Starting phenix.real_space_refine on Sun Mar 10 17:34:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2j_18109/03_2024/8q2j_18109.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2j_18109/03_2024/8q2j_18109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2j_18109/03_2024/8q2j_18109.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2j_18109/03_2024/8q2j_18109.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2j_18109/03_2024/8q2j_18109.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2j_18109/03_2024/8q2j_18109.pdb" } resolution = 2.23 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: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2193 2.51 5 N 648 2.21 5 O 660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 348": "OD1" <-> "OD2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 380": "OE1" <-> "OE2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 348": "OD1" <-> "OD2" Residue "D ASP 358": "OD1" <-> "OD2" Residue "D GLU 380": "OE1" <-> "OE2" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 348": "OD1" <-> "OD2" Residue "F PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 3507 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 582 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "B" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "C" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 582 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "D" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "E" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 582 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "F" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Time building chain proxies: 2.29, per 1000 atoms: 0.65 Number of scatterers: 3507 At special positions: 0 Unit cell: (117.047, 119.228, 37.804, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 660 8.00 N 648 7.00 C 2193 6.00 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: 1.18 Conformation dependent library (CDL) restraints added in 685.1 milliseconds 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 798 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 51.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.518A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.781A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.543A pdb=" N LYS A 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N SER C 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR A 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N CYS C 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LYS A 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 325 through 330 removed outlier: 6.872A pdb=" N GLY C 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASN A 327 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLY A 326 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN E 327 " --> pdb=" O GLY A 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 342 removed outlier: 6.537A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N GLU E 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER A 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.504A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 350 through 354 removed outlier: 6.261A pdb=" N VAL A 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LYS E 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER A 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.419A pdb=" N LEU A 357 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ILE E 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASN A 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N HIS E 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR A 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 369 through 378 removed outlier: 6.423A pdb=" N LYS A 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N GLU C 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N HIS C 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N THR A 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LEU C 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS A 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N PHE C 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR A 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.580A pdb=" N SER B 305 " --> pdb=" O VAL D 306 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE D 308 " --> pdb=" O SER B 305 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.935A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 317 through 325 removed outlier: 6.525A pdb=" N LYS B 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N SER D 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THR B 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N CYS D 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LYS B 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER D 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLY B 323 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.720A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 337 through 342 removed outlier: 6.684A pdb=" N VAL B 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LYS F 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL B 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N GLU F 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER B 341 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.358A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 350 through 354 removed outlier: 6.190A pdb=" N VAL B 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N LYS F 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N SER B 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 357 through 362 removed outlier: 6.733A pdb=" N ASP B 358 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N THR D 361 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE B 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU B 357 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ILE F 360 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASN B 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N HIS F 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR B 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 368 through 378 removed outlier: 6.486A pdb=" N LYS B 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N GLU D 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE B 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N HIS D 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR B 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N LEU D 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LYS B 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N PHE D 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR B 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) 76 hydrogen bonds defined for protein. 228 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: 0.86 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1074 1.33 - 1.45: 374 1.45 - 1.57: 2107 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3561 Sorted by residual: bond pdb=" CA LYS F 331 " pdb=" C LYS F 331 " ideal model delta sigma weight residual 1.532 1.555 -0.023 6.50e-03 2.37e+04 1.26e+01 bond pdb=" CZ ARG F 349 " pdb=" NH2 ARG F 349 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.64e+00 bond pdb=" CA LYS F 331 " pdb=" CB LYS F 331 " ideal model delta sigma weight residual 1.522 1.548 -0.026 8.90e-03 1.26e+04 8.32e+00 bond pdb=" CA LYS D 331 " pdb=" CB LYS D 331 " ideal model delta sigma weight residual 1.522 1.547 -0.025 8.90e-03 1.26e+04 7.63e+00 bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.17e+00 ... (remaining 3556 not shown) Histogram of bond angle deviations from ideal: 101.88 - 107.35: 183 107.35 - 112.82: 1758 112.82 - 118.29: 920 118.29 - 123.75: 1526 123.75 - 129.22: 374 Bond angle restraints: 4761 Sorted by residual: angle pdb=" N GLY A 326 " pdb=" CA GLY A 326 " pdb=" C GLY A 326 " ideal model delta sigma weight residual 110.69 117.51 -6.82 1.33e+00 5.65e-01 2.63e+01 angle pdb=" CA ASP B 358 " pdb=" CB ASP B 358 " pdb=" CG ASP B 358 " ideal model delta sigma weight residual 112.60 117.65 -5.05 1.00e+00 1.00e+00 2.55e+01 angle pdb=" OE1 GLN B 336 " pdb=" CD GLN B 336 " pdb=" NE2 GLN B 336 " ideal model delta sigma weight residual 122.60 117.74 4.86 1.00e+00 1.00e+00 2.37e+01 angle pdb=" C ASP F 348 " pdb=" N ARG F 349 " pdb=" CA ARG F 349 " ideal model delta sigma weight residual 121.05 127.81 -6.76 1.43e+00 4.89e-01 2.24e+01 angle pdb=" CB HIS B 374 " pdb=" CG HIS B 374 " pdb=" CD2 HIS B 374 " ideal model delta sigma weight residual 131.20 125.06 6.14 1.30e+00 5.92e-01 2.23e+01 ... (remaining 4756 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.74: 2053 17.74 - 35.48: 92 35.48 - 53.22: 13 53.22 - 70.96: 3 70.96 - 88.69: 2 Dihedral angle restraints: 2163 sinusoidal: 903 harmonic: 1260 Sorted by residual: dihedral pdb=" CA GLY A 355 " pdb=" C GLY A 355 " pdb=" N SER A 356 " pdb=" CA SER A 356 " ideal model delta harmonic sigma weight residual 180.00 151.73 28.27 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA LEU E 357 " pdb=" C LEU E 357 " pdb=" N ASP E 358 " pdb=" CA ASP E 358 " ideal model delta harmonic sigma weight residual 180.00 154.60 25.40 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA GLY B 355 " pdb=" C GLY B 355 " pdb=" N SER B 356 " pdb=" CA SER B 356 " ideal model delta harmonic sigma weight residual 180.00 154.81 25.19 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 2160 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 301 0.062 - 0.124: 175 0.124 - 0.186: 42 0.186 - 0.248: 9 0.248 - 0.311: 4 Chirality restraints: 531 Sorted by residual: chirality pdb=" CA GLU A 372 " pdb=" N GLU A 372 " pdb=" C GLU A 372 " pdb=" CB GLU A 372 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA GLU E 372 " pdb=" N GLU E 372 " pdb=" C GLU E 372 " pdb=" CB GLU E 372 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA THR B 319 " pdb=" N THR B 319 " pdb=" C THR B 319 " pdb=" CB THR B 319 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 528 not shown) Planarity restraints: 609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " 0.091 2.00e-02 2.50e+03 5.23e-02 5.48e+01 pdb=" CG TYR F 310 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " -0.036 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " -0.029 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " 0.083 2.00e-02 2.50e+03 4.63e-02 4.29e+01 pdb=" CG TYR E 310 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " -0.023 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " 0.072 2.00e-02 2.50e+03 4.13e-02 3.41e+01 pdb=" CG TYR A 310 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " -0.035 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " -0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " 0.070 2.00e-02 2.50e+03 ... (remaining 606 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 1505 2.97 - 3.45: 2687 3.45 - 3.94: 5705 3.94 - 4.42: 5591 4.42 - 4.90: 10696 Nonbonded interactions: 26184 Sorted by model distance: nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.490 2.440 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.499 2.440 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.519 2.440 nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.535 2.440 nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.535 2.440 ... (remaining 26179 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' and resid 304 through 379) selection = (chain 'B' and resid 304 through 379) selection = (chain 'C' and resid 304 through 379) selection = (chain 'D' and resid 304 through 379) selection = (chain 'E' and resid 304 through 379) selection = (chain 'F' and resid 304 through 379) } 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: 2.730 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: 0.010 Extract box with map and model: 11.330 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.650 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 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 0.038 3561 Z= 0.737 Angle : 1.720 6.824 4761 Z= 1.160 Chirality : 0.079 0.311 531 Planarity : 0.010 0.071 609 Dihedral : 11.078 88.693 1365 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 0.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % 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: -1.62 (0.31), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.004 HIS A 330 PHE 0.035 0.012 PHE A 346 TYR 0.091 0.026 TYR F 310 ARG 0.008 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7818 (mttt) cc_final: 0.7530 (mttm) REVERT: A 317 LYS cc_start: 0.7043 (mtmt) cc_final: 0.6683 (mtpt) REVERT: A 338 GLU cc_start: 0.6921 (tt0) cc_final: 0.5878 (mt-10) REVERT: A 342 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6604 (mt-10) REVERT: A 343 LYS cc_start: 0.7881 (mttt) cc_final: 0.7614 (mtpp) REVERT: A 353 LYS cc_start: 0.7411 (tttt) cc_final: 0.5931 (tptt) REVERT: A 358 ASP cc_start: 0.7242 (m-30) cc_final: 0.6818 (m-30) REVERT: A 369 LYS cc_start: 0.6714 (mttt) cc_final: 0.6034 (mtpp) REVERT: A 370 LYS cc_start: 0.7418 (tttp) cc_final: 0.6913 (ttmt) REVERT: A 373 THR cc_start: 0.7803 (m) cc_final: 0.7345 (p) REVERT: A 375 LYS cc_start: 0.7255 (tttt) cc_final: 0.7052 (tttt) REVERT: B 345 ASP cc_start: 0.6846 (m-30) cc_final: 0.6221 (t70) REVERT: B 348 ASP cc_start: 0.8206 (t70) cc_final: 0.7992 (t0) REVERT: B 353 LYS cc_start: 0.7015 (tttt) cc_final: 0.6591 (tttm) REVERT: B 375 LYS cc_start: 0.7608 (tttt) cc_final: 0.7061 (ttpp) REVERT: C 307 GLN cc_start: 0.8278 (tt0) cc_final: 0.7880 (tt0) REVERT: C 311 LYS cc_start: 0.8232 (mttt) cc_final: 0.7978 (mttm) REVERT: C 320 SER cc_start: 0.7604 (t) cc_final: 0.7339 (p) REVERT: C 336 GLN cc_start: 0.8206 (tt0) cc_final: 0.7923 (tt0) REVERT: C 338 GLU cc_start: 0.7444 (tt0) cc_final: 0.7002 (tm-30) REVERT: C 340 LYS cc_start: 0.7880 (mttt) cc_final: 0.7504 (mtmm) REVERT: C 342 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7127 (mt-10) REVERT: C 343 LYS cc_start: 0.8064 (mttt) cc_final: 0.7772 (mttm) REVERT: C 349 ARG cc_start: 0.6452 (mtm180) cc_final: 0.6051 (mtt180) REVERT: C 353 LYS cc_start: 0.7737 (tttt) cc_final: 0.6777 (tptt) REVERT: C 369 LYS cc_start: 0.7617 (mttt) cc_final: 0.6980 (mtpp) REVERT: C 370 LYS cc_start: 0.7871 (tttp) cc_final: 0.7520 (ttmt) REVERT: C 371 ILE cc_start: 0.8166 (mt) cc_final: 0.7738 (mp) REVERT: C 372 GLU cc_start: 0.7364 (mt-10) cc_final: 0.6269 (mm-30) REVERT: C 373 THR cc_start: 0.8235 (m) cc_final: 0.7848 (p) REVERT: C 375 LYS cc_start: 0.8036 (tttt) cc_final: 0.7709 (tttt) REVERT: D 314 ASP cc_start: 0.7230 (t0) cc_final: 0.6917 (t0) REVERT: D 315 LEU cc_start: 0.8312 (mt) cc_final: 0.7971 (mm) REVERT: D 317 LYS cc_start: 0.7720 (mttt) cc_final: 0.7358 (mtpt) REVERT: D 321 LYS cc_start: 0.7725 (mttt) cc_final: 0.7197 (mttp) REVERT: D 338 GLU cc_start: 0.7798 (tt0) cc_final: 0.7137 (tt0) REVERT: D 345 ASP cc_start: 0.7255 (m-30) cc_final: 0.6768 (t70) REVERT: D 347 LYS cc_start: 0.7951 (mttt) cc_final: 0.7634 (mmtm) REVERT: D 353 LYS cc_start: 0.7856 (tttt) cc_final: 0.7582 (tttm) REVERT: D 373 THR cc_start: 0.8328 (m) cc_final: 0.7952 (p) REVERT: D 375 LYS cc_start: 0.8246 (tttt) cc_final: 0.7726 (ttpp) REVERT: D 379 ARG cc_start: 0.6720 (mtt-85) cc_final: 0.6292 (mmp-170) REVERT: E 311 LYS cc_start: 0.7813 (mttt) cc_final: 0.6878 (mttm) REVERT: E 336 GLN cc_start: 0.7688 (tt0) cc_final: 0.7391 (tt0) REVERT: E 338 GLU cc_start: 0.6808 (tt0) cc_final: 0.6077 (mt-10) REVERT: E 342 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7128 (mt-10) REVERT: E 343 LYS cc_start: 0.8105 (mttt) cc_final: 0.7855 (mtpp) REVERT: E 347 LYS cc_start: 0.8048 (mttt) cc_final: 0.7808 (mttm) REVERT: E 348 ASP cc_start: 0.7897 (t0) cc_final: 0.7658 (t0) REVERT: E 349 ARG cc_start: 0.6798 (mtm180) cc_final: 0.5746 (mtp180) REVERT: E 353 LYS cc_start: 0.7295 (tttt) cc_final: 0.5997 (tptt) REVERT: E 356 SER cc_start: 0.7331 (p) cc_final: 0.7005 (t) REVERT: E 369 LYS cc_start: 0.6882 (mttt) cc_final: 0.6240 (mtpp) REVERT: E 373 THR cc_start: 0.7841 (m) cc_final: 0.7121 (p) REVERT: E 375 LYS cc_start: 0.7191 (tttt) cc_final: 0.6686 (tttp) REVERT: F 311 LYS cc_start: 0.7444 (mttt) cc_final: 0.6550 (mttm) REVERT: F 317 LYS cc_start: 0.7056 (mttt) cc_final: 0.6837 (mtpt) REVERT: F 321 LYS cc_start: 0.6984 (mttt) cc_final: 0.6605 (mttm) REVERT: F 336 GLN cc_start: 0.7452 (tt0) cc_final: 0.7223 (tt0) REVERT: F 338 GLU cc_start: 0.7380 (tt0) cc_final: 0.6342 (tt0) REVERT: F 340 LYS cc_start: 0.6749 (mttt) cc_final: 0.6081 (mmtt) REVERT: F 347 LYS cc_start: 0.7897 (mttt) cc_final: 0.7408 (mmtp) REVERT: F 348 ASP cc_start: 0.7818 (t0) cc_final: 0.7552 (t0) REVERT: F 353 LYS cc_start: 0.7234 (tttt) cc_final: 0.6750 (tttm) REVERT: F 356 SER cc_start: 0.7261 (p) cc_final: 0.7023 (t) REVERT: F 375 LYS cc_start: 0.7658 (tttt) cc_final: 0.7126 (ttpp) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 1.2650 time to fit residues: 264.1310 Evaluate side-chains 187 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 chunk 32 optimal weight: 0.2980 chunk 12 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 362 HIS B 351 GLN D 307 GLN D 327 ASN F 351 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3561 Z= 0.160 Angle : 0.561 5.420 4761 Z= 0.285 Chirality : 0.048 0.124 531 Planarity : 0.003 0.021 609 Dihedral : 5.130 18.305 474 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.50 % Allowed : 10.53 % Favored : 87.97 % 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 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 329 PHE 0.013 0.002 PHE C 378 TYR 0.010 0.003 TYR A 310 ARG 0.002 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 189 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7768 (mttt) cc_final: 0.7464 (mttm) REVERT: A 314 ASP cc_start: 0.7853 (t0) cc_final: 0.7560 (t0) REVERT: A 317 LYS cc_start: 0.6990 (mtmt) cc_final: 0.6732 (mtpt) REVERT: A 338 GLU cc_start: 0.6870 (tt0) cc_final: 0.5927 (tp30) REVERT: A 340 LYS cc_start: 0.6984 (mttm) cc_final: 0.6567 (mttm) REVERT: A 342 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6532 (mt-10) REVERT: A 343 LYS cc_start: 0.7891 (mttt) cc_final: 0.7639 (mtpp) REVERT: A 347 LYS cc_start: 0.8145 (mttt) cc_final: 0.7696 (mmtm) REVERT: A 353 LYS cc_start: 0.7431 (tttt) cc_final: 0.6215 (tptt) REVERT: A 358 ASP cc_start: 0.7127 (m-30) cc_final: 0.6734 (m-30) REVERT: A 369 LYS cc_start: 0.6777 (mttt) cc_final: 0.6098 (mtpp) REVERT: A 370 LYS cc_start: 0.7478 (tttp) cc_final: 0.6846 (ttmt) REVERT: A 371 ILE cc_start: 0.7477 (mt) cc_final: 0.7120 (mp) REVERT: A 373 THR cc_start: 0.7749 (m) cc_final: 0.7354 (p) REVERT: A 375 LYS cc_start: 0.7257 (tttt) cc_final: 0.7027 (tttp) REVERT: B 314 ASP cc_start: 0.7301 (t0) cc_final: 0.7019 (t0) REVERT: B 345 ASP cc_start: 0.6857 (m-30) cc_final: 0.6254 (t70) REVERT: B 353 LYS cc_start: 0.7126 (tttt) cc_final: 0.6681 (tttm) REVERT: B 375 LYS cc_start: 0.7591 (tttt) cc_final: 0.6999 (ttpt) REVERT: C 307 GLN cc_start: 0.8327 (tt0) cc_final: 0.8032 (tt0) REVERT: C 311 LYS cc_start: 0.8254 (mttt) cc_final: 0.7923 (mttm) REVERT: C 314 ASP cc_start: 0.7894 (t0) cc_final: 0.7623 (t0) REVERT: C 320 SER cc_start: 0.7727 (t) cc_final: 0.7416 (p) REVERT: C 321 LYS cc_start: 0.7595 (mttt) cc_final: 0.7375 (mttp) REVERT: C 336 GLN cc_start: 0.8143 (tt0) cc_final: 0.7934 (tt0) REVERT: C 338 GLU cc_start: 0.7455 (tt0) cc_final: 0.6807 (tm-30) REVERT: C 340 LYS cc_start: 0.7786 (mttt) cc_final: 0.7135 (mttm) REVERT: C 342 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7120 (mt-10) REVERT: C 343 LYS cc_start: 0.8014 (mttt) cc_final: 0.7727 (mttm) REVERT: C 345 ASP cc_start: 0.7956 (m-30) cc_final: 0.7116 (t70) REVERT: C 349 ARG cc_start: 0.6398 (mtm180) cc_final: 0.6190 (mtt180) REVERT: C 353 LYS cc_start: 0.7702 (tttt) cc_final: 0.6779 (tptt) REVERT: C 369 LYS cc_start: 0.7616 (mttt) cc_final: 0.6969 (mtpp) REVERT: C 370 LYS cc_start: 0.7808 (tttp) cc_final: 0.7355 (ttmt) REVERT: C 371 ILE cc_start: 0.8067 (mt) cc_final: 0.7650 (mp) REVERT: C 372 GLU cc_start: 0.7429 (mt-10) cc_final: 0.6338 (mm-30) REVERT: C 373 THR cc_start: 0.8336 (m) cc_final: 0.7931 (p) REVERT: D 314 ASP cc_start: 0.7462 (t0) cc_final: 0.7053 (t0) REVERT: D 315 LEU cc_start: 0.8236 (mt) cc_final: 0.7908 (mm) REVERT: D 317 LYS cc_start: 0.7687 (mttt) cc_final: 0.7292 (mtpm) REVERT: D 324 SER cc_start: 0.7596 (t) cc_final: 0.7197 (m) REVERT: D 338 GLU cc_start: 0.7894 (tt0) cc_final: 0.7204 (tt0) REVERT: D 345 ASP cc_start: 0.7126 (m-30) cc_final: 0.6727 (t70) REVERT: D 347 LYS cc_start: 0.8034 (mttt) cc_final: 0.7692 (mmtm) REVERT: D 353 LYS cc_start: 0.7853 (tttt) cc_final: 0.7581 (tttm) REVERT: D 375 LYS cc_start: 0.8244 (tttt) cc_final: 0.7715 (ttpp) REVERT: D 379 ARG cc_start: 0.6838 (mtt-85) cc_final: 0.6202 (mmp-170) REVERT: E 311 LYS cc_start: 0.7766 (mttt) cc_final: 0.6782 (mttm) REVERT: E 336 GLN cc_start: 0.7659 (tt0) cc_final: 0.7260 (tt0) REVERT: E 338 GLU cc_start: 0.6729 (tt0) cc_final: 0.5681 (mt-10) REVERT: E 340 LYS cc_start: 0.7145 (mttt) cc_final: 0.6936 (mtpt) REVERT: E 342 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7132 (mt-10) REVERT: E 349 ARG cc_start: 0.6821 (mtm180) cc_final: 0.5565 (mmp80) REVERT: E 353 LYS cc_start: 0.7310 (tttt) cc_final: 0.6089 (tptt) REVERT: E 369 LYS cc_start: 0.6891 (mttt) cc_final: 0.6281 (mtpp) REVERT: E 372 GLU cc_start: 0.7307 (tt0) cc_final: 0.7013 (tp30) REVERT: E 373 THR cc_start: 0.7902 (m) cc_final: 0.7317 (p) REVERT: E 375 LYS cc_start: 0.7356 (tttt) cc_final: 0.6768 (tttp) REVERT: F 311 LYS cc_start: 0.7434 (mttt) cc_final: 0.6435 (mttm) REVERT: F 317 LYS cc_start: 0.7327 (mttt) cc_final: 0.7106 (mtpt) REVERT: F 321 LYS cc_start: 0.6961 (mttt) cc_final: 0.6609 (mttm) REVERT: F 338 GLU cc_start: 0.7393 (tt0) cc_final: 0.6483 (tt0) REVERT: F 340 LYS cc_start: 0.6963 (mttt) cc_final: 0.6166 (mmtt) REVERT: F 345 ASP cc_start: 0.6781 (m-30) cc_final: 0.6504 (t70) REVERT: F 353 LYS cc_start: 0.7250 (tttt) cc_final: 0.6739 (tttm) REVERT: F 375 LYS cc_start: 0.7698 (tttt) cc_final: 0.7109 (ttpp) outliers start: 6 outliers final: 2 residues processed: 190 average time/residue: 1.2920 time to fit residues: 251.1477 Evaluate side-chains 177 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 175 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 3561 Z= 0.364 Angle : 0.647 4.972 4761 Z= 0.330 Chirality : 0.051 0.128 531 Planarity : 0.004 0.025 609 Dihedral : 5.146 18.368 474 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.75 % Allowed : 13.78 % Favored : 84.46 % 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: -1.75 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 329 PHE 0.015 0.003 PHE F 346 TYR 0.013 0.003 TYR E 310 ARG 0.003 0.001 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 170 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7775 (mttt) cc_final: 0.7425 (mttm) REVERT: A 317 LYS cc_start: 0.7013 (mtmt) cc_final: 0.6708 (mtpt) REVERT: A 321 LYS cc_start: 0.7012 (mtmt) cc_final: 0.6211 (mtpp) REVERT: A 338 GLU cc_start: 0.6952 (tt0) cc_final: 0.5672 (mt-10) REVERT: A 343 LYS cc_start: 0.7834 (mttt) cc_final: 0.7605 (mtpp) REVERT: A 347 LYS cc_start: 0.8097 (mttt) cc_final: 0.7680 (mmtm) REVERT: A 353 LYS cc_start: 0.7400 (tttt) cc_final: 0.6126 (tptt) REVERT: A 369 LYS cc_start: 0.6754 (mttt) cc_final: 0.6136 (mtpp) REVERT: A 370 LYS cc_start: 0.7667 (tttp) cc_final: 0.6876 (ttmt) REVERT: A 371 ILE cc_start: 0.7583 (mt) cc_final: 0.7366 (mp) REVERT: A 372 GLU cc_start: 0.7368 (tt0) cc_final: 0.7045 (tt0) REVERT: A 373 THR cc_start: 0.7798 (m) cc_final: 0.7351 (p) REVERT: B 314 ASP cc_start: 0.7363 (t0) cc_final: 0.7056 (t0) REVERT: B 345 ASP cc_start: 0.6828 (m-30) cc_final: 0.6210 (t70) REVERT: B 353 LYS cc_start: 0.7058 (tttt) cc_final: 0.6634 (tttm) REVERT: B 375 LYS cc_start: 0.7653 (tttt) cc_final: 0.7088 (ttpp) REVERT: C 307 GLN cc_start: 0.8284 (tt0) cc_final: 0.7974 (tt0) REVERT: C 311 LYS cc_start: 0.8175 (mttt) cc_final: 0.7840 (mttm) REVERT: C 320 SER cc_start: 0.7800 (t) cc_final: 0.7352 (p) REVERT: C 338 GLU cc_start: 0.7607 (tt0) cc_final: 0.6988 (tm-30) REVERT: C 342 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7232 (mt-10) REVERT: C 343 LYS cc_start: 0.8020 (mttt) cc_final: 0.7747 (mttm) REVERT: C 347 LYS cc_start: 0.8468 (mmtt) cc_final: 0.6569 (pmtt) REVERT: C 349 ARG cc_start: 0.6521 (mtm180) cc_final: 0.6213 (mtt180) REVERT: C 353 LYS cc_start: 0.7693 (tttt) cc_final: 0.6817 (tptt) REVERT: C 369 LYS cc_start: 0.7640 (mttt) cc_final: 0.7024 (mtpp) REVERT: C 370 LYS cc_start: 0.7824 (tttp) cc_final: 0.7420 (ttmt) REVERT: C 371 ILE cc_start: 0.8168 (mt) cc_final: 0.7765 (mp) REVERT: C 372 GLU cc_start: 0.7499 (mt-10) cc_final: 0.6262 (mm-30) REVERT: C 373 THR cc_start: 0.8415 (m) cc_final: 0.8004 (p) REVERT: D 314 ASP cc_start: 0.7407 (t0) cc_final: 0.7072 (t0) REVERT: D 317 LYS cc_start: 0.7755 (mttt) cc_final: 0.7414 (mtpt) REVERT: D 324 SER cc_start: 0.7726 (t) cc_final: 0.7299 (m) REVERT: D 338 GLU cc_start: 0.7825 (tt0) cc_final: 0.7122 (tt0) REVERT: D 345 ASP cc_start: 0.7135 (m-30) cc_final: 0.6827 (t70) REVERT: D 353 LYS cc_start: 0.7880 (tttt) cc_final: 0.7644 (tttm) REVERT: D 370 LYS cc_start: 0.7661 (tttp) cc_final: 0.7427 (tttt) REVERT: D 375 LYS cc_start: 0.8259 (tttt) cc_final: 0.7736 (ttpp) REVERT: D 379 ARG cc_start: 0.6867 (mtt-85) cc_final: 0.6611 (mtt-85) REVERT: E 311 LYS cc_start: 0.7980 (mttt) cc_final: 0.6885 (mttm) REVERT: E 336 GLN cc_start: 0.7632 (tt0) cc_final: 0.7283 (tt0) REVERT: E 338 GLU cc_start: 0.6986 (tt0) cc_final: 0.6014 (mt-10) REVERT: E 340 LYS cc_start: 0.7208 (OUTLIER) cc_final: 0.7001 (mtpt) REVERT: E 342 GLU cc_start: 0.7314 (mt-10) cc_final: 0.7068 (mt-10) REVERT: E 349 ARG cc_start: 0.6809 (mtm180) cc_final: 0.5210 (mmp-170) REVERT: E 353 LYS cc_start: 0.7198 (tttt) cc_final: 0.5969 (tptt) REVERT: E 369 LYS cc_start: 0.6859 (mttt) cc_final: 0.6245 (mtpp) REVERT: E 371 ILE cc_start: 0.7671 (mt) cc_final: 0.7353 (mp) REVERT: E 372 GLU cc_start: 0.7439 (tt0) cc_final: 0.7062 (tp30) REVERT: E 373 THR cc_start: 0.7925 (m) cc_final: 0.7368 (p) REVERT: E 375 LYS cc_start: 0.7364 (tttt) cc_final: 0.6749 (tttp) REVERT: F 317 LYS cc_start: 0.7318 (mttt) cc_final: 0.7061 (mtpt) REVERT: F 321 LYS cc_start: 0.7112 (mttt) cc_final: 0.6725 (mttm) REVERT: F 338 GLU cc_start: 0.7442 (tt0) cc_final: 0.6681 (tt0) REVERT: F 345 ASP cc_start: 0.6745 (m-30) cc_final: 0.6435 (t70) REVERT: F 347 LYS cc_start: 0.7905 (mttt) cc_final: 0.7213 (mmtp) REVERT: F 353 LYS cc_start: 0.7163 (tttt) cc_final: 0.6707 (tttm) REVERT: F 375 LYS cc_start: 0.7695 (tttt) cc_final: 0.7160 (ttpp) outliers start: 7 outliers final: 3 residues processed: 173 average time/residue: 1.4004 time to fit residues: 247.3729 Evaluate side-chains 171 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 167 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 0.1980 chunk 25 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 23 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 307 GLN C 330 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3561 Z= 0.288 Angle : 0.588 4.616 4761 Z= 0.298 Chirality : 0.049 0.123 531 Planarity : 0.003 0.024 609 Dihedral : 4.961 18.286 474 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.75 % Allowed : 13.53 % Favored : 84.71 % 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: -1.84 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 329 PHE 0.013 0.002 PHE F 346 TYR 0.012 0.003 TYR E 310 ARG 0.003 0.001 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 166 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7752 (mttt) cc_final: 0.7381 (mttm) REVERT: A 317 LYS cc_start: 0.7002 (mtmt) cc_final: 0.6650 (mtpt) REVERT: A 321 LYS cc_start: 0.7080 (mtmt) cc_final: 0.6245 (mtpp) REVERT: A 338 GLU cc_start: 0.7005 (tt0) cc_final: 0.5627 (mt-10) REVERT: A 343 LYS cc_start: 0.7837 (mttt) cc_final: 0.7626 (mtpp) REVERT: A 345 ASP cc_start: 0.7298 (m-30) cc_final: 0.6939 (m-30) REVERT: A 347 LYS cc_start: 0.8085 (mttt) cc_final: 0.7750 (mmtm) REVERT: A 353 LYS cc_start: 0.7380 (tttt) cc_final: 0.6183 (tptt) REVERT: A 369 LYS cc_start: 0.6786 (mttt) cc_final: 0.6140 (mtpp) REVERT: A 370 LYS cc_start: 0.7553 (tttp) cc_final: 0.6806 (ttmt) REVERT: A 371 ILE cc_start: 0.7581 (mt) cc_final: 0.7225 (mp) REVERT: A 373 THR cc_start: 0.7785 (m) cc_final: 0.7370 (p) REVERT: B 345 ASP cc_start: 0.6802 (m-30) cc_final: 0.6196 (t70) REVERT: B 353 LYS cc_start: 0.7079 (tttt) cc_final: 0.6643 (tttm) REVERT: B 375 LYS cc_start: 0.7676 (tttt) cc_final: 0.7125 (ttpt) REVERT: C 307 GLN cc_start: 0.8307 (tt0) cc_final: 0.8062 (tt0) REVERT: C 311 LYS cc_start: 0.8152 (mttt) cc_final: 0.7860 (mttm) REVERT: C 320 SER cc_start: 0.7799 (t) cc_final: 0.7340 (p) REVERT: C 338 GLU cc_start: 0.7542 (tt0) cc_final: 0.6923 (tm-30) REVERT: C 342 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7233 (mt-10) REVERT: C 343 LYS cc_start: 0.8026 (mttt) cc_final: 0.7761 (mttm) REVERT: C 347 LYS cc_start: 0.8463 (mmtt) cc_final: 0.6574 (pmtt) REVERT: C 349 ARG cc_start: 0.6461 (mtm180) cc_final: 0.6110 (mtt180) REVERT: C 353 LYS cc_start: 0.7675 (tttt) cc_final: 0.6910 (tptp) REVERT: C 369 LYS cc_start: 0.7659 (mttt) cc_final: 0.7021 (mtpp) REVERT: C 370 LYS cc_start: 0.7844 (tttp) cc_final: 0.7389 (ttmt) REVERT: C 371 ILE cc_start: 0.8148 (mt) cc_final: 0.7734 (mp) REVERT: C 372 GLU cc_start: 0.7549 (mt-10) cc_final: 0.6383 (mm-30) REVERT: C 373 THR cc_start: 0.8394 (m) cc_final: 0.8007 (p) REVERT: D 314 ASP cc_start: 0.7421 (t0) cc_final: 0.7118 (t0) REVERT: D 315 LEU cc_start: 0.8435 (mt) cc_final: 0.8036 (mm) REVERT: D 317 LYS cc_start: 0.7782 (mttt) cc_final: 0.7433 (mtpt) REVERT: D 324 SER cc_start: 0.7685 (t) cc_final: 0.7341 (m) REVERT: D 338 GLU cc_start: 0.7806 (tt0) cc_final: 0.7124 (tt0) REVERT: D 345 ASP cc_start: 0.7123 (m-30) cc_final: 0.6837 (t70) REVERT: D 353 LYS cc_start: 0.7869 (tttt) cc_final: 0.7374 (tttt) REVERT: D 370 LYS cc_start: 0.7665 (tttp) cc_final: 0.7452 (tttt) REVERT: D 375 LYS cc_start: 0.8245 (tttt) cc_final: 0.7704 (ttpp) REVERT: D 379 ARG cc_start: 0.6840 (mtt-85) cc_final: 0.6160 (mmp-170) REVERT: E 311 LYS cc_start: 0.7978 (mttt) cc_final: 0.6926 (mttm) REVERT: E 336 GLN cc_start: 0.7690 (tt0) cc_final: 0.7321 (tt0) REVERT: E 338 GLU cc_start: 0.6997 (tt0) cc_final: 0.6014 (mt-10) REVERT: E 349 ARG cc_start: 0.6840 (mtm180) cc_final: 0.5241 (mmp-170) REVERT: E 353 LYS cc_start: 0.7235 (tttt) cc_final: 0.6009 (tptt) REVERT: E 369 LYS cc_start: 0.6834 (mttt) cc_final: 0.6206 (mtpp) REVERT: E 371 ILE cc_start: 0.7666 (mt) cc_final: 0.7342 (mp) REVERT: E 372 GLU cc_start: 0.7467 (tt0) cc_final: 0.7160 (tp30) REVERT: E 373 THR cc_start: 0.7928 (m) cc_final: 0.7362 (p) REVERT: E 375 LYS cc_start: 0.7393 (tttt) cc_final: 0.6773 (tttp) REVERT: F 317 LYS cc_start: 0.7337 (mttt) cc_final: 0.7069 (mtpt) REVERT: F 321 LYS cc_start: 0.7108 (mttt) cc_final: 0.6738 (mttm) REVERT: F 338 GLU cc_start: 0.7451 (tt0) cc_final: 0.6526 (tt0) REVERT: F 340 LYS cc_start: 0.7207 (mtmt) cc_final: 0.6056 (mmtt) REVERT: F 345 ASP cc_start: 0.6741 (m-30) cc_final: 0.6430 (t70) REVERT: F 347 LYS cc_start: 0.7917 (mttt) cc_final: 0.7233 (mmtp) REVERT: F 353 LYS cc_start: 0.7177 (tttt) cc_final: 0.6717 (tttm) REVERT: F 375 LYS cc_start: 0.7712 (tttt) cc_final: 0.7134 (ttpp) outliers start: 7 outliers final: 3 residues processed: 170 average time/residue: 1.4388 time to fit residues: 249.8688 Evaluate side-chains 167 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 164 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3561 Z= 0.353 Angle : 0.619 4.682 4761 Z= 0.316 Chirality : 0.050 0.126 531 Planarity : 0.003 0.025 609 Dihedral : 5.028 18.041 474 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 1.75 % Allowed : 13.78 % Favored : 84.46 % 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: -1.91 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 329 PHE 0.013 0.003 PHE F 346 TYR 0.013 0.003 TYR F 310 ARG 0.002 0.001 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 166 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7789 (mttt) cc_final: 0.7411 (mttm) REVERT: A 317 LYS cc_start: 0.7005 (mtmt) cc_final: 0.6629 (mtpt) REVERT: A 321 LYS cc_start: 0.7098 (mtmt) cc_final: 0.6289 (mtpp) REVERT: A 338 GLU cc_start: 0.7068 (tt0) cc_final: 0.5622 (mt-10) REVERT: A 343 LYS cc_start: 0.7843 (mttt) cc_final: 0.7613 (mttp) REVERT: A 345 ASP cc_start: 0.7303 (m-30) cc_final: 0.6931 (m-30) REVERT: A 347 LYS cc_start: 0.8037 (mttt) cc_final: 0.7786 (mttm) REVERT: A 353 LYS cc_start: 0.7365 (tttt) cc_final: 0.6022 (tptt) REVERT: A 369 LYS cc_start: 0.6793 (mttt) cc_final: 0.6160 (mtpp) REVERT: A 370 LYS cc_start: 0.7530 (tttp) cc_final: 0.6816 (ttmt) REVERT: A 371 ILE cc_start: 0.7575 (mt) cc_final: 0.7360 (mp) REVERT: A 373 THR cc_start: 0.7772 (m) cc_final: 0.7370 (p) REVERT: B 345 ASP cc_start: 0.6790 (m-30) cc_final: 0.6184 (t70) REVERT: B 353 LYS cc_start: 0.7086 (tttt) cc_final: 0.6658 (tttm) REVERT: B 375 LYS cc_start: 0.7659 (tttt) cc_final: 0.7123 (ttpt) REVERT: C 307 GLN cc_start: 0.8300 (tt0) cc_final: 0.8063 (tt0) REVERT: C 311 LYS cc_start: 0.8130 (mttt) cc_final: 0.7804 (mttm) REVERT: C 320 SER cc_start: 0.7926 (t) cc_final: 0.7442 (p) REVERT: C 338 GLU cc_start: 0.7565 (tt0) cc_final: 0.6924 (tm-30) REVERT: C 342 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7255 (mt-10) REVERT: C 343 LYS cc_start: 0.8019 (mttt) cc_final: 0.7754 (mttm) REVERT: C 347 LYS cc_start: 0.8463 (mmtt) cc_final: 0.6634 (pmtt) REVERT: C 349 ARG cc_start: 0.6520 (mtm180) cc_final: 0.6112 (mtt180) REVERT: C 353 LYS cc_start: 0.7707 (tttt) cc_final: 0.6746 (tptt) REVERT: C 369 LYS cc_start: 0.7649 (mttt) cc_final: 0.7021 (mtpp) REVERT: C 370 LYS cc_start: 0.7829 (tttp) cc_final: 0.7357 (ttmt) REVERT: C 371 ILE cc_start: 0.8183 (mt) cc_final: 0.7785 (mp) REVERT: C 372 GLU cc_start: 0.7611 (mt-10) cc_final: 0.6429 (mm-30) REVERT: C 373 THR cc_start: 0.8378 (m) cc_final: 0.7996 (p) REVERT: D 317 LYS cc_start: 0.7781 (mttt) cc_final: 0.7440 (mtpt) REVERT: D 324 SER cc_start: 0.7699 (t) cc_final: 0.7339 (m) REVERT: D 338 GLU cc_start: 0.7812 (tt0) cc_final: 0.7140 (tt0) REVERT: D 345 ASP cc_start: 0.7070 (m-30) cc_final: 0.6772 (t70) REVERT: D 347 LYS cc_start: 0.8007 (mttt) cc_final: 0.7719 (mttm) REVERT: D 353 LYS cc_start: 0.7854 (tttt) cc_final: 0.7630 (tttm) REVERT: D 375 LYS cc_start: 0.8214 (tttt) cc_final: 0.7748 (ttpt) REVERT: D 379 ARG cc_start: 0.6807 (mtt-85) cc_final: 0.6124 (mmp-170) REVERT: E 311 LYS cc_start: 0.7984 (mttt) cc_final: 0.6891 (mttm) REVERT: E 336 GLN cc_start: 0.7637 (tt0) cc_final: 0.7304 (tt0) REVERT: E 338 GLU cc_start: 0.7019 (tt0) cc_final: 0.6214 (mt-10) REVERT: E 340 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.6814 (mttp) REVERT: E 349 ARG cc_start: 0.6790 (mtm180) cc_final: 0.5176 (mmp-170) REVERT: E 353 LYS cc_start: 0.7213 (tttt) cc_final: 0.5989 (tptt) REVERT: E 369 LYS cc_start: 0.6878 (mttt) cc_final: 0.6269 (mtpp) REVERT: E 370 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7839 (ttmp) REVERT: E 371 ILE cc_start: 0.7678 (mt) cc_final: 0.7367 (mp) REVERT: E 372 GLU cc_start: 0.7485 (tp30) cc_final: 0.7126 (tp30) REVERT: E 373 THR cc_start: 0.7925 (m) cc_final: 0.7364 (p) REVERT: E 375 LYS cc_start: 0.7398 (tttt) cc_final: 0.6780 (tttp) REVERT: F 317 LYS cc_start: 0.7341 (mttt) cc_final: 0.7066 (mtpt) REVERT: F 321 LYS cc_start: 0.7164 (mttt) cc_final: 0.6831 (mttm) REVERT: F 338 GLU cc_start: 0.7446 (tt0) cc_final: 0.6715 (tt0) REVERT: F 345 ASP cc_start: 0.6762 (m-30) cc_final: 0.6480 (t70) REVERT: F 347 LYS cc_start: 0.7920 (mttt) cc_final: 0.7285 (mmtm) REVERT: F 353 LYS cc_start: 0.7146 (tttt) cc_final: 0.6684 (tttm) REVERT: F 375 LYS cc_start: 0.7760 (tttt) cc_final: 0.7169 (ttpp) outliers start: 7 outliers final: 3 residues processed: 170 average time/residue: 1.4791 time to fit residues: 256.6851 Evaluate side-chains 169 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 164 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3561 Z= 0.268 Angle : 0.568 4.522 4761 Z= 0.289 Chirality : 0.049 0.122 531 Planarity : 0.003 0.025 609 Dihedral : 4.856 17.864 474 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.50 % Allowed : 15.29 % Favored : 83.21 % 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: -1.92 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 329 PHE 0.012 0.002 PHE F 346 TYR 0.012 0.003 TYR F 310 ARG 0.002 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 168 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7784 (mttt) cc_final: 0.7406 (mttm) REVERT: A 317 LYS cc_start: 0.6998 (mtmt) cc_final: 0.6629 (mtpt) REVERT: A 321 LYS cc_start: 0.7131 (mtmt) cc_final: 0.6301 (mtpp) REVERT: A 338 GLU cc_start: 0.7065 (tt0) cc_final: 0.5598 (mt-10) REVERT: A 343 LYS cc_start: 0.7822 (mttt) cc_final: 0.7612 (mtpp) REVERT: A 345 ASP cc_start: 0.7313 (m-30) cc_final: 0.6936 (m-30) REVERT: A 347 LYS cc_start: 0.7976 (mttt) cc_final: 0.7686 (mmtm) REVERT: A 353 LYS cc_start: 0.7411 (tttt) cc_final: 0.6063 (tptt) REVERT: A 369 LYS cc_start: 0.6777 (mttt) cc_final: 0.6135 (mtpp) REVERT: A 370 LYS cc_start: 0.7538 (tttp) cc_final: 0.6819 (ttmt) REVERT: A 371 ILE cc_start: 0.7589 (mt) cc_final: 0.7382 (mp) REVERT: A 373 THR cc_start: 0.7766 (m) cc_final: 0.7358 (p) REVERT: B 345 ASP cc_start: 0.6748 (m-30) cc_final: 0.6172 (t70) REVERT: B 353 LYS cc_start: 0.7066 (tttt) cc_final: 0.6642 (tttm) REVERT: B 375 LYS cc_start: 0.7667 (tttt) cc_final: 0.7170 (ttpt) REVERT: C 307 GLN cc_start: 0.8313 (tt0) cc_final: 0.8029 (tt0) REVERT: C 311 LYS cc_start: 0.8104 (mttt) cc_final: 0.7771 (mttm) REVERT: C 314 ASP cc_start: 0.7731 (t0) cc_final: 0.7525 (t0) REVERT: C 320 SER cc_start: 0.7895 (t) cc_final: 0.7440 (p) REVERT: C 338 GLU cc_start: 0.7568 (tt0) cc_final: 0.6917 (tm-30) REVERT: C 342 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7132 (mt-10) REVERT: C 343 LYS cc_start: 0.8027 (mttt) cc_final: 0.7765 (mttm) REVERT: C 347 LYS cc_start: 0.8457 (mmtt) cc_final: 0.6626 (pmtt) REVERT: C 349 ARG cc_start: 0.6534 (mtm180) cc_final: 0.6121 (mtt180) REVERT: C 353 LYS cc_start: 0.7690 (tttt) cc_final: 0.6746 (tptt) REVERT: C 369 LYS cc_start: 0.7596 (mttt) cc_final: 0.6964 (mtpp) REVERT: C 370 LYS cc_start: 0.7837 (tttp) cc_final: 0.7394 (ttmt) REVERT: C 371 ILE cc_start: 0.8184 (mt) cc_final: 0.7811 (mp) REVERT: C 372 GLU cc_start: 0.7625 (mt-10) cc_final: 0.6528 (mm-30) REVERT: C 373 THR cc_start: 0.8380 (m) cc_final: 0.8000 (p) REVERT: D 315 LEU cc_start: 0.8431 (mt) cc_final: 0.8092 (mm) REVERT: D 317 LYS cc_start: 0.7773 (mttt) cc_final: 0.7439 (mtpt) REVERT: D 324 SER cc_start: 0.7703 (t) cc_final: 0.7387 (m) REVERT: D 338 GLU cc_start: 0.7824 (tt0) cc_final: 0.7169 (tt0) REVERT: D 345 ASP cc_start: 0.7084 (m-30) cc_final: 0.6856 (t70) REVERT: D 353 LYS cc_start: 0.7845 (tttt) cc_final: 0.7360 (tttt) REVERT: D 375 LYS cc_start: 0.8241 (tttt) cc_final: 0.7775 (ttpt) REVERT: D 379 ARG cc_start: 0.6832 (mtt-85) cc_final: 0.6150 (mmp-170) REVERT: E 311 LYS cc_start: 0.7966 (mttt) cc_final: 0.6951 (mttm) REVERT: E 336 GLN cc_start: 0.7642 (tt0) cc_final: 0.7269 (tt0) REVERT: E 338 GLU cc_start: 0.7025 (tt0) cc_final: 0.6282 (mt-10) REVERT: E 340 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.6876 (mttm) REVERT: E 349 ARG cc_start: 0.6800 (mtm180) cc_final: 0.5177 (mmp-170) REVERT: E 353 LYS cc_start: 0.7288 (tttt) cc_final: 0.6038 (tptt) REVERT: E 369 LYS cc_start: 0.6837 (mttt) cc_final: 0.6205 (mtpp) REVERT: E 370 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7843 (ttmp) REVERT: E 371 ILE cc_start: 0.7681 (mt) cc_final: 0.7368 (mp) REVERT: E 372 GLU cc_start: 0.7517 (tp30) cc_final: 0.7218 (tp30) REVERT: E 373 THR cc_start: 0.7923 (m) cc_final: 0.7356 (p) REVERT: E 375 LYS cc_start: 0.7368 (tttt) cc_final: 0.6752 (tttp) REVERT: F 317 LYS cc_start: 0.7334 (mttt) cc_final: 0.7071 (mtpt) REVERT: F 321 LYS cc_start: 0.7127 (mttt) cc_final: 0.6797 (mttm) REVERT: F 338 GLU cc_start: 0.7417 (tt0) cc_final: 0.6749 (tt0) REVERT: F 345 ASP cc_start: 0.6770 (m-30) cc_final: 0.6415 (t70) REVERT: F 347 LYS cc_start: 0.7939 (mttt) cc_final: 0.7215 (mmtp) REVERT: F 353 LYS cc_start: 0.7141 (tttt) cc_final: 0.6677 (tttm) REVERT: F 375 LYS cc_start: 0.7803 (tttt) cc_final: 0.7135 (ttpt) outliers start: 6 outliers final: 3 residues processed: 172 average time/residue: 1.4703 time to fit residues: 258.2024 Evaluate side-chains 172 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 167 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 18 optimal weight: 0.4980 chunk 16 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3561 Z= 0.292 Angle : 0.580 4.566 4761 Z= 0.296 Chirality : 0.049 0.124 531 Planarity : 0.003 0.025 609 Dihedral : 4.869 17.751 474 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 1.50 % Allowed : 15.54 % Favored : 82.96 % 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: -1.95 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 329 PHE 0.012 0.002 PHE F 346 TYR 0.013 0.003 TYR F 310 ARG 0.002 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 164 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7772 (mttt) cc_final: 0.7391 (mttm) REVERT: A 317 LYS cc_start: 0.6977 (mtmt) cc_final: 0.6594 (mtpt) REVERT: A 321 LYS cc_start: 0.7129 (mtmt) cc_final: 0.6292 (mtpp) REVERT: A 338 GLU cc_start: 0.7042 (tt0) cc_final: 0.5589 (mt-10) REVERT: A 343 LYS cc_start: 0.7808 (mttt) cc_final: 0.7577 (mttp) REVERT: A 345 ASP cc_start: 0.7310 (m-30) cc_final: 0.6933 (m-30) REVERT: A 347 LYS cc_start: 0.7984 (mttt) cc_final: 0.7695 (mmtm) REVERT: A 353 LYS cc_start: 0.7409 (tttt) cc_final: 0.6066 (tptt) REVERT: A 369 LYS cc_start: 0.6772 (mttt) cc_final: 0.6130 (mtpp) REVERT: A 370 LYS cc_start: 0.7539 (tttp) cc_final: 0.6800 (ttmt) REVERT: A 371 ILE cc_start: 0.7580 (mt) cc_final: 0.7378 (mp) REVERT: A 373 THR cc_start: 0.7781 (m) cc_final: 0.7379 (p) REVERT: B 345 ASP cc_start: 0.6759 (m-30) cc_final: 0.6174 (t70) REVERT: B 353 LYS cc_start: 0.7071 (tttt) cc_final: 0.6639 (tttm) REVERT: B 375 LYS cc_start: 0.7733 (tttt) cc_final: 0.7314 (ttpt) REVERT: C 307 GLN cc_start: 0.8309 (tt0) cc_final: 0.8023 (tt0) REVERT: C 311 LYS cc_start: 0.8104 (mttt) cc_final: 0.7766 (mttm) REVERT: C 314 ASP cc_start: 0.7732 (t0) cc_final: 0.7513 (t0) REVERT: C 320 SER cc_start: 0.7904 (t) cc_final: 0.7408 (p) REVERT: C 338 GLU cc_start: 0.7584 (tt0) cc_final: 0.6901 (tm-30) REVERT: C 342 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7174 (mt-10) REVERT: C 343 LYS cc_start: 0.8010 (mttt) cc_final: 0.7761 (mttm) REVERT: C 347 LYS cc_start: 0.8459 (mmtt) cc_final: 0.6632 (pmtt) REVERT: C 349 ARG cc_start: 0.6545 (mtm180) cc_final: 0.6108 (mtt180) REVERT: C 353 LYS cc_start: 0.7695 (tttt) cc_final: 0.6746 (tptt) REVERT: C 369 LYS cc_start: 0.7598 (mttt) cc_final: 0.6971 (mtpp) REVERT: C 370 LYS cc_start: 0.7845 (tttp) cc_final: 0.7100 (ttmt) REVERT: C 371 ILE cc_start: 0.8189 (mt) cc_final: 0.7868 (mp) REVERT: C 373 THR cc_start: 0.8371 (m) cc_final: 0.7990 (p) REVERT: D 317 LYS cc_start: 0.7752 (mttt) cc_final: 0.7435 (mtpt) REVERT: D 324 SER cc_start: 0.7706 (t) cc_final: 0.7386 (m) REVERT: D 338 GLU cc_start: 0.7803 (tt0) cc_final: 0.7153 (tt0) REVERT: D 345 ASP cc_start: 0.7087 (m-30) cc_final: 0.6874 (t70) REVERT: D 353 LYS cc_start: 0.7846 (tttt) cc_final: 0.7610 (tttm) REVERT: D 375 LYS cc_start: 0.8257 (tttt) cc_final: 0.7818 (ttpt) REVERT: D 379 ARG cc_start: 0.6800 (mtt-85) cc_final: 0.6113 (mmp-170) REVERT: E 311 LYS cc_start: 0.7973 (mttt) cc_final: 0.6959 (mttm) REVERT: E 336 GLN cc_start: 0.7646 (tt0) cc_final: 0.7280 (tt0) REVERT: E 338 GLU cc_start: 0.7143 (tt0) cc_final: 0.6380 (mt-10) REVERT: E 340 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.6963 (mttm) REVERT: E 349 ARG cc_start: 0.6769 (mtm180) cc_final: 0.5172 (mmp-170) REVERT: E 353 LYS cc_start: 0.7286 (tttt) cc_final: 0.6055 (tptt) REVERT: E 369 LYS cc_start: 0.6865 (mttt) cc_final: 0.6228 (mtpp) REVERT: E 370 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7826 (ttmp) REVERT: E 371 ILE cc_start: 0.7685 (mt) cc_final: 0.7369 (mp) REVERT: E 373 THR cc_start: 0.7905 (m) cc_final: 0.7345 (p) REVERT: F 317 LYS cc_start: 0.7349 (mttt) cc_final: 0.7079 (mtpt) REVERT: F 321 LYS cc_start: 0.7155 (mttt) cc_final: 0.6840 (mttm) REVERT: F 338 GLU cc_start: 0.7394 (tt0) cc_final: 0.6663 (tt0) REVERT: F 345 ASP cc_start: 0.6773 (m-30) cc_final: 0.6495 (t70) REVERT: F 353 LYS cc_start: 0.7150 (tttt) cc_final: 0.6692 (tttm) REVERT: F 375 LYS cc_start: 0.7791 (tttt) cc_final: 0.7105 (ttpt) outliers start: 6 outliers final: 3 residues processed: 168 average time/residue: 1.4917 time to fit residues: 255.7888 Evaluate side-chains 169 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 164 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3561 Z= 0.282 Angle : 0.572 4.520 4761 Z= 0.291 Chirality : 0.049 0.124 531 Planarity : 0.003 0.025 609 Dihedral : 4.843 17.680 474 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.50 % Allowed : 16.04 % Favored : 82.46 % 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: -1.98 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 329 PHE 0.011 0.002 PHE F 346 TYR 0.013 0.003 TYR F 310 ARG 0.003 0.001 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 165 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7781 (mttt) cc_final: 0.7396 (mttm) REVERT: A 317 LYS cc_start: 0.6993 (mtmt) cc_final: 0.6597 (mtpt) REVERT: A 321 LYS cc_start: 0.7127 (mtmt) cc_final: 0.6294 (mtpp) REVERT: A 338 GLU cc_start: 0.7029 (tt0) cc_final: 0.5620 (mt-10) REVERT: A 343 LYS cc_start: 0.7809 (mttt) cc_final: 0.7578 (mttp) REVERT: A 345 ASP cc_start: 0.7309 (m-30) cc_final: 0.6932 (m-30) REVERT: A 347 LYS cc_start: 0.7975 (mttt) cc_final: 0.7713 (mmtm) REVERT: A 353 LYS cc_start: 0.7416 (tttt) cc_final: 0.6071 (tptt) REVERT: A 369 LYS cc_start: 0.6764 (mttt) cc_final: 0.6122 (mtpp) REVERT: A 370 LYS cc_start: 0.7543 (tttp) cc_final: 0.6820 (ttmt) REVERT: A 371 ILE cc_start: 0.7584 (mt) cc_final: 0.7383 (mp) REVERT: A 373 THR cc_start: 0.7787 (m) cc_final: 0.7373 (p) REVERT: B 345 ASP cc_start: 0.6771 (m-30) cc_final: 0.6180 (t70) REVERT: B 353 LYS cc_start: 0.7060 (tttt) cc_final: 0.6635 (tttm) REVERT: B 375 LYS cc_start: 0.7717 (tttt) cc_final: 0.7300 (ttpt) REVERT: C 307 GLN cc_start: 0.8307 (tt0) cc_final: 0.8023 (tt0) REVERT: C 311 LYS cc_start: 0.8103 (mttt) cc_final: 0.7763 (mttm) REVERT: C 320 SER cc_start: 0.7897 (t) cc_final: 0.7405 (p) REVERT: C 338 GLU cc_start: 0.7485 (tt0) cc_final: 0.6773 (tm-30) REVERT: C 342 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7162 (mt-10) REVERT: C 343 LYS cc_start: 0.8005 (mttt) cc_final: 0.7760 (mttm) REVERT: C 347 LYS cc_start: 0.8460 (mmtt) cc_final: 0.6633 (pmtt) REVERT: C 349 ARG cc_start: 0.6592 (mtm180) cc_final: 0.6113 (mtt180) REVERT: C 353 LYS cc_start: 0.7709 (tttt) cc_final: 0.6755 (tptt) REVERT: C 369 LYS cc_start: 0.7601 (mttt) cc_final: 0.6961 (mtpp) REVERT: C 370 LYS cc_start: 0.7860 (tttp) cc_final: 0.7127 (ttmt) REVERT: C 371 ILE cc_start: 0.8171 (mt) cc_final: 0.7854 (mp) REVERT: C 373 THR cc_start: 0.8402 (m) cc_final: 0.8020 (p) REVERT: D 315 LEU cc_start: 0.8416 (mt) cc_final: 0.8092 (mm) REVERT: D 317 LYS cc_start: 0.7764 (mttt) cc_final: 0.7438 (mtpt) REVERT: D 324 SER cc_start: 0.7705 (t) cc_final: 0.7389 (m) REVERT: D 338 GLU cc_start: 0.7815 (tt0) cc_final: 0.7172 (tt0) REVERT: D 345 ASP cc_start: 0.7075 (m-30) cc_final: 0.6860 (t70) REVERT: D 353 LYS cc_start: 0.7846 (tttt) cc_final: 0.7354 (tttt) REVERT: D 375 LYS cc_start: 0.8293 (tttt) cc_final: 0.7851 (ttpt) REVERT: D 379 ARG cc_start: 0.6825 (mtt-85) cc_final: 0.6147 (mmp-170) REVERT: E 311 LYS cc_start: 0.7966 (mttt) cc_final: 0.6953 (mttm) REVERT: E 336 GLN cc_start: 0.7639 (tt0) cc_final: 0.7274 (tt0) REVERT: E 338 GLU cc_start: 0.7151 (tt0) cc_final: 0.6381 (mt-10) REVERT: E 340 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.6921 (mttm) REVERT: E 349 ARG cc_start: 0.6812 (mtm180) cc_final: 0.5178 (mmp-170) REVERT: E 353 LYS cc_start: 0.7306 (tttt) cc_final: 0.6078 (tptt) REVERT: E 369 LYS cc_start: 0.6846 (mttt) cc_final: 0.6216 (mtpp) REVERT: E 370 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7846 (ttmp) REVERT: E 371 ILE cc_start: 0.7714 (mt) cc_final: 0.7384 (mp) REVERT: E 373 THR cc_start: 0.7935 (m) cc_final: 0.7368 (p) REVERT: F 317 LYS cc_start: 0.7349 (mttt) cc_final: 0.7081 (mtpt) REVERT: F 321 LYS cc_start: 0.7144 (mttt) cc_final: 0.6827 (mttm) REVERT: F 338 GLU cc_start: 0.7387 (tt0) cc_final: 0.6660 (tt0) REVERT: F 345 ASP cc_start: 0.6773 (m-30) cc_final: 0.6463 (t70) REVERT: F 347 LYS cc_start: 0.7950 (mttt) cc_final: 0.7309 (mmtm) REVERT: F 353 LYS cc_start: 0.7137 (tttt) cc_final: 0.6688 (tttm) REVERT: F 375 LYS cc_start: 0.7828 (tttt) cc_final: 0.7136 (ttpt) outliers start: 6 outliers final: 3 residues processed: 169 average time/residue: 1.5174 time to fit residues: 261.6978 Evaluate side-chains 169 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 164 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 307 GLN C 330 HIS F 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 3561 Z= 0.392 Angle : 0.633 4.724 4761 Z= 0.324 Chirality : 0.050 0.129 531 Planarity : 0.003 0.025 609 Dihedral : 5.053 18.079 474 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 1.50 % Allowed : 15.79 % Favored : 82.71 % 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: -2.01 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 329 PHE 0.014 0.003 PHE F 346 TYR 0.014 0.003 TYR A 310 ARG 0.005 0.001 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 164 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7800 (mttt) cc_final: 0.7424 (mttm) REVERT: A 317 LYS cc_start: 0.6994 (mtmt) cc_final: 0.6588 (mtpt) REVERT: A 321 LYS cc_start: 0.7114 (mtmt) cc_final: 0.6288 (mtpp) REVERT: A 338 GLU cc_start: 0.7059 (tt0) cc_final: 0.5645 (mt-10) REVERT: A 343 LYS cc_start: 0.7822 (mttt) cc_final: 0.7596 (mttp) REVERT: A 345 ASP cc_start: 0.7334 (m-30) cc_final: 0.6881 (m-30) REVERT: A 353 LYS cc_start: 0.7368 (tttt) cc_final: 0.6055 (tptt) REVERT: A 369 LYS cc_start: 0.6754 (mttt) cc_final: 0.6120 (mtpp) REVERT: A 370 LYS cc_start: 0.7577 (tttp) cc_final: 0.6827 (ttmt) REVERT: A 371 ILE cc_start: 0.7582 (mt) cc_final: 0.7376 (mp) REVERT: A 373 THR cc_start: 0.7780 (m) cc_final: 0.7388 (p) REVERT: B 345 ASP cc_start: 0.6779 (m-30) cc_final: 0.6182 (t70) REVERT: B 353 LYS cc_start: 0.7059 (tttt) cc_final: 0.6632 (tttm) REVERT: B 375 LYS cc_start: 0.7762 (tttt) cc_final: 0.7281 (ttpt) REVERT: C 307 GLN cc_start: 0.8275 (tt0) cc_final: 0.8031 (tt0) REVERT: C 311 LYS cc_start: 0.8115 (mttt) cc_final: 0.7772 (mttm) REVERT: C 320 SER cc_start: 0.7854 (t) cc_final: 0.7400 (p) REVERT: C 338 GLU cc_start: 0.7467 (tt0) cc_final: 0.6750 (tm-30) REVERT: C 342 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7223 (mt-10) REVERT: C 343 LYS cc_start: 0.7989 (mttt) cc_final: 0.7716 (mttm) REVERT: C 347 LYS cc_start: 0.8461 (mmtt) cc_final: 0.6670 (pmtt) REVERT: C 349 ARG cc_start: 0.6580 (mtm180) cc_final: 0.6109 (mtt180) REVERT: C 353 LYS cc_start: 0.7690 (tttt) cc_final: 0.6727 (tptt) REVERT: C 369 LYS cc_start: 0.7610 (mttt) cc_final: 0.6979 (mtpp) REVERT: C 370 LYS cc_start: 0.7849 (tttp) cc_final: 0.7113 (ttmt) REVERT: C 371 ILE cc_start: 0.8189 (mt) cc_final: 0.7876 (mp) REVERT: C 373 THR cc_start: 0.8387 (m) cc_final: 0.8006 (p) REVERT: D 317 LYS cc_start: 0.7778 (mttt) cc_final: 0.7459 (mtpt) REVERT: D 324 SER cc_start: 0.7706 (t) cc_final: 0.7328 (m) REVERT: D 338 GLU cc_start: 0.7824 (tt0) cc_final: 0.7174 (tt0) REVERT: D 345 ASP cc_start: 0.7097 (m-30) cc_final: 0.6869 (t70) REVERT: D 347 LYS cc_start: 0.8016 (mttt) cc_final: 0.7673 (mttm) REVERT: D 353 LYS cc_start: 0.7848 (tttt) cc_final: 0.7605 (tttm) REVERT: D 375 LYS cc_start: 0.8305 (tttt) cc_final: 0.7873 (ttpt) REVERT: D 379 ARG cc_start: 0.6799 (mtt-85) cc_final: 0.6078 (mmp-170) REVERT: E 311 LYS cc_start: 0.7988 (mttt) cc_final: 0.6919 (mttm) REVERT: E 336 GLN cc_start: 0.7632 (tt0) cc_final: 0.7303 (tt0) REVERT: E 338 GLU cc_start: 0.7169 (tt0) cc_final: 0.6393 (mt-10) REVERT: E 340 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.6875 (mttm) REVERT: E 349 ARG cc_start: 0.6702 (mtm180) cc_final: 0.5092 (mmp-170) REVERT: E 353 LYS cc_start: 0.7246 (tttt) cc_final: 0.6047 (tptt) REVERT: E 369 LYS cc_start: 0.6892 (mttt) cc_final: 0.6277 (mtpp) REVERT: E 370 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7844 (ttmp) REVERT: E 371 ILE cc_start: 0.7729 (mt) cc_final: 0.7409 (mp) REVERT: E 373 THR cc_start: 0.7917 (m) cc_final: 0.7326 (p) REVERT: F 307 GLN cc_start: 0.7938 (tt0) cc_final: 0.7700 (tt0) REVERT: F 317 LYS cc_start: 0.7343 (mttt) cc_final: 0.7086 (mtpt) REVERT: F 321 LYS cc_start: 0.7153 (mttt) cc_final: 0.6855 (mttm) REVERT: F 338 GLU cc_start: 0.7382 (tt0) cc_final: 0.6668 (tt0) REVERT: F 345 ASP cc_start: 0.6771 (m-30) cc_final: 0.6473 (t70) REVERT: F 347 LYS cc_start: 0.7940 (mttt) cc_final: 0.7282 (mmtm) REVERT: F 353 LYS cc_start: 0.7142 (tttt) cc_final: 0.6683 (tttm) REVERT: F 375 LYS cc_start: 0.7815 (tttt) cc_final: 0.7222 (ttpp) outliers start: 6 outliers final: 3 residues processed: 168 average time/residue: 1.4971 time to fit residues: 256.7840 Evaluate side-chains 167 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 162 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 9 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 307 GLN C 330 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3561 Z= 0.284 Angle : 0.578 4.488 4761 Z= 0.294 Chirality : 0.049 0.124 531 Planarity : 0.003 0.025 609 Dihedral : 4.883 17.692 474 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 1.25 % Allowed : 16.54 % Favored : 82.21 % 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: -2.00 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 329 PHE 0.012 0.002 PHE F 346 TYR 0.011 0.003 TYR F 310 ARG 0.004 0.001 ARG A 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 163 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7765 (mttt) cc_final: 0.7380 (mttm) REVERT: A 317 LYS cc_start: 0.6993 (mtmt) cc_final: 0.6595 (mtpt) REVERT: A 321 LYS cc_start: 0.7136 (mtmt) cc_final: 0.6309 (mtpp) REVERT: A 338 GLU cc_start: 0.7048 (tt0) cc_final: 0.5587 (mt-10) REVERT: A 343 LYS cc_start: 0.7792 (mttt) cc_final: 0.7559 (mttp) REVERT: A 345 ASP cc_start: 0.7362 (m-30) cc_final: 0.6863 (m-30) REVERT: A 353 LYS cc_start: 0.7378 (tttt) cc_final: 0.6053 (tptt) REVERT: A 369 LYS cc_start: 0.6739 (mttt) cc_final: 0.6106 (mtpp) REVERT: A 370 LYS cc_start: 0.7553 (tttp) cc_final: 0.6873 (ttmt) REVERT: A 371 ILE cc_start: 0.7603 (mt) cc_final: 0.7368 (mp) REVERT: A 372 GLU cc_start: 0.7414 (tt0) cc_final: 0.6740 (mm-30) REVERT: A 373 THR cc_start: 0.7781 (m) cc_final: 0.7365 (p) REVERT: B 345 ASP cc_start: 0.6769 (m-30) cc_final: 0.6172 (t70) REVERT: B 353 LYS cc_start: 0.7066 (tttt) cc_final: 0.6638 (tttm) REVERT: B 375 LYS cc_start: 0.7750 (tttt) cc_final: 0.7321 (ttpt) REVERT: C 307 GLN cc_start: 0.8285 (tt0) cc_final: 0.8047 (tt0) REVERT: C 311 LYS cc_start: 0.8106 (mttt) cc_final: 0.7771 (mttm) REVERT: C 320 SER cc_start: 0.7862 (t) cc_final: 0.7380 (p) REVERT: C 338 GLU cc_start: 0.7459 (tt0) cc_final: 0.6743 (tm-30) REVERT: C 342 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7209 (mt-10) REVERT: C 343 LYS cc_start: 0.8001 (mttt) cc_final: 0.7755 (mttm) REVERT: C 349 ARG cc_start: 0.6574 (mtm180) cc_final: 0.6105 (mtt180) REVERT: C 353 LYS cc_start: 0.7701 (tttt) cc_final: 0.6755 (tptt) REVERT: C 369 LYS cc_start: 0.7616 (mttt) cc_final: 0.6980 (mtpp) REVERT: C 370 LYS cc_start: 0.7854 (tttp) cc_final: 0.7136 (ttmt) REVERT: C 371 ILE cc_start: 0.8177 (mt) cc_final: 0.7866 (mp) REVERT: C 373 THR cc_start: 0.8399 (m) cc_final: 0.8009 (p) REVERT: D 315 LEU cc_start: 0.8408 (mt) cc_final: 0.8093 (mm) REVERT: D 317 LYS cc_start: 0.7783 (mttt) cc_final: 0.7462 (mtpt) REVERT: D 324 SER cc_start: 0.7687 (t) cc_final: 0.7363 (m) REVERT: D 338 GLU cc_start: 0.7814 (tt0) cc_final: 0.7173 (tt0) REVERT: D 345 ASP cc_start: 0.7066 (m-30) cc_final: 0.6810 (t70) REVERT: D 347 LYS cc_start: 0.8021 (mttt) cc_final: 0.7680 (mttm) REVERT: D 353 LYS cc_start: 0.7849 (tttt) cc_final: 0.7620 (tttm) REVERT: D 375 LYS cc_start: 0.8306 (tttt) cc_final: 0.7822 (tppp) REVERT: D 379 ARG cc_start: 0.6781 (mtt-85) cc_final: 0.6101 (mmp-170) REVERT: E 311 LYS cc_start: 0.7973 (mttt) cc_final: 0.6959 (mttm) REVERT: E 336 GLN cc_start: 0.7637 (tt0) cc_final: 0.7294 (tt0) REVERT: E 338 GLU cc_start: 0.7187 (tt0) cc_final: 0.6381 (mt-10) REVERT: E 340 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.6894 (mttm) REVERT: E 349 ARG cc_start: 0.6739 (mtm180) cc_final: 0.5125 (mmp-170) REVERT: E 353 LYS cc_start: 0.7285 (tttt) cc_final: 0.6067 (tptt) REVERT: E 369 LYS cc_start: 0.6838 (mttt) cc_final: 0.6215 (mtpp) REVERT: E 370 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7842 (ttmp) REVERT: E 371 ILE cc_start: 0.7731 (mt) cc_final: 0.7411 (mp) REVERT: E 373 THR cc_start: 0.7926 (m) cc_final: 0.7314 (p) REVERT: F 317 LYS cc_start: 0.7341 (mttt) cc_final: 0.7074 (mtpt) REVERT: F 321 LYS cc_start: 0.7149 (mttt) cc_final: 0.6838 (mttm) REVERT: F 338 GLU cc_start: 0.7386 (tt0) cc_final: 0.6663 (tt0) REVERT: F 345 ASP cc_start: 0.6774 (m-30) cc_final: 0.6465 (t70) REVERT: F 347 LYS cc_start: 0.7955 (mttt) cc_final: 0.7306 (mmtm) REVERT: F 353 LYS cc_start: 0.7131 (tttt) cc_final: 0.6685 (tttm) REVERT: F 375 LYS cc_start: 0.7807 (tttt) cc_final: 0.7126 (ttpt) outliers start: 5 outliers final: 3 residues processed: 167 average time/residue: 1.5124 time to fit residues: 257.7919 Evaluate side-chains 168 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 163 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 307 GLN F 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.121922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.107134 restraints weight = 3891.322| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.46 r_work: 0.3465 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3561 Z= 0.267 Angle : 0.566 4.495 4761 Z= 0.288 Chirality : 0.049 0.124 531 Planarity : 0.003 0.024 609 Dihedral : 4.812 17.587 474 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 1.25 % Allowed : 16.54 % Favored : 82.21 % 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: -1.99 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 329 PHE 0.011 0.002 PHE F 346 TYR 0.012 0.003 TYR F 310 ARG 0.003 0.000 ARG A 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3726.78 seconds wall clock time: 65 minutes 56.63 seconds (3956.63 seconds total)