Starting phenix.real_space_refine on Sun Aug 4 12:20:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bbl_44421/08_2024/9bbl_44421_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bbl_44421/08_2024/9bbl_44421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bbl_44421/08_2024/9bbl_44421.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bbl_44421/08_2024/9bbl_44421.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bbl_44421/08_2024/9bbl_44421_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bbl_44421/08_2024/9bbl_44421_neut.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 9 5.16 5 C 3198 2.51 5 N 936 2.21 5 O 951 1.98 5 H 5301 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 10395 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1121 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "B" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1121 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "E" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "G" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1121 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "H" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "I" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 4.93, per 1000 atoms: 0.47 Number of scatterers: 10395 At special positions: 0 Unit cell: (151.58, 134.62, 41.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 O 951 8.00 N 936 7.00 C 3198 6.00 H 5301 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.19 Conformation dependent library (CDL) restraints added in 1.0 seconds 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1170 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 25 sheets defined 0.0% alpha, 42.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.823A pdb=" N VAL A 313 " --> pdb=" O ASP G 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 317 through 321 removed outlier: 6.359A pdb=" N LYS A 317 " --> pdb=" O VAL G 318 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N SER G 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR A 319 " --> pdb=" O SER G 320 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 328 through 330 removed outlier: 6.561A pdb=" N HIS A 329 " --> pdb=" O HIS G 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 339 removed outlier: 6.437A pdb=" N GLN A 336 " --> pdb=" O VAL G 337 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N VAL G 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLU A 338 " --> pdb=" O VAL G 339 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 345 through 347 removed outlier: 6.431A pdb=" N PHE D 346 " --> pdb=" O LYS G 347 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 351 through 356 removed outlier: 6.836A pdb=" N SER G 356 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N SER D 352 " --> pdb=" O LYS G 353 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N GLY G 355 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ILE D 354 " --> pdb=" O GLY G 355 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 359 through 362 removed outlier: 6.252A pdb=" N ILE A 360 " --> pdb=" O THR G 361 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN D 359 " --> pdb=" O ILE G 360 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N HIS G 362 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR D 361 " --> pdb=" O HIS G 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 369 through 372 removed outlier: 6.737A pdb=" N LYS A 369 " --> pdb=" O LYS G 370 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N GLU G 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE A 371 " --> pdb=" O GLU G 372 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 306 through 308 Processing sheet with id=AB1, first strand: chain 'B' and resid 317 through 322 removed outlier: 6.377A pdb=" N LYS B 317 " --> pdb=" O VAL H 318 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N SER H 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR B 319 " --> pdb=" O SER H 320 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N CYS H 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LYS B 321 " --> pdb=" O CYS H 322 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 325 through 330 removed outlier: 8.725A pdb=" N LEU B 325 " --> pdb=" O GLY H 326 " (cutoff:3.500A) removed outlier: 9.780A pdb=" N ILE H 328 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASN B 327 " --> pdb=" O ILE H 328 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N HIS H 330 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N HIS B 329 " --> pdb=" O HIS H 330 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY E 326 " --> pdb=" O LEU H 325 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN H 327 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 336 through 340 removed outlier: 6.338A pdb=" N VAL E 337 " --> pdb=" O GLU H 338 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N LYS H 340 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL E 339 " --> pdb=" O LYS H 340 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 344 through 347 removed outlier: 6.695A pdb=" N LEU E 344 " --> pdb=" O ASP H 345 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LYS H 347 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE E 346 " --> pdb=" O LYS H 347 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 351 through 354 removed outlier: 6.448A pdb=" N GLN B 351 " --> pdb=" O SER H 352 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ILE H 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS B 353 " --> pdb=" O ILE H 354 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 357 through 362 removed outlier: 6.501A pdb=" N ASP B 358 " --> pdb=" O ASN H 359 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N THR H 361 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE B 360 " --> pdb=" O THR H 361 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 369 through 374 removed outlier: 6.634A pdb=" N LYS B 369 " --> pdb=" O LYS H 370 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N GLU H 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 371 " --> pdb=" O GLU H 372 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N HIS H 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N THR B 373 " --> pdb=" O HIS H 374 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 377 through 378 removed outlier: 6.394A pdb=" N THR B 377 " --> pdb=" O PHE H 378 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.567A pdb=" N GLN C 307 " --> pdb=" O ILE I 308 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TYR I 310 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL C 309 " --> pdb=" O TYR I 310 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL F 306 " --> pdb=" O GLN I 307 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N VAL I 309 " --> pdb=" O VAL F 306 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ILE F 308 " --> pdb=" O VAL I 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.399A pdb=" N LYS C 317 " --> pdb=" O VAL I 318 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N SER I 320 " --> pdb=" O LYS C 317 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR C 319 " --> pdb=" O SER I 320 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N CYS I 322 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LYS C 321 " --> pdb=" O CYS I 322 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 325 through 330 removed outlier: 8.706A pdb=" N LEU C 325 " --> pdb=" O GLY I 326 " (cutoff:3.500A) removed outlier: 9.917A pdb=" N ILE I 328 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASN C 327 " --> pdb=" O ILE I 328 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N HIS I 330 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N HIS C 329 " --> pdb=" O HIS I 330 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLY F 326 " --> pdb=" O LEU I 325 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN I 327 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 336 through 340 removed outlier: 6.430A pdb=" N VAL F 337 " --> pdb=" O GLU I 338 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N LYS I 340 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL F 339 " --> pdb=" O LYS I 340 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 344 through 347 removed outlier: 6.483A pdb=" N LEU F 344 " --> pdb=" O ASP I 345 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LYS I 347 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE F 346 " --> pdb=" O LYS I 347 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 350 through 356 removed outlier: 6.829A pdb=" N SER I 356 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL F 350 " --> pdb=" O GLN I 351 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LYS I 353 " --> pdb=" O VAL F 350 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER F 352 " --> pdb=" O LYS I 353 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N GLY I 355 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N ILE F 354 " --> pdb=" O GLY I 355 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 359 through 362 removed outlier: 6.553A pdb=" N ASN F 359 " --> pdb=" O ILE I 360 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N HIS I 362 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR F 361 " --> pdb=" O HIS I 362 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 369 through 377 91 hydrogen bonds defined for protein. 273 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: 3.06 Time building geometry restraints manager: 7.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.09: 5292 1.09 - 1.27: 846 1.27 - 1.45: 1242 1.45 - 1.63: 3087 1.63 - 1.81: 9 Bond restraints: 10476 Sorted by residual: bond pdb=" N THR G 361 " pdb=" H THR G 361 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" ND1 HIS D 330 " pdb=" HD1 HIS D 330 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CE2 PHE D 378 " pdb=" HE2 PHE D 378 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" CD1 PHE D 378 " pdb=" HD1 PHE D 378 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N SER D 324 " pdb=" H SER D 324 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 ... (remaining 10471 not shown) Histogram of bond angle deviations from ideal: 96.68 - 103.28: 48 103.28 - 109.88: 9141 109.88 - 116.47: 4651 116.47 - 123.07: 4460 123.07 - 129.67: 795 Bond angle restraints: 19095 Sorted by residual: angle pdb=" CA ASP D 358 " pdb=" CB ASP D 358 " pdb=" CG ASP D 358 " ideal model delta sigma weight residual 112.60 118.26 -5.66 1.00e+00 1.00e+00 3.20e+01 angle pdb=" C GLU C 342 " pdb=" CA GLU C 342 " pdb=" CB GLU C 342 " ideal model delta sigma weight residual 110.42 121.14 -10.72 1.99e+00 2.53e-01 2.90e+01 angle pdb=" CA PHE D 346 " pdb=" CB PHE D 346 " pdb=" CG PHE D 346 " ideal model delta sigma weight residual 113.80 119.17 -5.37 1.00e+00 1.00e+00 2.89e+01 angle pdb=" CA ASP G 358 " pdb=" CB ASP G 358 " pdb=" CG ASP G 358 " ideal model delta sigma weight residual 112.60 117.77 -5.17 1.00e+00 1.00e+00 2.67e+01 angle pdb=" CB HIS G 329 " pdb=" CG HIS G 329 " pdb=" CD2 HIS G 329 " ideal model delta sigma weight residual 131.20 124.51 6.69 1.30e+00 5.92e-01 2.65e+01 ... (remaining 19090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 4344 17.30 - 34.61: 233 34.61 - 51.91: 101 51.91 - 69.22: 143 69.22 - 86.52: 6 Dihedral angle restraints: 4827 sinusoidal: 2757 harmonic: 2070 Sorted by residual: dihedral pdb=" C GLU C 342 " pdb=" N GLU C 342 " pdb=" CA GLU C 342 " pdb=" CB GLU C 342 " ideal model delta harmonic sigma weight residual -122.60 -134.00 11.40 0 2.50e+00 1.60e-01 2.08e+01 dihedral pdb=" C GLU I 342 " pdb=" N GLU I 342 " pdb=" CA GLU I 342 " pdb=" CB GLU I 342 " ideal model delta harmonic sigma weight residual -122.60 -132.42 9.82 0 2.50e+00 1.60e-01 1.54e+01 dihedral pdb=" C ARG B 349 " pdb=" N ARG B 349 " pdb=" CA ARG B 349 " pdb=" CB ARG B 349 " ideal model delta harmonic sigma weight residual -122.60 -131.72 9.12 0 2.50e+00 1.60e-01 1.33e+01 ... (remaining 4824 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 463 0.081 - 0.161: 238 0.161 - 0.242: 63 0.242 - 0.323: 11 0.323 - 0.403: 5 Chirality restraints: 780 Sorted by residual: chirality pdb=" CA PRO I 332 " pdb=" N PRO I 332 " pdb=" C PRO I 332 " pdb=" CB PRO I 332 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" CA LEU A 325 " pdb=" N LEU A 325 " pdb=" C LEU A 325 " pdb=" CB LEU A 325 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CG LEU C 357 " pdb=" CB LEU C 357 " pdb=" CD1 LEU C 357 " pdb=" CD2 LEU C 357 " both_signs ideal model delta sigma weight residual False -2.59 -2.93 0.34 2.00e-01 2.50e+01 2.93e+00 ... (remaining 777 not shown) Planarity restraints: 1509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 329 " 0.040 2.00e-02 2.50e+03 6.00e-02 8.11e+01 pdb=" CG HIS B 329 " -0.118 2.00e-02 2.50e+03 pdb=" ND1 HIS B 329 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 HIS B 329 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 HIS B 329 " -0.013 2.00e-02 2.50e+03 pdb=" NE2 HIS B 329 " -0.022 2.00e-02 2.50e+03 pdb=" HD1 HIS B 329 " 0.058 2.00e-02 2.50e+03 pdb=" HD2 HIS B 329 " 0.091 2.00e-02 2.50e+03 pdb=" HE1 HIS B 329 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS H 329 " 0.045 2.00e-02 2.50e+03 5.67e-02 7.23e+01 pdb=" CG HIS H 329 " -0.131 2.00e-02 2.50e+03 pdb=" ND1 HIS H 329 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS H 329 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 HIS H 329 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS H 329 " -0.015 2.00e-02 2.50e+03 pdb=" HD1 HIS H 329 " 0.032 2.00e-02 2.50e+03 pdb=" HD2 HIS H 329 " 0.077 2.00e-02 2.50e+03 pdb=" HE1 HIS H 329 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 329 " -0.058 2.00e-02 2.50e+03 5.00e-02 5.62e+01 pdb=" CG HIS C 329 " 0.101 2.00e-02 2.50e+03 pdb=" ND1 HIS C 329 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 HIS C 329 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 HIS C 329 " 0.009 2.00e-02 2.50e+03 pdb=" NE2 HIS C 329 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 HIS C 329 " -0.032 2.00e-02 2.50e+03 pdb=" HD2 HIS C 329 " -0.054 2.00e-02 2.50e+03 pdb=" HE1 HIS C 329 " -0.045 2.00e-02 2.50e+03 ... (remaining 1506 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 542 2.15 - 2.76: 17211 2.76 - 3.37: 28116 3.37 - 3.99: 36273 3.99 - 4.60: 52416 Nonbonded interactions: 134558 Sorted by model distance: nonbonded pdb=" OD1 ASP G 314 " pdb=" HG SER G 316 " model vdw 1.532 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.539 2.450 nonbonded pdb=" OD1 ASP I 314 " pdb=" HG SER I 316 " model vdw 1.543 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.548 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.552 2.450 ... (remaining 134553 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' selection = (chain 'B' and resid 307 through 378) selection = (chain 'C' and resid 307 through 378) selection = chain 'D' selection = (chain 'E' and resid 307 through 378) selection = (chain 'F' and resid 307 through 378) selection = chain 'G' selection = (chain 'H' and resid 307 through 378) selection = (chain 'I' and resid 307 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: 3.970 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: 0.150 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 32.660 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6397 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 0.045 5175 Z= 0.738 Angle : 2.112 10.719 6924 Z= 1.371 Chirality : 0.102 0.403 780 Planarity : 0.013 0.110 879 Dihedral : 10.019 86.521 1986 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 0.19 Ramachandran Plot: Outliers : 1.39 % Allowed : 9.72 % Favored : 88.89 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.34 % 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: -2.48 (0.26), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.20), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.043 0.008 HIS H 329 PHE 0.027 0.010 PHE I 346 TYR 0.059 0.014 TYR B 310 ARG 0.009 0.002 ARG H 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.8083 (mtmt) cc_final: 0.6036 (tptp) REVERT: A 342 GLU cc_start: 0.7620 (mt-10) cc_final: 0.6624 (mp0) REVERT: A 343 LYS cc_start: 0.8253 (mttt) cc_final: 0.8044 (mtmt) REVERT: A 356 SER cc_start: 0.7966 (p) cc_final: 0.7681 (t) REVERT: A 358 ASP cc_start: 0.7916 (m-30) cc_final: 0.7523 (m-30) REVERT: B 307 GLN cc_start: 0.7736 (pt0) cc_final: 0.7487 (pt0) REVERT: B 311 LYS cc_start: 0.7880 (mttt) cc_final: 0.6900 (mmtm) REVERT: B 317 LYS cc_start: 0.7429 (mtmt) cc_final: 0.6527 (tttp) REVERT: B 321 LYS cc_start: 0.7563 (tttt) cc_final: 0.7139 (tmmm) REVERT: B 336 GLN cc_start: 0.7656 (mt0) cc_final: 0.7398 (mt0) REVERT: B 338 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6766 (mt-10) REVERT: B 340 LYS cc_start: 0.7572 (tttt) cc_final: 0.7152 (mtpp) REVERT: B 345 ASP cc_start: 0.7816 (t0) cc_final: 0.7469 (t0) REVERT: B 347 LYS cc_start: 0.7145 (mttp) cc_final: 0.6716 (mttp) REVERT: B 348 ASP cc_start: 0.7527 (t0) cc_final: 0.7217 (t0) REVERT: C 311 LYS cc_start: 0.7807 (mttt) cc_final: 0.6969 (mmtm) REVERT: C 321 LYS cc_start: 0.7327 (ttmt) cc_final: 0.6426 (tmtm) REVERT: C 331 LYS cc_start: 0.7388 (mttt) cc_final: 0.6965 (mtpt) REVERT: C 338 GLU cc_start: 0.7151 (tt0) cc_final: 0.6913 (tt0) REVERT: C 345 ASP cc_start: 0.8198 (t0) cc_final: 0.7530 (t0) REVERT: C 347 LYS cc_start: 0.7187 (mttt) cc_final: 0.6769 (mtpp) REVERT: C 348 ASP cc_start: 0.7867 (t0) cc_final: 0.7647 (t0) REVERT: C 372 GLU cc_start: 0.8161 (tt0) cc_final: 0.7899 (tt0) REVERT: D 311 LYS cc_start: 0.8118 (tttt) cc_final: 0.7580 (ttmp) REVERT: D 317 LYS cc_start: 0.8165 (mttt) cc_final: 0.7523 (mtpt) REVERT: D 321 LYS cc_start: 0.8220 (mttt) cc_final: 0.7463 (tptp) REVERT: D 331 LYS cc_start: 0.8116 (mtmt) cc_final: 0.7851 (mtpt) REVERT: D 340 LYS cc_start: 0.8093 (mttt) cc_final: 0.7431 (mttm) REVERT: D 341 SER cc_start: 0.8729 (m) cc_final: 0.8525 (m) REVERT: D 342 GLU cc_start: 0.7791 (mt-10) cc_final: 0.6985 (mp0) REVERT: D 343 LYS cc_start: 0.8306 (mttt) cc_final: 0.7838 (mttm) REVERT: D 347 LYS cc_start: 0.7821 (mttt) cc_final: 0.7319 (mtmm) REVERT: D 356 SER cc_start: 0.8138 (p) cc_final: 0.7878 (t) REVERT: D 358 ASP cc_start: 0.7682 (m-30) cc_final: 0.7250 (m-30) REVERT: D 369 LYS cc_start: 0.8145 (mttt) cc_final: 0.7845 (mttp) REVERT: D 372 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7603 (mt-10) REVERT: D 375 LYS cc_start: 0.8076 (ttpt) cc_final: 0.7831 (ttmt) REVERT: E 317 LYS cc_start: 0.7738 (mtmt) cc_final: 0.7509 (mtpm) REVERT: E 320 SER cc_start: 0.7993 (t) cc_final: 0.7773 (p) REVERT: E 321 LYS cc_start: 0.7950 (tttt) cc_final: 0.7587 (tmmt) REVERT: E 331 LYS cc_start: 0.8589 (mttt) cc_final: 0.8358 (mttp) REVERT: E 336 GLN cc_start: 0.8036 (mt0) cc_final: 0.7421 (mt0) REVERT: E 338 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7235 (tt0) REVERT: E 340 LYS cc_start: 0.7734 (tttt) cc_final: 0.7431 (tptp) REVERT: E 341 SER cc_start: 0.8173 (m) cc_final: 0.7835 (t) REVERT: E 342 GLU cc_start: 0.7662 (mt-10) cc_final: 0.6370 (mp0) REVERT: E 347 LYS cc_start: 0.7662 (mttp) cc_final: 0.7173 (mmtm) REVERT: E 369 LYS cc_start: 0.8492 (mttt) cc_final: 0.8172 (mttp) REVERT: F 311 LYS cc_start: 0.8344 (mttt) cc_final: 0.7480 (ttpp) REVERT: F 317 LYS cc_start: 0.7870 (pttt) cc_final: 0.7669 (ptmt) REVERT: F 342 GLU cc_start: 0.7678 (mt-10) cc_final: 0.6057 (mp0) REVERT: F 345 ASP cc_start: 0.8372 (t0) cc_final: 0.7979 (t0) REVERT: F 347 LYS cc_start: 0.7694 (mttt) cc_final: 0.6913 (mtmm) REVERT: F 349 ARG cc_start: 0.7266 (mtt180) cc_final: 0.6836 (mtp180) REVERT: F 353 LYS cc_start: 0.8380 (tttt) cc_final: 0.8022 (tttp) REVERT: F 369 LYS cc_start: 0.7983 (mttt) cc_final: 0.7404 (mtpp) REVERT: F 375 LYS cc_start: 0.8054 (tttt) cc_final: 0.7849 (ttmt) REVERT: G 311 LYS cc_start: 0.7831 (tttt) cc_final: 0.7403 (tppp) REVERT: G 317 LYS cc_start: 0.7457 (mttt) cc_final: 0.7166 (mtpm) REVERT: G 321 LYS cc_start: 0.7936 (mttt) cc_final: 0.7362 (mptt) REVERT: G 340 LYS cc_start: 0.7876 (mttt) cc_final: 0.6960 (mtpp) REVERT: G 342 GLU cc_start: 0.7607 (mt-10) cc_final: 0.6768 (mp0) REVERT: G 343 LYS cc_start: 0.8061 (mttt) cc_final: 0.7729 (mttp) REVERT: G 345 ASP cc_start: 0.7417 (m-30) cc_final: 0.7113 (m-30) REVERT: G 353 LYS cc_start: 0.7471 (mttt) cc_final: 0.7243 (mtmt) REVERT: G 356 SER cc_start: 0.8045 (p) cc_final: 0.7759 (p) REVERT: G 358 ASP cc_start: 0.7738 (m-30) cc_final: 0.7379 (m-30) REVERT: G 369 LYS cc_start: 0.7434 (mttt) cc_final: 0.7052 (mttp) REVERT: G 371 ILE cc_start: 0.8054 (mt) cc_final: 0.7747 (mp) REVERT: H 317 LYS cc_start: 0.7620 (mtmt) cc_final: 0.7378 (ttmm) REVERT: H 321 LYS cc_start: 0.7702 (tttt) cc_final: 0.7142 (mttp) REVERT: H 331 LYS cc_start: 0.8066 (mttt) cc_final: 0.7774 (mttp) REVERT: H 336 GLN cc_start: 0.7517 (mt0) cc_final: 0.6995 (mt0) REVERT: H 347 LYS cc_start: 0.7097 (mttp) cc_final: 0.6517 (mmtm) REVERT: H 356 SER cc_start: 0.8112 (m) cc_final: 0.7533 (p) REVERT: H 375 LYS cc_start: 0.7688 (tttt) cc_final: 0.7232 (tttm) REVERT: I 317 LYS cc_start: 0.7575 (pttt) cc_final: 0.7242 (pttt) REVERT: I 321 LYS cc_start: 0.7401 (ttmt) cc_final: 0.6922 (ttmm) REVERT: I 331 LYS cc_start: 0.7229 (mttt) cc_final: 0.6750 (mtpt) REVERT: I 338 GLU cc_start: 0.7508 (tt0) cc_final: 0.6791 (tt0) REVERT: I 347 LYS cc_start: 0.7326 (mttt) cc_final: 0.6226 (mmtm) REVERT: I 349 ARG cc_start: 0.7024 (mtt180) cc_final: 0.6545 (mtm180) REVERT: I 369 LYS cc_start: 0.7510 (mttt) cc_final: 0.6963 (mtpm) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 2.7365 time to fit residues: 735.8587 Evaluate side-chains 206 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN I 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5175 Z= 0.232 Angle : 0.714 5.357 6924 Z= 0.369 Chirality : 0.051 0.151 780 Planarity : 0.004 0.040 879 Dihedral : 6.450 18.856 681 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 0.34 % Allowed : 11.79 % Favored : 87.86 % 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: -2.68 (0.25), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.19), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS B 362 PHE 0.016 0.002 PHE E 378 TYR 0.007 0.001 TYR F 310 ARG 0.004 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 202 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.7676 (mt-10) cc_final: 0.6585 (mp0) REVERT: A 345 ASP cc_start: 0.7203 (t0) cc_final: 0.6534 (m-30) REVERT: B 311 LYS cc_start: 0.7920 (mttt) cc_final: 0.6948 (mmtm) REVERT: B 321 LYS cc_start: 0.7810 (tttt) cc_final: 0.7228 (tmmm) REVERT: B 336 GLN cc_start: 0.7681 (mt0) cc_final: 0.7441 (mt0) REVERT: B 338 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6546 (tt0) REVERT: B 340 LYS cc_start: 0.7582 (tttt) cc_final: 0.7267 (mtpp) REVERT: B 348 ASP cc_start: 0.7932 (t0) cc_final: 0.7435 (t0) REVERT: B 375 LYS cc_start: 0.7684 (tttt) cc_final: 0.7478 (ttpp) REVERT: C 311 LYS cc_start: 0.7920 (mttt) cc_final: 0.7070 (mmtm) REVERT: C 321 LYS cc_start: 0.7541 (ttmt) cc_final: 0.6627 (tmtm) REVERT: C 331 LYS cc_start: 0.7355 (mttt) cc_final: 0.6930 (mtpt) REVERT: C 338 GLU cc_start: 0.7149 (tt0) cc_final: 0.6858 (tt0) REVERT: C 345 ASP cc_start: 0.7706 (t0) cc_final: 0.6782 (t0) REVERT: C 347 LYS cc_start: 0.7031 (mttt) cc_final: 0.6620 (mtpp) REVERT: C 348 ASP cc_start: 0.7827 (t0) cc_final: 0.7615 (t0) REVERT: C 351 GLN cc_start: 0.7659 (mt0) cc_final: 0.7425 (mt0) REVERT: C 369 LYS cc_start: 0.7716 (mttt) cc_final: 0.7324 (ttmm) REVERT: D 311 LYS cc_start: 0.8154 (tttt) cc_final: 0.7613 (ttmp) REVERT: D 317 LYS cc_start: 0.8029 (mttt) cc_final: 0.7357 (mtpt) REVERT: D 321 LYS cc_start: 0.8132 (mttt) cc_final: 0.7393 (tptp) REVERT: D 340 LYS cc_start: 0.8334 (mttt) cc_final: 0.7917 (mttm) REVERT: D 341 SER cc_start: 0.8698 (m) cc_final: 0.8431 (m) REVERT: D 342 GLU cc_start: 0.7714 (mt-10) cc_final: 0.6822 (mp0) REVERT: D 343 LYS cc_start: 0.8194 (mttt) cc_final: 0.7812 (mttm) REVERT: D 369 LYS cc_start: 0.8171 (mttt) cc_final: 0.7864 (mttp) REVERT: E 317 LYS cc_start: 0.7647 (mtmt) cc_final: 0.7365 (mtpm) REVERT: E 320 SER cc_start: 0.7860 (t) cc_final: 0.7464 (p) REVERT: E 321 LYS cc_start: 0.7981 (tttt) cc_final: 0.7659 (tmmt) REVERT: E 336 GLN cc_start: 0.8043 (mt0) cc_final: 0.7433 (mt0) REVERT: E 338 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7130 (tt0) REVERT: E 340 LYS cc_start: 0.7803 (tttt) cc_final: 0.7468 (tptp) REVERT: E 347 LYS cc_start: 0.7505 (mttp) cc_final: 0.6944 (mmtm) REVERT: E 356 SER cc_start: 0.8238 (m) cc_final: 0.7915 (p) REVERT: E 369 LYS cc_start: 0.8528 (mttt) cc_final: 0.8213 (mttp) REVERT: E 379 ARG cc_start: 0.5251 (pmt170) cc_final: 0.4836 (pmt-80) REVERT: F 311 LYS cc_start: 0.8367 (mttt) cc_final: 0.7425 (ttpp) REVERT: F 338 GLU cc_start: 0.7641 (tt0) cc_final: 0.7395 (tt0) REVERT: F 345 ASP cc_start: 0.8011 (t0) cc_final: 0.7662 (t0) REVERT: F 349 ARG cc_start: 0.7168 (mtt180) cc_final: 0.6833 (mtp180) REVERT: F 353 LYS cc_start: 0.8309 (tttt) cc_final: 0.7908 (tttt) REVERT: F 369 LYS cc_start: 0.7975 (mttt) cc_final: 0.7410 (mtpp) REVERT: F 373 THR cc_start: 0.8326 (m) cc_final: 0.7995 (p) REVERT: G 311 LYS cc_start: 0.7784 (tttt) cc_final: 0.7509 (tttm) REVERT: G 317 LYS cc_start: 0.7413 (mttt) cc_final: 0.7179 (mtpm) REVERT: G 321 LYS cc_start: 0.7794 (mttt) cc_final: 0.7214 (mptt) REVERT: G 340 LYS cc_start: 0.7919 (mttt) cc_final: 0.7140 (mttm) REVERT: G 342 GLU cc_start: 0.7664 (mt-10) cc_final: 0.6694 (mp0) REVERT: G 343 LYS cc_start: 0.7818 (mttt) cc_final: 0.7601 (mttp) REVERT: G 353 LYS cc_start: 0.7577 (mttt) cc_final: 0.7258 (mtmt) REVERT: G 356 SER cc_start: 0.8213 (p) cc_final: 0.7887 (t) REVERT: G 369 LYS cc_start: 0.7405 (mttt) cc_final: 0.7007 (mttp) REVERT: G 371 ILE cc_start: 0.7896 (mt) cc_final: 0.7587 (mp) REVERT: H 317 LYS cc_start: 0.7587 (mtmt) cc_final: 0.7309 (mtpm) REVERT: H 321 LYS cc_start: 0.7747 (tttt) cc_final: 0.7052 (mptp) REVERT: H 331 LYS cc_start: 0.7976 (mttt) cc_final: 0.7682 (mttp) REVERT: H 336 GLN cc_start: 0.7575 (mt0) cc_final: 0.7033 (mt0) REVERT: H 338 GLU cc_start: 0.7030 (mt-10) cc_final: 0.6350 (mt-10) REVERT: H 341 SER cc_start: 0.7772 (m) cc_final: 0.7316 (t) REVERT: H 347 LYS cc_start: 0.7110 (mttp) cc_final: 0.6489 (mmtm) REVERT: H 356 SER cc_start: 0.7946 (m) cc_final: 0.7511 (t) REVERT: H 358 ASP cc_start: 0.6856 (m-30) cc_final: 0.6529 (m-30) REVERT: I 311 LYS cc_start: 0.7549 (mtpt) cc_final: 0.6584 (tttp) REVERT: I 317 LYS cc_start: 0.7634 (pttt) cc_final: 0.7266 (ptpp) REVERT: I 321 LYS cc_start: 0.7320 (ttmt) cc_final: 0.6821 (ttmm) REVERT: I 331 LYS cc_start: 0.6996 (mttt) cc_final: 0.6430 (mtpt) REVERT: I 341 SER cc_start: 0.7615 (p) cc_final: 0.7271 (t) REVERT: I 347 LYS cc_start: 0.7358 (mttt) cc_final: 0.6231 (mmtm) REVERT: I 349 ARG cc_start: 0.6863 (mtt180) cc_final: 0.6425 (mtm180) REVERT: I 369 LYS cc_start: 0.7466 (mttt) cc_final: 0.7167 (ttmm) outliers start: 2 outliers final: 1 residues processed: 203 average time/residue: 2.9482 time to fit residues: 617.6293 Evaluate side-chains 183 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 182 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 315 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 351 GLN C 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5175 Z= 0.192 Angle : 0.568 4.703 6924 Z= 0.291 Chirality : 0.051 0.137 780 Planarity : 0.003 0.036 879 Dihedral : 6.196 17.613 681 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 0.68 % Allowed : 13.50 % Favored : 85.81 % 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: -2.65 (0.25), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.19), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS H 329 PHE 0.004 0.001 PHE D 346 TYR 0.008 0.001 TYR F 310 ARG 0.004 0.001 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 186 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.7662 (mt-10) cc_final: 0.6538 (mp0) REVERT: A 345 ASP cc_start: 0.6852 (t0) cc_final: 0.6543 (m-30) REVERT: B 311 LYS cc_start: 0.7997 (mttt) cc_final: 0.7010 (mmtm) REVERT: B 321 LYS cc_start: 0.7783 (tttt) cc_final: 0.7208 (tmmm) REVERT: B 336 GLN cc_start: 0.7658 (mt0) cc_final: 0.7422 (mt0) REVERT: B 338 GLU cc_start: 0.7296 (mt-10) cc_final: 0.6606 (tt0) REVERT: B 340 LYS cc_start: 0.7521 (tttt) cc_final: 0.7184 (mtpp) REVERT: B 347 LYS cc_start: 0.6990 (mttp) cc_final: 0.6466 (mttp) REVERT: B 348 ASP cc_start: 0.7646 (t0) cc_final: 0.7350 (t70) REVERT: B 356 SER cc_start: 0.8297 (m) cc_final: 0.7796 (t) REVERT: B 358 ASP cc_start: 0.6958 (m-30) cc_final: 0.6633 (m-30) REVERT: B 375 LYS cc_start: 0.7721 (tttt) cc_final: 0.7454 (ttpp) REVERT: C 311 LYS cc_start: 0.7898 (mttt) cc_final: 0.7026 (mmtm) REVERT: C 321 LYS cc_start: 0.7417 (ttmt) cc_final: 0.6495 (tmtm) REVERT: C 331 LYS cc_start: 0.7314 (mttt) cc_final: 0.6871 (mtpt) REVERT: C 338 GLU cc_start: 0.7163 (tt0) cc_final: 0.6868 (tt0) REVERT: C 345 ASP cc_start: 0.7653 (t0) cc_final: 0.6775 (t0) REVERT: C 347 LYS cc_start: 0.7027 (mttt) cc_final: 0.6643 (mtpp) REVERT: C 369 LYS cc_start: 0.7723 (mttt) cc_final: 0.7349 (ttmm) REVERT: D 311 LYS cc_start: 0.8146 (tttt) cc_final: 0.7620 (ttmp) REVERT: D 314 ASP cc_start: 0.8440 (t0) cc_final: 0.8077 (t0) REVERT: D 317 LYS cc_start: 0.7973 (mttt) cc_final: 0.7331 (mtpt) REVERT: D 321 LYS cc_start: 0.8107 (mttt) cc_final: 0.7355 (tptp) REVERT: D 340 LYS cc_start: 0.8329 (mttt) cc_final: 0.7927 (mttm) REVERT: D 341 SER cc_start: 0.8688 (m) cc_final: 0.8452 (m) REVERT: D 342 GLU cc_start: 0.7739 (mt-10) cc_final: 0.6858 (mp0) REVERT: D 343 LYS cc_start: 0.8169 (mttt) cc_final: 0.7860 (mttm) REVERT: D 347 LYS cc_start: 0.7976 (mtpt) cc_final: 0.7683 (mtmp) REVERT: D 369 LYS cc_start: 0.8120 (mttt) cc_final: 0.7793 (mttp) REVERT: D 378 PHE cc_start: 0.5571 (t80) cc_final: 0.5307 (m-80) REVERT: E 317 LYS cc_start: 0.7678 (mtmt) cc_final: 0.7464 (mtpm) REVERT: E 320 SER cc_start: 0.7832 (t) cc_final: 0.7355 (p) REVERT: E 321 LYS cc_start: 0.8059 (tttt) cc_final: 0.7662 (tmmt) REVERT: E 336 GLN cc_start: 0.7976 (mt0) cc_final: 0.7364 (mt0) REVERT: E 338 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7190 (tt0) REVERT: E 340 LYS cc_start: 0.7921 (tttt) cc_final: 0.7534 (tptp) REVERT: E 342 GLU cc_start: 0.7551 (mt-10) cc_final: 0.6203 (mp0) REVERT: E 347 LYS cc_start: 0.7543 (mttp) cc_final: 0.6898 (mmtm) REVERT: E 356 SER cc_start: 0.8254 (m) cc_final: 0.7885 (t) REVERT: E 369 LYS cc_start: 0.8511 (mttt) cc_final: 0.8158 (mttp) REVERT: F 311 LYS cc_start: 0.8377 (mttt) cc_final: 0.6612 (pmtt) REVERT: F 338 GLU cc_start: 0.7638 (tt0) cc_final: 0.7365 (tt0) REVERT: F 345 ASP cc_start: 0.7949 (t0) cc_final: 0.7539 (t0) REVERT: F 349 ARG cc_start: 0.7204 (mtt180) cc_final: 0.6749 (mtm180) REVERT: F 353 LYS cc_start: 0.8272 (tttt) cc_final: 0.7879 (tttp) REVERT: F 369 LYS cc_start: 0.7975 (mttt) cc_final: 0.7416 (mtpp) REVERT: F 373 THR cc_start: 0.8380 (m) cc_final: 0.8043 (p) REVERT: G 311 LYS cc_start: 0.7762 (tttt) cc_final: 0.7497 (tttm) REVERT: G 317 LYS cc_start: 0.7447 (mttt) cc_final: 0.7160 (mtpm) REVERT: G 321 LYS cc_start: 0.7780 (mttt) cc_final: 0.7490 (mttm) REVERT: G 340 LYS cc_start: 0.7894 (mttt) cc_final: 0.7329 (mttm) REVERT: G 342 GLU cc_start: 0.7652 (mt-10) cc_final: 0.6679 (mp0) REVERT: G 343 LYS cc_start: 0.7790 (mttt) cc_final: 0.7494 (mttp) REVERT: G 345 ASP cc_start: 0.7554 (m-30) cc_final: 0.7322 (m-30) REVERT: G 349 ARG cc_start: 0.7183 (mtm180) cc_final: 0.6459 (mtm180) REVERT: G 353 LYS cc_start: 0.7563 (mttt) cc_final: 0.7196 (mtmt) REVERT: G 356 SER cc_start: 0.8143 (p) cc_final: 0.7832 (t) REVERT: G 369 LYS cc_start: 0.7409 (mttt) cc_final: 0.7065 (mttp) REVERT: G 371 ILE cc_start: 0.7895 (mt) cc_final: 0.7600 (mp) REVERT: H 321 LYS cc_start: 0.7748 (tttt) cc_final: 0.7005 (mptp) REVERT: H 331 LYS cc_start: 0.7960 (mttt) cc_final: 0.7702 (mttp) REVERT: H 336 GLN cc_start: 0.7565 (mt0) cc_final: 0.7028 (mt0) REVERT: H 338 GLU cc_start: 0.7039 (mt-10) cc_final: 0.6371 (mt-10) REVERT: H 341 SER cc_start: 0.7848 (m) cc_final: 0.7451 (t) REVERT: H 347 LYS cc_start: 0.7117 (mttp) cc_final: 0.6453 (mmtm) REVERT: H 356 SER cc_start: 0.8042 (m) cc_final: 0.7620 (t) REVERT: H 358 ASP cc_start: 0.6853 (m-30) cc_final: 0.6558 (m-30) REVERT: H 375 LYS cc_start: 0.7837 (tttt) cc_final: 0.7422 (tttm) REVERT: I 311 LYS cc_start: 0.7371 (mtpt) cc_final: 0.6572 (tttp) REVERT: I 317 LYS cc_start: 0.7655 (pttt) cc_final: 0.7300 (ptpp) REVERT: I 321 LYS cc_start: 0.7327 (ttmt) cc_final: 0.6811 (ttmm) REVERT: I 331 LYS cc_start: 0.6990 (mttt) cc_final: 0.6423 (mtpt) REVERT: I 341 SER cc_start: 0.7589 (p) cc_final: 0.7287 (t) REVERT: I 347 LYS cc_start: 0.7124 (mttt) cc_final: 0.5970 (mmtm) REVERT: I 349 ARG cc_start: 0.6823 (mtt180) cc_final: 0.6446 (mtm180) REVERT: I 369 LYS cc_start: 0.7464 (mttt) cc_final: 0.7193 (ttmm) outliers start: 4 outliers final: 0 residues processed: 189 average time/residue: 3.0137 time to fit residues: 588.6134 Evaluate side-chains 181 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 30 optimal weight: 0.0050 chunk 54 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 351 GLN C 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5175 Z= 0.256 Angle : 0.586 5.343 6924 Z= 0.299 Chirality : 0.050 0.153 780 Planarity : 0.004 0.040 879 Dihedral : 6.164 17.840 681 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.68 % Allowed : 14.36 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.25), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.19), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS B 362 PHE 0.005 0.001 PHE D 378 TYR 0.009 0.002 TYR E 310 ARG 0.003 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 191 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8504 (mp) cc_final: 0.8292 (mp) REVERT: A 342 GLU cc_start: 0.7662 (mt-10) cc_final: 0.6375 (mp0) REVERT: A 378 PHE cc_start: 0.5474 (t80) cc_final: 0.5202 (m-80) REVERT: B 311 LYS cc_start: 0.8127 (mttt) cc_final: 0.7071 (mmtm) REVERT: B 321 LYS cc_start: 0.7851 (tttt) cc_final: 0.7284 (tmmm) REVERT: B 336 GLN cc_start: 0.7685 (mt0) cc_final: 0.7448 (mt0) REVERT: B 338 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6581 (tt0) REVERT: B 340 LYS cc_start: 0.7524 (tttt) cc_final: 0.7226 (mtpp) REVERT: B 347 LYS cc_start: 0.6934 (mttp) cc_final: 0.6405 (mttp) REVERT: B 348 ASP cc_start: 0.7585 (t0) cc_final: 0.7304 (t70) REVERT: B 356 SER cc_start: 0.8510 (m) cc_final: 0.7980 (t) REVERT: B 358 ASP cc_start: 0.6876 (m-30) cc_final: 0.6559 (m-30) REVERT: B 375 LYS cc_start: 0.7793 (tttt) cc_final: 0.7466 (ttpp) REVERT: B 379 ARG cc_start: 0.6383 (ttp-110) cc_final: 0.5964 (mtt90) REVERT: C 311 LYS cc_start: 0.7949 (mttt) cc_final: 0.7060 (mmtm) REVERT: C 321 LYS cc_start: 0.7360 (ttmt) cc_final: 0.6451 (tmtm) REVERT: C 331 LYS cc_start: 0.7272 (mttt) cc_final: 0.6808 (mtpt) REVERT: C 338 GLU cc_start: 0.7126 (tt0) cc_final: 0.6827 (tt0) REVERT: C 345 ASP cc_start: 0.7581 (t0) cc_final: 0.6750 (t70) REVERT: C 347 LYS cc_start: 0.6932 (mttt) cc_final: 0.6583 (mtpp) REVERT: C 369 LYS cc_start: 0.7707 (mttt) cc_final: 0.7269 (ttmm) REVERT: D 311 LYS cc_start: 0.8228 (tttt) cc_final: 0.7712 (ttmp) REVERT: D 317 LYS cc_start: 0.7928 (mttt) cc_final: 0.7411 (mtpt) REVERT: D 321 LYS cc_start: 0.8167 (mttt) cc_final: 0.7363 (tptp) REVERT: D 340 LYS cc_start: 0.8309 (mttt) cc_final: 0.7998 (mttm) REVERT: D 343 LYS cc_start: 0.8250 (mttt) cc_final: 0.7932 (mttm) REVERT: D 347 LYS cc_start: 0.7962 (mtpt) cc_final: 0.7721 (mtpt) REVERT: D 369 LYS cc_start: 0.8099 (mttt) cc_final: 0.7773 (mttp) REVERT: E 317 LYS cc_start: 0.7744 (mtmt) cc_final: 0.7493 (mtpm) REVERT: E 320 SER cc_start: 0.7895 (t) cc_final: 0.7509 (p) REVERT: E 321 LYS cc_start: 0.8050 (tttt) cc_final: 0.7606 (tmmt) REVERT: E 336 GLN cc_start: 0.7963 (mt0) cc_final: 0.7467 (mt0) REVERT: E 338 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7211 (tt0) REVERT: E 340 LYS cc_start: 0.7939 (tttt) cc_final: 0.7551 (tptp) REVERT: E 342 GLU cc_start: 0.7572 (mt-10) cc_final: 0.6181 (mp0) REVERT: E 347 LYS cc_start: 0.7503 (mttp) cc_final: 0.6902 (mmtm) REVERT: E 356 SER cc_start: 0.8471 (m) cc_final: 0.8088 (t) REVERT: E 369 LYS cc_start: 0.8545 (mttt) cc_final: 0.8159 (mttp) REVERT: E 372 GLU cc_start: 0.7628 (tt0) cc_final: 0.7316 (tt0) REVERT: F 311 LYS cc_start: 0.8313 (mttt) cc_final: 0.6719 (pmtt) REVERT: F 338 GLU cc_start: 0.7706 (tt0) cc_final: 0.7342 (tt0) REVERT: F 349 ARG cc_start: 0.7229 (mtt180) cc_final: 0.6691 (mtm180) REVERT: F 353 LYS cc_start: 0.8252 (tttt) cc_final: 0.7868 (tttt) REVERT: G 311 LYS cc_start: 0.7685 (tttt) cc_final: 0.7451 (tttm) REVERT: G 317 LYS cc_start: 0.7389 (mttt) cc_final: 0.7108 (mtpm) REVERT: G 321 LYS cc_start: 0.7765 (mttt) cc_final: 0.7499 (mttm) REVERT: G 340 LYS cc_start: 0.7838 (mttt) cc_final: 0.7443 (mttm) REVERT: G 342 GLU cc_start: 0.7578 (mt-10) cc_final: 0.6642 (mp0) REVERT: G 343 LYS cc_start: 0.7785 (mttt) cc_final: 0.7505 (mttp) REVERT: G 349 ARG cc_start: 0.7241 (mtm180) cc_final: 0.6439 (mtm180) REVERT: G 353 LYS cc_start: 0.7519 (mttt) cc_final: 0.7236 (mtpt) REVERT: G 356 SER cc_start: 0.8198 (p) cc_final: 0.7778 (t) REVERT: G 369 LYS cc_start: 0.7411 (mttt) cc_final: 0.7069 (mttp) REVERT: G 371 ILE cc_start: 0.7844 (mt) cc_final: 0.7555 (mp) REVERT: H 321 LYS cc_start: 0.7833 (tttt) cc_final: 0.7039 (mptp) REVERT: H 331 LYS cc_start: 0.7909 (mttt) cc_final: 0.7667 (mttp) REVERT: H 336 GLN cc_start: 0.7654 (mt0) cc_final: 0.7098 (mt0) REVERT: H 341 SER cc_start: 0.7897 (m) cc_final: 0.7507 (t) REVERT: H 345 ASP cc_start: 0.7830 (t0) cc_final: 0.7223 (t70) REVERT: H 347 LYS cc_start: 0.7055 (mttp) cc_final: 0.6399 (mmtm) REVERT: H 356 SER cc_start: 0.8307 (m) cc_final: 0.7883 (t) REVERT: H 358 ASP cc_start: 0.6961 (m-30) cc_final: 0.6647 (m-30) REVERT: H 375 LYS cc_start: 0.7800 (tttt) cc_final: 0.7349 (tttm) REVERT: I 311 LYS cc_start: 0.7353 (mtpt) cc_final: 0.6573 (tttp) REVERT: I 317 LYS cc_start: 0.7657 (pttt) cc_final: 0.7359 (ptmt) REVERT: I 321 LYS cc_start: 0.7336 (ttmt) cc_final: 0.6831 (ttmm) REVERT: I 331 LYS cc_start: 0.6931 (mttt) cc_final: 0.6297 (mtpt) REVERT: I 338 GLU cc_start: 0.7769 (tt0) cc_final: 0.7438 (tt0) REVERT: I 341 SER cc_start: 0.7588 (p) cc_final: 0.7268 (t) REVERT: I 347 LYS cc_start: 0.6996 (mttt) cc_final: 0.5838 (mmtm) REVERT: I 349 ARG cc_start: 0.6880 (mtt180) cc_final: 0.6446 (mtm180) REVERT: I 369 LYS cc_start: 0.7489 (mttt) cc_final: 0.7204 (ttmm) outliers start: 4 outliers final: 1 residues processed: 193 average time/residue: 2.9319 time to fit residues: 584.3250 Evaluate side-chains 182 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 181 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 345 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 351 GLN C 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5175 Z= 0.272 Angle : 0.571 4.807 6924 Z= 0.294 Chirality : 0.049 0.133 780 Planarity : 0.004 0.039 879 Dihedral : 6.162 17.507 681 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 1.37 % Allowed : 14.87 % Favored : 83.76 % 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: -2.80 (0.26), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.19), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 362 PHE 0.015 0.001 PHE E 378 TYR 0.009 0.002 TYR B 310 ARG 0.003 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 188 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7834 (mttt) cc_final: 0.7190 (mttp) REVERT: A 342 GLU cc_start: 0.7623 (mt-10) cc_final: 0.6374 (mp0) REVERT: B 311 LYS cc_start: 0.8174 (mttt) cc_final: 0.7052 (mmtm) REVERT: B 321 LYS cc_start: 0.7837 (tttt) cc_final: 0.7204 (tmmt) REVERT: B 338 GLU cc_start: 0.7264 (mt-10) cc_final: 0.6548 (tt0) REVERT: B 340 LYS cc_start: 0.7528 (tttt) cc_final: 0.7207 (mtpp) REVERT: B 347 LYS cc_start: 0.6936 (mttp) cc_final: 0.6467 (mttp) REVERT: B 348 ASP cc_start: 0.7375 (t0) cc_final: 0.7102 (t70) REVERT: B 356 SER cc_start: 0.8505 (m) cc_final: 0.7964 (t) REVERT: B 375 LYS cc_start: 0.7903 (tttt) cc_final: 0.7538 (ttpp) REVERT: C 311 LYS cc_start: 0.7966 (mttt) cc_final: 0.7083 (mmtm) REVERT: C 321 LYS cc_start: 0.7345 (ttmt) cc_final: 0.6426 (tmtm) REVERT: C 331 LYS cc_start: 0.7351 (mttt) cc_final: 0.6861 (mtpt) REVERT: C 338 GLU cc_start: 0.7116 (tt0) cc_final: 0.6786 (tt0) REVERT: C 345 ASP cc_start: 0.7530 (t0) cc_final: 0.6838 (t70) REVERT: C 347 LYS cc_start: 0.7016 (mttt) cc_final: 0.6660 (mtpp) REVERT: D 311 LYS cc_start: 0.8243 (tttt) cc_final: 0.7774 (ttmt) REVERT: D 317 LYS cc_start: 0.7848 (mttt) cc_final: 0.7290 (mtpt) REVERT: D 321 LYS cc_start: 0.8305 (mttt) cc_final: 0.7429 (tptm) REVERT: D 340 LYS cc_start: 0.8295 (mttt) cc_final: 0.8009 (mttm) REVERT: D 343 LYS cc_start: 0.8237 (mttt) cc_final: 0.7933 (mttm) REVERT: D 347 LYS cc_start: 0.7932 (mtpt) cc_final: 0.7716 (mtpt) REVERT: D 369 LYS cc_start: 0.8060 (mttt) cc_final: 0.7584 (mmtp) REVERT: E 317 LYS cc_start: 0.7762 (mtmt) cc_final: 0.7474 (mtpm) REVERT: E 320 SER cc_start: 0.7837 (t) cc_final: 0.7435 (p) REVERT: E 321 LYS cc_start: 0.8035 (tttt) cc_final: 0.7598 (tmmt) REVERT: E 336 GLN cc_start: 0.7984 (mt0) cc_final: 0.7481 (mt0) REVERT: E 338 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7256 (tt0) REVERT: E 340 LYS cc_start: 0.7905 (tttt) cc_final: 0.7427 (tptp) REVERT: E 342 GLU cc_start: 0.7536 (mt-10) cc_final: 0.6074 (mp0) REVERT: E 347 LYS cc_start: 0.7601 (mttp) cc_final: 0.7013 (mmtm) REVERT: E 369 LYS cc_start: 0.8595 (mttt) cc_final: 0.8226 (mttp) REVERT: E 379 ARG cc_start: 0.5781 (OUTLIER) cc_final: 0.3211 (ptt90) REVERT: F 311 LYS cc_start: 0.8309 (mttt) cc_final: 0.6760 (pmtt) REVERT: F 338 GLU cc_start: 0.7599 (tt0) cc_final: 0.7344 (tt0) REVERT: F 347 LYS cc_start: 0.7644 (mttt) cc_final: 0.7332 (mtmm) REVERT: F 349 ARG cc_start: 0.7278 (mtt180) cc_final: 0.6736 (mtm180) REVERT: F 353 LYS cc_start: 0.8253 (tttt) cc_final: 0.7873 (tttt) REVERT: G 317 LYS cc_start: 0.7351 (mttt) cc_final: 0.7044 (mtpm) REVERT: G 321 LYS cc_start: 0.7763 (mttt) cc_final: 0.6913 (mtpp) REVERT: G 340 LYS cc_start: 0.7871 (mttt) cc_final: 0.7197 (mttp) REVERT: G 342 GLU cc_start: 0.7630 (mt-10) cc_final: 0.6659 (mp0) REVERT: G 343 LYS cc_start: 0.7727 (mttt) cc_final: 0.7508 (mttp) REVERT: G 349 ARG cc_start: 0.7157 (mtm180) cc_final: 0.6400 (mtm180) REVERT: G 353 LYS cc_start: 0.7477 (mttt) cc_final: 0.7208 (mtmt) REVERT: G 356 SER cc_start: 0.8191 (p) cc_final: 0.7748 (t) REVERT: G 369 LYS cc_start: 0.7417 (mttt) cc_final: 0.7099 (mttp) REVERT: G 371 ILE cc_start: 0.7829 (mt) cc_final: 0.7522 (mp) REVERT: H 321 LYS cc_start: 0.7922 (tttt) cc_final: 0.7030 (mttp) REVERT: H 331 LYS cc_start: 0.7988 (mttt) cc_final: 0.7708 (mttp) REVERT: H 336 GLN cc_start: 0.7719 (mt0) cc_final: 0.7185 (mt0) REVERT: H 341 SER cc_start: 0.7846 (m) cc_final: 0.7462 (t) REVERT: H 347 LYS cc_start: 0.6994 (mttp) cc_final: 0.6306 (mmtm) REVERT: H 356 SER cc_start: 0.8259 (m) cc_final: 0.7842 (t) REVERT: H 358 ASP cc_start: 0.6937 (m-30) cc_final: 0.6725 (m-30) REVERT: H 375 LYS cc_start: 0.7869 (tttt) cc_final: 0.7387 (tttm) REVERT: I 311 LYS cc_start: 0.7283 (mtpt) cc_final: 0.6452 (tttp) REVERT: I 317 LYS cc_start: 0.7644 (pttt) cc_final: 0.7347 (ptmt) REVERT: I 321 LYS cc_start: 0.7330 (ttmt) cc_final: 0.6821 (ttmm) REVERT: I 331 LYS cc_start: 0.6939 (mttt) cc_final: 0.6346 (mtpt) REVERT: I 338 GLU cc_start: 0.7744 (tt0) cc_final: 0.7361 (tt0) REVERT: I 341 SER cc_start: 0.7644 (p) cc_final: 0.7328 (t) REVERT: I 347 LYS cc_start: 0.7001 (mttt) cc_final: 0.5859 (mptp) REVERT: I 349 ARG cc_start: 0.6876 (mtt180) cc_final: 0.6458 (mtm180) REVERT: I 369 LYS cc_start: 0.7516 (mttt) cc_final: 0.7198 (ttmm) outliers start: 8 outliers final: 1 residues processed: 190 average time/residue: 3.0213 time to fit residues: 592.2148 Evaluate side-chains 185 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 183 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5175 Z= 0.291 Angle : 0.578 5.515 6924 Z= 0.296 Chirality : 0.049 0.133 780 Planarity : 0.005 0.060 879 Dihedral : 6.147 17.531 681 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 0.85 % Allowed : 16.24 % Favored : 82.91 % 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: -2.87 (0.26), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.20), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS G 330 PHE 0.011 0.001 PHE E 378 TYR 0.009 0.002 TYR E 310 ARG 0.005 0.001 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 188 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7803 (mttt) cc_final: 0.7139 (mttp) REVERT: A 342 GLU cc_start: 0.7535 (mt-10) cc_final: 0.6314 (mp0) REVERT: A 378 PHE cc_start: 0.5821 (t80) cc_final: 0.5358 (m-80) REVERT: B 311 LYS cc_start: 0.8207 (mttt) cc_final: 0.7043 (mmtm) REVERT: B 321 LYS cc_start: 0.7793 (tttt) cc_final: 0.7206 (tmmm) REVERT: B 338 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6544 (tt0) REVERT: B 340 LYS cc_start: 0.7545 (tttt) cc_final: 0.7216 (mtpp) REVERT: B 347 LYS cc_start: 0.6912 (mttp) cc_final: 0.6442 (mttp) REVERT: B 348 ASP cc_start: 0.7281 (t0) cc_final: 0.7042 (t70) REVERT: B 356 SER cc_start: 0.8518 (m) cc_final: 0.7988 (t) REVERT: C 311 LYS cc_start: 0.7989 (mttt) cc_final: 0.7110 (mmtm) REVERT: C 321 LYS cc_start: 0.7347 (ttmt) cc_final: 0.6413 (tmtm) REVERT: C 331 LYS cc_start: 0.7334 (mttt) cc_final: 0.6881 (mtpt) REVERT: C 338 GLU cc_start: 0.7121 (tt0) cc_final: 0.6786 (tt0) REVERT: C 345 ASP cc_start: 0.7534 (t0) cc_final: 0.6832 (t70) REVERT: C 347 LYS cc_start: 0.6891 (mttt) cc_final: 0.6513 (mtpp) REVERT: D 311 LYS cc_start: 0.8286 (tttt) cc_final: 0.7804 (ttmt) REVERT: D 317 LYS cc_start: 0.7892 (mttt) cc_final: 0.7376 (mtpt) REVERT: D 321 LYS cc_start: 0.8329 (mttt) cc_final: 0.7449 (tptm) REVERT: D 340 LYS cc_start: 0.8330 (mttt) cc_final: 0.7986 (mttm) REVERT: D 342 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7026 (mp0) REVERT: D 343 LYS cc_start: 0.8263 (mttt) cc_final: 0.8014 (mttm) REVERT: D 347 LYS cc_start: 0.7926 (mtpt) cc_final: 0.7717 (mtpt) REVERT: D 378 PHE cc_start: 0.5707 (t80) cc_final: 0.5240 (m-80) REVERT: E 317 LYS cc_start: 0.7772 (mtmt) cc_final: 0.7466 (mtpm) REVERT: E 320 SER cc_start: 0.7831 (t) cc_final: 0.7403 (p) REVERT: E 321 LYS cc_start: 0.8032 (tttt) cc_final: 0.7591 (tmmt) REVERT: E 336 GLN cc_start: 0.7987 (mt0) cc_final: 0.7470 (mt0) REVERT: E 338 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7228 (tt0) REVERT: E 340 LYS cc_start: 0.7913 (tttt) cc_final: 0.7435 (tptp) REVERT: E 342 GLU cc_start: 0.7522 (mt-10) cc_final: 0.6037 (mp0) REVERT: E 347 LYS cc_start: 0.7615 (mttp) cc_final: 0.7016 (mmtm) REVERT: E 369 LYS cc_start: 0.8627 (mttt) cc_final: 0.8303 (mttp) REVERT: E 379 ARG cc_start: 0.5927 (OUTLIER) cc_final: 0.3336 (ptt90) REVERT: F 311 LYS cc_start: 0.8299 (mttt) cc_final: 0.6793 (pmtt) REVERT: F 338 GLU cc_start: 0.7754 (tt0) cc_final: 0.7454 (tt0) REVERT: F 347 LYS cc_start: 0.7765 (mttt) cc_final: 0.7406 (mtmm) REVERT: F 349 ARG cc_start: 0.7260 (mtt180) cc_final: 0.6721 (mtm180) REVERT: F 353 LYS cc_start: 0.8236 (tttt) cc_final: 0.7851 (tttt) REVERT: G 317 LYS cc_start: 0.7321 (mttt) cc_final: 0.7009 (mtpm) REVERT: G 321 LYS cc_start: 0.7733 (mttt) cc_final: 0.7474 (mttm) REVERT: G 340 LYS cc_start: 0.7864 (mttt) cc_final: 0.6995 (mttp) REVERT: G 342 GLU cc_start: 0.7575 (mt-10) cc_final: 0.6380 (mp0) REVERT: G 343 LYS cc_start: 0.7712 (mttt) cc_final: 0.7482 (mttp) REVERT: G 349 ARG cc_start: 0.7163 (mtm180) cc_final: 0.6392 (mtm180) REVERT: G 353 LYS cc_start: 0.7457 (mttt) cc_final: 0.7193 (mtmt) REVERT: G 356 SER cc_start: 0.8208 (p) cc_final: 0.7750 (t) REVERT: G 369 LYS cc_start: 0.7413 (mttt) cc_final: 0.7027 (mttp) REVERT: G 371 ILE cc_start: 0.7818 (mt) cc_final: 0.7522 (mp) REVERT: G 378 PHE cc_start: 0.5498 (t80) cc_final: 0.5115 (m-80) REVERT: H 321 LYS cc_start: 0.7885 (tttt) cc_final: 0.6954 (mttp) REVERT: H 331 LYS cc_start: 0.7939 (mttt) cc_final: 0.7656 (mttp) REVERT: H 341 SER cc_start: 0.7852 (m) cc_final: 0.7512 (t) REVERT: H 347 LYS cc_start: 0.6985 (mttp) cc_final: 0.6294 (mmtm) REVERT: H 375 LYS cc_start: 0.7878 (tttt) cc_final: 0.7322 (tttm) REVERT: I 311 LYS cc_start: 0.7281 (mtpt) cc_final: 0.6447 (tttp) REVERT: I 317 LYS cc_start: 0.7641 (pttt) cc_final: 0.7347 (ptmt) REVERT: I 321 LYS cc_start: 0.7334 (ttmt) cc_final: 0.6820 (ttmm) REVERT: I 331 LYS cc_start: 0.6904 (mttt) cc_final: 0.6334 (mtpt) REVERT: I 338 GLU cc_start: 0.7671 (tt0) cc_final: 0.7331 (tt0) REVERT: I 341 SER cc_start: 0.7650 (p) cc_final: 0.7336 (t) REVERT: I 345 ASP cc_start: 0.7690 (t0) cc_final: 0.7228 (t0) REVERT: I 347 LYS cc_start: 0.6989 (mttt) cc_final: 0.5841 (mptp) REVERT: I 349 ARG cc_start: 0.6884 (mtt180) cc_final: 0.6458 (mtm180) REVERT: I 369 LYS cc_start: 0.7548 (mttt) cc_final: 0.7229 (ttmm) outliers start: 5 outliers final: 3 residues processed: 188 average time/residue: 3.1109 time to fit residues: 603.2696 Evaluate side-chains 189 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 185 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 37 optimal weight: 0.3980 chunk 28 optimal weight: 0.0470 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 351 GLN H 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5175 Z= 0.149 Angle : 0.515 5.361 6924 Z= 0.264 Chirality : 0.050 0.132 780 Planarity : 0.003 0.034 879 Dihedral : 5.787 17.152 681 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.17 % Allowed : 18.12 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.26), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.20), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 329 PHE 0.012 0.001 PHE E 378 TYR 0.006 0.001 TYR E 310 ARG 0.005 0.001 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 191 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7879 (mttt) cc_final: 0.7277 (mttp) REVERT: A 342 GLU cc_start: 0.7576 (mt-10) cc_final: 0.6443 (mp0) REVERT: A 378 PHE cc_start: 0.5731 (t80) cc_final: 0.5426 (m-80) REVERT: B 311 LYS cc_start: 0.8250 (mttt) cc_final: 0.7116 (mmtm) REVERT: B 321 LYS cc_start: 0.7798 (tttt) cc_final: 0.7162 (tmmt) REVERT: B 338 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6563 (tt0) REVERT: B 340 LYS cc_start: 0.7552 (tttt) cc_final: 0.7223 (mtpp) REVERT: B 347 LYS cc_start: 0.6812 (mttp) cc_final: 0.6363 (mttp) REVERT: B 356 SER cc_start: 0.8496 (m) cc_final: 0.7973 (t) REVERT: C 311 LYS cc_start: 0.7937 (mttt) cc_final: 0.7078 (mmtm) REVERT: C 321 LYS cc_start: 0.7374 (ttmt) cc_final: 0.6440 (tmtm) REVERT: C 331 LYS cc_start: 0.7423 (mttt) cc_final: 0.6981 (mtpt) REVERT: C 338 GLU cc_start: 0.7119 (tt0) cc_final: 0.6693 (tm-30) REVERT: C 345 ASP cc_start: 0.7519 (t0) cc_final: 0.6847 (t0) REVERT: C 347 LYS cc_start: 0.6910 (mttt) cc_final: 0.6536 (mtpp) REVERT: C 349 ARG cc_start: 0.7016 (mtt180) cc_final: 0.6650 (mtm180) REVERT: D 311 LYS cc_start: 0.8269 (tttt) cc_final: 0.7759 (ttmp) REVERT: D 317 LYS cc_start: 0.7814 (mttt) cc_final: 0.7328 (mtpt) REVERT: D 321 LYS cc_start: 0.8292 (mttt) cc_final: 0.7421 (tptm) REVERT: D 340 LYS cc_start: 0.8269 (mttt) cc_final: 0.7875 (mttm) REVERT: D 342 GLU cc_start: 0.7825 (mt-10) cc_final: 0.6986 (mp0) REVERT: D 343 LYS cc_start: 0.8257 (mttt) cc_final: 0.8017 (mttm) REVERT: D 369 LYS cc_start: 0.8292 (mttm) cc_final: 0.7924 (mmtp) REVERT: D 378 PHE cc_start: 0.5750 (t80) cc_final: 0.5271 (m-80) REVERT: E 317 LYS cc_start: 0.7725 (mtmt) cc_final: 0.7439 (mtpm) REVERT: E 320 SER cc_start: 0.7803 (t) cc_final: 0.7392 (p) REVERT: E 321 LYS cc_start: 0.8027 (tttt) cc_final: 0.7608 (tmmt) REVERT: E 336 GLN cc_start: 0.7953 (mt0) cc_final: 0.7438 (mt0) REVERT: E 338 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7232 (tt0) REVERT: E 340 LYS cc_start: 0.7926 (tttt) cc_final: 0.7439 (tptp) REVERT: E 342 GLU cc_start: 0.7491 (mt-10) cc_final: 0.6062 (mp0) REVERT: E 347 LYS cc_start: 0.7542 (mttp) cc_final: 0.6949 (mmtm) REVERT: E 353 LYS cc_start: 0.8184 (tttt) cc_final: 0.7914 (tttp) REVERT: E 369 LYS cc_start: 0.8576 (mttt) cc_final: 0.8241 (mttp) REVERT: F 311 LYS cc_start: 0.8352 (mttt) cc_final: 0.7453 (tttp) REVERT: F 338 GLU cc_start: 0.7531 (tt0) cc_final: 0.7293 (tt0) REVERT: F 347 LYS cc_start: 0.7669 (mttt) cc_final: 0.7340 (mtmm) REVERT: F 349 ARG cc_start: 0.7211 (mtt180) cc_final: 0.6792 (mtm180) REVERT: F 353 LYS cc_start: 0.8223 (tttt) cc_final: 0.7808 (tttp) REVERT: G 317 LYS cc_start: 0.7338 (mttt) cc_final: 0.7046 (mtpm) REVERT: G 321 LYS cc_start: 0.7659 (mttt) cc_final: 0.6837 (mtpp) REVERT: G 340 LYS cc_start: 0.7882 (mttt) cc_final: 0.6961 (mttp) REVERT: G 342 GLU cc_start: 0.7501 (mt-10) cc_final: 0.6459 (mp0) REVERT: G 343 LYS cc_start: 0.7788 (mttt) cc_final: 0.7581 (mttp) REVERT: G 349 ARG cc_start: 0.7127 (mtm180) cc_final: 0.6337 (mtm180) REVERT: G 353 LYS cc_start: 0.7455 (mttt) cc_final: 0.7192 (mtmt) REVERT: G 356 SER cc_start: 0.7983 (p) cc_final: 0.7600 (t) REVERT: G 358 ASP cc_start: 0.7472 (m-30) cc_final: 0.7124 (m-30) REVERT: G 369 LYS cc_start: 0.7406 (mttt) cc_final: 0.7027 (mttp) REVERT: G 371 ILE cc_start: 0.7820 (mt) cc_final: 0.7519 (mp) REVERT: G 378 PHE cc_start: 0.5551 (t80) cc_final: 0.5196 (m-80) REVERT: H 321 LYS cc_start: 0.7839 (tttt) cc_final: 0.6936 (mttp) REVERT: H 331 LYS cc_start: 0.8006 (mttt) cc_final: 0.7717 (mttp) REVERT: H 336 GLN cc_start: 0.7688 (mt0) cc_final: 0.7178 (mt0) REVERT: H 341 SER cc_start: 0.7928 (m) cc_final: 0.7552 (t) REVERT: H 347 LYS cc_start: 0.6959 (mttp) cc_final: 0.6243 (mmtm) REVERT: H 356 SER cc_start: 0.8230 (m) cc_final: 0.7789 (t) REVERT: H 375 LYS cc_start: 0.7881 (tttt) cc_final: 0.7360 (tttm) REVERT: I 311 LYS cc_start: 0.7347 (mtpt) cc_final: 0.6420 (tttp) REVERT: I 317 LYS cc_start: 0.7632 (pttt) cc_final: 0.7356 (ptmt) REVERT: I 321 LYS cc_start: 0.7328 (ttmt) cc_final: 0.6819 (ttmm) REVERT: I 331 LYS cc_start: 0.7024 (mttt) cc_final: 0.6377 (mtpt) REVERT: I 338 GLU cc_start: 0.7631 (tt0) cc_final: 0.7215 (tt0) REVERT: I 341 SER cc_start: 0.7580 (p) cc_final: 0.7265 (t) REVERT: I 345 ASP cc_start: 0.7724 (t0) cc_final: 0.7227 (t0) REVERT: I 347 LYS cc_start: 0.6959 (mttt) cc_final: 0.5809 (mptp) REVERT: I 349 ARG cc_start: 0.6882 (mtt180) cc_final: 0.6366 (mtm180) REVERT: I 369 LYS cc_start: 0.7527 (mttt) cc_final: 0.7239 (ttmm) outliers start: 1 outliers final: 1 residues processed: 191 average time/residue: 3.0338 time to fit residues: 597.8788 Evaluate side-chains 188 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 187 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 34 optimal weight: 0.4980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5175 Z= 0.204 Angle : 0.526 4.680 6924 Z= 0.268 Chirality : 0.049 0.130 780 Planarity : 0.004 0.062 879 Dihedral : 5.782 16.947 681 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 0.68 % Allowed : 18.29 % Favored : 81.03 % 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: -2.86 (0.26), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.19), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 330 PHE 0.013 0.001 PHE E 378 TYR 0.008 0.001 TYR E 310 ARG 0.005 0.001 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 192 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7829 (mttt) cc_final: 0.7233 (mttp) REVERT: A 342 GLU cc_start: 0.7576 (mt-10) cc_final: 0.6434 (mp0) REVERT: A 378 PHE cc_start: 0.6035 (t80) cc_final: 0.5655 (m-80) REVERT: B 311 LYS cc_start: 0.8283 (mttt) cc_final: 0.7151 (mmtm) REVERT: B 321 LYS cc_start: 0.7794 (tttt) cc_final: 0.7156 (tmmt) REVERT: B 338 GLU cc_start: 0.7302 (mt-10) cc_final: 0.6621 (tt0) REVERT: B 340 LYS cc_start: 0.7571 (tttt) cc_final: 0.7221 (mtpp) REVERT: B 347 LYS cc_start: 0.6867 (mttp) cc_final: 0.6404 (mttp) REVERT: B 356 SER cc_start: 0.8500 (m) cc_final: 0.7984 (t) REVERT: C 311 LYS cc_start: 0.7962 (mttt) cc_final: 0.7095 (mmtm) REVERT: C 321 LYS cc_start: 0.7368 (ttmt) cc_final: 0.6433 (tmtm) REVERT: C 331 LYS cc_start: 0.7367 (mttt) cc_final: 0.6915 (mtpt) REVERT: C 338 GLU cc_start: 0.7126 (tt0) cc_final: 0.6688 (tm-30) REVERT: C 345 ASP cc_start: 0.7509 (t0) cc_final: 0.6831 (t0) REVERT: C 347 LYS cc_start: 0.6865 (mttt) cc_final: 0.6487 (mtpp) REVERT: C 349 ARG cc_start: 0.7020 (mtt180) cc_final: 0.6652 (mtm180) REVERT: D 311 LYS cc_start: 0.8263 (tttt) cc_final: 0.7764 (ttmp) REVERT: D 317 LYS cc_start: 0.7826 (mttt) cc_final: 0.7365 (mtpt) REVERT: D 321 LYS cc_start: 0.8269 (mttt) cc_final: 0.7356 (tptm) REVERT: D 340 LYS cc_start: 0.8325 (mttt) cc_final: 0.7970 (mttm) REVERT: D 342 GLU cc_start: 0.7806 (mt-10) cc_final: 0.6965 (mp0) REVERT: D 343 LYS cc_start: 0.8261 (mttt) cc_final: 0.8024 (mttm) REVERT: D 369 LYS cc_start: 0.8265 (mttm) cc_final: 0.7891 (mmtp) REVERT: D 378 PHE cc_start: 0.5791 (t80) cc_final: 0.5310 (m-80) REVERT: E 317 LYS cc_start: 0.7742 (mtmt) cc_final: 0.7433 (mtpm) REVERT: E 320 SER cc_start: 0.7818 (t) cc_final: 0.7398 (p) REVERT: E 321 LYS cc_start: 0.8029 (tttt) cc_final: 0.7604 (tmmt) REVERT: E 336 GLN cc_start: 0.7962 (mt0) cc_final: 0.7453 (mt0) REVERT: E 338 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7228 (tt0) REVERT: E 340 LYS cc_start: 0.7923 (tttt) cc_final: 0.7432 (tptp) REVERT: E 342 GLU cc_start: 0.7545 (mt-10) cc_final: 0.6062 (mp0) REVERT: E 347 LYS cc_start: 0.7488 (mttp) cc_final: 0.6928 (mmtm) REVERT: E 369 LYS cc_start: 0.8586 (mttt) cc_final: 0.8247 (mttp) REVERT: F 311 LYS cc_start: 0.8340 (mttt) cc_final: 0.6811 (pmtt) REVERT: F 338 GLU cc_start: 0.7545 (tt0) cc_final: 0.7291 (tt0) REVERT: F 347 LYS cc_start: 0.7679 (mttt) cc_final: 0.7331 (mtmm) REVERT: F 349 ARG cc_start: 0.7201 (mtt180) cc_final: 0.6815 (mtm180) REVERT: F 353 LYS cc_start: 0.8227 (tttt) cc_final: 0.7810 (tttp) REVERT: F 379 ARG cc_start: 0.7644 (ttm-80) cc_final: 0.7338 (mtt90) REVERT: G 317 LYS cc_start: 0.7367 (mttt) cc_final: 0.7075 (mtpm) REVERT: G 321 LYS cc_start: 0.7670 (mttt) cc_final: 0.6819 (mtpp) REVERT: G 340 LYS cc_start: 0.7842 (mttt) cc_final: 0.6937 (mttp) REVERT: G 342 GLU cc_start: 0.7503 (mt-10) cc_final: 0.6460 (mp0) REVERT: G 343 LYS cc_start: 0.7786 (mttt) cc_final: 0.7581 (mttp) REVERT: G 349 ARG cc_start: 0.7168 (mtm180) cc_final: 0.6548 (mtm180) REVERT: G 353 LYS cc_start: 0.7445 (mttt) cc_final: 0.7192 (mtmt) REVERT: G 356 SER cc_start: 0.7990 (p) cc_final: 0.7591 (t) REVERT: G 369 LYS cc_start: 0.7410 (mttt) cc_final: 0.7029 (mttp) REVERT: G 371 ILE cc_start: 0.7816 (mt) cc_final: 0.7514 (mp) REVERT: G 378 PHE cc_start: 0.5537 (t80) cc_final: 0.5232 (m-80) REVERT: H 321 LYS cc_start: 0.7856 (tttt) cc_final: 0.6957 (mttp) REVERT: H 331 LYS cc_start: 0.7991 (mttt) cc_final: 0.7691 (mttp) REVERT: H 336 GLN cc_start: 0.7744 (mt0) cc_final: 0.7313 (mt0) REVERT: H 341 SER cc_start: 0.7991 (m) cc_final: 0.7619 (t) REVERT: H 345 ASP cc_start: 0.7813 (t0) cc_final: 0.7241 (t70) REVERT: H 347 LYS cc_start: 0.6925 (mttp) cc_final: 0.6253 (mmtm) REVERT: H 375 LYS cc_start: 0.7880 (tttt) cc_final: 0.7326 (tttm) REVERT: I 311 LYS cc_start: 0.7347 (mtpt) cc_final: 0.6489 (tttp) REVERT: I 317 LYS cc_start: 0.7654 (pttt) cc_final: 0.7393 (ptmt) REVERT: I 321 LYS cc_start: 0.7330 (ttmt) cc_final: 0.6819 (ttmm) REVERT: I 331 LYS cc_start: 0.7009 (mttt) cc_final: 0.6359 (mtpt) REVERT: I 338 GLU cc_start: 0.7649 (tt0) cc_final: 0.7216 (tt0) REVERT: I 341 SER cc_start: 0.7618 (p) cc_final: 0.7321 (t) REVERT: I 345 ASP cc_start: 0.7706 (t0) cc_final: 0.7173 (t0) REVERT: I 347 LYS cc_start: 0.6941 (mttt) cc_final: 0.5767 (mptp) REVERT: I 349 ARG cc_start: 0.6852 (mtt180) cc_final: 0.6383 (mtm180) REVERT: I 369 LYS cc_start: 0.7528 (mttt) cc_final: 0.7235 (ttmm) outliers start: 4 outliers final: 4 residues processed: 192 average time/residue: 3.0377 time to fit residues: 601.7852 Evaluate side-chains 195 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 191 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain G residue 345 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5175 Z= 0.165 Angle : 0.513 5.321 6924 Z= 0.261 Chirality : 0.049 0.131 780 Planarity : 0.004 0.041 879 Dihedral : 5.665 16.884 681 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 0.85 % Allowed : 18.29 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.26), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.19), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 329 PHE 0.011 0.001 PHE E 378 TYR 0.006 0.001 TYR E 310 ARG 0.010 0.001 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 193 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7830 (mttt) cc_final: 0.7235 (mttp) REVERT: A 342 GLU cc_start: 0.7575 (mt-10) cc_final: 0.6440 (mp0) REVERT: A 378 PHE cc_start: 0.6033 (t80) cc_final: 0.5651 (m-80) REVERT: B 311 LYS cc_start: 0.8291 (mttt) cc_final: 0.7139 (mmtm) REVERT: B 321 LYS cc_start: 0.7794 (tttt) cc_final: 0.7153 (tmmt) REVERT: B 338 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6619 (tt0) REVERT: B 340 LYS cc_start: 0.7571 (tttt) cc_final: 0.7233 (mtpp) REVERT: B 347 LYS cc_start: 0.6865 (mttp) cc_final: 0.6426 (mttp) REVERT: B 356 SER cc_start: 0.8498 (m) cc_final: 0.7965 (t) REVERT: C 311 LYS cc_start: 0.7951 (mttt) cc_final: 0.7074 (mmtm) REVERT: C 321 LYS cc_start: 0.7397 (ttmt) cc_final: 0.6449 (tmtm) REVERT: C 331 LYS cc_start: 0.7418 (mttt) cc_final: 0.6973 (mtpt) REVERT: C 338 GLU cc_start: 0.7122 (tt0) cc_final: 0.6710 (tm-30) REVERT: C 345 ASP cc_start: 0.7544 (t0) cc_final: 0.6853 (t0) REVERT: C 347 LYS cc_start: 0.6856 (mttt) cc_final: 0.6490 (mtpp) REVERT: C 349 ARG cc_start: 0.7016 (mtt180) cc_final: 0.6655 (mtm180) REVERT: D 311 LYS cc_start: 0.8261 (tttt) cc_final: 0.7748 (ttmp) REVERT: D 317 LYS cc_start: 0.7861 (mttt) cc_final: 0.7405 (mtpt) REVERT: D 321 LYS cc_start: 0.8244 (mttt) cc_final: 0.7322 (tptm) REVERT: D 340 LYS cc_start: 0.8306 (mttt) cc_final: 0.7938 (mttm) REVERT: D 342 GLU cc_start: 0.7769 (mt-10) cc_final: 0.6898 (mp0) REVERT: D 345 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7177 (m-30) REVERT: D 369 LYS cc_start: 0.8263 (mttm) cc_final: 0.7889 (mmtp) REVERT: D 378 PHE cc_start: 0.5791 (t80) cc_final: 0.5303 (m-80) REVERT: E 317 LYS cc_start: 0.7729 (mtmt) cc_final: 0.7435 (mtpm) REVERT: E 320 SER cc_start: 0.7807 (t) cc_final: 0.7393 (p) REVERT: E 321 LYS cc_start: 0.8018 (tttt) cc_final: 0.7597 (tmmt) REVERT: E 336 GLN cc_start: 0.7954 (mt0) cc_final: 0.7448 (mt0) REVERT: E 338 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7217 (tt0) REVERT: E 340 LYS cc_start: 0.7929 (tttt) cc_final: 0.7439 (tptp) REVERT: E 342 GLU cc_start: 0.7491 (mt-10) cc_final: 0.6056 (mp0) REVERT: E 347 LYS cc_start: 0.7411 (mttp) cc_final: 0.6882 (mmtm) REVERT: E 353 LYS cc_start: 0.8233 (tttt) cc_final: 0.7929 (tttp) REVERT: E 369 LYS cc_start: 0.8572 (mttt) cc_final: 0.8227 (mttp) REVERT: F 311 LYS cc_start: 0.8322 (mttt) cc_final: 0.7255 (tmtm) REVERT: F 338 GLU cc_start: 0.7540 (tt0) cc_final: 0.7300 (tt0) REVERT: F 347 LYS cc_start: 0.7493 (mttt) cc_final: 0.7148 (mtmm) REVERT: F 349 ARG cc_start: 0.7188 (mtt180) cc_final: 0.6829 (mtm180) REVERT: F 353 LYS cc_start: 0.8220 (tttt) cc_final: 0.7796 (tttp) REVERT: G 317 LYS cc_start: 0.7374 (mttt) cc_final: 0.7088 (mtpm) REVERT: G 321 LYS cc_start: 0.7662 (mttt) cc_final: 0.6816 (mtpp) REVERT: G 340 LYS cc_start: 0.7864 (mttt) cc_final: 0.6945 (mttp) REVERT: G 342 GLU cc_start: 0.7561 (mt-10) cc_final: 0.6549 (mp0) REVERT: G 343 LYS cc_start: 0.7790 (mttt) cc_final: 0.7587 (mttp) REVERT: G 349 ARG cc_start: 0.7141 (mtm180) cc_final: 0.6521 (mtm180) REVERT: G 353 LYS cc_start: 0.7455 (mttt) cc_final: 0.7208 (mtmt) REVERT: G 356 SER cc_start: 0.7989 (p) cc_final: 0.7628 (t) REVERT: G 369 LYS cc_start: 0.7404 (mttt) cc_final: 0.7026 (mttp) REVERT: G 371 ILE cc_start: 0.7730 (mt) cc_final: 0.7415 (mp) REVERT: G 378 PHE cc_start: 0.5544 (t80) cc_final: 0.5238 (m-80) REVERT: H 321 LYS cc_start: 0.7855 (tttt) cc_final: 0.6931 (mttp) REVERT: H 331 LYS cc_start: 0.8018 (mttt) cc_final: 0.7714 (mttp) REVERT: H 336 GLN cc_start: 0.7735 (mt0) cc_final: 0.7314 (mt0) REVERT: H 341 SER cc_start: 0.7936 (m) cc_final: 0.7557 (t) REVERT: H 347 LYS cc_start: 0.6915 (mttp) cc_final: 0.6218 (mmtm) REVERT: H 356 SER cc_start: 0.8196 (m) cc_final: 0.7763 (t) REVERT: H 375 LYS cc_start: 0.7887 (tttt) cc_final: 0.7328 (tttm) REVERT: I 311 LYS cc_start: 0.7342 (mtpt) cc_final: 0.6436 (tttp) REVERT: I 317 LYS cc_start: 0.7625 (pttt) cc_final: 0.7364 (ptmt) REVERT: I 321 LYS cc_start: 0.7326 (ttmt) cc_final: 0.6815 (ttmm) REVERT: I 331 LYS cc_start: 0.7004 (mttt) cc_final: 0.6343 (mtpt) REVERT: I 341 SER cc_start: 0.7575 (OUTLIER) cc_final: 0.7263 (t) REVERT: I 345 ASP cc_start: 0.7609 (t0) cc_final: 0.7040 (t0) REVERT: I 347 LYS cc_start: 0.6931 (mttt) cc_final: 0.5756 (mmtm) REVERT: I 349 ARG cc_start: 0.6930 (mtt180) cc_final: 0.6363 (mtm180) REVERT: I 369 LYS cc_start: 0.7505 (mttt) cc_final: 0.7219 (ttmm) outliers start: 5 outliers final: 3 residues processed: 193 average time/residue: 3.0200 time to fit residues: 602.0736 Evaluate side-chains 196 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 191 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain I residue 341 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5175 Z= 0.213 Angle : 0.531 5.252 6924 Z= 0.270 Chirality : 0.049 0.131 780 Planarity : 0.004 0.041 879 Dihedral : 5.714 16.943 681 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 0.68 % Allowed : 18.97 % Favored : 80.34 % 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: -2.91 (0.25), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.19), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 330 PHE 0.012 0.001 PHE E 378 TYR 0.008 0.002 TYR E 310 ARG 0.006 0.001 ARG F 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 189 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7811 (mttt) cc_final: 0.7249 (mttp) REVERT: A 342 GLU cc_start: 0.7578 (mt-10) cc_final: 0.6436 (mp0) REVERT: A 378 PHE cc_start: 0.6011 (t80) cc_final: 0.5624 (m-80) REVERT: B 311 LYS cc_start: 0.8344 (mttt) cc_final: 0.7189 (mmtm) REVERT: B 321 LYS cc_start: 0.7691 (tttt) cc_final: 0.7109 (tmmt) REVERT: B 338 GLU cc_start: 0.7305 (mt-10) cc_final: 0.6624 (tt0) REVERT: B 340 LYS cc_start: 0.7601 (tttt) cc_final: 0.7237 (mtpp) REVERT: B 347 LYS cc_start: 0.6876 (mttp) cc_final: 0.6409 (mttp) REVERT: B 356 SER cc_start: 0.8501 (m) cc_final: 0.7972 (t) REVERT: C 311 LYS cc_start: 0.7973 (mttt) cc_final: 0.7085 (mmtm) REVERT: C 321 LYS cc_start: 0.7395 (ttmt) cc_final: 0.6429 (tmtm) REVERT: C 331 LYS cc_start: 0.7371 (mttt) cc_final: 0.6922 (mtpt) REVERT: C 338 GLU cc_start: 0.7138 (tt0) cc_final: 0.6647 (tm-30) REVERT: C 340 LYS cc_start: 0.7706 (tttt) cc_final: 0.6641 (tptt) REVERT: C 345 ASP cc_start: 0.7545 (t0) cc_final: 0.6841 (t0) REVERT: C 347 LYS cc_start: 0.6871 (mttt) cc_final: 0.6497 (mtpp) REVERT: C 349 ARG cc_start: 0.6941 (mtt180) cc_final: 0.6555 (mtm180) REVERT: D 311 LYS cc_start: 0.8271 (tttt) cc_final: 0.7765 (ttmp) REVERT: D 317 LYS cc_start: 0.7858 (mttt) cc_final: 0.7417 (mtpt) REVERT: D 321 LYS cc_start: 0.8276 (mttt) cc_final: 0.7322 (tptm) REVERT: D 340 LYS cc_start: 0.8323 (mttt) cc_final: 0.7977 (mttm) REVERT: D 342 GLU cc_start: 0.7789 (mt-10) cc_final: 0.6901 (mp0) REVERT: D 345 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7176 (m-30) REVERT: D 369 LYS cc_start: 0.8281 (mttm) cc_final: 0.7906 (mmtp) REVERT: D 378 PHE cc_start: 0.5799 (t80) cc_final: 0.5309 (m-80) REVERT: E 317 LYS cc_start: 0.7748 (mtmt) cc_final: 0.7453 (mtpm) REVERT: E 320 SER cc_start: 0.7818 (t) cc_final: 0.7396 (p) REVERT: E 321 LYS cc_start: 0.8025 (tttt) cc_final: 0.7600 (tmmt) REVERT: E 336 GLN cc_start: 0.7967 (mt0) cc_final: 0.7471 (mt0) REVERT: E 338 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7205 (tt0) REVERT: E 340 LYS cc_start: 0.7932 (tttt) cc_final: 0.7438 (tptp) REVERT: E 342 GLU cc_start: 0.7547 (mt-10) cc_final: 0.6077 (mp0) REVERT: E 347 LYS cc_start: 0.7451 (mttp) cc_final: 0.6905 (mmtm) REVERT: E 369 LYS cc_start: 0.8589 (mttt) cc_final: 0.8237 (mttp) REVERT: F 311 LYS cc_start: 0.8321 (mttt) cc_final: 0.7272 (tmtm) REVERT: F 338 GLU cc_start: 0.7551 (tt0) cc_final: 0.7284 (tt0) REVERT: F 347 LYS cc_start: 0.7454 (mttt) cc_final: 0.7114 (mtmm) REVERT: F 349 ARG cc_start: 0.7187 (mtt180) cc_final: 0.6835 (mtm180) REVERT: F 353 LYS cc_start: 0.8230 (tttt) cc_final: 0.7831 (tttt) REVERT: G 317 LYS cc_start: 0.7388 (mttt) cc_final: 0.7091 (mtpm) REVERT: G 321 LYS cc_start: 0.7665 (mttt) cc_final: 0.6814 (mtpp) REVERT: G 340 LYS cc_start: 0.7837 (mttt) cc_final: 0.6929 (mttp) REVERT: G 342 GLU cc_start: 0.7503 (mt-10) cc_final: 0.6458 (mp0) REVERT: G 343 LYS cc_start: 0.7797 (mttt) cc_final: 0.7589 (mttp) REVERT: G 349 ARG cc_start: 0.7129 (mtm180) cc_final: 0.6528 (mtm180) REVERT: G 353 LYS cc_start: 0.7536 (mttt) cc_final: 0.7184 (mtpt) REVERT: G 356 SER cc_start: 0.7997 (p) cc_final: 0.7595 (t) REVERT: G 369 LYS cc_start: 0.7411 (mttt) cc_final: 0.7032 (mttp) REVERT: G 371 ILE cc_start: 0.7697 (mt) cc_final: 0.7491 (mp) REVERT: G 378 PHE cc_start: 0.5357 (t80) cc_final: 0.5099 (m-80) REVERT: H 321 LYS cc_start: 0.7857 (tttt) cc_final: 0.6959 (mptp) REVERT: H 331 LYS cc_start: 0.8022 (mttt) cc_final: 0.7725 (mttp) REVERT: H 341 SER cc_start: 0.7866 (m) cc_final: 0.7570 (t) REVERT: H 347 LYS cc_start: 0.6914 (mttp) cc_final: 0.6205 (mmtm) REVERT: H 375 LYS cc_start: 0.7916 (tttt) cc_final: 0.7363 (tttm) REVERT: I 311 LYS cc_start: 0.7341 (mtpt) cc_final: 0.6438 (tttp) REVERT: I 317 LYS cc_start: 0.7608 (pttt) cc_final: 0.7352 (ptmt) REVERT: I 321 LYS cc_start: 0.7322 (ttmt) cc_final: 0.6810 (ttmm) REVERT: I 331 LYS cc_start: 0.6963 (mttt) cc_final: 0.6330 (mtpt) REVERT: I 338 GLU cc_start: 0.7770 (tt0) cc_final: 0.7268 (tt0) REVERT: I 341 SER cc_start: 0.7622 (OUTLIER) cc_final: 0.7317 (t) REVERT: I 345 ASP cc_start: 0.7601 (t0) cc_final: 0.7012 (t0) REVERT: I 347 LYS cc_start: 0.6944 (mttt) cc_final: 0.5762 (mmtm) REVERT: I 349 ARG cc_start: 0.6860 (mtt180) cc_final: 0.6387 (mtm180) REVERT: I 369 LYS cc_start: 0.7528 (mttt) cc_final: 0.7238 (ttmm) outliers start: 4 outliers final: 2 residues processed: 189 average time/residue: 3.0337 time to fit residues: 591.4965 Evaluate side-chains 193 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 189 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain I residue 341 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 6 optimal weight: 0.0030 chunk 9 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 36 optimal weight: 0.0040 chunk 57 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 overall best weight: 0.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 351 GLN H 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.145016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.129850 restraints weight = 19062.306| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 1.43 r_work: 0.3908 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3835 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5175 Z= 0.126 Angle : 0.490 5.172 6924 Z= 0.250 Chirality : 0.050 0.132 780 Planarity : 0.003 0.034 879 Dihedral : 5.413 16.503 681 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.17 % Allowed : 19.49 % Favored : 80.34 % 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: -2.88 (0.26), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.19), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 330 PHE 0.010 0.001 PHE E 378 TYR 0.005 0.001 TYR I 310 ARG 0.003 0.000 ARG B 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9077.99 seconds wall clock time: 156 minutes 7.16 seconds (9367.16 seconds total)