Starting phenix.real_space_refine on Sun Mar 10 17:12:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8x_18264/03_2024/8q8x_18264.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8x_18264/03_2024/8q8x_18264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8x_18264/03_2024/8q8x_18264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8x_18264/03_2024/8q8x_18264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8x_18264/03_2024/8q8x_18264.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8x_18264/03_2024/8q8x_18264.pdb" } resolution = 2.54 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= 0.003 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 2154 2.51 5 N 630 2.21 5 O 645 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 GLU 338": "OE1" <-> "OE2" 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 GLU 338": "OE1" <-> "OE2" Residue "B ASP 348": "OD1" <-> "OD2" Residue "B ASP 358": "OD1" <-> "OD2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D ASP 358": "OD1" <-> "OD2" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 338": "OE1" <-> "OE2" 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 GLU 338": "OE1" <-> "OE2" Residue "F ASP 358": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3435 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 571 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 571 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "E" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 571 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Time building chain proxies: 2.18, per 1000 atoms: 0.63 Number of scatterers: 3435 At special positions: 0 Unit cell: (133.768, 135.222, 56.706, 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 645 8.00 N 630 7.00 C 2154 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: 1.14 Conformation dependent library (CDL) restraints added in 656.5 milliseconds 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 57.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.547A pdb=" N VAL A 306 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL C 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE A 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLN A 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N TYR E 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL A 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.878A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 325 removed outlier: 6.561A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLY C 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N CYS A 322 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU C 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER A 324 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.665A pdb=" N ILE A 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 346 removed outlier: 6.773A pdb=" N LEU C 344 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASP A 345 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N PHE C 346 " --> pdb=" O ASP A 345 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 9.814A pdb=" N GLU E 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N SER A 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) removed outlier: 9.397A pdb=" N LEU E 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LYS A 343 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N PHE E 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 350 through 362 removed outlier: 8.982A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 10.259A pdb=" N ILE C 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 9.061A pdb=" N LYS A 353 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 10.211A pdb=" N SER C 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLY A 355 " --> pdb=" O SER C 356 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ASP C 358 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU A 357 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ILE C 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASN A 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N HIS C 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLN E 351 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N SER A 352 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LYS E 353 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE A 354 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLY E 355 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER A 356 " --> pdb=" O GLY E 355 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 368 through 378 removed outlier: 6.486A pdb=" N LYS A 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N GLU E 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE A 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N HIS E 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR A 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU E 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS A 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE E 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR A 377 " --> pdb=" O PHE E 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.543A pdb=" N GLN B 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N TYR F 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL B 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.832A pdb=" N VAL B 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 317 through 325 removed outlier: 6.295A pdb=" N LYS B 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N SER F 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR B 319 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N CYS F 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LYS B 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N SER F 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY B 323 " --> pdb=" O SER F 324 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.516A pdb=" N ILE B 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 336 through 340 removed outlier: 6.545A pdb=" N VAL B 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LYS D 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL B 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 343 through 347 removed outlier: 6.418A pdb=" N LEU B 344 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LYS D 347 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE B 346 " --> pdb=" O LYS D 347 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 350 through 354 removed outlier: 6.347A pdb=" N GLN B 351 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE F 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS B 353 " --> pdb=" O ILE F 354 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 357 through 362 Processing sheet with id=AB7, first strand: chain 'D' and resid 368 through 377 88 hydrogen bonds defined for protein. 264 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: 0.77 Time building geometry restraints manager: 1.27 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: 1021 1.33 - 1.46: 381 1.46 - 1.58: 2081 1.58 - 1.70: 0 1.70 - 1.82: 6 Bond restraints: 3489 Sorted by residual: bond pdb=" CZ ARG E 349 " pdb=" NH2 ARG E 349 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.69e+00 bond pdb=" CZ ARG A 349 " pdb=" NH2 ARG A 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.37e+00 bond pdb=" CZ ARG C 349 " pdb=" NH2 ARG C 349 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.66e+00 bond pdb=" CZ ARG A 379 " pdb=" NH2 ARG A 379 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.54e+00 bond pdb=" CA LYS C 331 " pdb=" C LYS C 331 " ideal model delta sigma weight residual 1.532 1.548 -0.016 6.50e-03 2.37e+04 6.24e+00 ... (remaining 3484 not shown) Histogram of bond angle deviations from ideal: 101.27 - 106.85: 162 106.85 - 112.43: 1614 112.43 - 118.01: 972 118.01 - 123.59: 1534 123.59 - 129.17: 386 Bond angle restraints: 4668 Sorted by residual: angle pdb=" CA ASP B 358 " pdb=" CB ASP B 358 " pdb=" CG ASP B 358 " ideal model delta sigma weight residual 112.60 118.91 -6.31 1.00e+00 1.00e+00 3.98e+01 angle pdb=" CA ASP F 358 " pdb=" CB ASP F 358 " pdb=" CG ASP F 358 " ideal model delta sigma weight residual 112.60 118.64 -6.04 1.00e+00 1.00e+00 3.65e+01 angle pdb=" CA ASP A 358 " pdb=" CB ASP A 358 " pdb=" CG ASP A 358 " ideal model delta sigma weight residual 112.60 118.56 -5.96 1.00e+00 1.00e+00 3.55e+01 angle pdb=" OE1 GLN A 336 " pdb=" CD GLN A 336 " pdb=" NE2 GLN A 336 " ideal model delta sigma weight residual 122.60 116.93 5.67 1.00e+00 1.00e+00 3.22e+01 angle pdb=" CA GLY C 355 " pdb=" C GLY C 355 " pdb=" N SER C 356 " ideal model delta sigma weight residual 114.58 119.19 -4.61 8.60e-01 1.35e+00 2.88e+01 ... (remaining 4663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 2014 17.67 - 35.35: 76 35.35 - 53.02: 18 53.02 - 70.69: 7 70.69 - 88.37: 3 Dihedral angle restraints: 2118 sinusoidal: 879 harmonic: 1239 Sorted by residual: dihedral pdb=" CA LYS F 343 " pdb=" C LYS F 343 " pdb=" N LEU F 344 " pdb=" CA LEU F 344 " ideal model delta harmonic sigma weight residual 180.00 155.22 24.78 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA ASP E 358 " pdb=" C ASP E 358 " pdb=" N ASN E 359 " pdb=" CA ASN E 359 " ideal model delta harmonic sigma weight residual 180.00 155.72 24.28 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA SER B 341 " pdb=" C SER B 341 " pdb=" N GLU B 342 " pdb=" CA GLU B 342 " ideal model delta harmonic sigma weight residual 180.00 156.72 23.28 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 2115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 276 0.058 - 0.117: 185 0.117 - 0.175: 48 0.175 - 0.233: 14 0.233 - 0.291: 2 Chirality restraints: 525 Sorted by residual: chirality pdb=" CA THR A 319 " pdb=" N THR A 319 " pdb=" C THR A 319 " pdb=" CB THR A 319 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA THR E 319 " pdb=" N THR E 319 " pdb=" C THR E 319 " pdb=" CB THR E 319 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA GLU E 342 " pdb=" N GLU E 342 " pdb=" C GLU E 342 " pdb=" CB GLU E 342 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 522 not shown) Planarity restraints: 594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.110 2.00e-02 2.50e+03 6.34e-02 8.03e+01 pdb=" CG TYR C 310 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " -0.052 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " -0.044 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " -0.036 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " -0.014 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " 0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " 0.064 2.00e-02 2.50e+03 3.56e-02 2.53e+01 pdb=" CG TYR A 310 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " 0.049 2.00e-02 2.50e+03 2.60e-02 1.35e+01 pdb=" CG TYR E 310 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " 0.036 2.00e-02 2.50e+03 ... (remaining 591 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 1594 2.99 - 3.47: 2668 3.47 - 3.95: 5618 3.95 - 4.42: 5438 4.42 - 4.90: 10758 Nonbonded interactions: 26076 Sorted by model distance: nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.517 2.440 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.521 2.440 nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.529 2.440 nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.532 2.440 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.535 2.440 ... (remaining 26071 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 305 through 378) selection = (chain 'B' and resid 305 through 378) selection = (chain 'C' and resid 305 through 378) selection = (chain 'D' and resid 305 through 378) selection = (chain 'E' and resid 305 through 378) selection = (chain 'F' and resid 305 through 378) } 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: 2.320 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: 11.380 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.700 Find NCS groups from input model: 0.260 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:11.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 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 0.036 3489 Z= 0.747 Angle : 1.745 6.308 4668 Z= 1.165 Chirality : 0.079 0.291 525 Planarity : 0.009 0.063 594 Dihedral : 11.916 88.368 1332 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.27 % Allowed : 4.33 % Favored : 94.40 % 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: -1.63 (0.34), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS C 362 PHE 0.034 0.011 PHE E 346 TYR 0.110 0.022 TYR C 310 ARG 0.005 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 193 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.6907 (mttt) cc_final: 0.6561 (mttp) REVERT: A 319 THR cc_start: 0.7218 (p) cc_final: 0.6909 (m) REVERT: A 340 LYS cc_start: 0.6452 (mttt) cc_final: 0.6212 (mtpt) REVERT: A 353 LYS cc_start: 0.6522 (mttt) cc_final: 0.6138 (tttm) REVERT: A 360 ILE cc_start: 0.7388 (mt) cc_final: 0.7123 (mm) REVERT: A 375 LYS cc_start: 0.7862 (ttmt) cc_final: 0.7636 (ttpt) REVERT: B 317 LYS cc_start: 0.7768 (mttt) cc_final: 0.7187 (mtpt) REVERT: B 340 LYS cc_start: 0.7795 (tttt) cc_final: 0.7100 (ttpp) REVERT: B 343 LYS cc_start: 0.6437 (ttmt) cc_final: 0.6233 (tppt) REVERT: B 369 LYS cc_start: 0.7528 (tttt) cc_final: 0.7197 (tttm) REVERT: C 317 LYS cc_start: 0.6966 (mttt) cc_final: 0.6617 (mttm) REVERT: C 347 LYS cc_start: 0.7934 (mttt) cc_final: 0.7723 (mptp) REVERT: C 349 ARG cc_start: 0.6327 (mtm180) cc_final: 0.5897 (mmp-170) REVERT: C 353 LYS cc_start: 0.6576 (mttt) cc_final: 0.6256 (tttp) REVERT: C 360 ILE cc_start: 0.7478 (mt) cc_final: 0.7230 (mp) REVERT: D 311 LYS cc_start: 0.7803 (mttt) cc_final: 0.6972 (mttm) REVERT: D 317 LYS cc_start: 0.7712 (mttt) cc_final: 0.7230 (mtpt) REVERT: D 340 LYS cc_start: 0.7711 (tttt) cc_final: 0.7270 (tptt) REVERT: D 369 LYS cc_start: 0.7514 (tttt) cc_final: 0.7255 (tttm) REVERT: D 375 LYS cc_start: 0.7125 (tttt) cc_final: 0.6874 (ttpt) REVERT: E 317 LYS cc_start: 0.7829 (mttt) cc_final: 0.7495 (mttm) REVERT: E 320 SER cc_start: 0.8379 (m) cc_final: 0.7846 (p) REVERT: E 340 LYS cc_start: 0.7676 (mttt) cc_final: 0.7251 (mtpt) REVERT: F 315 LEU cc_start: 0.8983 (mp) cc_final: 0.8775 (mp) REVERT: F 317 LYS cc_start: 0.8233 (mttt) cc_final: 0.7728 (mtpt) REVERT: F 340 LYS cc_start: 0.8303 (tttt) cc_final: 0.7869 (tppt) REVERT: F 343 LYS cc_start: 0.6977 (ttmt) cc_final: 0.6744 (tppt) REVERT: F 369 LYS cc_start: 0.8123 (tttt) cc_final: 0.7811 (tttm) outliers start: 5 outliers final: 0 residues processed: 193 average time/residue: 1.2738 time to fit residues: 251.7364 Evaluate side-chains 138 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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: 0.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN C 351 GLN D 351 GLN E 327 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3489 Z= 0.187 Angle : 0.623 7.597 4668 Z= 0.303 Chirality : 0.050 0.125 525 Planarity : 0.003 0.018 594 Dihedral : 5.472 16.301 462 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.02 % Allowed : 13.99 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.34), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.06 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 329 PHE 0.009 0.002 PHE C 346 TYR 0.017 0.003 TYR B 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 146 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7091 (mttt) cc_final: 0.6688 (mttp) REVERT: A 320 SER cc_start: 0.8345 (m) cc_final: 0.8133 (p) REVERT: A 338 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6373 (tt0) REVERT: A 340 LYS cc_start: 0.6790 (mttt) cc_final: 0.6576 (mtpt) REVERT: A 347 LYS cc_start: 0.8076 (mptm) cc_final: 0.7705 (mptt) REVERT: A 353 LYS cc_start: 0.6630 (mttt) cc_final: 0.6292 (tttm) REVERT: A 360 ILE cc_start: 0.7430 (mt) cc_final: 0.7199 (mp) REVERT: A 375 LYS cc_start: 0.7886 (ttmt) cc_final: 0.7629 (ttpt) REVERT: B 315 LEU cc_start: 0.8644 (mt) cc_final: 0.8404 (mp) REVERT: B 317 LYS cc_start: 0.7752 (mttt) cc_final: 0.7217 (mtpt) REVERT: B 340 LYS cc_start: 0.7808 (tttt) cc_final: 0.7455 (tttm) REVERT: B 358 ASP cc_start: 0.7914 (m-30) cc_final: 0.7551 (m-30) REVERT: B 369 LYS cc_start: 0.7557 (tttt) cc_final: 0.7199 (tttm) REVERT: C 307 GLN cc_start: 0.8141 (tt0) cc_final: 0.7825 (tt0) REVERT: C 317 LYS cc_start: 0.7139 (mttt) cc_final: 0.6728 (mtmt) REVERT: C 347 LYS cc_start: 0.8157 (mttt) cc_final: 0.7718 (mptp) REVERT: C 349 ARG cc_start: 0.6242 (mtm180) cc_final: 0.5753 (tpt90) REVERT: C 353 LYS cc_start: 0.6835 (mttt) cc_final: 0.6546 (tttp) REVERT: C 360 ILE cc_start: 0.7531 (mt) cc_final: 0.7304 (mp) REVERT: D 311 LYS cc_start: 0.7865 (mttt) cc_final: 0.6939 (mttm) REVERT: D 317 LYS cc_start: 0.7702 (mttt) cc_final: 0.7296 (mtpt) REVERT: D 340 LYS cc_start: 0.7712 (tttt) cc_final: 0.7102 (tptm) REVERT: D 342 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7258 (mt-10) REVERT: D 358 ASP cc_start: 0.7728 (m-30) cc_final: 0.7407 (m-30) REVERT: D 369 LYS cc_start: 0.7590 (tttt) cc_final: 0.7310 (tttm) REVERT: D 375 LYS cc_start: 0.7285 (tttt) cc_final: 0.6997 (ttpt) REVERT: E 311 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7515 (mttt) REVERT: E 314 ASP cc_start: 0.7638 (t0) cc_final: 0.7430 (t0) REVERT: E 317 LYS cc_start: 0.7812 (mttt) cc_final: 0.7426 (mttp) REVERT: E 320 SER cc_start: 0.8346 (m) cc_final: 0.7810 (p) REVERT: E 338 GLU cc_start: 0.7398 (mt-10) cc_final: 0.7196 (mt-10) REVERT: E 340 LYS cc_start: 0.7758 (mttt) cc_final: 0.7298 (mtpt) REVERT: F 317 LYS cc_start: 0.8157 (mttt) cc_final: 0.7688 (mtpt) REVERT: F 340 LYS cc_start: 0.8435 (tttt) cc_final: 0.7815 (tptp) REVERT: F 343 LYS cc_start: 0.7226 (ttmt) cc_final: 0.6993 (ttpt) REVERT: F 369 LYS cc_start: 0.8098 (tttt) cc_final: 0.7716 (tttm) outliers start: 4 outliers final: 3 residues processed: 147 average time/residue: 1.4281 time to fit residues: 214.6833 Evaluate side-chains 130 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 126 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 347 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 28 optimal weight: 0.0770 chunk 19 optimal weight: 0.0010 overall best weight: 0.4944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN C 351 GLN F 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3489 Z= 0.115 Angle : 0.530 8.351 4668 Z= 0.254 Chirality : 0.049 0.125 525 Planarity : 0.002 0.018 594 Dihedral : 4.726 12.466 462 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.53 % Allowed : 16.28 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.34), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 329 PHE 0.004 0.001 PHE A 346 TYR 0.011 0.002 TYR F 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 137 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7041 (mttt) cc_final: 0.6624 (mttp) REVERT: A 338 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6462 (tt0) REVERT: A 340 LYS cc_start: 0.6806 (mttt) cc_final: 0.6586 (mtpt) REVERT: A 347 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7540 (mptt) REVERT: A 353 LYS cc_start: 0.6628 (mttt) cc_final: 0.6355 (tttm) REVERT: A 360 ILE cc_start: 0.7415 (mt) cc_final: 0.7191 (mp) REVERT: A 375 LYS cc_start: 0.7913 (ttmt) cc_final: 0.7627 (ttpt) REVERT: B 317 LYS cc_start: 0.7709 (mttt) cc_final: 0.7200 (mtpt) REVERT: B 340 LYS cc_start: 0.7824 (tttt) cc_final: 0.7477 (tttm) REVERT: B 343 LYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6744 (tptm) REVERT: B 358 ASP cc_start: 0.7878 (m-30) cc_final: 0.7547 (m-30) REVERT: B 369 LYS cc_start: 0.7597 (tttt) cc_final: 0.7161 (tttm) REVERT: C 307 GLN cc_start: 0.8127 (tt0) cc_final: 0.7850 (tt0) REVERT: C 317 LYS cc_start: 0.7139 (mttt) cc_final: 0.6777 (mtmt) REVERT: C 349 ARG cc_start: 0.6379 (mtm180) cc_final: 0.5719 (tpt90) REVERT: C 353 LYS cc_start: 0.6824 (mttt) cc_final: 0.6529 (tttp) REVERT: C 360 ILE cc_start: 0.7586 (mt) cc_final: 0.7373 (mp) REVERT: D 311 LYS cc_start: 0.7839 (mttt) cc_final: 0.6953 (mttm) REVERT: D 317 LYS cc_start: 0.7732 (mttt) cc_final: 0.7297 (mtpt) REVERT: D 340 LYS cc_start: 0.7708 (tttt) cc_final: 0.7106 (tptm) REVERT: D 342 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7241 (mt-10) REVERT: D 358 ASP cc_start: 0.7694 (m-30) cc_final: 0.7420 (m-30) REVERT: D 369 LYS cc_start: 0.7658 (tttt) cc_final: 0.7360 (tttm) REVERT: D 375 LYS cc_start: 0.7374 (tttt) cc_final: 0.7009 (ttpt) REVERT: E 311 LYS cc_start: 0.8065 (ptmt) cc_final: 0.7440 (mttt) REVERT: E 315 LEU cc_start: 0.8636 (mp) cc_final: 0.8429 (mm) REVERT: E 317 LYS cc_start: 0.7786 (mttt) cc_final: 0.7283 (mtmt) REVERT: E 320 SER cc_start: 0.8258 (m) cc_final: 0.7880 (p) REVERT: E 338 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7252 (mt-10) REVERT: E 340 LYS cc_start: 0.7771 (mttt) cc_final: 0.7324 (mtpt) REVERT: E 347 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7959 (mptp) REVERT: F 317 LYS cc_start: 0.8111 (mttt) cc_final: 0.7626 (mtpt) REVERT: F 340 LYS cc_start: 0.8405 (tttt) cc_final: 0.7789 (tptm) REVERT: F 343 LYS cc_start: 0.7407 (ttmt) cc_final: 0.7114 (tppt) REVERT: F 369 LYS cc_start: 0.8119 (tttt) cc_final: 0.7725 (tttm) outliers start: 6 outliers final: 0 residues processed: 137 average time/residue: 1.3823 time to fit residues: 193.6542 Evaluate side-chains 129 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 126 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain E residue 347 LYS 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: 0.7980 chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 0.0030 chunk 23 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN C 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3489 Z= 0.135 Angle : 0.516 7.268 4668 Z= 0.244 Chirality : 0.049 0.118 525 Planarity : 0.002 0.015 594 Dihedral : 4.465 10.947 462 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.02 % Allowed : 17.05 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.34), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 329 PHE 0.005 0.001 PHE A 346 TYR 0.020 0.003 TYR D 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 136 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7114 (mttt) cc_final: 0.6672 (mttp) REVERT: A 338 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6446 (tt0) REVERT: A 347 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7589 (mptt) REVERT: A 353 LYS cc_start: 0.6668 (mttt) cc_final: 0.6375 (tttm) REVERT: A 360 ILE cc_start: 0.7413 (mt) cc_final: 0.7200 (mp) REVERT: A 375 LYS cc_start: 0.7894 (ttmt) cc_final: 0.7630 (ttpt) REVERT: B 317 LYS cc_start: 0.7765 (mttt) cc_final: 0.7195 (mtpt) REVERT: B 340 LYS cc_start: 0.7815 (tttt) cc_final: 0.7514 (tttm) REVERT: B 343 LYS cc_start: 0.7279 (tppt) cc_final: 0.6778 (tptm) REVERT: B 358 ASP cc_start: 0.7892 (m-30) cc_final: 0.7623 (m-30) REVERT: B 369 LYS cc_start: 0.7596 (tttt) cc_final: 0.7211 (tttm) REVERT: C 307 GLN cc_start: 0.8159 (tt0) cc_final: 0.7894 (tt0) REVERT: C 317 LYS cc_start: 0.7133 (mttt) cc_final: 0.6739 (mtmt) REVERT: C 349 ARG cc_start: 0.6416 (mtm180) cc_final: 0.5715 (tpt90) REVERT: C 353 LYS cc_start: 0.6843 (mttt) cc_final: 0.6496 (tttp) REVERT: C 360 ILE cc_start: 0.7667 (mt) cc_final: 0.7450 (mp) REVERT: D 311 LYS cc_start: 0.7825 (mttt) cc_final: 0.6861 (mttm) REVERT: D 317 LYS cc_start: 0.7791 (mttt) cc_final: 0.7323 (mtpt) REVERT: D 340 LYS cc_start: 0.7787 (tttt) cc_final: 0.7131 (tptm) REVERT: D 342 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7334 (mt-10) REVERT: D 343 LYS cc_start: 0.7587 (tttt) cc_final: 0.6238 (tppt) REVERT: D 369 LYS cc_start: 0.7728 (tttt) cc_final: 0.7466 (tttp) REVERT: D 375 LYS cc_start: 0.7448 (tttt) cc_final: 0.7063 (ttpt) REVERT: E 311 LYS cc_start: 0.8121 (ptmt) cc_final: 0.7476 (mttt) REVERT: E 317 LYS cc_start: 0.7801 (mttt) cc_final: 0.7336 (mtmt) REVERT: E 320 SER cc_start: 0.8221 (m) cc_final: 0.7923 (p) REVERT: E 338 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7245 (mt-10) REVERT: E 340 LYS cc_start: 0.7860 (mttt) cc_final: 0.7395 (mtpt) REVERT: E 347 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7966 (mptp) REVERT: E 372 GLU cc_start: 0.8133 (tt0) cc_final: 0.7637 (tt0) REVERT: F 317 LYS cc_start: 0.8101 (mttt) cc_final: 0.7574 (mtpt) REVERT: F 340 LYS cc_start: 0.8423 (tttt) cc_final: 0.7785 (tptm) REVERT: F 343 LYS cc_start: 0.7599 (ttmt) cc_final: 0.7262 (tppt) REVERT: F 369 LYS cc_start: 0.8148 (tttt) cc_final: 0.7764 (tttm) outliers start: 4 outliers final: 0 residues processed: 136 average time/residue: 1.3765 time to fit residues: 191.3104 Evaluate side-chains 132 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain E residue 347 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 0.0670 overall best weight: 3.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 327 ASN C 351 GLN E 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3489 Z= 0.319 Angle : 0.626 8.727 4668 Z= 0.299 Chirality : 0.048 0.118 525 Planarity : 0.003 0.018 594 Dihedral : 4.933 11.710 462 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.53 % Allowed : 16.03 % Favored : 82.44 % 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: -1.65 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.010 0.002 PHE C 346 TYR 0.020 0.002 TYR B 310 ARG 0.002 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 132 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6408 (tt0) REVERT: A 347 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7587 (mptt) REVERT: A 353 LYS cc_start: 0.6732 (mttt) cc_final: 0.6424 (tttm) REVERT: A 372 GLU cc_start: 0.8148 (tt0) cc_final: 0.7878 (tt0) REVERT: A 375 LYS cc_start: 0.7896 (ttmt) cc_final: 0.7600 (ttpt) REVERT: B 317 LYS cc_start: 0.7714 (mttt) cc_final: 0.7132 (mtpt) REVERT: B 340 LYS cc_start: 0.7836 (tttt) cc_final: 0.7126 (ttpp) REVERT: B 343 LYS cc_start: 0.7279 (tppt) cc_final: 0.6778 (tptm) REVERT: B 358 ASP cc_start: 0.7997 (m-30) cc_final: 0.7697 (m-30) REVERT: B 369 LYS cc_start: 0.7677 (tttt) cc_final: 0.7256 (tttm) REVERT: C 307 GLN cc_start: 0.8209 (tt0) cc_final: 0.7961 (tt0) REVERT: C 349 ARG cc_start: 0.6329 (mtm180) cc_final: 0.5711 (tpt90) REVERT: C 353 LYS cc_start: 0.6854 (mttt) cc_final: 0.6513 (tttp) REVERT: C 360 ILE cc_start: 0.7577 (mt) cc_final: 0.7354 (mp) REVERT: D 311 LYS cc_start: 0.7968 (mttt) cc_final: 0.6993 (mttm) REVERT: D 317 LYS cc_start: 0.7783 (mttt) cc_final: 0.7287 (mtpt) REVERT: D 340 LYS cc_start: 0.7827 (tttt) cc_final: 0.7401 (tptt) REVERT: D 342 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7364 (mt-10) REVERT: D 343 LYS cc_start: 0.7389 (tttt) cc_final: 0.6004 (tppt) REVERT: D 369 LYS cc_start: 0.7712 (tttt) cc_final: 0.7450 (tttp) REVERT: D 375 LYS cc_start: 0.7485 (tttt) cc_final: 0.6996 (ttpt) REVERT: E 317 LYS cc_start: 0.7819 (mttt) cc_final: 0.7424 (mtmt) REVERT: E 320 SER cc_start: 0.8438 (m) cc_final: 0.7905 (p) REVERT: E 338 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7266 (mt-10) REVERT: E 340 LYS cc_start: 0.7831 (mttt) cc_final: 0.7325 (mtpt) REVERT: E 347 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7989 (mptp) REVERT: E 370 LYS cc_start: 0.8170 (tttt) cc_final: 0.7944 (tttt) REVERT: E 372 GLU cc_start: 0.8251 (tt0) cc_final: 0.7835 (tt0) REVERT: F 317 LYS cc_start: 0.8167 (mttt) cc_final: 0.7650 (mtpt) REVERT: F 340 LYS cc_start: 0.8434 (tttt) cc_final: 0.7736 (tptm) REVERT: F 343 LYS cc_start: 0.7594 (ttmt) cc_final: 0.7244 (tppt) REVERT: F 358 ASP cc_start: 0.8154 (m-30) cc_final: 0.7952 (m-30) REVERT: F 369 LYS cc_start: 0.8209 (tttt) cc_final: 0.7789 (tttm) REVERT: F 372 GLU cc_start: 0.8105 (tt0) cc_final: 0.7795 (tt0) outliers start: 6 outliers final: 3 residues processed: 132 average time/residue: 1.5057 time to fit residues: 202.9452 Evaluate side-chains 134 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 373 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN C 351 GLN E 336 GLN E 351 GLN F 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3489 Z= 0.263 Angle : 0.584 7.726 4668 Z= 0.280 Chirality : 0.048 0.117 525 Planarity : 0.003 0.019 594 Dihedral : 4.846 11.436 462 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.04 % Allowed : 15.78 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 329 PHE 0.010 0.002 PHE C 346 TYR 0.023 0.002 TYR B 310 ARG 0.002 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6406 (tt0) REVERT: A 347 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7603 (mptt) REVERT: A 353 LYS cc_start: 0.6751 (mttt) cc_final: 0.6442 (tttm) REVERT: A 372 GLU cc_start: 0.8140 (tt0) cc_final: 0.7911 (tt0) REVERT: A 375 LYS cc_start: 0.7907 (ttmt) cc_final: 0.7617 (ttpt) REVERT: B 317 LYS cc_start: 0.7661 (mttt) cc_final: 0.7071 (mtpt) REVERT: B 340 LYS cc_start: 0.7801 (tttt) cc_final: 0.7448 (tttm) REVERT: B 343 LYS cc_start: 0.7306 (tppt) cc_final: 0.6760 (tptm) REVERT: B 358 ASP cc_start: 0.7991 (m-30) cc_final: 0.7679 (m-30) REVERT: B 369 LYS cc_start: 0.7633 (tttt) cc_final: 0.7209 (tttm) REVERT: C 307 GLN cc_start: 0.8209 (tt0) cc_final: 0.7944 (tt0) REVERT: C 349 ARG cc_start: 0.6311 (mtm180) cc_final: 0.5671 (tpt90) REVERT: C 353 LYS cc_start: 0.6865 (mttt) cc_final: 0.6522 (tttp) REVERT: C 360 ILE cc_start: 0.7575 (mt) cc_final: 0.7361 (mp) REVERT: D 311 LYS cc_start: 0.7986 (mttt) cc_final: 0.6965 (mttm) REVERT: D 317 LYS cc_start: 0.7795 (mttt) cc_final: 0.7283 (mtpt) REVERT: D 340 LYS cc_start: 0.7867 (tttt) cc_final: 0.7556 (tttm) REVERT: D 342 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7352 (mt-10) REVERT: D 343 LYS cc_start: 0.7451 (tttt) cc_final: 0.6078 (tppt) REVERT: D 369 LYS cc_start: 0.7762 (tttt) cc_final: 0.7497 (tttp) REVERT: D 375 LYS cc_start: 0.7555 (tttt) cc_final: 0.7070 (ttpt) REVERT: E 317 LYS cc_start: 0.7788 (mttt) cc_final: 0.7397 (mtmt) REVERT: E 320 SER cc_start: 0.8426 (m) cc_final: 0.7915 (p) REVERT: E 338 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7235 (mt-10) REVERT: E 340 LYS cc_start: 0.7842 (mttt) cc_final: 0.7233 (mtpt) REVERT: E 347 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7882 (mptp) REVERT: E 370 LYS cc_start: 0.8189 (tttt) cc_final: 0.7950 (tttt) REVERT: E 372 GLU cc_start: 0.8247 (tt0) cc_final: 0.7961 (mt-10) REVERT: F 311 LYS cc_start: 0.8294 (mtpt) cc_final: 0.7620 (mtmt) REVERT: F 317 LYS cc_start: 0.8158 (mttt) cc_final: 0.7642 (mtpt) REVERT: F 340 LYS cc_start: 0.8426 (tttt) cc_final: 0.7713 (tptm) REVERT: F 343 LYS cc_start: 0.7626 (ttmt) cc_final: 0.6992 (tptm) REVERT: F 369 LYS cc_start: 0.8216 (tttt) cc_final: 0.7770 (tttm) REVERT: F 372 GLU cc_start: 0.8093 (tt0) cc_final: 0.7806 (tt0) outliers start: 8 outliers final: 3 residues processed: 131 average time/residue: 1.5091 time to fit residues: 201.8531 Evaluate side-chains 134 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 373 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN C 351 GLN E 336 GLN E 351 GLN F 307 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 3489 Z= 0.392 Angle : 0.647 8.558 4668 Z= 0.314 Chirality : 0.049 0.120 525 Planarity : 0.003 0.021 594 Dihedral : 5.101 12.442 462 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.04 % Allowed : 16.03 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.32), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.24), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 374 PHE 0.013 0.002 PHE C 346 TYR 0.025 0.003 TYR B 310 ARG 0.003 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 129 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6397 (tt0) REVERT: A 347 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7043 (mptm) REVERT: A 353 LYS cc_start: 0.6768 (mttt) cc_final: 0.6431 (tttm) REVERT: A 372 GLU cc_start: 0.8135 (tt0) cc_final: 0.7882 (tt0) REVERT: A 375 LYS cc_start: 0.7917 (ttmt) cc_final: 0.7627 (ttpt) REVERT: B 317 LYS cc_start: 0.7649 (mttt) cc_final: 0.7062 (mtpt) REVERT: B 340 LYS cc_start: 0.7814 (tttt) cc_final: 0.7462 (tttm) REVERT: B 358 ASP cc_start: 0.8068 (m-30) cc_final: 0.7741 (m-30) REVERT: B 369 LYS cc_start: 0.7652 (tttt) cc_final: 0.7239 (tttm) REVERT: C 307 GLN cc_start: 0.8222 (tt0) cc_final: 0.8011 (tt0) REVERT: C 349 ARG cc_start: 0.6350 (mtm180) cc_final: 0.5645 (tpt90) REVERT: C 353 LYS cc_start: 0.6863 (mttt) cc_final: 0.6514 (tttp) REVERT: C 360 ILE cc_start: 0.7542 (mt) cc_final: 0.7299 (mp) REVERT: C 369 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7818 (tttt) REVERT: D 311 LYS cc_start: 0.8002 (mttt) cc_final: 0.6985 (mttm) REVERT: D 317 LYS cc_start: 0.7792 (mttt) cc_final: 0.7270 (mtpt) REVERT: D 340 LYS cc_start: 0.7848 (tttt) cc_final: 0.7579 (tttm) REVERT: D 343 LYS cc_start: 0.7394 (tttt) cc_final: 0.6044 (tppt) REVERT: D 369 LYS cc_start: 0.7683 (tttt) cc_final: 0.7409 (tttp) REVERT: D 375 LYS cc_start: 0.7544 (tttt) cc_final: 0.7013 (ttpt) REVERT: E 317 LYS cc_start: 0.7790 (mttt) cc_final: 0.7388 (mtmt) REVERT: E 338 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7335 (mt-10) REVERT: E 340 LYS cc_start: 0.7808 (mttt) cc_final: 0.7216 (mtpt) REVERT: E 347 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7995 (mptp) REVERT: E 370 LYS cc_start: 0.8200 (tttt) cc_final: 0.7979 (tttt) REVERT: E 372 GLU cc_start: 0.8256 (tt0) cc_final: 0.7986 (mt-10) REVERT: F 311 LYS cc_start: 0.8291 (mtpt) cc_final: 0.7631 (mtmt) REVERT: F 317 LYS cc_start: 0.8170 (mttt) cc_final: 0.7638 (mtpt) REVERT: F 340 LYS cc_start: 0.8437 (tttt) cc_final: 0.7698 (tptm) REVERT: F 343 LYS cc_start: 0.7596 (ttmt) cc_final: 0.7235 (tppt) REVERT: F 369 LYS cc_start: 0.8179 (tttt) cc_final: 0.7696 (tttm) REVERT: F 372 GLU cc_start: 0.8144 (tt0) cc_final: 0.7749 (tt0) outliers start: 8 outliers final: 4 residues processed: 129 average time/residue: 1.5154 time to fit residues: 199.4396 Evaluate side-chains 134 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 127 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 373 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: 5.9990 chunk 36 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 35 optimal weight: 0.0870 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN C 351 GLN D 307 GLN E 351 GLN F 307 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3489 Z= 0.313 Angle : 0.609 8.106 4668 Z= 0.294 Chirality : 0.048 0.120 525 Planarity : 0.003 0.021 594 Dihedral : 4.977 11.817 462 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.04 % Allowed : 16.79 % Favored : 81.17 % 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: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.24), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 329 PHE 0.010 0.002 PHE C 346 TYR 0.026 0.003 TYR B 310 ARG 0.003 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 126 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6396 (tt0) REVERT: A 347 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7578 (mptt) REVERT: A 353 LYS cc_start: 0.6746 (mttt) cc_final: 0.6433 (tttm) REVERT: A 372 GLU cc_start: 0.8089 (tt0) cc_final: 0.7870 (tt0) REVERT: A 375 LYS cc_start: 0.7928 (ttmt) cc_final: 0.7637 (ttpt) REVERT: B 317 LYS cc_start: 0.7648 (mttt) cc_final: 0.7061 (mtpt) REVERT: B 340 LYS cc_start: 0.7797 (tttt) cc_final: 0.7444 (tttm) REVERT: B 358 ASP cc_start: 0.8023 (m-30) cc_final: 0.7713 (m-30) REVERT: B 369 LYS cc_start: 0.7639 (tttt) cc_final: 0.7229 (tttm) REVERT: C 307 GLN cc_start: 0.8219 (tt0) cc_final: 0.8006 (tt0) REVERT: C 349 ARG cc_start: 0.6284 (mtm180) cc_final: 0.5638 (tpt90) REVERT: C 353 LYS cc_start: 0.6856 (mttt) cc_final: 0.6517 (tttp) REVERT: C 360 ILE cc_start: 0.7565 (mt) cc_final: 0.7337 (mp) REVERT: C 369 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7819 (tttt) REVERT: D 311 LYS cc_start: 0.8041 (mttt) cc_final: 0.7019 (mttm) REVERT: D 317 LYS cc_start: 0.7785 (mttt) cc_final: 0.7267 (mtpt) REVERT: D 340 LYS cc_start: 0.7819 (tttt) cc_final: 0.7580 (tttm) REVERT: D 343 LYS cc_start: 0.7476 (tttt) cc_final: 0.6107 (tppt) REVERT: D 369 LYS cc_start: 0.7685 (tttt) cc_final: 0.7398 (tttp) REVERT: D 375 LYS cc_start: 0.7586 (tttt) cc_final: 0.7035 (ttpt) REVERT: E 317 LYS cc_start: 0.7774 (mttt) cc_final: 0.7377 (mtmt) REVERT: E 338 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7368 (mt-10) REVERT: E 340 LYS cc_start: 0.7860 (mttt) cc_final: 0.7274 (mtpt) REVERT: E 347 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.8023 (mptp) REVERT: E 370 LYS cc_start: 0.8209 (tttt) cc_final: 0.7977 (tttt) REVERT: E 372 GLU cc_start: 0.8253 (tt0) cc_final: 0.7992 (mt-10) REVERT: F 311 LYS cc_start: 0.8255 (mtpt) cc_final: 0.7607 (mtmt) REVERT: F 317 LYS cc_start: 0.8129 (mttt) cc_final: 0.7610 (mtpt) REVERT: F 340 LYS cc_start: 0.8439 (tttt) cc_final: 0.7705 (tptm) REVERT: F 343 LYS cc_start: 0.7601 (ttmt) cc_final: 0.7234 (tppt) REVERT: F 369 LYS cc_start: 0.8143 (tttt) cc_final: 0.7653 (tttm) REVERT: F 372 GLU cc_start: 0.8128 (tt0) cc_final: 0.7779 (tt0) outliers start: 8 outliers final: 4 residues processed: 126 average time/residue: 1.5228 time to fit residues: 195.8636 Evaluate side-chains 132 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 125 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 373 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 18 optimal weight: 0.3980 chunk 27 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN C 351 GLN D 307 GLN E 336 GLN E 351 GLN F 307 GLN F 351 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3489 Z= 0.290 Angle : 0.591 8.326 4668 Z= 0.287 Chirality : 0.048 0.120 525 Planarity : 0.003 0.020 594 Dihedral : 4.917 11.669 462 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.29 % Allowed : 16.03 % Favored : 81.68 % 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 (0.31), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.24), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 362 PHE 0.010 0.002 PHE C 346 TYR 0.029 0.003 TYR B 310 ARG 0.002 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 125 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6388 (tt0) REVERT: A 347 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7594 (mptt) REVERT: A 353 LYS cc_start: 0.6759 (mttt) cc_final: 0.6442 (tttm) REVERT: A 372 GLU cc_start: 0.8137 (tt0) cc_final: 0.7912 (tt0) REVERT: A 375 LYS cc_start: 0.7912 (ttmt) cc_final: 0.7614 (ttpt) REVERT: B 317 LYS cc_start: 0.7626 (mttt) cc_final: 0.7031 (mtpt) REVERT: B 340 LYS cc_start: 0.7795 (tttt) cc_final: 0.7439 (tttm) REVERT: B 358 ASP cc_start: 0.8016 (m-30) cc_final: 0.7701 (m-30) REVERT: B 369 LYS cc_start: 0.7642 (tttt) cc_final: 0.7234 (tttm) REVERT: C 307 GLN cc_start: 0.8222 (tt0) cc_final: 0.8009 (tt0) REVERT: C 349 ARG cc_start: 0.6283 (mtm180) cc_final: 0.5637 (tpt90) REVERT: C 353 LYS cc_start: 0.6853 (mttt) cc_final: 0.6515 (tttp) REVERT: C 360 ILE cc_start: 0.7572 (mt) cc_final: 0.7346 (mp) REVERT: C 369 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7844 (tttt) REVERT: D 311 LYS cc_start: 0.8042 (mttt) cc_final: 0.7026 (mttm) REVERT: D 317 LYS cc_start: 0.7817 (mttt) cc_final: 0.7293 (mtpt) REVERT: D 340 LYS cc_start: 0.7817 (tttt) cc_final: 0.7200 (ttpp) REVERT: D 343 LYS cc_start: 0.7506 (tttt) cc_final: 0.6138 (tppt) REVERT: D 375 LYS cc_start: 0.7625 (tttt) cc_final: 0.7079 (ttpt) REVERT: E 317 LYS cc_start: 0.7776 (mttt) cc_final: 0.7381 (mtmt) REVERT: E 338 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7326 (mt-10) REVERT: E 340 LYS cc_start: 0.7860 (mttt) cc_final: 0.7256 (mtpt) REVERT: E 347 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.8031 (mptp) REVERT: E 370 LYS cc_start: 0.8212 (tttt) cc_final: 0.7989 (tttt) REVERT: E 372 GLU cc_start: 0.8243 (tt0) cc_final: 0.7978 (mt-10) REVERT: F 317 LYS cc_start: 0.8173 (mttt) cc_final: 0.7619 (mtpt) REVERT: F 340 LYS cc_start: 0.8436 (tttt) cc_final: 0.7727 (tptm) REVERT: F 343 LYS cc_start: 0.7624 (ttmt) cc_final: 0.7364 (ttpt) REVERT: F 369 LYS cc_start: 0.8157 (tttt) cc_final: 0.7668 (tttm) REVERT: F 372 GLU cc_start: 0.8139 (tt0) cc_final: 0.7718 (tt0) outliers start: 9 outliers final: 5 residues processed: 125 average time/residue: 1.5205 time to fit residues: 194.0302 Evaluate side-chains 133 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 125 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 373 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 327 ASN C 351 GLN D 351 GLN E 351 GLN F 307 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3489 Z= 0.145 Angle : 0.533 8.661 4668 Z= 0.253 Chirality : 0.048 0.121 525 Planarity : 0.002 0.019 594 Dihedral : 4.535 10.603 462 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.27 % Allowed : 18.07 % Favored : 80.66 % 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: -1.94 (0.32), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.24), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 374 PHE 0.006 0.001 PHE C 346 TYR 0.027 0.002 TYR B 310 ARG 0.001 0.000 ARG D 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 130 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7025 (mt-10) cc_final: 0.6340 (tt0) REVERT: A 347 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7555 (mptt) REVERT: A 353 LYS cc_start: 0.6732 (mttt) cc_final: 0.6465 (tttm) REVERT: A 372 GLU cc_start: 0.8109 (tt0) cc_final: 0.7845 (tt0) REVERT: A 375 LYS cc_start: 0.7862 (ttmt) cc_final: 0.7593 (ttpt) REVERT: B 317 LYS cc_start: 0.7627 (mttt) cc_final: 0.7044 (mtpt) REVERT: B 340 LYS cc_start: 0.7794 (tttt) cc_final: 0.7456 (tttm) REVERT: B 343 LYS cc_start: 0.7387 (tppt) cc_final: 0.7054 (tptm) REVERT: B 358 ASP cc_start: 0.7945 (m-30) cc_final: 0.7664 (m-30) REVERT: B 369 LYS cc_start: 0.7650 (tttt) cc_final: 0.7249 (tttm) REVERT: C 307 GLN cc_start: 0.8227 (tt0) cc_final: 0.7960 (tt0) REVERT: C 340 LYS cc_start: 0.7199 (mtmm) cc_final: 0.6942 (mttm) REVERT: C 349 ARG cc_start: 0.6320 (mtm180) cc_final: 0.5651 (tpt90) REVERT: C 353 LYS cc_start: 0.6860 (mttt) cc_final: 0.6526 (tttp) REVERT: D 311 LYS cc_start: 0.7977 (mttt) cc_final: 0.6956 (mttm) REVERT: D 317 LYS cc_start: 0.7790 (mttt) cc_final: 0.7270 (mtpt) REVERT: D 340 LYS cc_start: 0.7902 (tttt) cc_final: 0.7605 (tttm) REVERT: D 343 LYS cc_start: 0.7569 (tttt) cc_final: 0.6163 (tppt) REVERT: D 375 LYS cc_start: 0.7625 (tttt) cc_final: 0.7084 (ttpt) REVERT: E 317 LYS cc_start: 0.7746 (mttt) cc_final: 0.7345 (mtmt) REVERT: E 320 SER cc_start: 0.8476 (m) cc_final: 0.7906 (p) REVERT: E 338 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7360 (mt-10) REVERT: E 340 LYS cc_start: 0.7892 (mttt) cc_final: 0.7314 (mtpt) REVERT: E 347 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7920 (mptp) REVERT: E 370 LYS cc_start: 0.8212 (tttt) cc_final: 0.7954 (tttt) REVERT: E 372 GLU cc_start: 0.8235 (tt0) cc_final: 0.7837 (tt0) REVERT: F 317 LYS cc_start: 0.8098 (mttt) cc_final: 0.7572 (mtpt) REVERT: F 340 LYS cc_start: 0.8399 (tttt) cc_final: 0.7721 (tptm) REVERT: F 343 LYS cc_start: 0.7597 (ttmt) cc_final: 0.6951 (tptm) REVERT: F 351 GLN cc_start: 0.8127 (tt0) cc_final: 0.7882 (tt0) REVERT: F 369 LYS cc_start: 0.8141 (tttt) cc_final: 0.7659 (tttm) outliers start: 5 outliers final: 1 residues processed: 130 average time/residue: 1.4266 time to fit residues: 189.5903 Evaluate side-chains 127 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 124 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain E residue 347 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 GLN E 336 GLN E 351 GLN F 307 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.114214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.100720 restraints weight = 4123.914| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.43 r_work: 0.3308 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3489 Z= 0.288 Angle : 0.593 8.740 4668 Z= 0.285 Chirality : 0.048 0.119 525 Planarity : 0.003 0.020 594 Dihedral : 4.792 11.387 462 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.27 % Allowed : 18.83 % Favored : 79.90 % 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 (0.32), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.24), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 362 PHE 0.010 0.002 PHE C 346 TYR 0.022 0.003 TYR D 310 ARG 0.002 0.001 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3260.27 seconds wall clock time: 57 minutes 47.80 seconds (3467.80 seconds total)