtpm) REVERT: C 319 THR cc_start: 0.7292 (m) cc_final: 0.6573 (p) REVERT: C 349 ARG cc_start: 0.7374 (mtt180) cc_final: 0.5527 (mmp-170) REVERT: C 372 GLU cc_start: 0.7754 (tt0) cc_final: 0.7392 (tt0) REVERT: C 373 THR cc_start: 0.6076 (m) cc_final: 0.5680 (p) REVERT: D 314 ASP cc_start: 0.5458 (t70) cc_final: 0.5140 (t0) REVERT: D 316 SER cc_start: 0.6619 (m) cc_final: 0.6210 (p) REVERT: D 349 ARG cc_start: 0.7292 (mtt180) cc_final: 0.5194 (pmt-80) REVERT: E 314 ASP cc_start: 0.5582 (t0) cc_final: 0.5295 (t0) REVERT: E 349 ARG cc_start: 0.7536 (mtt180) cc_final: 0.5382 (pmt-80) REVERT: G 311 LYS cc_start: 0.5984 (mtpt) cc_final: 0.5529 (mttt) REVERT: G 349 ARG cc_start: 0.7087 (mtp85) cc_final: 0.6812 (mtt180) outliers start: 4 outliers final: 3 residues processed: 101 average time/residue: 2.5587 time to fit residues: 265.7086 Evaluate side-chains 99 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 96 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain E residue 324 SER 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: 7.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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: 0.7778 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 3396 Z= 0.396 Angle : 0.667 5.220 4548 Z= 0.355 Chirality : 0.051 0.157 516 Planarity : 0.003 0.026 576 Dihedral : 5.364 13.805 444 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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: -1.55 (0.34), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 329 PHE 0.010 0.002 PHE D 378 TYR 0.021 0.005 TYR C 310 ARG 0.002 0.001 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 97 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.4986 (t0) cc_final: 0.4730 (t0) REVERT: A 349 ARG cc_start: 0.7162 (mtt180) cc_final: 0.6695 (mtp85) REVERT: A 372 GLU cc_start: 0.7195 (tt0) cc_final: 0.6689 (tt0) REVERT: B 311 LYS cc_start: 0.6363 (ttpt) cc_final: 0.5860 (mmtm) REVERT: B 319 THR cc_start: 0.7196 (m) cc_final: 0.6546 (p) REVERT: B 349 ARG cc_start: 0.7228 (mtt180) cc_final: 0.5348 (mmp-170) REVERT: C 319 THR cc_start: 0.7266 (m) cc_final: 0.6576 (p) REVERT: C 349 ARG cc_start: 0.7378 (mtt180) cc_final: 0.5532 (mmp-170) REVERT: C 372 GLU cc_start: 0.7732 (tt0) cc_final: 0.7342 (tt0) REVERT: C 373 THR cc_start: 0.6137 (m) cc_final: 0.5737 (p) REVERT: D 316 SER cc_start: 0.6637 (m) cc_final: 0.6204 (p) REVERT: D 349 ARG cc_start: 0.7271 (mtt180) cc_final: 0.5141 (pmt-80) REVERT: E 314 ASP cc_start: 0.5527 (t0) cc_final: 0.5280 (t0) REVERT: E 349 ARG cc_start: 0.7460 (mtt180) cc_final: 0.5319 (pmt-80) outliers start: 3 outliers final: 3 residues processed: 97 average time/residue: 2.3008 time to fit residues: 229.9190 Evaluate side-chains 97 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain E residue 324 SER 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: 6.9990 chunk 34 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4973 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= 0.143 Angle : 0.511 3.863 4548 Z= 0.262 Chirality : 0.050 0.140 516 Planarity : 0.002 0.022 576 Dihedral : 4.774 12.311 444 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.26 % Allowed : 23.70 % Favored : 76.04 % 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: -1.51 (0.34), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.004 0.001 PHE D 378 TYR 0.007 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 97 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 349 ARG cc_start: 0.7165 (mtt180) cc_final: 0.6702 (mtp85) REVERT: A 372 GLU cc_start: 0.7225 (tt0) cc_final: 0.6672 (tt0) REVERT: B 311 LYS cc_start: 0.6323 (ttpt) cc_final: 0.5853 (mttm) REVERT: B 319 THR cc_start: 0.7143 (m) cc_final: 0.6488 (p) REVERT: B 340 LYS cc_start: 0.7830 (mtpp) cc_final: 0.7245 (mttm) REVERT: B 343 LYS cc_start: 0.8371 (mttt) cc_final: 0.8105 (mttm) REVERT: B 349 ARG cc_start: 0.7302 (mtt180) cc_final: 0.5402 (mmp-170) REVERT: C 319 THR cc_start: 0.7314 (m) cc_final: 0.6713 (p) REVERT: C 349 ARG cc_start: 0.7413 (mtt180) cc_final: 0.5579 (mmp-170) REVERT: C 372 GLU cc_start: 0.7620 (tt0) cc_final: 0.7217 (tt0) REVERT: C 373 THR cc_start: 0.6143 (m) cc_final: 0.5763 (p) REVERT: D 314 ASP cc_start: 0.5425 (t0) cc_final: 0.5216 (t0) REVERT: D 316 SER cc_start: 0.6450 (m) cc_final: 0.6064 (p) REVERT: D 349 ARG cc_start: 0.7252 (mtt180) cc_final: 0.5233 (pmt-80) REVERT: E 314 ASP cc_start: 0.5799 (t0) cc_final: 0.5469 (t0) REVERT: E 319 THR cc_start: 0.7998 (m) cc_final: 0.7492 (p) REVERT: E 349 ARG cc_start: 0.7485 (mtt180) cc_final: 0.5399 (pmt-80) REVERT: E 372 GLU cc_start: 0.7348 (tt0) cc_final: 0.6988 (tt0) REVERT: G 314 ASP cc_start: 0.5256 (t0) cc_final: 0.5029 (t0) outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 2.1301 time to fit residues: 213.1458 Evaluate side-chains 95 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.5013 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= 0.313 Angle : 0.601 4.746 4548 Z= 0.318 Chirality : 0.051 0.155 516 Planarity : 0.002 0.023 576 Dihedral : 5.096 13.450 444 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.78 % Allowed : 23.70 % Favored : 75.52 % 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: -1.55 (0.34), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (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 G 346 TYR 0.018 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 : 0.584 Fit side-chains REVERT: A 349 ARG cc_start: 0.7177 (mtt180) cc_final: 0.6702 (mtp85) REVERT: A 372 GLU cc_start: 0.7216 (tt0) cc_final: 0.6668 (tt0) REVERT: B 311 LYS cc_start: 0.6385 (ttpt) cc_final: 0.6036 (mmtm) REVERT: B 319 THR cc_start: 0.7187 (m) cc_final: 0.6549 (p) REVERT: B 340 LYS cc_start: 0.7869 (mtpp) cc_final: 0.7284 (mttm) REVERT: B 349 ARG cc_start: 0.7241 (mtt180) cc_final: 0.5334 (mmp-170) REVERT: C 319 THR cc_start: 0.7298 (m) cc_final: 0.6660 (p) REVERT: C 349 ARG cc_start: 0.7375 (mtt180) cc_final: 0.5553 (mmp-170) REVERT: C 372 GLU cc_start: 0.7699 (tt0) cc_final: 0.7293 (tt0) REVERT: C 373 THR cc_start: 0.6128 (m) cc_final: 0.5736 (p) REVERT: D 316 SER cc_start: 0.6596 (m) cc_final: 0.6189 (p) REVERT: D 349 ARG cc_start: 0.7291 (mtt180) cc_final: 0.5216 (pmt-80) REVERT: E 314 ASP cc_start: 0.5657 (t0) cc_final: 0.5198 (t0) REVERT: E 319 THR cc_start: 0.8051 (m) cc_final: 0.7536 (p) REVERT: E 349 ARG cc_start: 0.7529 (mtt180) cc_final: 0.5393 (pmt-80) REVERT: G 311 LYS cc_start: 0.5889 (mtpt) cc_final: 0.5462 (mttp) outliers start: 3 outliers final: 1 residues processed: 99 average time/residue: 2.2266 time to fit residues: 227.2924 Evaluate side-chains 96 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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: 7.9990 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 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 : 0.003 0.023 3396 Z= 0.236 Angle : 0.572 4.374 4548 Z= 0.298 Chirality : 0.050 0.150 516 Planarity : 0.002 0.024 576 Dihedral : 4.999 12.918 444 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.26 % Allowed : 23.70 % Favored : 76.04 % 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: -1.57 (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 A 329 PHE 0.004 0.001 PHE G 346 TYR 0.013 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 96 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.578 Fit side-chains REVERT: A 314 ASP cc_start: 0.5124 (t0) cc_final: 0.4923 (t0) REVERT: A 349 ARG cc_start: 0.7208 (mtt180) cc_final: 0.6739 (mtp85) REVERT: A 372 GLU cc_start: 0.7214 (tt0) cc_final: 0.6663 (tt0) REVERT: B 311 LYS cc_start: 0.6435 (ttpt) cc_final: 0.6144 (mmtm) REVERT: B 319 THR cc_start: 0.7193 (m) cc_final: 0.6541 (p) REVERT: B 340 LYS cc_start: 0.7870 (mtpp) cc_final: 0.7287 (mttm) REVERT: B 343 LYS cc_start: 0.8362 (mttt) cc_final: 0.8104 (mttm) REVERT: B 349 ARG cc_start: 0.7285 (mtt180) cc_final: 0.5391 (mmp-170) REVERT: C 319 THR cc_start: 0.7304 (m) cc_final: 0.6677 (p) REVERT: C 349 ARG cc_start: 0.7344 (mtt180) cc_final: 0.5488 (mmp-170) REVERT: C 372 GLU cc_start: 0.7628 (tt0) cc_final: 0.7216 (tt0) REVERT: C 373 THR cc_start: 0.6134 (m) cc_final: 0.5736 (p) REVERT: D 316 SER cc_start: 0.6405 (m) cc_final: 0.6007 (p) REVERT: D 349 ARG cc_start: 0.7303 (mtt180) cc_final: 0.5250 (pmt-80) REVERT: E 314 ASP cc_start: 0.5697 (t0) cc_final: 0.5283 (t0) REVERT: E 319 THR cc_start: 0.8047 (m) cc_final: 0.7537 (p) REVERT: E 349 ARG cc_start: 0.7513 (mtt180) cc_final: 0.5417 (pmt-80) REVERT: G 311 LYS cc_start: 0.5881 (mtpt) cc_final: 0.5460 (mttm) outliers start: 1 outliers final: 1 residues processed: 96 average time/residue: 2.2302 time to fit residues: 220.6824 Evaluate side-chains 96 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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: 9.9990 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 8.9990 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.5103 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= 0.137 Angle : 0.500 3.916 4548 Z= 0.254 Chirality : 0.050 0.141 516 Planarity : 0.002 0.021 576 Dihedral : 4.648 11.977 444 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.26 % Allowed : 23.70 % Favored : 76.04 % 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: -1.50 (0.35), 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 0.003 0.001 HIS B 362 PHE 0.002 0.000 PHE A 346 TYR 0.006 0.002 TYR A 310 ARG 0.000 0.000 ARG G 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: 1 poor density : 97 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 314 ASP cc_start: 0.5100 (t0) cc_final: 0.4896 (t0) REVERT: A 349 ARG cc_start: 0.7246 (mtt180) cc_final: 0.6782 (mtp85) REVERT: A 372 GLU cc_start: 0.7222 (tt0) cc_final: 0.6677 (tt0) REVERT: B 311 LYS cc_start: 0.6351 (ttpt) cc_final: 0.5856 (mmtm) REVERT: B 319 THR cc_start: 0.7177 (m) cc_final: 0.6524 (p) REVERT: B 340 LYS cc_start: 0.7837 (mtpp) cc_final: 0.7261 (mttm) REVERT: B 343 LYS cc_start: 0.8389 (mttt) cc_final: 0.8125 (mttm) REVERT: B 349 ARG cc_start: 0.7325 (mtt180) cc_final: 0.5488 (mmp-170) REVERT: C 319 THR cc_start: 0.7355 (m) cc_final: 0.6772 (p) REVERT: C 349 ARG cc_start: 0.7405 (mtt180) cc_final: 0.5574 (mmp-170) REVERT: C 372 GLU cc_start: 0.7627 (tt0) cc_final: 0.7216 (tt0) REVERT: C 373 THR cc_start: 0.6145 (m) cc_final: 0.5765 (p) REVERT: D 316 SER cc_start: 0.6419 (m) cc_final: 0.6040 (p) REVERT: D 349 ARG cc_start: 0.7304 (mtt180) cc_final: 0.5213 (pmt-80) REVERT: E 314 ASP cc_start: 0.5729 (t0) cc_final: 0.5322 (t0) REVERT: E 319 THR cc_start: 0.8003 (m) cc_final: 0.7500 (p) REVERT: E 349 ARG cc_start: 0.7517 (mtt180) cc_final: 0.5418 (pmt-80) REVERT: G 349 ARG cc_start: 0.7107 (mtp85) cc_final: 0.6716 (mtt180) outliers start: 1 outliers final: 1 residues processed: 98 average time/residue: 2.1380 time to fit residues: 216.3556 Evaluate side-chains 95 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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: 0.8980 chunk 1 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 25 optimal weight: 0.0470 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.168174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.143039 restraints weight = 9959.638| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 1.38 r_work: 0.4058 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3992 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.5201 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= 0.128 Angle : 0.479 3.884 4548 Z= 0.243 Chirality : 0.050 0.139 516 Planarity : 0.002 0.019 576 Dihedral : 4.334 10.931 444 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.26 % Allowed : 23.96 % Favored : 75.78 % 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: -1.45 (0.35), residues: 426 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.002 0.001 PHE C 378 TYR 0.006 0.001 TYR A 310 ARG 0.001 0.000 ARG G 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5459.34 seconds wall clock time: 95 minutes 42.53 seconds (5742.53 seconds total)