Starting phenix.real_space_refine on Fri Aug 2 16:27:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2j_18109/08_2024/8q2j_18109.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2j_18109/08_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_18109/08_2024/8q2j_18109.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2j_18109/08_2024/8q2j_18109.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2j_18109/08_2024/8q2j_18109.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q2j_18109/08_2024/8q2j_18109.cif" } 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-5409/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: 3.32, per 1000 atoms: 0.95 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: 1.28 Conformation dependent library (CDL) restraints added in 645.0 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: 0.58 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: 0.82 Time building geometry restraints manager: 1.41 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 3.040 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.499 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.519 3.040 nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.535 3.040 nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.535 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.240 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 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:14.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.350 ------------------------------------------------------------------------------- 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 : 0.457 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: 1.3014 time to fit residues: 271.6612 Evaluate side-chains 187 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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: 4.9990 chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 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 351 GLN D 307 GLN D 327 ASN F 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3561 Z= 0.269 Angle : 0.645 5.499 4761 Z= 0.330 Chirality : 0.051 0.131 531 Planarity : 0.004 0.026 609 Dihedral : 5.389 19.164 474 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.25 % Allowed : 10.28 % Favored : 88.47 % 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 (0.32), 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 0.004 0.001 HIS D 329 PHE 0.016 0.003 PHE F 346 TYR 0.011 0.003 TYR A 310 ARG 0.003 0.001 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 188 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 183 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7797 (mttt) cc_final: 0.7434 (mttm) REVERT: A 314 ASP cc_start: 0.7945 (t0) cc_final: 0.7626 (t0) REVERT: A 317 LYS cc_start: 0.7027 (mtmt) cc_final: 0.6761 (mtpt) REVERT: A 338 GLU cc_start: 0.6852 (tt0) cc_final: 0.5638 (mt-10) REVERT: A 343 LYS cc_start: 0.7899 (mttt) cc_final: 0.7665 (mtpp) REVERT: A 347 LYS cc_start: 0.8176 (mttt) cc_final: 0.7734 (mmtm) REVERT: A 353 LYS cc_start: 0.7428 (tttt) cc_final: 0.6109 (tptt) REVERT: A 369 LYS cc_start: 0.6809 (mttt) cc_final: 0.6138 (mtpp) REVERT: A 370 LYS cc_start: 0.7550 (tttp) cc_final: 0.6838 (ttmt) REVERT: A 371 ILE cc_start: 0.7524 (mt) cc_final: 0.7189 (mp) REVERT: A 373 THR cc_start: 0.7840 (m) cc_final: 0.7421 (p) REVERT: A 375 LYS cc_start: 0.7365 (tttt) cc_final: 0.7140 (tttp) REVERT: B 314 ASP cc_start: 0.7478 (t0) cc_final: 0.7184 (t0) REVERT: B 324 SER cc_start: 0.7388 (t) cc_final: 0.6994 (m) REVERT: B 345 ASP cc_start: 0.6896 (m-30) cc_final: 0.6334 (t70) REVERT: B 353 LYS cc_start: 0.7068 (tttt) cc_final: 0.6632 (tttm) REVERT: B 375 LYS cc_start: 0.7641 (tttt) cc_final: 0.7033 (ttpt) REVERT: C 307 GLN cc_start: 0.8308 (tt0) cc_final: 0.7993 (tt0) REVERT: C 311 LYS cc_start: 0.8242 (mttt) cc_final: 0.7912 (mttm) REVERT: C 320 SER cc_start: 0.7776 (t) cc_final: 0.7404 (p) REVERT: C 324 SER cc_start: 0.8374 (p) cc_final: 0.8135 (t) REVERT: C 338 GLU cc_start: 0.7580 (tt0) cc_final: 0.7047 (tm-30) REVERT: C 340 LYS cc_start: 0.7810 (mttt) cc_final: 0.7522 (mtmm) REVERT: C 342 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7140 (mt-10) REVERT: C 343 LYS cc_start: 0.8029 (mttt) cc_final: 0.7770 (mttm) REVERT: C 345 ASP cc_start: 0.7930 (m-30) cc_final: 0.7098 (t70) REVERT: C 349 ARG cc_start: 0.6486 (mtm180) cc_final: 0.6225 (mtt180) REVERT: C 353 LYS cc_start: 0.7733 (tttt) cc_final: 0.6731 (tptt) REVERT: C 369 LYS cc_start: 0.7679 (mttt) cc_final: 0.7034 (mtpp) REVERT: C 370 LYS cc_start: 0.7844 (tttp) cc_final: 0.7365 (ttmt) REVERT: C 371 ILE cc_start: 0.8138 (mt) cc_final: 0.7729 (mp) REVERT: C 372 GLU cc_start: 0.7453 (mt-10) cc_final: 0.6319 (mm-30) REVERT: C 373 THR cc_start: 0.8398 (m) cc_final: 0.7975 (p) REVERT: C 375 LYS cc_start: 0.8028 (tttt) cc_final: 0.7727 (tttt) REVERT: D 307 GLN cc_start: 0.8624 (tt0) cc_final: 0.8383 (tt0) REVERT: D 314 ASP cc_start: 0.7564 (t0) cc_final: 0.7126 (t0) REVERT: D 315 LEU cc_start: 0.8311 (mt) cc_final: 0.7915 (mm) REVERT: D 317 LYS cc_start: 0.7751 (mttt) cc_final: 0.7386 (mtpt) REVERT: D 338 GLU cc_start: 0.7821 (tt0) cc_final: 0.7133 (tt0) REVERT: D 345 ASP cc_start: 0.7215 (m-30) cc_final: 0.6859 (t70) REVERT: D 353 LYS cc_start: 0.7882 (tttt) cc_final: 0.7623 (tttm) REVERT: D 375 LYS cc_start: 0.8274 (tttt) cc_final: 0.7699 (ttpp) REVERT: E 307 GLN cc_start: 0.7800 (tt0) cc_final: 0.7241 (tt0) REVERT: E 311 LYS cc_start: 0.7828 (mttt) cc_final: 0.6778 (mttm) REVERT: E 336 GLN cc_start: 0.7683 (tt0) cc_final: 0.7272 (tt0) REVERT: E 338 GLU cc_start: 0.6826 (tt0) cc_final: 0.5954 (mt-10) REVERT: E 340 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6884 (mtpt) REVERT: E 342 GLU cc_start: 0.7349 (mt-10) cc_final: 0.7085 (mt-10) REVERT: E 343 LYS cc_start: 0.8177 (mttt) cc_final: 0.7908 (mtpp) REVERT: E 353 LYS cc_start: 0.7351 (tttt) cc_final: 0.6090 (tptt) REVERT: E 369 LYS cc_start: 0.6911 (mttt) cc_final: 0.6300 (mtpp) REVERT: E 372 GLU cc_start: 0.7339 (tt0) cc_final: 0.7006 (tp30) REVERT: E 373 THR cc_start: 0.7908 (m) cc_final: 0.7349 (p) REVERT: F 311 LYS cc_start: 0.7526 (mttt) cc_final: 0.6516 (mttm) REVERT: F 317 LYS cc_start: 0.7366 (mttt) cc_final: 0.7112 (mtpt) REVERT: F 321 LYS cc_start: 0.7023 (mttt) cc_final: 0.6654 (mttm) REVERT: F 338 GLU cc_start: 0.7456 (tt0) cc_final: 0.6562 (tt0) REVERT: F 340 LYS cc_start: 0.7036 (mttt) cc_final: 0.6199 (mmtt) REVERT: F 345 ASP cc_start: 0.6762 (m-30) cc_final: 0.6455 (t70) REVERT: F 347 LYS cc_start: 0.7928 (mttt) cc_final: 0.7255 (mmtp) REVERT: F 353 LYS cc_start: 0.7304 (tttt) cc_final: 0.6864 (tttm) REVERT: F 375 LYS cc_start: 0.7661 (tttt) cc_final: 0.7119 (ttpp) outliers start: 5 outliers final: 2 residues processed: 185 average time/residue: 1.3234 time to fit residues: 250.4432 Evaluate side-chains 173 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 170 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 37 optimal weight: 0.0980 chunk 13 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 overall best weight: 3.0188 ------------------------------------------------------------------------------- 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: 0.7295 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3561 Z= 0.256 Angle : 0.604 5.332 4761 Z= 0.304 Chirality : 0.050 0.125 531 Planarity : 0.003 0.023 609 Dihedral : 5.001 17.796 474 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.25 % Allowed : 14.29 % 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: -1.76 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 329 PHE 0.012 0.002 PHE F 346 TYR 0.012 0.002 TYR E 310 ARG 0.003 0.001 ARG E 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 178 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 173 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7771 (mttt) cc_final: 0.7421 (mttm) REVERT: A 317 LYS cc_start: 0.7049 (mtmt) cc_final: 0.6746 (mtpt) REVERT: A 321 LYS cc_start: 0.7148 (mtmt) cc_final: 0.6272 (mtpp) REVERT: A 338 GLU cc_start: 0.6809 (tt0) cc_final: 0.5579 (mt-10) REVERT: A 343 LYS cc_start: 0.7859 (mttt) cc_final: 0.7640 (mtpp) REVERT: A 347 LYS cc_start: 0.8073 (mttt) cc_final: 0.7701 (mmtm) REVERT: A 353 LYS cc_start: 0.7400 (tttt) cc_final: 0.5963 (tptt) REVERT: A 369 LYS cc_start: 0.6809 (mttt) cc_final: 0.6148 (mtpp) REVERT: A 370 LYS cc_start: 0.7576 (tttp) cc_final: 0.6792 (ttmt) REVERT: A 371 ILE cc_start: 0.7582 (mt) cc_final: 0.7235 (mp) REVERT: A 372 GLU cc_start: 0.7398 (tt0) cc_final: 0.7114 (tt0) REVERT: A 373 THR cc_start: 0.7816 (m) cc_final: 0.7398 (p) REVERT: B 314 ASP cc_start: 0.7453 (t0) cc_final: 0.7147 (t0) REVERT: B 324 SER cc_start: 0.7379 (t) cc_final: 0.6967 (m) REVERT: B 345 ASP cc_start: 0.6915 (m-30) cc_final: 0.6325 (t70) REVERT: B 353 LYS cc_start: 0.7066 (tttt) cc_final: 0.6633 (tttm) REVERT: B 375 LYS cc_start: 0.7691 (tttt) cc_final: 0.7113 (ttpp) REVERT: C 307 GLN cc_start: 0.8299 (tt0) cc_final: 0.8039 (tt0) REVERT: C 311 LYS cc_start: 0.8197 (mttt) cc_final: 0.7866 (mttm) REVERT: C 314 ASP cc_start: 0.7854 (t0) cc_final: 0.7608 (t0) REVERT: C 320 SER cc_start: 0.7859 (t) cc_final: 0.7408 (p) REVERT: C 338 GLU cc_start: 0.7604 (tt0) cc_final: 0.7003 (tm-30) REVERT: C 340 LYS cc_start: 0.7765 (mttt) cc_final: 0.7482 (mtmm) REVERT: C 342 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7120 (mt-10) REVERT: C 343 LYS cc_start: 0.8036 (mttt) cc_final: 0.7777 (mttm) REVERT: C 345 ASP cc_start: 0.7937 (m-30) cc_final: 0.7248 (t70) REVERT: C 347 LYS cc_start: 0.8470 (mmtt) cc_final: 0.6614 (pmtt) REVERT: C 349 ARG cc_start: 0.6546 (mtm180) cc_final: 0.6225 (mtt180) REVERT: C 353 LYS cc_start: 0.7734 (tttt) cc_final: 0.6710 (tptt) REVERT: C 369 LYS cc_start: 0.7646 (mttt) cc_final: 0.7014 (mtpp) REVERT: C 370 LYS cc_start: 0.7875 (tttp) cc_final: 0.7456 (ttmt) REVERT: C 371 ILE cc_start: 0.8130 (mt) cc_final: 0.7732 (mp) REVERT: C 372 GLU cc_start: 0.7540 (mt-10) cc_final: 0.6344 (mm-30) REVERT: C 373 THR cc_start: 0.8400 (m) cc_final: 0.7986 (p) REVERT: C 375 LYS cc_start: 0.8041 (tttt) cc_final: 0.7748 (tttt) REVERT: D 314 ASP cc_start: 0.7568 (t0) cc_final: 0.7138 (t0) REVERT: D 315 LEU cc_start: 0.8400 (mt) cc_final: 0.7936 (mm) REVERT: D 317 LYS cc_start: 0.7733 (mttt) cc_final: 0.7392 (mtpt) REVERT: D 324 SER cc_start: 0.7727 (t) cc_final: 0.7286 (m) REVERT: D 338 GLU cc_start: 0.7804 (tt0) cc_final: 0.7064 (tt0) REVERT: D 345 ASP cc_start: 0.7289 (m-30) cc_final: 0.6947 (t70) REVERT: D 353 LYS cc_start: 0.7872 (tttt) cc_final: 0.7328 (tttt) REVERT: D 375 LYS cc_start: 0.8310 (tttt) cc_final: 0.7766 (ttpp) REVERT: E 311 LYS cc_start: 0.7931 (mttt) cc_final: 0.6828 (mttm) REVERT: E 336 GLN cc_start: 0.7675 (tt0) cc_final: 0.7464 (tt0) REVERT: E 338 GLU cc_start: 0.6913 (tt0) cc_final: 0.6009 (mt-10) REVERT: E 340 LYS cc_start: 0.7226 (mttt) cc_final: 0.6935 (mtpt) REVERT: E 342 GLU cc_start: 0.7321 (mt-10) cc_final: 0.7060 (mt-10) REVERT: E 343 LYS cc_start: 0.8148 (mttt) cc_final: 0.7919 (mttm) REVERT: E 349 ARG cc_start: 0.7363 (mtt180) cc_final: 0.4989 (mmp-170) REVERT: E 353 LYS cc_start: 0.7347 (tttt) cc_final: 0.6017 (tptt) REVERT: E 369 LYS cc_start: 0.6840 (mttt) cc_final: 0.6213 (mtpp) REVERT: E 371 ILE cc_start: 0.7647 (mt) cc_final: 0.7332 (mp) REVERT: E 372 GLU cc_start: 0.7428 (tt0) cc_final: 0.7067 (tp30) REVERT: E 373 THR cc_start: 0.7926 (m) cc_final: 0.7366 (p) REVERT: E 375 LYS cc_start: 0.7378 (tttt) cc_final: 0.6767 (tttp) REVERT: F 311 LYS cc_start: 0.7542 (mttt) cc_final: 0.6492 (mttm) REVERT: F 317 LYS cc_start: 0.7327 (mttt) cc_final: 0.7090 (mtpt) REVERT: F 321 LYS cc_start: 0.7045 (mttt) cc_final: 0.6657 (mttm) REVERT: F 338 GLU cc_start: 0.7488 (tt0) cc_final: 0.6698 (tt0) REVERT: F 345 ASP cc_start: 0.6762 (m-30) cc_final: 0.6447 (t70) REVERT: F 347 LYS cc_start: 0.7941 (mttt) cc_final: 0.7281 (mmtp) REVERT: F 353 LYS cc_start: 0.7237 (tttt) cc_final: 0.6787 (tttm) REVERT: F 375 LYS cc_start: 0.7697 (tttt) cc_final: 0.7141 (ttpp) outliers start: 5 outliers final: 2 residues processed: 175 average time/residue: 1.4111 time to fit residues: 252.2593 Evaluate side-chains 170 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 168 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 0.3980 chunk 25 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 0.0470 chunk 23 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.8884 ------------------------------------------------------------------------------- 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: 0.7305 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 3561 Z= 0.393 Angle : 0.668 5.714 4761 Z= 0.340 Chirality : 0.051 0.135 531 Planarity : 0.004 0.024 609 Dihedral : 5.186 18.791 474 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.25 % Allowed : 14.04 % 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: -1.93 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 329 PHE 0.014 0.003 PHE F 346 TYR 0.014 0.003 TYR E 310 ARG 0.004 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 169 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 164 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7789 (mttt) cc_final: 0.7371 (mttm) REVERT: A 317 LYS cc_start: 0.7026 (mtmt) cc_final: 0.6687 (mtpt) REVERT: A 338 GLU cc_start: 0.6860 (tt0) cc_final: 0.5622 (mt-10) REVERT: A 343 LYS cc_start: 0.7843 (mttt) cc_final: 0.7607 (mttp) REVERT: A 353 LYS cc_start: 0.7360 (tttt) cc_final: 0.6014 (tptt) REVERT: A 369 LYS cc_start: 0.6751 (mttt) cc_final: 0.6138 (mtpp) REVERT: A 370 LYS cc_start: 0.7571 (tttp) cc_final: 0.6798 (ttmt) REVERT: A 371 ILE cc_start: 0.7604 (mt) cc_final: 0.7397 (mp) REVERT: A 372 GLU cc_start: 0.7389 (tt0) cc_final: 0.7101 (tt0) REVERT: A 373 THR cc_start: 0.7798 (m) cc_final: 0.7419 (p) REVERT: B 345 ASP cc_start: 0.6922 (m-30) cc_final: 0.6289 (t70) REVERT: B 353 LYS cc_start: 0.7052 (tttt) cc_final: 0.6639 (tttm) REVERT: B 375 LYS cc_start: 0.7714 (tttt) cc_final: 0.7156 (ttpt) REVERT: C 307 GLN cc_start: 0.8300 (tt0) cc_final: 0.8033 (tt0) REVERT: C 311 LYS cc_start: 0.8160 (mttt) cc_final: 0.7823 (mttm) REVERT: C 320 SER cc_start: 0.7932 (t) cc_final: 0.7429 (p) REVERT: C 338 GLU cc_start: 0.7592 (tt0) cc_final: 0.6921 (tm-30) REVERT: C 340 LYS cc_start: 0.7761 (mttt) cc_final: 0.7509 (mtmm) REVERT: C 342 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7236 (mt-10) REVERT: C 343 LYS cc_start: 0.8014 (mttt) cc_final: 0.7746 (mttm) REVERT: C 347 LYS cc_start: 0.8471 (mmtt) cc_final: 0.6626 (pmtt) REVERT: C 349 ARG cc_start: 0.6490 (mtm180) cc_final: 0.6114 (mtt180) REVERT: C 353 LYS cc_start: 0.7758 (tttt) cc_final: 0.6712 (tptt) REVERT: C 369 LYS cc_start: 0.7658 (mttt) cc_final: 0.7020 (mtpp) REVERT: C 370 LYS cc_start: 0.7864 (tttp) cc_final: 0.7390 (ttmt) REVERT: C 371 ILE cc_start: 0.8185 (mt) cc_final: 0.7784 (mp) REVERT: C 372 GLU cc_start: 0.7566 (mt-10) cc_final: 0.6392 (mm-30) REVERT: C 373 THR cc_start: 0.8405 (m) cc_final: 0.8021 (p) REVERT: C 375 LYS cc_start: 0.8060 (tttt) cc_final: 0.7798 (tttt) REVERT: D 314 ASP cc_start: 0.7512 (t0) cc_final: 0.7169 (t0) REVERT: D 317 LYS cc_start: 0.7752 (mttt) cc_final: 0.7424 (mtpt) REVERT: D 338 GLU cc_start: 0.7833 (tt0) cc_final: 0.7127 (tt0) REVERT: D 345 ASP cc_start: 0.7285 (m-30) cc_final: 0.6948 (t70) REVERT: D 347 LYS cc_start: 0.7968 (mttt) cc_final: 0.7645 (mttm) REVERT: D 353 LYS cc_start: 0.7861 (tttt) cc_final: 0.7623 (tttm) REVERT: D 375 LYS cc_start: 0.8275 (tttt) cc_final: 0.7751 (ttpp) REVERT: E 311 LYS cc_start: 0.7982 (mttt) cc_final: 0.6958 (mttm) REVERT: E 338 GLU cc_start: 0.6979 (tt0) cc_final: 0.6172 (mt-10) REVERT: E 343 LYS cc_start: 0.8161 (mttt) cc_final: 0.7908 (mtpp) REVERT: E 349 ARG cc_start: 0.7323 (mtt180) cc_final: 0.4924 (mmp-170) REVERT: E 353 LYS cc_start: 0.7320 (tttt) cc_final: 0.5998 (tptt) REVERT: E 369 LYS cc_start: 0.6880 (mttt) cc_final: 0.6260 (mtpp) REVERT: E 370 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7891 (ttmp) REVERT: E 371 ILE cc_start: 0.7707 (mt) cc_final: 0.7402 (mp) REVERT: E 372 GLU cc_start: 0.7539 (tt0) cc_final: 0.7228 (tp30) REVERT: E 373 THR cc_start: 0.7912 (m) cc_final: 0.7364 (p) REVERT: E 375 LYS cc_start: 0.7397 (tttt) cc_final: 0.6779 (tttp) REVERT: F 317 LYS cc_start: 0.7310 (mttt) cc_final: 0.7039 (mtpt) REVERT: F 321 LYS cc_start: 0.7167 (mttt) cc_final: 0.6791 (mttm) REVERT: F 338 GLU cc_start: 0.7465 (tt0) cc_final: 0.6645 (tt0) REVERT: F 345 ASP cc_start: 0.6746 (m-30) cc_final: 0.6491 (t70) REVERT: F 353 LYS cc_start: 0.7246 (tttt) cc_final: 0.6783 (tttm) REVERT: F 375 LYS cc_start: 0.7752 (tttt) cc_final: 0.7170 (ttpp) outliers start: 5 outliers final: 2 residues processed: 167 average time/residue: 1.4634 time to fit residues: 249.4640 Evaluate side-chains 165 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 162 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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: 0.7307 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3561 Z= 0.353 Angle : 0.636 5.656 4761 Z= 0.323 Chirality : 0.050 0.132 531 Planarity : 0.003 0.024 609 Dihedral : 5.103 18.244 474 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 1.50 % Allowed : 14.54 % Favored : 83.96 % 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: -1.99 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 329 PHE 0.013 0.003 PHE F 346 TYR 0.013 0.003 TYR E 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 170 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 164 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7828 (mttt) cc_final: 0.7454 (mttm) REVERT: A 317 LYS cc_start: 0.7019 (mtmt) cc_final: 0.6649 (mtpt) REVERT: A 338 GLU cc_start: 0.7005 (tt0) cc_final: 0.5642 (mt-10) REVERT: A 343 LYS cc_start: 0.7843 (mttt) cc_final: 0.7611 (mttp) REVERT: A 347 LYS cc_start: 0.8269 (mttt) cc_final: 0.7938 (mmtm) REVERT: A 353 LYS cc_start: 0.7374 (tttt) cc_final: 0.6027 (tptt) REVERT: A 369 LYS cc_start: 0.6801 (mttt) cc_final: 0.6157 (mtpp) REVERT: A 370 LYS cc_start: 0.7553 (tttp) cc_final: 0.6804 (ttmt) REVERT: A 373 THR cc_start: 0.7800 (m) cc_final: 0.7432 (p) REVERT: B 314 ASP cc_start: 0.7496 (t0) cc_final: 0.7284 (t0) REVERT: B 345 ASP cc_start: 0.6905 (m-30) cc_final: 0.6289 (t70) REVERT: B 353 LYS cc_start: 0.7063 (tttt) cc_final: 0.6648 (tttm) REVERT: B 375 LYS cc_start: 0.7718 (tttt) cc_final: 0.7161 (ttpt) REVERT: C 307 GLN cc_start: 0.8296 (tt0) cc_final: 0.8028 (tt0) REVERT: C 311 LYS cc_start: 0.8144 (mttt) cc_final: 0.7801 (mttm) REVERT: C 320 SER cc_start: 0.7909 (t) cc_final: 0.7411 (p) REVERT: C 338 GLU cc_start: 0.7611 (tt0) cc_final: 0.6965 (tm-30) REVERT: C 340 LYS cc_start: 0.7760 (mttt) cc_final: 0.7488 (mtmm) REVERT: C 342 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7251 (mt-10) REVERT: C 343 LYS cc_start: 0.8020 (mttt) cc_final: 0.7755 (mttm) REVERT: C 347 LYS cc_start: 0.8454 (mmtt) cc_final: 0.6637 (pmtt) REVERT: C 349 ARG cc_start: 0.6535 (mtm180) cc_final: 0.6080 (mtt180) REVERT: C 353 LYS cc_start: 0.7748 (tttt) cc_final: 0.6708 (tptt) REVERT: C 369 LYS cc_start: 0.7614 (mttt) cc_final: 0.6984 (mtpp) REVERT: C 370 LYS cc_start: 0.7847 (tttp) cc_final: 0.7121 (ttmt) REVERT: C 371 ILE cc_start: 0.8194 (mt) cc_final: 0.7874 (mp) REVERT: C 372 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7392 (mm-30) REVERT: C 373 THR cc_start: 0.8402 (m) cc_final: 0.8017 (p) REVERT: C 375 LYS cc_start: 0.8008 (tttt) cc_final: 0.7768 (tttt) REVERT: D 314 ASP cc_start: 0.7559 (t0) cc_final: 0.7293 (t0) REVERT: D 317 LYS cc_start: 0.7749 (mttt) cc_final: 0.7436 (mtpt) REVERT: D 338 GLU cc_start: 0.7827 (tt0) cc_final: 0.7153 (tt0) REVERT: D 345 ASP cc_start: 0.7208 (m-30) cc_final: 0.6855 (t70) REVERT: D 347 LYS cc_start: 0.8010 (mttt) cc_final: 0.7714 (mttm) REVERT: D 353 LYS cc_start: 0.7855 (tttt) cc_final: 0.7620 (tttm) REVERT: D 375 LYS cc_start: 0.8268 (tttt) cc_final: 0.7721 (ttpp) REVERT: E 311 LYS cc_start: 0.7992 (mttt) cc_final: 0.6973 (mttm) REVERT: E 338 GLU cc_start: 0.7049 (tt0) cc_final: 0.6178 (mt-10) REVERT: E 349 ARG cc_start: 0.7303 (mtt180) cc_final: 0.4927 (mmp-170) REVERT: E 353 LYS cc_start: 0.7339 (tttt) cc_final: 0.6005 (tptt) REVERT: E 369 LYS cc_start: 0.6885 (mttt) cc_final: 0.6268 (mtpp) REVERT: E 370 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7841 (ttmp) REVERT: E 371 ILE cc_start: 0.7701 (mt) cc_final: 0.7390 (mp) REVERT: E 373 THR cc_start: 0.7911 (m) cc_final: 0.7365 (p) REVERT: F 317 LYS cc_start: 0.7341 (mttt) cc_final: 0.7066 (mtpt) REVERT: F 321 LYS cc_start: 0.7158 (mttt) cc_final: 0.6806 (mttm) REVERT: F 338 GLU cc_start: 0.7441 (tt0) cc_final: 0.6687 (tt0) REVERT: F 345 ASP cc_start: 0.6799 (m-30) cc_final: 0.6458 (t70) REVERT: F 347 LYS cc_start: 0.7973 (mttt) cc_final: 0.7339 (mmtp) REVERT: F 353 LYS cc_start: 0.7219 (tttt) cc_final: 0.6753 (tttm) REVERT: F 375 LYS cc_start: 0.7792 (tttt) cc_final: 0.7192 (ttpp) outliers start: 6 outliers final: 2 residues processed: 167 average time/residue: 1.4890 time to fit residues: 253.7929 Evaluate side-chains 166 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 163 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 0.0870 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 0.0060 chunk 29 optimal weight: 4.9990 overall best weight: 0.9978 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3561 Z= 0.130 Angle : 0.501 5.004 4761 Z= 0.250 Chirality : 0.049 0.123 531 Planarity : 0.002 0.021 609 Dihedral : 4.519 16.490 474 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.25 % Allowed : 15.79 % Favored : 83.96 % 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: -1.89 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.009 0.001 PHE C 378 TYR 0.009 0.002 TYR F 310 ARG 0.002 0.000 ARG A 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: 1 poor density : 173 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7760 (mttt) cc_final: 0.7387 (mttt) REVERT: A 314 ASP cc_start: 0.7930 (t0) cc_final: 0.7559 (t0) REVERT: A 317 LYS cc_start: 0.7064 (mtmt) cc_final: 0.6681 (mtpt) REVERT: A 321 LYS cc_start: 0.7207 (mtmt) cc_final: 0.6335 (mtpp) REVERT: A 338 GLU cc_start: 0.6942 (tt0) cc_final: 0.5561 (mt-10) REVERT: A 340 LYS cc_start: 0.7204 (mttm) cc_final: 0.6872 (mttt) REVERT: A 342 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6646 (mt-10) REVERT: A 353 LYS cc_start: 0.7470 (tttt) cc_final: 0.6251 (tptt) REVERT: A 369 LYS cc_start: 0.6847 (mttt) cc_final: 0.6181 (mtpp) REVERT: A 370 LYS cc_start: 0.7521 (tttp) cc_final: 0.6780 (ttmt) REVERT: A 372 GLU cc_start: 0.7393 (tt0) cc_final: 0.7113 (tt0) REVERT: A 373 THR cc_start: 0.7808 (m) cc_final: 0.7405 (p) REVERT: B 314 ASP cc_start: 0.7538 (t0) cc_final: 0.7283 (t0) REVERT: B 324 SER cc_start: 0.7116 (t) cc_final: 0.6897 (m) REVERT: B 345 ASP cc_start: 0.6951 (m-30) cc_final: 0.6353 (t70) REVERT: B 353 LYS cc_start: 0.7079 (tttt) cc_final: 0.6664 (tttm) REVERT: B 375 LYS cc_start: 0.7696 (tttt) cc_final: 0.7208 (ttpt) REVERT: C 307 GLN cc_start: 0.8302 (tt0) cc_final: 0.8063 (tt0) REVERT: C 311 LYS cc_start: 0.8092 (mttt) cc_final: 0.7800 (mttm) REVERT: C 314 ASP cc_start: 0.7803 (t0) cc_final: 0.7594 (t0) REVERT: C 320 SER cc_start: 0.7977 (t) cc_final: 0.7529 (p) REVERT: C 338 GLU cc_start: 0.7618 (tt0) cc_final: 0.6982 (tm-30) REVERT: C 342 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7139 (mt-10) REVERT: C 343 LYS cc_start: 0.8055 (mttt) cc_final: 0.7751 (mttm) REVERT: C 347 LYS cc_start: 0.8453 (mmtt) cc_final: 0.6605 (pmtt) REVERT: C 349 ARG cc_start: 0.6491 (mtm180) cc_final: 0.6075 (mtt180) REVERT: C 353 LYS cc_start: 0.7764 (tttt) cc_final: 0.6715 (tptt) REVERT: C 369 LYS cc_start: 0.7549 (mttt) cc_final: 0.6920 (mtpp) REVERT: C 370 LYS cc_start: 0.7919 (tttp) cc_final: 0.7459 (ttmt) REVERT: C 371 ILE cc_start: 0.8144 (mt) cc_final: 0.7768 (mp) REVERT: C 372 GLU cc_start: 0.7623 (mt-10) cc_final: 0.6525 (mm-30) REVERT: C 373 THR cc_start: 0.8395 (m) cc_final: 0.7983 (p) REVERT: C 375 LYS cc_start: 0.7997 (tttt) cc_final: 0.7743 (tttt) REVERT: D 314 ASP cc_start: 0.7593 (t0) cc_final: 0.7324 (t0) REVERT: D 315 LEU cc_start: 0.8254 (mt) cc_final: 0.8027 (mm) REVERT: D 317 LYS cc_start: 0.7682 (mttt) cc_final: 0.7394 (mtpt) REVERT: D 324 SER cc_start: 0.7670 (t) cc_final: 0.7253 (m) REVERT: D 338 GLU cc_start: 0.7812 (tt0) cc_final: 0.7171 (tt0) REVERT: D 345 ASP cc_start: 0.7248 (m-30) cc_final: 0.6891 (t70) REVERT: D 347 LYS cc_start: 0.8015 (mttt) cc_final: 0.7680 (mmtm) REVERT: D 353 LYS cc_start: 0.7795 (tttt) cc_final: 0.7304 (tttt) REVERT: D 358 ASP cc_start: 0.7635 (p0) cc_final: 0.7244 (p0) REVERT: D 375 LYS cc_start: 0.8278 (tttt) cc_final: 0.7714 (tppp) REVERT: E 311 LYS cc_start: 0.7892 (mttt) cc_final: 0.6827 (mttm) REVERT: E 338 GLU cc_start: 0.7011 (tt0) cc_final: 0.6447 (tm-30) REVERT: E 340 LYS cc_start: 0.7278 (mttm) cc_final: 0.6591 (mttm) REVERT: E 349 ARG cc_start: 0.7336 (mtt180) cc_final: 0.5421 (mtp180) REVERT: E 353 LYS cc_start: 0.7422 (tttt) cc_final: 0.6133 (tptt) REVERT: E 369 LYS cc_start: 0.6798 (mttt) cc_final: 0.6177 (mtpp) REVERT: E 371 ILE cc_start: 0.7676 (mt) cc_final: 0.7371 (mp) REVERT: E 372 GLU cc_start: 0.7718 (tp30) cc_final: 0.7426 (tp30) REVERT: E 373 THR cc_start: 0.7954 (m) cc_final: 0.7361 (p) REVERT: F 317 LYS cc_start: 0.7368 (mttt) cc_final: 0.7095 (mtpt) REVERT: F 321 LYS cc_start: 0.7060 (mttt) cc_final: 0.6699 (mttm) REVERT: F 338 GLU cc_start: 0.7447 (tt0) cc_final: 0.6690 (tt0) REVERT: F 345 ASP cc_start: 0.6834 (m-30) cc_final: 0.6478 (t70) REVERT: F 347 LYS cc_start: 0.7945 (mttt) cc_final: 0.7233 (mmtp) REVERT: F 353 LYS cc_start: 0.7244 (tttt) cc_final: 0.6802 (tttm) REVERT: F 375 LYS cc_start: 0.7776 (tttt) cc_final: 0.7127 (ttpt) outliers start: 1 outliers final: 1 residues processed: 174 average time/residue: 1.4460 time to fit residues: 257.0042 Evaluate side-chains 167 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 34 optimal weight: 5.9990 chunk 40 optimal weight: 0.2980 chunk 25 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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: 0.7303 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3561 Z= 0.193 Angle : 0.534 5.225 4761 Z= 0.268 Chirality : 0.049 0.123 531 Planarity : 0.003 0.023 609 Dihedral : 4.542 17.023 474 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.25 % Allowed : 16.04 % Favored : 83.71 % 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: -1.90 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 329 PHE 0.008 0.002 PHE F 346 TYR 0.012 0.002 TYR F 310 ARG 0.001 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 166 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7755 (mttt) cc_final: 0.7380 (mttt) REVERT: A 317 LYS cc_start: 0.7040 (mtmt) cc_final: 0.6653 (mtpt) REVERT: A 321 LYS cc_start: 0.7192 (mtmt) cc_final: 0.6331 (mtpp) REVERT: A 338 GLU cc_start: 0.7035 (tt0) cc_final: 0.5681 (mt-10) REVERT: A 340 LYS cc_start: 0.7208 (mttm) cc_final: 0.6880 (mttt) REVERT: A 353 LYS cc_start: 0.7463 (tttt) cc_final: 0.6123 (tptt) REVERT: A 369 LYS cc_start: 0.6831 (mttt) cc_final: 0.6164 (mtpp) REVERT: A 370 LYS cc_start: 0.7538 (tttp) cc_final: 0.6764 (ttmt) REVERT: A 372 GLU cc_start: 0.7391 (tt0) cc_final: 0.7121 (tt0) REVERT: A 373 THR cc_start: 0.7801 (m) cc_final: 0.7404 (p) REVERT: B 314 ASP cc_start: 0.7534 (t0) cc_final: 0.7274 (t0) REVERT: B 324 SER cc_start: 0.7167 (t) cc_final: 0.6910 (m) REVERT: B 345 ASP cc_start: 0.6940 (m-30) cc_final: 0.6335 (t70) REVERT: B 353 LYS cc_start: 0.7076 (tttt) cc_final: 0.6656 (tttm) REVERT: B 375 LYS cc_start: 0.7765 (tttt) cc_final: 0.7277 (ttpt) REVERT: C 307 GLN cc_start: 0.8312 (tt0) cc_final: 0.8072 (tt0) REVERT: C 311 LYS cc_start: 0.8101 (mttt) cc_final: 0.7789 (mttm) REVERT: C 320 SER cc_start: 0.7904 (t) cc_final: 0.7468 (p) REVERT: C 338 GLU cc_start: 0.7533 (tt0) cc_final: 0.6946 (tm-30) REVERT: C 342 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7184 (mt-10) REVERT: C 343 LYS cc_start: 0.8047 (mttt) cc_final: 0.7753 (mttm) REVERT: C 349 ARG cc_start: 0.6543 (mtm180) cc_final: 0.6069 (mtt180) REVERT: C 353 LYS cc_start: 0.7746 (tttt) cc_final: 0.6747 (tptt) REVERT: C 369 LYS cc_start: 0.7607 (mttt) cc_final: 0.6988 (mtpp) REVERT: C 370 LYS cc_start: 0.7896 (tttp) cc_final: 0.7445 (ttmt) REVERT: C 371 ILE cc_start: 0.8160 (mt) cc_final: 0.7782 (mp) REVERT: C 372 GLU cc_start: 0.7644 (mm-30) cc_final: 0.6522 (mm-30) REVERT: C 373 THR cc_start: 0.8436 (m) cc_final: 0.8017 (p) REVERT: C 375 LYS cc_start: 0.8002 (tttt) cc_final: 0.7755 (tttt) REVERT: D 315 LEU cc_start: 0.8400 (mt) cc_final: 0.8076 (mm) REVERT: D 317 LYS cc_start: 0.7696 (mttt) cc_final: 0.7401 (mtpt) REVERT: D 324 SER cc_start: 0.7658 (t) cc_final: 0.7250 (m) REVERT: D 338 GLU cc_start: 0.7827 (tt0) cc_final: 0.7191 (tt0) REVERT: D 345 ASP cc_start: 0.7239 (m-30) cc_final: 0.6872 (t70) REVERT: D 347 LYS cc_start: 0.7982 (mttt) cc_final: 0.7630 (mmtm) REVERT: D 353 LYS cc_start: 0.7806 (tttt) cc_final: 0.7313 (tttt) REVERT: D 358 ASP cc_start: 0.7650 (p0) cc_final: 0.7211 (p0) REVERT: D 375 LYS cc_start: 0.8291 (tttt) cc_final: 0.7728 (tppp) REVERT: E 311 LYS cc_start: 0.7895 (mttt) cc_final: 0.6821 (mttm) REVERT: E 338 GLU cc_start: 0.7018 (tt0) cc_final: 0.6133 (mt-10) REVERT: E 349 ARG cc_start: 0.7324 (mtt180) cc_final: 0.5013 (mmp-170) REVERT: E 353 LYS cc_start: 0.7392 (tttt) cc_final: 0.6090 (tptt) REVERT: E 369 LYS cc_start: 0.6822 (mttt) cc_final: 0.6195 (mtpp) REVERT: E 371 ILE cc_start: 0.7701 (mt) cc_final: 0.7394 (mp) REVERT: E 373 THR cc_start: 0.7941 (m) cc_final: 0.7360 (p) REVERT: F 317 LYS cc_start: 0.7368 (mttt) cc_final: 0.7090 (mtpt) REVERT: F 321 LYS cc_start: 0.7089 (mttt) cc_final: 0.6719 (mttm) REVERT: F 338 GLU cc_start: 0.7433 (tt0) cc_final: 0.6759 (tt0) REVERT: F 345 ASP cc_start: 0.6844 (m-30) cc_final: 0.6545 (t70) REVERT: F 353 LYS cc_start: 0.7229 (tttt) cc_final: 0.6794 (tttm) REVERT: F 375 LYS cc_start: 0.7805 (tttt) cc_final: 0.7137 (ttpt) outliers start: 1 outliers final: 1 residues processed: 166 average time/residue: 1.4635 time to fit residues: 247.9673 Evaluate side-chains 165 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 34 optimal weight: 0.0270 overall best weight: 2.5642 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3561 Z= 0.230 Angle : 0.559 5.253 4761 Z= 0.283 Chirality : 0.049 0.124 531 Planarity : 0.003 0.025 609 Dihedral : 4.670 17.244 474 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 0.50 % Allowed : 16.54 % 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 0.010 0.002 PHE F 346 TYR 0.012 0.002 TYR F 310 ARG 0.004 0.000 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 167 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 165 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7760 (mttt) cc_final: 0.7385 (mttm) REVERT: A 314 ASP cc_start: 0.7899 (t0) cc_final: 0.7569 (t0) REVERT: A 317 LYS cc_start: 0.7071 (mtmt) cc_final: 0.6653 (mtpt) REVERT: A 321 LYS cc_start: 0.7167 (mtmt) cc_final: 0.6311 (mtpp) REVERT: A 338 GLU cc_start: 0.7025 (tt0) cc_final: 0.5680 (mt-10) REVERT: A 340 LYS cc_start: 0.7180 (mttm) cc_final: 0.6897 (mttt) REVERT: A 347 LYS cc_start: 0.8185 (mptm) cc_final: 0.7779 (mmtm) REVERT: A 353 LYS cc_start: 0.7425 (tttt) cc_final: 0.6113 (tptt) REVERT: A 369 LYS cc_start: 0.6815 (mttt) cc_final: 0.6149 (mtpp) REVERT: A 370 LYS cc_start: 0.7540 (tttp) cc_final: 0.6759 (ttmt) REVERT: A 372 GLU cc_start: 0.7398 (tt0) cc_final: 0.7133 (tt0) REVERT: A 373 THR cc_start: 0.7810 (m) cc_final: 0.7411 (p) REVERT: B 314 ASP cc_start: 0.7527 (t0) cc_final: 0.7246 (t0) REVERT: B 324 SER cc_start: 0.7244 (t) cc_final: 0.6914 (m) REVERT: B 345 ASP cc_start: 0.6909 (m-30) cc_final: 0.6297 (t70) REVERT: B 353 LYS cc_start: 0.7079 (tttt) cc_final: 0.6648 (tttm) REVERT: B 375 LYS cc_start: 0.7769 (tttt) cc_final: 0.7339 (ttpt) REVERT: C 307 GLN cc_start: 0.8315 (tt0) cc_final: 0.8074 (tt0) REVERT: C 311 LYS cc_start: 0.8098 (mttt) cc_final: 0.7767 (mttm) REVERT: C 314 ASP cc_start: 0.7794 (t0) cc_final: 0.7583 (t0) REVERT: C 320 SER cc_start: 0.7921 (t) cc_final: 0.7459 (p) REVERT: C 338 GLU cc_start: 0.7544 (tt0) cc_final: 0.6910 (tm-30) REVERT: C 342 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7170 (mt-10) REVERT: C 343 LYS cc_start: 0.8017 (mttt) cc_final: 0.7772 (mttm) REVERT: C 347 LYS cc_start: 0.8450 (mmtt) cc_final: 0.6605 (pmtt) REVERT: C 349 ARG cc_start: 0.6556 (mtm180) cc_final: 0.6066 (mtt180) REVERT: C 353 LYS cc_start: 0.7770 (tttt) cc_final: 0.6772 (tptt) REVERT: C 369 LYS cc_start: 0.7621 (mttt) cc_final: 0.6991 (mtpp) REVERT: C 370 LYS cc_start: 0.7903 (tttp) cc_final: 0.7166 (ttmt) REVERT: C 371 ILE cc_start: 0.8196 (mt) cc_final: 0.7879 (mp) REVERT: C 373 THR cc_start: 0.8424 (m) cc_final: 0.8010 (p) REVERT: C 375 LYS cc_start: 0.7993 (tttt) cc_final: 0.7756 (tttt) REVERT: D 317 LYS cc_start: 0.7702 (mttt) cc_final: 0.7403 (mtpt) REVERT: D 324 SER cc_start: 0.7674 (t) cc_final: 0.7250 (m) REVERT: D 338 GLU cc_start: 0.7815 (tt0) cc_final: 0.7171 (tt0) REVERT: D 345 ASP cc_start: 0.7247 (m-30) cc_final: 0.6938 (t70) REVERT: D 347 LYS cc_start: 0.8004 (mttt) cc_final: 0.7666 (mttm) REVERT: D 353 LYS cc_start: 0.7817 (tttt) cc_final: 0.7324 (tttt) REVERT: D 375 LYS cc_start: 0.8278 (tttt) cc_final: 0.7773 (tppp) REVERT: E 311 LYS cc_start: 0.7890 (mttt) cc_final: 0.6856 (mttm) REVERT: E 338 GLU cc_start: 0.6982 (tt0) cc_final: 0.6116 (mt-10) REVERT: E 353 LYS cc_start: 0.7387 (tttt) cc_final: 0.6088 (tptt) REVERT: E 369 LYS cc_start: 0.6868 (mttt) cc_final: 0.6229 (mtpp) REVERT: E 371 ILE cc_start: 0.7708 (mt) cc_final: 0.7378 (mp) REVERT: E 373 THR cc_start: 0.7940 (m) cc_final: 0.7374 (p) REVERT: F 311 LYS cc_start: 0.7561 (mtpt) cc_final: 0.5990 (tppt) REVERT: F 317 LYS cc_start: 0.7337 (mttt) cc_final: 0.7060 (mtpt) REVERT: F 321 LYS cc_start: 0.7113 (mttt) cc_final: 0.6754 (mttm) REVERT: F 338 GLU cc_start: 0.7449 (tt0) cc_final: 0.6781 (tt0) REVERT: F 345 ASP cc_start: 0.6850 (m-30) cc_final: 0.6526 (t70) REVERT: F 353 LYS cc_start: 0.7220 (tttt) cc_final: 0.6784 (tttm) REVERT: F 375 LYS cc_start: 0.7765 (tttt) cc_final: 0.7091 (ttpt) outliers start: 2 outliers final: 2 residues processed: 166 average time/residue: 1.4965 time to fit residues: 253.5445 Evaluate side-chains 165 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 163 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 315 LEU 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: 6.9990 chunk 18 optimal weight: 8.9990 chunk 27 optimal weight: 0.2980 chunk 41 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 33 optimal weight: 0.0020 chunk 3 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 overall best weight: 3.2594 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.2786 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= 0.279 Angle : 0.590 5.390 4761 Z= 0.300 Chirality : 0.050 0.124 531 Planarity : 0.003 0.025 609 Dihedral : 4.801 17.669 474 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.50 % Allowed : 17.04 % 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 0.003 0.001 HIS C 329 PHE 0.012 0.002 PHE F 346 TYR 0.013 0.003 TYR F 310 ARG 0.004 0.000 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 164 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 162 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7792 (mttt) cc_final: 0.7422 (mttm) REVERT: A 317 LYS cc_start: 0.7045 (mtmt) cc_final: 0.6637 (mtpt) REVERT: A 321 LYS cc_start: 0.7196 (mtmt) cc_final: 0.6317 (mtpp) REVERT: A 338 GLU cc_start: 0.7064 (tt0) cc_final: 0.5623 (mt-10) REVERT: A 340 LYS cc_start: 0.7181 (mttm) cc_final: 0.6849 (mttt) REVERT: A 353 LYS cc_start: 0.7393 (tttt) cc_final: 0.6111 (tptt) REVERT: A 369 LYS cc_start: 0.6806 (mttt) cc_final: 0.6138 (mtpp) REVERT: A 370 LYS cc_start: 0.7553 (tttp) cc_final: 0.6788 (ttmt) REVERT: A 373 THR cc_start: 0.7804 (m) cc_final: 0.7411 (p) REVERT: B 314 ASP cc_start: 0.7535 (t0) cc_final: 0.7268 (t0) REVERT: B 324 SER cc_start: 0.7311 (t) cc_final: 0.6925 (m) REVERT: B 345 ASP cc_start: 0.6904 (m-30) cc_final: 0.6294 (t70) REVERT: B 353 LYS cc_start: 0.7064 (tttt) cc_final: 0.6628 (tttm) REVERT: B 375 LYS cc_start: 0.7777 (tttt) cc_final: 0.7300 (ttpt) REVERT: C 307 GLN cc_start: 0.8310 (tt0) cc_final: 0.8068 (tt0) REVERT: C 311 LYS cc_start: 0.8118 (mttt) cc_final: 0.7777 (mttm) REVERT: C 314 ASP cc_start: 0.7783 (t0) cc_final: 0.7580 (t0) REVERT: C 320 SER cc_start: 0.7871 (t) cc_final: 0.7388 (p) REVERT: C 338 GLU cc_start: 0.7553 (tt0) cc_final: 0.6891 (tm-30) REVERT: C 342 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7106 (mt-10) REVERT: C 343 LYS cc_start: 0.8014 (mttt) cc_final: 0.7774 (mttm) REVERT: C 349 ARG cc_start: 0.6583 (mtm180) cc_final: 0.6103 (mtt180) REVERT: C 353 LYS cc_start: 0.7769 (tttt) cc_final: 0.6769 (tptt) REVERT: C 369 LYS cc_start: 0.7624 (mttt) cc_final: 0.6990 (mtpp) REVERT: C 370 LYS cc_start: 0.7878 (tttp) cc_final: 0.7153 (ttmt) REVERT: C 371 ILE cc_start: 0.8207 (mt) cc_final: 0.7891 (mp) REVERT: C 373 THR cc_start: 0.8412 (m) cc_final: 0.8009 (p) REVERT: C 375 LYS cc_start: 0.8024 (tttt) cc_final: 0.7778 (tttt) REVERT: D 317 LYS cc_start: 0.7722 (mttt) cc_final: 0.7417 (mtpt) REVERT: D 324 SER cc_start: 0.7705 (t) cc_final: 0.7266 (m) REVERT: D 338 GLU cc_start: 0.7808 (tt0) cc_final: 0.7159 (tt0) REVERT: D 345 ASP cc_start: 0.7206 (m-30) cc_final: 0.6915 (t70) REVERT: D 347 LYS cc_start: 0.8001 (mttt) cc_final: 0.7659 (mttm) REVERT: D 353 LYS cc_start: 0.7814 (tttt) cc_final: 0.7322 (tttt) REVERT: D 375 LYS cc_start: 0.8311 (tttt) cc_final: 0.7865 (ttpt) REVERT: E 311 LYS cc_start: 0.7972 (mttt) cc_final: 0.6950 (mttm) REVERT: E 338 GLU cc_start: 0.7046 (tt0) cc_final: 0.6116 (mt-10) REVERT: E 353 LYS cc_start: 0.7372 (tttt) cc_final: 0.6056 (tptt) REVERT: E 369 LYS cc_start: 0.6863 (mttt) cc_final: 0.6236 (mtpp) REVERT: E 371 ILE cc_start: 0.7725 (mt) cc_final: 0.7405 (mp) REVERT: E 373 THR cc_start: 0.7925 (m) cc_final: 0.7321 (p) REVERT: F 317 LYS cc_start: 0.7331 (mttt) cc_final: 0.7063 (mtpt) REVERT: F 321 LYS cc_start: 0.7121 (mttt) cc_final: 0.6783 (mttm) REVERT: F 338 GLU cc_start: 0.7441 (tt0) cc_final: 0.6784 (tt0) REVERT: F 345 ASP cc_start: 0.6837 (m-30) cc_final: 0.6520 (t70) REVERT: F 353 LYS cc_start: 0.7228 (tttt) cc_final: 0.6808 (tttm) REVERT: F 375 LYS cc_start: 0.7779 (tttt) cc_final: 0.7161 (ttpp) outliers start: 2 outliers final: 1 residues processed: 163 average time/residue: 1.4975 time to fit residues: 249.3131 Evaluate side-chains 161 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 26 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN F 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 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 : 0.003 0.028 3561 Z= 0.209 Angle : 0.557 5.146 4761 Z= 0.282 Chirality : 0.049 0.122 531 Planarity : 0.003 0.025 609 Dihedral : 4.644 17.367 474 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 0.25 % Allowed : 17.79 % Favored : 81.95 % 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: -1.97 (0.33), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 329 PHE 0.009 0.002 PHE F 346 TYR 0.012 0.002 TYR F 310 ARG 0.003 0.000 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 164 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7748 (mttt) cc_final: 0.7383 (mttt) REVERT: A 314 ASP cc_start: 0.7907 (t0) cc_final: 0.7563 (t0) REVERT: A 317 LYS cc_start: 0.7075 (mtmt) cc_final: 0.6652 (mtpt) REVERT: A 321 LYS cc_start: 0.7208 (mtmt) cc_final: 0.6332 (mtpp) REVERT: A 336 GLN cc_start: 0.7790 (tt0) cc_final: 0.7584 (tt0) REVERT: A 338 GLU cc_start: 0.7060 (tt0) cc_final: 0.5502 (mp0) REVERT: A 340 LYS cc_start: 0.7160 (mttm) cc_final: 0.6884 (mttt) REVERT: A 353 LYS cc_start: 0.7435 (tttt) cc_final: 0.6255 (tptt) REVERT: A 369 LYS cc_start: 0.6811 (mttt) cc_final: 0.6152 (mtpp) REVERT: A 370 LYS cc_start: 0.7552 (tttp) cc_final: 0.6775 (ttmt) REVERT: A 372 GLU cc_start: 0.7413 (tt0) cc_final: 0.7151 (tt0) REVERT: A 373 THR cc_start: 0.7806 (m) cc_final: 0.7402 (p) REVERT: B 314 ASP cc_start: 0.7542 (t0) cc_final: 0.7272 (t0) REVERT: B 324 SER cc_start: 0.7233 (t) cc_final: 0.6911 (m) REVERT: B 345 ASP cc_start: 0.6905 (m-30) cc_final: 0.6299 (t70) REVERT: B 353 LYS cc_start: 0.7063 (tttt) cc_final: 0.6623 (tttm) REVERT: B 375 LYS cc_start: 0.7777 (tttt) cc_final: 0.7293 (ttpt) REVERT: C 307 GLN cc_start: 0.8309 (tt0) cc_final: 0.8071 (tt0) REVERT: C 311 LYS cc_start: 0.8097 (mttt) cc_final: 0.7764 (mttm) REVERT: C 320 SER cc_start: 0.7881 (t) cc_final: 0.7409 (p) REVERT: C 338 GLU cc_start: 0.7507 (tt0) cc_final: 0.6847 (tm-30) REVERT: C 342 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7176 (mt-10) REVERT: C 343 LYS cc_start: 0.8027 (mttt) cc_final: 0.7791 (mttm) REVERT: C 349 ARG cc_start: 0.6534 (mtm180) cc_final: 0.6094 (mtt180) REVERT: C 353 LYS cc_start: 0.7789 (tttt) cc_final: 0.6778 (tptt) REVERT: C 369 LYS cc_start: 0.7599 (mttt) cc_final: 0.6971 (mtpp) REVERT: C 370 LYS cc_start: 0.7919 (tttp) cc_final: 0.7182 (ttmt) REVERT: C 371 ILE cc_start: 0.8187 (mt) cc_final: 0.7866 (mp) REVERT: C 373 THR cc_start: 0.8418 (m) cc_final: 0.8004 (p) REVERT: C 375 LYS cc_start: 0.7995 (tttt) cc_final: 0.7750 (tttt) REVERT: D 315 LEU cc_start: 0.8381 (mt) cc_final: 0.8111 (mm) REVERT: D 317 LYS cc_start: 0.7688 (mttt) cc_final: 0.7403 (mtpt) REVERT: D 324 SER cc_start: 0.7702 (t) cc_final: 0.7288 (m) REVERT: D 338 GLU cc_start: 0.7838 (tt0) cc_final: 0.7202 (tt0) REVERT: D 345 ASP cc_start: 0.7234 (m-30) cc_final: 0.6931 (t70) REVERT: D 347 LYS cc_start: 0.8011 (mttt) cc_final: 0.7665 (mttm) REVERT: D 353 LYS cc_start: 0.7808 (tttt) cc_final: 0.7314 (tttt) REVERT: D 375 LYS cc_start: 0.8323 (tttt) cc_final: 0.7823 (tppp) REVERT: E 311 LYS cc_start: 0.7885 (mttt) cc_final: 0.6860 (mttm) REVERT: E 338 GLU cc_start: 0.7085 (tt0) cc_final: 0.6150 (mt-10) REVERT: E 353 LYS cc_start: 0.7392 (tttt) cc_final: 0.6088 (tptt) REVERT: E 369 LYS cc_start: 0.6858 (mttt) cc_final: 0.6226 (mtpp) REVERT: E 371 ILE cc_start: 0.7738 (mt) cc_final: 0.7379 (mp) REVERT: E 372 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7682 (tp30) REVERT: E 373 THR cc_start: 0.7950 (m) cc_final: 0.7313 (p) REVERT: F 317 LYS cc_start: 0.7348 (mttt) cc_final: 0.7072 (mtpt) REVERT: F 321 LYS cc_start: 0.7078 (mttt) cc_final: 0.6722 (mttm) REVERT: F 338 GLU cc_start: 0.7443 (tt0) cc_final: 0.6779 (tt0) REVERT: F 345 ASP cc_start: 0.6848 (m-30) cc_final: 0.6523 (t70) REVERT: F 353 LYS cc_start: 0.7235 (tttt) cc_final: 0.6814 (tttm) REVERT: F 375 LYS cc_start: 0.7788 (tttt) cc_final: 0.7159 (ttpp) outliers start: 1 outliers final: 1 residues processed: 164 average time/residue: 1.4992 time to fit residues: 250.8943 Evaluate side-chains 162 residues out of total 399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.123692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.108960 restraints weight = 3840.946| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.47 r_work: 0.3460 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2807 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= 0.313 Angle : 0.610 5.435 4761 Z= 0.312 Chirality : 0.050 0.125 531 Planarity : 0.003 0.026 609 Dihedral : 4.850 17.973 474 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 0.25 % Allowed : 18.05 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 329 PHE 0.011 0.002 PHE F 346 TYR 0.013 0.003 TYR F 310 ARG 0.005 0.001 ARG A 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3821.12 seconds wall clock time: 66 minutes 41.27 seconds (4001.27 seconds total)