Starting phenix.real_space_refine on Fri Aug 2 16:00:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8x_18264/08_2024/8q8x_18264.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8x_18264/08_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_18264/08_2024/8q8x_18264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8x_18264/08_2024/8q8x_18264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8x_18264/08_2024/8q8x_18264.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8x_18264/08_2024/8q8x_18264.cif" } 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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 3.17, per 1000 atoms: 0.92 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: 0.96 Conformation dependent library (CDL) restraints added in 826.3 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: 0.49 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: 1.10 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 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.521 3.040 nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.529 3.040 nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.532 3.040 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.535 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 3.950 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.400 Find NCS groups from input model: 0.160 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:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.630 ------------------------------------------------------------------------------- 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 : 0.578 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: 1.2385 time to fit residues: 244.9763 Evaluate side-chains 138 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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: 0.8980 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN B 351 GLN C 327 ASN C 351 GLN D 351 GLN E 327 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 3489 Z= 0.177 Angle : 0.610 7.980 4668 Z= 0.296 Chirality : 0.051 0.137 525 Planarity : 0.003 0.019 594 Dihedral : 5.499 16.195 462 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.02 % Allowed : 14.50 % Favored : 84.48 % 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: -1.41 (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 0.003 0.001 HIS D 329 PHE 0.007 0.001 PHE A 346 TYR 0.019 0.003 TYR B 310 ARG 0.001 0.000 ARG D 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 152 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 148 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.7759 (t0) cc_final: 0.7558 (t0) REVERT: A 317 LYS cc_start: 0.7130 (mttt) cc_final: 0.6735 (mttp) REVERT: A 320 SER cc_start: 0.8544 (m) cc_final: 0.8332 (p) REVERT: A 338 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6437 (tt0) REVERT: A 340 LYS cc_start: 0.6832 (mttt) cc_final: 0.6610 (mtpt) REVERT: A 347 LYS cc_start: 0.8092 (mptm) cc_final: 0.7769 (mptt) REVERT: A 353 LYS cc_start: 0.6613 (mttt) cc_final: 0.6310 (tttm) REVERT: A 360 ILE cc_start: 0.7478 (mt) cc_final: 0.7254 (mp) REVERT: A 375 LYS cc_start: 0.7942 (ttmt) cc_final: 0.7664 (ttpt) REVERT: B 315 LEU cc_start: 0.8728 (mt) cc_final: 0.8470 (mp) REVERT: B 317 LYS cc_start: 0.7829 (mttt) cc_final: 0.7283 (mtpt) REVERT: B 340 LYS cc_start: 0.7805 (tttt) cc_final: 0.7490 (tttm) REVERT: B 358 ASP cc_start: 0.7880 (m-30) cc_final: 0.7611 (m-30) REVERT: B 369 LYS cc_start: 0.7581 (tttt) cc_final: 0.7226 (tttm) REVERT: C 307 GLN cc_start: 0.8225 (tt0) cc_final: 0.7920 (tt0) REVERT: C 317 LYS cc_start: 0.7210 (mttt) cc_final: 0.6811 (mtmt) REVERT: C 347 LYS cc_start: 0.8200 (mttt) cc_final: 0.7647 (mptp) REVERT: C 349 ARG cc_start: 0.6546 (mtm180) cc_final: 0.5781 (tpt90) REVERT: C 353 LYS cc_start: 0.6841 (mttt) cc_final: 0.6558 (tttp) REVERT: C 360 ILE cc_start: 0.7677 (mt) cc_final: 0.7458 (mp) REVERT: D 311 LYS cc_start: 0.7871 (mttt) cc_final: 0.6941 (mttm) REVERT: D 317 LYS cc_start: 0.7742 (mttt) cc_final: 0.7298 (mtpt) REVERT: D 340 LYS cc_start: 0.7755 (tttt) cc_final: 0.7349 (tptt) REVERT: D 358 ASP cc_start: 0.7784 (m-30) cc_final: 0.7500 (m-30) REVERT: D 369 LYS cc_start: 0.7590 (tttt) cc_final: 0.7313 (tttm) REVERT: D 375 LYS cc_start: 0.7288 (tttt) cc_final: 0.7008 (ttpt) REVERT: E 311 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7530 (mttt) REVERT: E 317 LYS cc_start: 0.7779 (mttt) cc_final: 0.7443 (mttp) REVERT: E 320 SER cc_start: 0.8397 (m) cc_final: 0.7879 (p) REVERT: E 338 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7204 (mt-10) REVERT: E 340 LYS cc_start: 0.7735 (mttt) cc_final: 0.7237 (mtpt) REVERT: F 317 LYS cc_start: 0.8133 (mttt) cc_final: 0.7652 (mtpt) REVERT: F 340 LYS cc_start: 0.8439 (tttt) cc_final: 0.7889 (tptp) REVERT: F 343 LYS cc_start: 0.7249 (ttmt) cc_final: 0.7017 (ttpt) REVERT: F 369 LYS cc_start: 0.8128 (tttt) cc_final: 0.7742 (tttm) outliers start: 4 outliers final: 1 residues processed: 150 average time/residue: 1.3306 time to fit residues: 204.2811 Evaluate side-chains 133 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 311 LYS 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: 7.9990 chunk 10 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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: 0.7580 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3489 Z= 0.292 Angle : 0.646 9.512 4668 Z= 0.309 Chirality : 0.050 0.128 525 Planarity : 0.003 0.019 594 Dihedral : 5.267 13.611 462 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.80 % Allowed : 16.54 % 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: -1.58 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 329 PHE 0.009 0.002 PHE C 346 TYR 0.007 0.001 TYR F 310 ARG 0.003 0.001 ARG A 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 146 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 135 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7061 (mttt) cc_final: 0.6627 (mttp) REVERT: A 338 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6413 (tt0) REVERT: A 347 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7638 (mptt) REVERT: A 353 LYS cc_start: 0.6762 (mttt) cc_final: 0.6446 (tttm) REVERT: A 375 LYS cc_start: 0.7976 (ttmt) cc_final: 0.7683 (ttpt) REVERT: B 317 LYS cc_start: 0.7741 (mttt) cc_final: 0.7173 (mtpt) REVERT: B 340 LYS cc_start: 0.7812 (tttt) cc_final: 0.7504 (tttm) REVERT: B 358 ASP cc_start: 0.8051 (m-30) cc_final: 0.7796 (m-30) REVERT: B 369 LYS cc_start: 0.7622 (tttt) cc_final: 0.7204 (tttm) REVERT: C 307 GLN cc_start: 0.8206 (tt0) cc_final: 0.7941 (tt0) REVERT: C 349 ARG cc_start: 0.6595 (mtm180) cc_final: 0.5743 (tpt90) REVERT: C 353 LYS cc_start: 0.6898 (mttt) cc_final: 0.6559 (tttp) REVERT: C 360 ILE cc_start: 0.7638 (mt) cc_final: 0.7435 (mp) REVERT: D 311 LYS cc_start: 0.7974 (mttt) cc_final: 0.6998 (mttm) REVERT: D 317 LYS cc_start: 0.7781 (mttt) cc_final: 0.7295 (mtpt) REVERT: D 340 LYS cc_start: 0.7844 (tttt) cc_final: 0.7164 (tptm) REVERT: D 369 LYS cc_start: 0.7685 (tttt) cc_final: 0.7362 (tttm) REVERT: D 375 LYS cc_start: 0.7426 (tttt) cc_final: 0.7030 (ttpt) REVERT: E 311 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7604 (mttt) REVERT: E 317 LYS cc_start: 0.7834 (mttt) cc_final: 0.7412 (mtmt) REVERT: E 320 SER cc_start: 0.8475 (m) cc_final: 0.7883 (p) REVERT: E 338 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7287 (mt-10) REVERT: E 340 LYS cc_start: 0.7843 (mttt) cc_final: 0.7343 (mtpt) REVERT: E 347 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7943 (mptp) REVERT: E 370 LYS cc_start: 0.8205 (tttt) cc_final: 0.7975 (tttt) REVERT: F 317 LYS cc_start: 0.8124 (mttt) cc_final: 0.7623 (mtpt) REVERT: F 340 LYS cc_start: 0.8432 (tttt) cc_final: 0.7762 (tptm) REVERT: F 343 LYS cc_start: 0.7646 (ttmt) cc_final: 0.7227 (tppt) REVERT: F 345 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7874 (t0) REVERT: F 369 LYS cc_start: 0.8171 (tttt) cc_final: 0.7778 (tttm) REVERT: F 372 GLU cc_start: 0.8139 (tt0) cc_final: 0.7798 (tt0) outliers start: 11 outliers final: 3 residues processed: 136 average time/residue: 1.4134 time to fit residues: 196.3468 Evaluate side-chains 133 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 126 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 311 LYS Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 345 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 0.4980 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3489 Z= 0.211 Angle : 0.556 6.617 4668 Z= 0.269 Chirality : 0.049 0.119 525 Planarity : 0.003 0.018 594 Dihedral : 4.928 12.100 462 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.80 % Allowed : 15.78 % Favored : 81.42 % 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: -1.68 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 329 PHE 0.007 0.002 PHE A 346 TYR 0.020 0.003 TYR D 310 ARG 0.002 0.001 ARG E 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 143 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 132 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6419 (tt0) REVERT: A 347 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7609 (mptt) REVERT: A 353 LYS cc_start: 0.6730 (mttt) cc_final: 0.6444 (tttm) REVERT: A 372 GLU cc_start: 0.8069 (tt0) cc_final: 0.7822 (tt0) REVERT: A 375 LYS cc_start: 0.7967 (ttmt) cc_final: 0.7659 (ttpt) REVERT: B 317 LYS cc_start: 0.7748 (mttt) cc_final: 0.7160 (mtpt) REVERT: B 340 LYS cc_start: 0.7837 (tttt) cc_final: 0.7125 (ttpp) REVERT: B 343 LYS cc_start: 0.7240 (tppt) cc_final: 0.6920 (tptm) REVERT: B 358 ASP cc_start: 0.8013 (m-30) cc_final: 0.7754 (m-30) REVERT: B 369 LYS cc_start: 0.7638 (tttt) cc_final: 0.7225 (tttm) REVERT: C 307 GLN cc_start: 0.8206 (tt0) cc_final: 0.7978 (tt0) REVERT: C 317 LYS cc_start: 0.7400 (mttm) cc_final: 0.7171 (mtmt) REVERT: C 349 ARG cc_start: 0.6623 (mtm180) cc_final: 0.5733 (tpt90) REVERT: C 353 LYS cc_start: 0.6904 (mttt) cc_final: 0.6573 (tttp) REVERT: D 311 LYS cc_start: 0.7975 (mttt) cc_final: 0.7004 (mttm) REVERT: D 317 LYS cc_start: 0.7783 (mttt) cc_final: 0.7302 (mtpt) REVERT: D 340 LYS cc_start: 0.7861 (tttt) cc_final: 0.7431 (tptt) REVERT: D 343 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.6041 (tppt) REVERT: D 369 LYS cc_start: 0.7729 (tttt) cc_final: 0.7470 (tttp) REVERT: D 375 LYS cc_start: 0.7485 (tttt) cc_final: 0.7021 (ttpt) REVERT: E 311 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7569 (mttt) REVERT: E 317 LYS cc_start: 0.7791 (mttt) cc_final: 0.7377 (mtmt) REVERT: E 320 SER cc_start: 0.8459 (m) cc_final: 0.7903 (p) REVERT: E 338 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7263 (mt-10) REVERT: E 340 LYS cc_start: 0.7814 (mttt) cc_final: 0.7344 (mtpt) REVERT: E 347 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7983 (mptp) REVERT: E 370 LYS cc_start: 0.8244 (tttt) cc_final: 0.7994 (tttt) REVERT: E 372 GLU cc_start: 0.8282 (tt0) cc_final: 0.7884 (tt0) REVERT: F 317 LYS cc_start: 0.8092 (mttt) cc_final: 0.7561 (mtpt) REVERT: F 340 LYS cc_start: 0.8433 (tttt) cc_final: 0.7716 (tptm) REVERT: F 343 LYS cc_start: 0.7670 (ttmt) cc_final: 0.7259 (tppt) REVERT: F 369 LYS cc_start: 0.8194 (tttt) cc_final: 0.7780 (tttm) outliers start: 11 outliers final: 3 residues processed: 132 average time/residue: 1.4375 time to fit residues: 193.8008 Evaluate side-chains 133 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 126 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 D residue 343 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 overall best weight: 3.4986 ------------------------------------------------------------------------------- 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 F 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3489 Z= 0.313 Angle : 0.606 6.860 4668 Z= 0.294 Chirality : 0.048 0.120 525 Planarity : 0.003 0.018 594 Dihedral : 5.014 12.543 462 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.54 % Allowed : 15.27 % 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: -1.80 (0.32), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 330 PHE 0.009 0.002 PHE C 346 TYR 0.008 0.001 TYR A 310 ARG 0.002 0.001 ARG E 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: 10 poor density : 128 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6438 (tt0) REVERT: A 347 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7616 (mptt) REVERT: A 353 LYS cc_start: 0.6716 (mttt) cc_final: 0.6420 (tttm) REVERT: A 375 LYS cc_start: 0.7972 (ttmt) cc_final: 0.7678 (ttpt) REVERT: B 317 LYS cc_start: 0.7690 (mttt) cc_final: 0.7105 (mtpt) REVERT: B 340 LYS cc_start: 0.7867 (tttt) cc_final: 0.7145 (ttpp) REVERT: B 358 ASP cc_start: 0.8013 (m-30) cc_final: 0.7777 (m-30) REVERT: B 369 LYS cc_start: 0.7633 (tttt) cc_final: 0.7214 (tttm) REVERT: C 307 GLN cc_start: 0.8234 (tt0) cc_final: 0.7979 (tt0) REVERT: C 317 LYS cc_start: 0.7361 (mttm) cc_final: 0.7132 (mtmt) REVERT: C 349 ARG cc_start: 0.6582 (mtm180) cc_final: 0.5721 (tpt90) REVERT: C 353 LYS cc_start: 0.6883 (mttt) cc_final: 0.6556 (tttp) REVERT: C 369 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7829 (tttt) REVERT: D 311 LYS cc_start: 0.7992 (mttt) cc_final: 0.6979 (mttm) REVERT: D 317 LYS cc_start: 0.7826 (mttt) cc_final: 0.7319 (mtpt) REVERT: D 340 LYS cc_start: 0.7908 (tttt) cc_final: 0.7586 (tttm) REVERT: D 343 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.6014 (tppt) REVERT: D 369 LYS cc_start: 0.7690 (tttt) cc_final: 0.7417 (tttp) REVERT: D 375 LYS cc_start: 0.7510 (tttt) cc_final: 0.7018 (ttpt) REVERT: E 311 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7613 (mttt) REVERT: E 317 LYS cc_start: 0.7799 (mttt) cc_final: 0.7374 (mtmt) REVERT: E 320 SER cc_start: 0.8501 (m) cc_final: 0.7888 (p) REVERT: E 338 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7317 (mt-10) REVERT: E 340 LYS cc_start: 0.7868 (mttt) cc_final: 0.7354 (mtpt) REVERT: E 347 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.8023 (mptp) REVERT: E 370 LYS cc_start: 0.8239 (tttt) cc_final: 0.7996 (tttt) REVERT: E 372 GLU cc_start: 0.8267 (tt0) cc_final: 0.8000 (mt-10) REVERT: F 317 LYS cc_start: 0.8122 (mttt) cc_final: 0.7610 (mtpt) REVERT: F 340 LYS cc_start: 0.8434 (tttt) cc_final: 0.7701 (tptm) REVERT: F 343 LYS cc_start: 0.7630 (ttmt) cc_final: 0.7270 (tppt) REVERT: F 369 LYS cc_start: 0.8222 (tttt) cc_final: 0.7775 (tttm) REVERT: F 372 GLU cc_start: 0.8122 (tt0) cc_final: 0.7803 (tt0) outliers start: 10 outliers final: 4 residues processed: 129 average time/residue: 1.5059 time to fit residues: 198.2338 Evaluate side-chains 135 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 126 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 D residue 343 LYS Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 344 LEU 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: 6.9990 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 18 optimal weight: 0.0570 chunk 3 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 overall best weight: 0.6300 ------------------------------------------------------------------------------- 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 351 GLN E 351 GLN F 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3489 Z= 0.124 Angle : 0.502 6.018 4668 Z= 0.241 Chirality : 0.049 0.122 525 Planarity : 0.002 0.017 594 Dihedral : 4.445 10.646 462 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.78 % Allowed : 17.56 % 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: -1.80 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 329 PHE 0.004 0.001 PHE C 346 TYR 0.020 0.002 TYR D 310 ARG 0.001 0.000 ARG D 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 143 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 136 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6422 (tt0) REVERT: A 347 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7628 (mptt) REVERT: A 353 LYS cc_start: 0.6688 (mttt) cc_final: 0.6453 (tttm) REVERT: A 375 LYS cc_start: 0.7927 (ttmt) cc_final: 0.7652 (ttpt) REVERT: B 317 LYS cc_start: 0.7707 (mttt) cc_final: 0.7127 (mtpt) REVERT: B 340 LYS cc_start: 0.7853 (tttt) cc_final: 0.7520 (tttm) REVERT: B 343 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.7066 (tptm) REVERT: B 358 ASP cc_start: 0.7924 (m-30) cc_final: 0.7672 (m-30) REVERT: B 369 LYS cc_start: 0.7647 (tttt) cc_final: 0.7236 (tttm) REVERT: C 340 LYS cc_start: 0.7183 (mtmm) cc_final: 0.6938 (mttm) REVERT: C 349 ARG cc_start: 0.6712 (mtm180) cc_final: 0.5698 (tpt170) REVERT: C 353 LYS cc_start: 0.6916 (mttt) cc_final: 0.6629 (tttp) REVERT: D 311 LYS cc_start: 0.7962 (mttt) cc_final: 0.7025 (mttm) REVERT: D 317 LYS cc_start: 0.7843 (mttt) cc_final: 0.7321 (mtpt) REVERT: D 340 LYS cc_start: 0.7933 (tttt) cc_final: 0.7515 (tptt) REVERT: D 343 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.6133 (tppt) REVERT: D 351 GLN cc_start: 0.7481 (tt0) cc_final: 0.7261 (tt0) REVERT: D 369 LYS cc_start: 0.7801 (tttt) cc_final: 0.7508 (tttp) REVERT: D 375 LYS cc_start: 0.7566 (tttt) cc_final: 0.7064 (ttpt) REVERT: E 311 LYS cc_start: 0.8098 (ptmt) cc_final: 0.7542 (mttt) REVERT: E 317 LYS cc_start: 0.7709 (mttt) cc_final: 0.7295 (mtmt) REVERT: E 320 SER cc_start: 0.8310 (m) cc_final: 0.7932 (p) REVERT: E 338 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7314 (mt-10) REVERT: E 340 LYS cc_start: 0.7902 (mttt) cc_final: 0.7411 (mtpt) REVERT: E 347 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7959 (mptp) REVERT: E 372 GLU cc_start: 0.8294 (tt0) cc_final: 0.7918 (tt0) REVERT: F 317 LYS cc_start: 0.8038 (mttt) cc_final: 0.7525 (mtpt) REVERT: F 340 LYS cc_start: 0.8345 (tttt) cc_final: 0.7693 (tptm) REVERT: F 343 LYS cc_start: 0.7660 (ttmt) cc_final: 0.7020 (tptm) REVERT: F 351 GLN cc_start: 0.8122 (tt0) cc_final: 0.7837 (tt0) REVERT: F 369 LYS cc_start: 0.8165 (tttt) cc_final: 0.7713 (tttm) outliers start: 7 outliers final: 0 residues processed: 136 average time/residue: 1.3734 time to fit residues: 190.9741 Evaluate side-chains 129 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 125 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain E residue 347 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 3.9990 chunk 34 optimal weight: 0.0020 chunk 40 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 overall best weight: 4.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN C 307 GLN C 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3489 Z= 0.357 Angle : 0.608 6.656 4668 Z= 0.298 Chirality : 0.049 0.120 525 Planarity : 0.003 0.018 594 Dihedral : 4.940 12.470 462 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.80 % Allowed : 17.30 % 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: -1.85 (0.32), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.24), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 362 PHE 0.012 0.002 PHE C 346 TYR 0.008 0.002 TYR A 310 ARG 0.002 0.001 ARG C 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 139 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6428 (tt0) REVERT: A 347 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7568 (mptt) REVERT: A 353 LYS cc_start: 0.6743 (mttt) cc_final: 0.6427 (tttm) REVERT: A 375 LYS cc_start: 0.7916 (ttmt) cc_final: 0.7645 (ttpt) REVERT: B 317 LYS cc_start: 0.7652 (mttt) cc_final: 0.7063 (mtpt) REVERT: B 340 LYS cc_start: 0.7844 (tttt) cc_final: 0.7490 (tttm) REVERT: B 343 LYS cc_start: 0.7296 (tppt) cc_final: 0.6999 (tptm) REVERT: B 358 ASP cc_start: 0.8011 (m-30) cc_final: 0.7753 (m-30) REVERT: B 369 LYS cc_start: 0.7633 (tttt) cc_final: 0.7219 (tttm) REVERT: C 349 ARG cc_start: 0.6565 (mtm180) cc_final: 0.5688 (tpt90) REVERT: C 353 LYS cc_start: 0.6857 (mttt) cc_final: 0.6523 (tttp) REVERT: D 311 LYS cc_start: 0.7999 (mttt) cc_final: 0.6998 (mttm) REVERT: D 317 LYS cc_start: 0.7826 (mttt) cc_final: 0.7319 (mtpt) REVERT: D 340 LYS cc_start: 0.7904 (tttt) cc_final: 0.7611 (tttm) REVERT: D 343 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.5999 (tppt) REVERT: D 369 LYS cc_start: 0.7710 (tttt) cc_final: 0.7441 (tttp) REVERT: D 375 LYS cc_start: 0.7558 (tttt) cc_final: 0.7017 (ttpt) REVERT: E 311 LYS cc_start: 0.8171 (ptmt) cc_final: 0.7586 (mttt) REVERT: E 317 LYS cc_start: 0.7772 (mttt) cc_final: 0.7369 (mtmt) REVERT: E 320 SER cc_start: 0.8482 (m) cc_final: 0.7861 (p) REVERT: E 338 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7339 (mt-10) REVERT: E 340 LYS cc_start: 0.7870 (mttt) cc_final: 0.7344 (mtpt) REVERT: E 372 GLU cc_start: 0.8268 (tt0) cc_final: 0.8000 (mt-10) REVERT: F 311 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7672 (mtmt) REVERT: F 317 LYS cc_start: 0.8141 (mttt) cc_final: 0.7606 (mtpt) REVERT: F 340 LYS cc_start: 0.8420 (tttt) cc_final: 0.7677 (tptm) REVERT: F 343 LYS cc_start: 0.7638 (ttmt) cc_final: 0.7279 (tppt) REVERT: F 351 GLN cc_start: 0.8216 (tt0) cc_final: 0.7905 (tt0) REVERT: F 369 LYS cc_start: 0.8190 (tttt) cc_final: 0.7710 (tttm) REVERT: F 372 GLU cc_start: 0.8147 (tt0) cc_final: 0.7718 (tt0) outliers start: 11 outliers final: 3 residues processed: 128 average time/residue: 1.5543 time to fit residues: 203.0213 Evaluate side-chains 133 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 127 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 D residue 343 LYS Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 311 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN C 307 GLN C 351 GLN D 307 GLN F 307 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 3489 Z= 0.510 Angle : 0.684 7.642 4668 Z= 0.339 Chirality : 0.050 0.129 525 Planarity : 0.003 0.023 594 Dihedral : 5.259 13.857 462 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.05 % Allowed : 17.30 % Favored : 79.64 % 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: -2.04 (0.31), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.24), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 329 PHE 0.013 0.002 PHE C 346 TYR 0.019 0.003 TYR D 310 ARG 0.003 0.001 ARG C 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 140 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7024 (mttt) cc_final: 0.6742 (mttm) REVERT: A 347 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7584 (mptt) REVERT: A 353 LYS cc_start: 0.6735 (mttt) cc_final: 0.6447 (tttm) REVERT: A 375 LYS cc_start: 0.7947 (ttmt) cc_final: 0.7651 (ttpt) REVERT: B 317 LYS cc_start: 0.7652 (mttt) cc_final: 0.7048 (mtpt) REVERT: B 340 LYS cc_start: 0.7840 (tttt) cc_final: 0.7505 (tttm) REVERT: B 358 ASP cc_start: 0.8053 (m-30) cc_final: 0.7743 (m-30) REVERT: B 369 LYS cc_start: 0.7655 (tttt) cc_final: 0.7300 (tttm) REVERT: C 349 ARG cc_start: 0.6527 (mtm180) cc_final: 0.5699 (tpt90) REVERT: C 353 LYS cc_start: 0.6876 (mttt) cc_final: 0.6522 (tttp) REVERT: D 311 LYS cc_start: 0.8048 (mttt) cc_final: 0.7807 (mttt) REVERT: D 317 LYS cc_start: 0.7791 (mttt) cc_final: 0.7248 (mtpt) REVERT: D 340 LYS cc_start: 0.7824 (tttt) cc_final: 0.7584 (tttm) REVERT: D 369 LYS cc_start: 0.7710 (tttt) cc_final: 0.7430 (tttp) REVERT: D 375 LYS cc_start: 0.7587 (tttt) cc_final: 0.7041 (ttpt) REVERT: E 311 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7603 (mttt) REVERT: E 317 LYS cc_start: 0.7819 (mttt) cc_final: 0.7434 (mtmt) REVERT: E 338 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7346 (mt-10) REVERT: E 340 LYS cc_start: 0.7847 (mttt) cc_final: 0.7226 (mtpt) REVERT: E 372 GLU cc_start: 0.8260 (tt0) cc_final: 0.8018 (mt-10) REVERT: F 317 LYS cc_start: 0.8188 (mttt) cc_final: 0.7653 (mtpt) REVERT: F 340 LYS cc_start: 0.8438 (tttt) cc_final: 0.7713 (tptm) REVERT: F 343 LYS cc_start: 0.7568 (ttmt) cc_final: 0.7211 (tppt) REVERT: F 351 GLN cc_start: 0.8259 (tt0) cc_final: 0.7960 (tt0) REVERT: F 372 GLU cc_start: 0.8178 (tt0) cc_final: 0.7765 (tt0) outliers start: 12 outliers final: 3 residues processed: 128 average time/residue: 1.5704 time to fit residues: 205.0836 Evaluate side-chains 129 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 124 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 311 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: 7.9990 chunk 37 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN C 307 GLN C 351 GLN D 307 GLN E 351 GLN F 307 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3662 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= 0.249 Angle : 0.579 7.264 4668 Z= 0.279 Chirality : 0.049 0.121 525 Planarity : 0.003 0.020 594 Dihedral : 4.941 12.776 462 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.53 % Allowed : 19.08 % Favored : 79.39 % 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: -2.03 (0.31), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.24), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 329 PHE 0.008 0.002 PHE C 346 TYR 0.007 0.001 TYR F 310 ARG 0.002 0.001 ARG C 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 132 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7029 (mttt) cc_final: 0.6745 (mttm) REVERT: A 347 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7556 (mptt) REVERT: A 353 LYS cc_start: 0.6748 (mttt) cc_final: 0.6445 (tttm) REVERT: A 375 LYS cc_start: 0.7966 (ttmt) cc_final: 0.7663 (ttpt) REVERT: B 317 LYS cc_start: 0.7648 (mttt) cc_final: 0.7058 (mtpt) REVERT: B 340 LYS cc_start: 0.7791 (tttt) cc_final: 0.7447 (tttm) REVERT: B 343 LYS cc_start: 0.7204 (ttpt) cc_final: 0.6909 (tptm) REVERT: B 358 ASP cc_start: 0.8009 (m-30) cc_final: 0.7744 (m-30) REVERT: B 369 LYS cc_start: 0.7636 (tttt) cc_final: 0.7228 (tttm) REVERT: C 349 ARG cc_start: 0.6545 (mtm180) cc_final: 0.5699 (tpt90) REVERT: C 353 LYS cc_start: 0.6878 (mttt) cc_final: 0.6557 (tttp) REVERT: D 311 LYS cc_start: 0.8028 (mttt) cc_final: 0.7011 (mttm) REVERT: D 317 LYS cc_start: 0.7804 (mttt) cc_final: 0.7282 (mtpt) REVERT: D 340 LYS cc_start: 0.7912 (tttt) cc_final: 0.7628 (tttm) REVERT: D 369 LYS cc_start: 0.7751 (tttt) cc_final: 0.7456 (tttp) REVERT: D 375 LYS cc_start: 0.7605 (tttt) cc_final: 0.7061 (ttpt) REVERT: E 317 LYS cc_start: 0.7764 (mttt) cc_final: 0.7342 (mtmt) REVERT: E 338 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7333 (mt-10) REVERT: E 340 LYS cc_start: 0.7874 (mttt) cc_final: 0.7288 (mtpt) REVERT: E 369 LYS cc_start: 0.8243 (tttt) cc_final: 0.8018 (tttt) REVERT: E 372 GLU cc_start: 0.8271 (tt0) cc_final: 0.7928 (tt0) REVERT: F 317 LYS cc_start: 0.8136 (mttt) cc_final: 0.7586 (mtpt) REVERT: F 340 LYS cc_start: 0.8431 (tttt) cc_final: 0.7710 (tptm) REVERT: F 343 LYS cc_start: 0.7596 (ttmt) cc_final: 0.7332 (ttpt) REVERT: F 351 GLN cc_start: 0.8184 (tt0) cc_final: 0.7891 (tt0) outliers start: 6 outliers final: 3 residues processed: 126 average time/residue: 1.5555 time to fit residues: 199.9690 Evaluate side-chains 128 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 124 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 373 THR 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: 10.0000 chunk 26 optimal weight: 7.9990 chunk 35 optimal weight: 0.0370 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN C 307 GLN C 351 GLN D 307 GLN E 351 GLN F 307 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3489 Z= 0.224 Angle : 0.564 8.021 4668 Z= 0.270 Chirality : 0.049 0.120 525 Planarity : 0.003 0.020 594 Dihedral : 4.804 12.355 462 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.53 % Allowed : 19.34 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.32), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.24), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 329 PHE 0.008 0.001 PHE C 346 TYR 0.021 0.003 TYR D 310 ARG 0.002 0.000 ARG C 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 132 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7037 (mttt) cc_final: 0.6741 (mttm) REVERT: A 347 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7545 (mptt) REVERT: A 353 LYS cc_start: 0.6743 (mttt) cc_final: 0.6454 (tttm) REVERT: A 375 LYS cc_start: 0.7951 (ttmt) cc_final: 0.7657 (ttpt) REVERT: B 317 LYS cc_start: 0.7638 (mttt) cc_final: 0.7046 (mtpt) REVERT: B 340 LYS cc_start: 0.7793 (tttt) cc_final: 0.7452 (tttm) REVERT: B 343 LYS cc_start: 0.7255 (ttpt) cc_final: 0.6957 (tptm) REVERT: B 358 ASP cc_start: 0.8029 (m-30) cc_final: 0.7742 (m-30) REVERT: B 369 LYS cc_start: 0.7638 (tttt) cc_final: 0.7231 (tttm) REVERT: C 349 ARG cc_start: 0.6553 (mtm180) cc_final: 0.5693 (tpt90) REVERT: C 353 LYS cc_start: 0.6877 (mttt) cc_final: 0.6559 (tttp) REVERT: D 311 LYS cc_start: 0.8000 (mttt) cc_final: 0.7009 (mttm) REVERT: D 317 LYS cc_start: 0.7834 (mttt) cc_final: 0.7292 (mtpt) REVERT: D 340 LYS cc_start: 0.7931 (tttt) cc_final: 0.7634 (tttm) REVERT: D 343 LYS cc_start: 0.7487 (tppt) cc_final: 0.6029 (tppt) REVERT: D 375 LYS cc_start: 0.7608 (tttt) cc_final: 0.7070 (ttpt) REVERT: E 311 LYS cc_start: 0.8262 (pttt) cc_final: 0.7536 (mttt) REVERT: E 317 LYS cc_start: 0.7760 (mttt) cc_final: 0.7342 (mtmt) REVERT: E 320 SER cc_start: 0.8487 (m) cc_final: 0.7843 (p) REVERT: E 338 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7336 (mt-10) REVERT: E 340 LYS cc_start: 0.7880 (mttt) cc_final: 0.7302 (mtpt) REVERT: E 372 GLU cc_start: 0.8278 (tt0) cc_final: 0.7934 (tt0) REVERT: F 317 LYS cc_start: 0.8111 (mttt) cc_final: 0.7569 (mtpt) REVERT: F 340 LYS cc_start: 0.8417 (tttt) cc_final: 0.7694 (tptm) REVERT: F 343 LYS cc_start: 0.7601 (ttmt) cc_final: 0.7336 (ttpt) REVERT: F 351 GLN cc_start: 0.8168 (tt0) cc_final: 0.7916 (tt0) outliers start: 6 outliers final: 3 residues processed: 126 average time/residue: 1.5496 time to fit residues: 199.2476 Evaluate side-chains 129 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 125 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 373 THR 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: 7.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 28 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 0.0980 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN C 307 GLN C 351 GLN D 307 GLN E 351 GLN F 307 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.116214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.102518 restraints weight = 4075.689| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.45 r_work: 0.3345 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3489 Z= 0.220 Angle : 0.568 8.318 4668 Z= 0.271 Chirality : 0.049 0.120 525 Planarity : 0.002 0.019 594 Dihedral : 4.763 11.801 462 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.27 % Allowed : 20.10 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.32), residues: 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 0.000 HIS B 362 PHE 0.008 0.001 PHE C 346 TYR 0.021 0.002 TYR B 310 ARG 0.002 0.000 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3275.22 seconds wall clock time: 57 minutes 26.16 seconds (3446.16 seconds total)