Starting phenix.real_space_refine on Sun Aug 4 09:38:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9l_18285/08_2024/8q9l_18285.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9l_18285/08_2024/8q9l_18285.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9l_18285/08_2024/8q9l_18285.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9l_18285/08_2024/8q9l_18285.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9l_18285/08_2024/8q9l_18285.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9l_18285/08_2024/8q9l_18285.cif" } resolution = 2.76 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 3159 2.51 5 N 909 2.21 5 O 936 1.98 5 H 5220 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 "A GLU 372": "OE1" <-> "OE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 372": "OE1" <-> "OE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 372": "OE1" <-> "OE2" Residue "B ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 372": "OE1" <-> "OE2" Residue "D ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 372": "OE1" <-> "OE2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 372": "OE1" <-> "OE2" Residue "G ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 372": "OE1" <-> "OE2" Residue "H ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 372": "OE1" <-> "OE2" Residue "I GLU 372": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 10233 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "C" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "E" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "B" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "D" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "F" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "G" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "H" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "I" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 5.15, per 1000 atoms: 0.50 Number of scatterers: 10233 At special positions: 0 Unit cell: (138.13, 136.676, 43.62, 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 936 8.00 N 909 7.00 C 3159 6.00 H 5220 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: 7.84 Conformation dependent library (CDL) restraints added in 1.0 seconds 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1152 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 24 sheets defined 0.0% alpha, 55.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 307 through 310 removed outlier: 6.400A pdb=" N ILE A 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.818A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 330 removed outlier: 6.399A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N GLY C 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N CYS A 322 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU C 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 9.483A pdb=" N SER A 324 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 10.128A pdb=" N ASN C 327 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLY A 326 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N HIS C 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER E 324 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU A 325 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLY E 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN A 327 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 336 through 342 removed outlier: 6.711A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N LYS C 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLU C 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N SER A 341 " --> pdb=" O GLU C 342 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.540A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 350 through 355 removed outlier: 6.368A pdb=" N VAL A 350 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LYS C 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N SER A 352 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N GLY C 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE A 354 " --> pdb=" O GLY C 355 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.323A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 369 through 377 removed outlier: 6.660A pdb=" N LYS A 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N GLU E 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE A 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N HIS E 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR A 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LEU E 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS A 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 307 through 310 removed outlier: 6.695A pdb=" N GLN B 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N TYR F 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL B 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.845A pdb=" N VAL B 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 317 through 330 removed outlier: 6.760A pdb=" N SER B 324 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU D 325 " --> pdb=" O SER B 324 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLY B 326 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN D 327 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER F 324 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU B 325 " --> pdb=" O SER F 324 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY F 326 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN B 327 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 336 through 342 removed outlier: 6.418A pdb=" N GLN B 336 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL F 339 " --> pdb=" O GLN B 336 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLU B 338 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N SER F 341 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LYS B 340 " --> pdb=" O SER F 341 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.489A pdb=" N ASP B 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 350 through 355 Processing sheet with id=AB6, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.357A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 369 through 377 removed outlier: 6.641A pdb=" N LYS B 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N GLU F 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE B 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N HIS F 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR B 373 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N LEU F 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS B 375 " --> pdb=" O LEU F 376 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 307 through 310 removed outlier: 6.757A pdb=" N GLN G 307 " --> pdb=" O ILE I 308 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N TYR I 310 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL G 309 " --> pdb=" O TYR I 310 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 313 through 314 removed outlier: 6.862A pdb=" N VAL G 313 " --> pdb=" O ASP I 314 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 317 through 330 removed outlier: 6.725A pdb=" N SER G 324 " --> pdb=" O GLY H 323 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU H 325 " --> pdb=" O SER G 324 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLY G 326 " --> pdb=" O LEU H 325 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN H 327 " --> pdb=" O GLY G 326 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER I 324 " --> pdb=" O GLY G 323 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU G 325 " --> pdb=" O SER I 324 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLY I 326 " --> pdb=" O LEU G 325 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASN G 327 " --> pdb=" O GLY I 326 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 336 through 342 removed outlier: 6.661A pdb=" N VAL G 337 " --> pdb=" O GLU H 338 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N LYS H 340 " --> pdb=" O VAL G 337 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL G 339 " --> pdb=" O LYS H 340 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N GLU H 342 " --> pdb=" O VAL G 339 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER G 341 " --> pdb=" O GLU H 342 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 345 through 346 removed outlier: 6.520A pdb=" N ASP G 345 " --> pdb=" O PHE I 346 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 350 through 355 removed outlier: 6.333A pdb=" N VAL G 350 " --> pdb=" O GLN H 351 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N LYS H 353 " --> pdb=" O VAL G 350 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER G 352 " --> pdb=" O LYS H 353 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N GLY H 355 " --> pdb=" O SER G 352 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE G 354 " --> pdb=" O GLY H 355 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLN G 351 " --> pdb=" O SER I 352 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ILE I 354 " --> pdb=" O GLN G 351 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS G 353 " --> pdb=" O ILE I 354 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N SER I 356 " --> pdb=" O LYS G 353 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLY G 355 " --> pdb=" O SER I 356 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'H' and resid 360 through 362 removed outlier: 6.362A pdb=" N THR G 361 " --> pdb=" O HIS H 362 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 369 through 377 removed outlier: 6.631A pdb=" N LYS G 369 " --> pdb=" O LYS I 370 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N GLU I 372 " --> pdb=" O LYS G 369 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE G 371 " --> pdb=" O GLU I 372 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N HIS I 374 " --> pdb=" O ILE G 371 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR G 373 " --> pdb=" O HIS I 374 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LEU I 376 " --> pdb=" O THR G 373 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS G 375 " --> pdb=" O LEU I 376 " (cutoff:3.500A) 128 hydrogen bonds defined for protein. 384 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: 3.18 Time building geometry restraints manager: 8.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.11: 5211 1.11 - 1.28: 837 1.28 - 1.46: 1329 1.46 - 1.63: 2928 1.63 - 1.81: 9 Bond restraints: 10314 Sorted by residual: bond pdb=" ND2 ASN H 359 " pdb="HD22 ASN H 359 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N LYS A 340 " pdb=" H LYS A 340 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N LYS I 347 " pdb=" H LYS I 347 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N ILE C 360 " pdb=" H ILE C 360 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" N THR A 361 " pdb=" H THR A 361 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 ... (remaining 10309 not shown) Histogram of bond angle deviations from ideal: 96.39 - 102.97: 39 102.97 - 109.56: 8016 109.56 - 116.14: 5528 116.14 - 122.73: 4260 122.73 - 129.31: 976 Bond angle restraints: 18819 Sorted by residual: angle pdb=" CB HIS F 374 " pdb=" CG HIS F 374 " pdb=" CD2 HIS F 374 " ideal model delta sigma weight residual 131.20 124.93 6.27 1.30e+00 5.92e-01 2.33e+01 angle pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " pdb=" CD2 HIS A 374 " ideal model delta sigma weight residual 131.20 124.93 6.27 1.30e+00 5.92e-01 2.32e+01 angle pdb=" CB HIS I 374 " pdb=" CG HIS I 374 " pdb=" CD2 HIS I 374 " ideal model delta sigma weight residual 131.20 124.97 6.23 1.30e+00 5.92e-01 2.29e+01 angle pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " pdb=" CD2 HIS E 374 " ideal model delta sigma weight residual 131.20 125.02 6.18 1.30e+00 5.92e-01 2.26e+01 angle pdb=" CB HIS B 374 " pdb=" CG HIS B 374 " pdb=" CD2 HIS B 374 " ideal model delta sigma weight residual 131.20 125.10 6.10 1.30e+00 5.92e-01 2.20e+01 ... (remaining 18814 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.54: 4119 13.54 - 27.08: 294 27.08 - 40.62: 97 40.62 - 54.16: 123 54.16 - 67.70: 119 Dihedral angle restraints: 4752 sinusoidal: 2709 harmonic: 2043 Sorted by residual: dihedral pdb=" CA ILE G 371 " pdb=" C ILE G 371 " pdb=" N GLU G 372 " pdb=" CA GLU G 372 " ideal model delta harmonic sigma weight residual -180.00 -157.59 -22.41 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA SER H 316 " pdb=" C SER H 316 " pdb=" N LYS H 317 " pdb=" CA LYS H 317 " ideal model delta harmonic sigma weight residual 180.00 158.19 21.81 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA ILE A 371 " pdb=" C ILE A 371 " pdb=" N GLU A 372 " pdb=" CA GLU A 372 " ideal model delta harmonic sigma weight residual 180.00 -158.21 -21.79 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 4749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 435 0.064 - 0.129: 243 0.129 - 0.193: 72 0.193 - 0.258: 18 0.258 - 0.322: 6 Chirality restraints: 774 Sorted by residual: chirality pdb=" CA LYS H 317 " pdb=" N LYS H 317 " pdb=" C LYS H 317 " pdb=" CB LYS H 317 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA LYS C 317 " pdb=" N LYS C 317 " pdb=" C LYS C 317 " pdb=" CB LYS C 317 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA LYS D 317 " pdb=" N LYS D 317 " pdb=" C LYS D 317 " pdb=" CB LYS D 317 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 771 not shown) Planarity restraints: 1485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 368 " 0.073 2.00e-02 2.50e+03 6.46e-02 6.25e+01 pdb=" CG ASN F 368 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN F 368 " -0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN F 368 " -0.042 2.00e-02 2.50e+03 pdb="HD21 ASN F 368 " -0.061 2.00e-02 2.50e+03 pdb="HD22 ASN F 368 " 0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 368 " -0.070 2.00e-02 2.50e+03 6.41e-02 6.16e+01 pdb=" CG ASN A 368 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN A 368 " 0.056 2.00e-02 2.50e+03 pdb=" ND2 ASN A 368 " 0.031 2.00e-02 2.50e+03 pdb="HD21 ASN A 368 " 0.070 2.00e-02 2.50e+03 pdb="HD22 ASN A 368 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 310 " -0.090 2.00e-02 2.50e+03 4.17e-02 5.23e+01 pdb=" CG TYR B 310 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR B 310 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR B 310 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR B 310 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 TYR B 310 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR B 310 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 310 " -0.085 2.00e-02 2.50e+03 pdb=" HD1 TYR B 310 " -0.007 2.00e-02 2.50e+03 pdb=" HD2 TYR B 310 " 0.035 2.00e-02 2.50e+03 pdb=" HE1 TYR B 310 " 0.029 2.00e-02 2.50e+03 pdb=" HE2 TYR B 310 " -0.005 2.00e-02 2.50e+03 ... (remaining 1482 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 873 2.18 - 2.79: 18013 2.79 - 3.39: 26435 3.39 - 4.00: 37363 4.00 - 4.60: 50819 Nonbonded interactions: 133503 Sorted by model distance: nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.581 2.450 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.581 2.450 nonbonded pdb=" OD1 ASP I 314 " pdb=" HG SER I 316 " model vdw 1.587 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.602 2.450 nonbonded pdb=" OD1 ASP G 314 " pdb=" HG SER G 316 " model vdw 1.605 2.450 ... (remaining 133498 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 20.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 33.040 Find NCS groups from input model: 0.270 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:10.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 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 0.034 5094 Z= 0.743 Angle : 1.762 8.654 6822 Z= 1.160 Chirality : 0.086 0.322 774 Planarity : 0.011 0.048 864 Dihedral : 11.628 51.205 1944 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.003 HIS H 330 PHE 0.030 0.009 PHE A 346 TYR 0.083 0.026 TYR B 310 ARG 0.006 0.002 ARG I 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 0.887 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: 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 309 VAL cc_start: 0.5819 (t) cc_final: 0.5517 (p) REVERT: A 324 SER cc_start: 0.8584 (p) cc_final: 0.8251 (m) REVERT: A 340 LYS cc_start: 0.8088 (mtpt) cc_final: 0.7686 (mttp) REVERT: A 342 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7651 (mm-30) REVERT: A 347 LYS cc_start: 0.8284 (mttt) cc_final: 0.8012 (mttp) REVERT: A 372 GLU cc_start: 0.7135 (tt0) cc_final: 0.6586 (mm-30) REVERT: A 377 THR cc_start: 0.7169 (m) cc_final: 0.6629 (p) REVERT: C 324 SER cc_start: 0.8585 (p) cc_final: 0.8298 (m) REVERT: C 340 LYS cc_start: 0.7959 (mtpt) cc_final: 0.7541 (mttt) REVERT: C 342 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7591 (mm-30) REVERT: C 343 LYS cc_start: 0.8730 (mttt) cc_final: 0.8508 (mttm) REVERT: C 345 ASP cc_start: 0.8195 (t0) cc_final: 0.7933 (t70) REVERT: C 372 GLU cc_start: 0.7988 (tt0) cc_final: 0.7520 (mm-30) REVERT: C 374 HIS cc_start: 0.8072 (m-70) cc_final: 0.7760 (m-70) REVERT: C 375 LYS cc_start: 0.5754 (tttt) cc_final: 0.5384 (tppt) REVERT: C 376 LEU cc_start: 0.7456 (tt) cc_final: 0.7253 (tt) REVERT: C 378 PHE cc_start: 0.5176 (t80) cc_final: 0.4857 (t80) REVERT: E 310 TYR cc_start: 0.4492 (t80) cc_final: 0.4177 (t80) REVERT: E 320 SER cc_start: 0.8155 (t) cc_final: 0.7583 (p) REVERT: E 324 SER cc_start: 0.8541 (p) cc_final: 0.8158 (m) REVERT: E 340 LYS cc_start: 0.8463 (mtpt) cc_final: 0.8166 (mttt) REVERT: E 342 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7872 (mm-30) REVERT: E 347 LYS cc_start: 0.8562 (mttt) cc_final: 0.7879 (mppt) REVERT: E 349 ARG cc_start: 0.6815 (mtt180) cc_final: 0.5220 (pmt-80) REVERT: E 369 LYS cc_start: 0.8091 (mttt) cc_final: 0.7664 (ttmp) REVERT: E 375 LYS cc_start: 0.7341 (tttt) cc_final: 0.6139 (pptt) REVERT: E 378 PHE cc_start: 0.4387 (t80) cc_final: 0.4181 (t80) REVERT: B 309 VAL cc_start: 0.5755 (t) cc_final: 0.5427 (p) REVERT: B 320 SER cc_start: 0.8638 (t) cc_final: 0.8286 (p) REVERT: B 321 LYS cc_start: 0.7466 (mtpt) cc_final: 0.7080 (mtmt) REVERT: B 340 LYS cc_start: 0.7939 (mtpt) cc_final: 0.7590 (mttt) REVERT: B 342 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7622 (mm-30) REVERT: B 372 GLU cc_start: 0.7352 (tt0) cc_final: 0.6542 (mm-30) REVERT: B 375 LYS cc_start: 0.6009 (tttt) cc_final: 0.5746 (tptt) REVERT: B 377 THR cc_start: 0.7037 (m) cc_final: 0.6703 (p) REVERT: D 342 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7459 (mm-30) REVERT: D 345 ASP cc_start: 0.8153 (t0) cc_final: 0.7628 (t0) REVERT: D 372 GLU cc_start: 0.8025 (tt0) cc_final: 0.7584 (mm-30) REVERT: D 373 THR cc_start: 0.5821 (m) cc_final: 0.5615 (m) REVERT: D 374 HIS cc_start: 0.8008 (m-70) cc_final: 0.7372 (m-70) REVERT: D 375 LYS cc_start: 0.5800 (tttt) cc_final: 0.5569 (tppt) REVERT: D 377 THR cc_start: 0.6655 (m) cc_final: 0.6015 (p) REVERT: F 310 TYR cc_start: 0.4497 (t80) cc_final: 0.4165 (t80) REVERT: F 340 LYS cc_start: 0.8470 (mtpt) cc_final: 0.8178 (mttt) REVERT: F 342 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8005 (mm-30) REVERT: F 349 ARG cc_start: 0.6828 (mtt180) cc_final: 0.5349 (ppt90) REVERT: F 369 LYS cc_start: 0.7982 (mttt) cc_final: 0.7778 (mtmm) REVERT: F 375 LYS cc_start: 0.7226 (tttt) cc_final: 0.5927 (pptt) REVERT: F 378 PHE cc_start: 0.4768 (t80) cc_final: 0.4545 (t80) REVERT: G 309 VAL cc_start: 0.5700 (t) cc_final: 0.5433 (p) REVERT: G 310 TYR cc_start: 0.4789 (t80) cc_final: 0.4543 (t80) REVERT: G 342 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7671 (mm-30) REVERT: G 345 ASP cc_start: 0.8364 (t0) cc_final: 0.8116 (t0) REVERT: G 372 GLU cc_start: 0.7231 (tt0) cc_final: 0.6863 (mm-30) REVERT: G 378 PHE cc_start: 0.4375 (t80) cc_final: 0.4156 (t80) REVERT: H 331 LYS cc_start: 0.8573 (mtmt) cc_final: 0.8355 (mtpt) REVERT: H 342 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7672 (mm-30) REVERT: H 345 ASP cc_start: 0.8242 (t0) cc_final: 0.7738 (t0) REVERT: H 347 LYS cc_start: 0.8511 (mttt) cc_final: 0.8299 (mtmt) REVERT: H 372 GLU cc_start: 0.8020 (tt0) cc_final: 0.7632 (mm-30) REVERT: H 374 HIS cc_start: 0.7980 (m-70) cc_final: 0.7551 (m-70) REVERT: H 375 LYS cc_start: 0.5712 (tttt) cc_final: 0.5417 (tppt) REVERT: I 309 VAL cc_start: 0.7306 (t) cc_final: 0.7096 (p) REVERT: I 310 TYR cc_start: 0.4767 (t80) cc_final: 0.4418 (t80) REVERT: I 320 SER cc_start: 0.8304 (t) cc_final: 0.7840 (p) REVERT: I 340 LYS cc_start: 0.8512 (mtpt) cc_final: 0.8252 (mttt) REVERT: I 342 GLU cc_start: 0.8419 (mt-10) cc_final: 0.7929 (mm-30) REVERT: I 347 LYS cc_start: 0.8611 (mttt) cc_final: 0.7850 (mppt) REVERT: I 349 ARG cc_start: 0.6703 (mtt180) cc_final: 0.5267 (pmt-80) REVERT: I 369 LYS cc_start: 0.8060 (mttt) cc_final: 0.7825 (ttmt) REVERT: I 375 LYS cc_start: 0.7280 (tttt) cc_final: 0.6052 (pptt) REVERT: I 378 PHE cc_start: 0.4593 (t80) cc_final: 0.4387 (t80) outliers start: 0 outliers final: 1 residues processed: 272 average time/residue: 2.4440 time to fit residues: 689.7360 Evaluate side-chains 220 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 219 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS B 307 GLN B 374 HIS H 307 GLN I 374 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5094 Z= 0.265 Angle : 0.610 4.468 6822 Z= 0.324 Chirality : 0.052 0.142 774 Planarity : 0.003 0.020 864 Dihedral : 7.864 120.248 668 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 0.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 2.08 % Allowed : 12.50 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 374 PHE 0.005 0.001 PHE D 346 TYR 0.011 0.002 TYR D 310 ARG 0.002 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 203 time to evaluate : 0.953 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: A 309 VAL cc_start: 0.5878 (t) cc_final: 0.5400 (p) REVERT: A 342 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7659 (mm-30) REVERT: A 345 ASP cc_start: 0.8386 (t0) cc_final: 0.8031 (t0) REVERT: A 369 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.7133 (ttmm) REVERT: A 372 GLU cc_start: 0.6944 (tt0) cc_final: 0.6567 (mm-30) REVERT: C 311 LYS cc_start: 0.6326 (mtpt) cc_final: 0.5712 (mmpt) REVERT: C 340 LYS cc_start: 0.8143 (mtpt) cc_final: 0.7763 (mttt) REVERT: C 342 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7844 (mm-30) REVERT: C 345 ASP cc_start: 0.8427 (t0) cc_final: 0.8034 (t0) REVERT: C 372 GLU cc_start: 0.8254 (tt0) cc_final: 0.7788 (mm-30) REVERT: C 375 LYS cc_start: 0.6051 (tttt) cc_final: 0.5583 (tppt) REVERT: C 376 LEU cc_start: 0.7507 (tt) cc_final: 0.7186 (tt) REVERT: C 378 PHE cc_start: 0.5625 (t80) cc_final: 0.5353 (t80) REVERT: E 311 LYS cc_start: 0.7093 (ttpt) cc_final: 0.6791 (mtpp) REVERT: E 317 LYS cc_start: 0.5419 (pttt) cc_final: 0.5185 (mtpp) REVERT: E 321 LYS cc_start: 0.7922 (mtpt) cc_final: 0.7696 (mtpt) REVERT: E 340 LYS cc_start: 0.8488 (mtpt) cc_final: 0.8176 (mttt) REVERT: E 342 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7927 (mm-30) REVERT: E 347 LYS cc_start: 0.8629 (mttt) cc_final: 0.7899 (mppt) REVERT: E 349 ARG cc_start: 0.6754 (mtt180) cc_final: 0.5161 (pmt-80) REVERT: E 369 LYS cc_start: 0.8041 (mttt) cc_final: 0.7595 (ttmp) REVERT: E 372 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7222 (mm-30) REVERT: E 375 LYS cc_start: 0.7446 (tttt) cc_final: 0.6431 (tmmt) REVERT: E 378 PHE cc_start: 0.4570 (t80) cc_final: 0.4339 (t80) REVERT: B 309 VAL cc_start: 0.5786 (t) cc_final: 0.5464 (p) REVERT: B 310 TYR cc_start: 0.4850 (t80) cc_final: 0.4583 (t80) REVERT: B 324 SER cc_start: 0.8324 (OUTLIER) cc_final: 0.8060 (m) REVERT: B 331 LYS cc_start: 0.8655 (mtmt) cc_final: 0.8410 (mtmt) REVERT: B 342 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7821 (mm-30) REVERT: B 372 GLU cc_start: 0.6900 (tt0) cc_final: 0.6401 (mm-30) REVERT: D 324 SER cc_start: 0.8440 (OUTLIER) cc_final: 0.8186 (m) REVERT: D 331 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8415 (mtmm) REVERT: D 342 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7796 (mm-30) REVERT: D 345 ASP cc_start: 0.8325 (t0) cc_final: 0.7930 (t0) REVERT: D 372 GLU cc_start: 0.8134 (tt0) cc_final: 0.7620 (mm-30) REVERT: D 373 THR cc_start: 0.5925 (m) cc_final: 0.5582 (m) REVERT: D 375 LYS cc_start: 0.5968 (tttt) cc_final: 0.5546 (tppt) REVERT: F 311 LYS cc_start: 0.6982 (ttpt) cc_final: 0.6666 (mtpp) REVERT: F 317 LYS cc_start: 0.5558 (pttt) cc_final: 0.5308 (mtpp) REVERT: F 324 SER cc_start: 0.8616 (p) cc_final: 0.8378 (m) REVERT: F 338 GLU cc_start: 0.7521 (tt0) cc_final: 0.7294 (tt0) REVERT: F 340 LYS cc_start: 0.8419 (mtpt) cc_final: 0.8129 (mttt) REVERT: F 342 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8005 (mm-30) REVERT: F 347 LYS cc_start: 0.8630 (mttt) cc_final: 0.7847 (mppt) REVERT: F 349 ARG cc_start: 0.6776 (mtt180) cc_final: 0.5244 (pmt-80) REVERT: F 375 LYS cc_start: 0.7507 (tttt) cc_final: 0.6385 (tmmt) REVERT: G 309 VAL cc_start: 0.5811 (t) cc_final: 0.5473 (p) REVERT: G 324 SER cc_start: 0.8269 (OUTLIER) cc_final: 0.8037 (m) REVERT: G 331 LYS cc_start: 0.8736 (mtmm) cc_final: 0.8443 (mmmm) REVERT: G 340 LYS cc_start: 0.8083 (mtpt) cc_final: 0.7609 (mttt) REVERT: G 342 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7704 (mm-30) REVERT: G 349 ARG cc_start: 0.6725 (mtm180) cc_final: 0.6332 (mtp85) REVERT: H 309 VAL cc_start: 0.5314 (t) cc_final: 0.4945 (p) REVERT: H 340 LYS cc_start: 0.8179 (mtpt) cc_final: 0.7760 (mttt) REVERT: H 342 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7881 (mm-30) REVERT: H 345 ASP cc_start: 0.8386 (t0) cc_final: 0.8164 (t70) REVERT: H 372 GLU cc_start: 0.8188 (tt0) cc_final: 0.7737 (mm-30) REVERT: H 375 LYS cc_start: 0.5985 (tttt) cc_final: 0.5490 (tppt) REVERT: I 310 TYR cc_start: 0.4969 (t80) cc_final: 0.4626 (t80) REVERT: I 311 LYS cc_start: 0.6947 (ttpt) cc_final: 0.6635 (mttp) REVERT: I 317 LYS cc_start: 0.5400 (pttt) cc_final: 0.5182 (mtpt) REVERT: I 324 SER cc_start: 0.8431 (p) cc_final: 0.8215 (m) REVERT: I 340 LYS cc_start: 0.8518 (mtpt) cc_final: 0.8235 (mttt) REVERT: I 342 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7950 (mm-30) REVERT: I 347 LYS cc_start: 0.8648 (mttt) cc_final: 0.7861 (mppt) REVERT: I 349 ARG cc_start: 0.6763 (mtt180) cc_final: 0.5128 (pmt-80) REVERT: I 369 LYS cc_start: 0.8033 (mttt) cc_final: 0.7548 (ttmp) REVERT: I 372 GLU cc_start: 0.7596 (mm-30) cc_final: 0.6999 (mm-30) REVERT: I 375 LYS cc_start: 0.7415 (tttt) cc_final: 0.6036 (pptt) outliers start: 12 outliers final: 2 residues processed: 205 average time/residue: 2.9567 time to fit residues: 625.8006 Evaluate side-chains 179 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 172 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain G residue 324 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 307 GLN H 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5094 Z= 0.214 Angle : 0.532 4.180 6822 Z= 0.279 Chirality : 0.052 0.140 774 Planarity : 0.002 0.018 864 Dihedral : 5.534 16.386 666 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 0.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 2.26 % Allowed : 14.24 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 374 PHE 0.006 0.001 PHE C 346 TYR 0.006 0.001 TYR G 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 170 time to evaluate : 0.832 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: A 309 VAL cc_start: 0.5830 (t) cc_final: 0.5273 (p) REVERT: A 342 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7641 (mm-30) REVERT: A 345 ASP cc_start: 0.8336 (t0) cc_final: 0.8062 (t0) REVERT: A 369 LYS cc_start: 0.7385 (OUTLIER) cc_final: 0.7092 (ttmm) REVERT: A 372 GLU cc_start: 0.7116 (tt0) cc_final: 0.6770 (mm-30) REVERT: C 320 SER cc_start: 0.8848 (t) cc_final: 0.8602 (p) REVERT: C 340 LYS cc_start: 0.8174 (mtpt) cc_final: 0.7805 (mttt) REVERT: C 342 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7848 (mm-30) REVERT: C 345 ASP cc_start: 0.8381 (t0) cc_final: 0.8155 (t0) REVERT: C 372 GLU cc_start: 0.8281 (tt0) cc_final: 0.7799 (mm-30) REVERT: C 375 LYS cc_start: 0.5942 (tttt) cc_final: 0.5511 (tppt) REVERT: C 378 PHE cc_start: 0.5678 (t80) cc_final: 0.5412 (t80) REVERT: E 311 LYS cc_start: 0.7058 (ttpt) cc_final: 0.6734 (mtpp) REVERT: E 321 LYS cc_start: 0.7922 (mtpt) cc_final: 0.7405 (mtpt) REVERT: E 340 LYS cc_start: 0.8483 (mtpt) cc_final: 0.8185 (mttm) REVERT: E 342 GLU cc_start: 0.8400 (mt-10) cc_final: 0.7927 (mm-30) REVERT: E 347 LYS cc_start: 0.8622 (mttt) cc_final: 0.7545 (ttpt) REVERT: E 349 ARG cc_start: 0.6881 (mtt180) cc_final: 0.5153 (pmt-80) REVERT: E 369 LYS cc_start: 0.8045 (mttt) cc_final: 0.7586 (ttmp) REVERT: E 372 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7412 (mm-30) REVERT: E 375 LYS cc_start: 0.7410 (tttt) cc_final: 0.6379 (tmmt) REVERT: E 378 PHE cc_start: 0.4652 (t80) cc_final: 0.4396 (t80) REVERT: B 340 LYS cc_start: 0.8149 (mtpt) cc_final: 0.7717 (mttt) REVERT: B 342 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7774 (mm-30) REVERT: B 372 GLU cc_start: 0.7163 (tt0) cc_final: 0.6571 (mm-30) REVERT: D 340 LYS cc_start: 0.8111 (mtpt) cc_final: 0.7722 (mttt) REVERT: D 342 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7743 (mm-30) REVERT: D 345 ASP cc_start: 0.8363 (t0) cc_final: 0.8044 (t0) REVERT: D 372 GLU cc_start: 0.8262 (tt0) cc_final: 0.7732 (mm-30) REVERT: D 375 LYS cc_start: 0.6061 (tttt) cc_final: 0.5612 (tppt) REVERT: F 311 LYS cc_start: 0.6962 (ttpt) cc_final: 0.6632 (mttt) REVERT: F 338 GLU cc_start: 0.7506 (tt0) cc_final: 0.7269 (tp30) REVERT: F 340 LYS cc_start: 0.8440 (mtpt) cc_final: 0.8135 (mttt) REVERT: F 342 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8006 (mm-30) REVERT: F 347 LYS cc_start: 0.8614 (mttt) cc_final: 0.7576 (ttpt) REVERT: F 349 ARG cc_start: 0.6924 (mtt180) cc_final: 0.5249 (pmt-80) REVERT: F 375 LYS cc_start: 0.7516 (tttt) cc_final: 0.6409 (tmmt) REVERT: G 314 ASP cc_start: 0.5520 (t0) cc_final: 0.5307 (t0) REVERT: G 324 SER cc_start: 0.8380 (OUTLIER) cc_final: 0.8168 (m) REVERT: G 342 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7727 (mm-30) REVERT: G 349 ARG cc_start: 0.6812 (mtm180) cc_final: 0.6309 (mtp85) REVERT: H 340 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7777 (mttt) REVERT: H 342 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7855 (mm-30) REVERT: H 372 GLU cc_start: 0.8181 (tt0) cc_final: 0.7777 (mm-30) REVERT: H 375 LYS cc_start: 0.5934 (tttt) cc_final: 0.5517 (tppt) REVERT: I 311 LYS cc_start: 0.6985 (ttpt) cc_final: 0.6650 (mttt) REVERT: I 314 ASP cc_start: 0.5816 (t0) cc_final: 0.5551 (t0) REVERT: I 340 LYS cc_start: 0.8514 (mtpt) cc_final: 0.8246 (mttt) REVERT: I 342 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8006 (mm-30) REVERT: I 347 LYS cc_start: 0.8672 (mttt) cc_final: 0.7916 (mppt) REVERT: I 349 ARG cc_start: 0.6921 (mtt180) cc_final: 0.5159 (pmt-80) REVERT: I 369 LYS cc_start: 0.8043 (mttt) cc_final: 0.7555 (ttmp) REVERT: I 375 LYS cc_start: 0.7431 (tttt) cc_final: 0.6040 (pptt) outliers start: 13 outliers final: 2 residues processed: 173 average time/residue: 3.0653 time to fit residues: 547.4119 Evaluate side-chains 162 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 158 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 345 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 16 optimal weight: 0.0970 overall best weight: 4.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 307 GLN H 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 5094 Z= 0.303 Angle : 0.560 4.276 6822 Z= 0.294 Chirality : 0.051 0.143 774 Planarity : 0.003 0.016 864 Dihedral : 5.531 17.606 666 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.43 % Allowed : 14.58 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 374 PHE 0.007 0.001 PHE C 346 TYR 0.016 0.002 TYR G 310 ARG 0.002 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 160 time to evaluate : 0.900 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: A 342 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7653 (mm-30) REVERT: C 311 LYS cc_start: 0.6347 (mtpt) cc_final: 0.5673 (mmpt) REVERT: C 331 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8475 (mmmm) REVERT: C 340 LYS cc_start: 0.8159 (mtpt) cc_final: 0.7754 (mttt) REVERT: C 342 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7758 (mm-30) REVERT: C 375 LYS cc_start: 0.5997 (tttt) cc_final: 0.5573 (tppt) REVERT: C 378 PHE cc_start: 0.5770 (t80) cc_final: 0.5496 (t80) REVERT: E 311 LYS cc_start: 0.7043 (ttpt) cc_final: 0.6704 (mttt) REVERT: E 321 LYS cc_start: 0.7866 (mtpt) cc_final: 0.7630 (mtpt) REVERT: E 338 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7769 (tm-30) REVERT: E 342 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7977 (mm-30) REVERT: E 347 LYS cc_start: 0.8655 (mttt) cc_final: 0.7937 (mppt) REVERT: E 349 ARG cc_start: 0.7196 (mtt180) cc_final: 0.5115 (pmt-80) REVERT: E 369 LYS cc_start: 0.8115 (mttt) cc_final: 0.7642 (ttmp) REVERT: E 375 LYS cc_start: 0.7405 (tttt) cc_final: 0.6344 (tmmt) REVERT: B 340 LYS cc_start: 0.8110 (mtpt) cc_final: 0.7664 (mttt) REVERT: B 342 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7753 (mm-30) REVERT: D 320 SER cc_start: 0.8952 (t) cc_final: 0.8749 (p) REVERT: D 340 LYS cc_start: 0.8099 (mtpt) cc_final: 0.7692 (mttt) REVERT: D 342 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7705 (mm-30) REVERT: D 345 ASP cc_start: 0.8311 (t0) cc_final: 0.7973 (t0) REVERT: D 375 LYS cc_start: 0.5917 (tttt) cc_final: 0.5494 (tppt) REVERT: F 310 TYR cc_start: 0.5030 (t80) cc_final: 0.4698 (t80) REVERT: F 311 LYS cc_start: 0.6990 (ttpt) cc_final: 0.6650 (mttt) REVERT: F 338 GLU cc_start: 0.7567 (tt0) cc_final: 0.7345 (tt0) REVERT: F 340 LYS cc_start: 0.8482 (mtpt) cc_final: 0.8168 (mttt) REVERT: F 342 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8035 (mm-30) REVERT: F 347 LYS cc_start: 0.8638 (mttt) cc_final: 0.7867 (mppt) REVERT: F 375 LYS cc_start: 0.7526 (tttt) cc_final: 0.6429 (tmmt) REVERT: G 342 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7686 (mm-30) REVERT: H 340 LYS cc_start: 0.8199 (mtpt) cc_final: 0.7766 (mttt) REVERT: H 342 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7868 (mm-30) REVERT: H 375 LYS cc_start: 0.5872 (tttt) cc_final: 0.5509 (tppt) REVERT: I 310 TYR cc_start: 0.5175 (t80) cc_final: 0.4896 (t80) REVERT: I 311 LYS cc_start: 0.6960 (ttpt) cc_final: 0.6653 (mttt) REVERT: I 340 LYS cc_start: 0.8552 (mtpt) cc_final: 0.8245 (mttt) REVERT: I 342 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8091 (mm-30) REVERT: I 347 LYS cc_start: 0.8681 (mttt) cc_final: 0.7906 (mppt) REVERT: I 369 LYS cc_start: 0.8150 (mttt) cc_final: 0.7641 (ttmp) REVERT: I 375 LYS cc_start: 0.7444 (tttt) cc_final: 0.6413 (tmmt) outliers start: 14 outliers final: 5 residues processed: 162 average time/residue: 3.1637 time to fit residues: 528.0904 Evaluate side-chains 153 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 146 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain G residue 309 VAL Chi-restraints excluded: chain G 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: 7.9990 chunk 34 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 42 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN H 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5094 Z= 0.207 Angle : 0.503 4.159 6822 Z= 0.262 Chirality : 0.051 0.139 774 Planarity : 0.002 0.017 864 Dihedral : 5.149 16.409 666 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.56 % Allowed : 17.01 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS C 374 PHE 0.008 0.001 PHE C 346 TYR 0.009 0.001 TYR G 310 ARG 0.003 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 151 time to evaluate : 0.877 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: A 309 VAL cc_start: 0.5694 (t) cc_final: 0.5479 (t) REVERT: A 342 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7641 (mm-30) REVERT: C 311 LYS cc_start: 0.6383 (mtpt) cc_final: 0.5671 (mmpt) REVERT: C 340 LYS cc_start: 0.8174 (mtpt) cc_final: 0.7749 (mttt) REVERT: C 342 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7751 (mm-30) REVERT: C 375 LYS cc_start: 0.5931 (tttt) cc_final: 0.5546 (tppt) REVERT: C 378 PHE cc_start: 0.5647 (t80) cc_final: 0.5391 (t80) REVERT: E 311 LYS cc_start: 0.7049 (ttpt) cc_final: 0.6715 (mttt) REVERT: E 340 LYS cc_start: 0.8559 (mtpt) cc_final: 0.8245 (mttm) REVERT: E 342 GLU cc_start: 0.8430 (mt-10) cc_final: 0.7978 (mm-30) REVERT: E 347 LYS cc_start: 0.8641 (mttt) cc_final: 0.7926 (mppt) REVERT: E 369 LYS cc_start: 0.8070 (mttt) cc_final: 0.7608 (ttmp) REVERT: E 375 LYS cc_start: 0.7473 (tttt) cc_final: 0.6400 (tmmt) REVERT: E 378 PHE cc_start: 0.4671 (t80) cc_final: 0.4453 (t80) REVERT: B 340 LYS cc_start: 0.8170 (mtpt) cc_final: 0.7725 (mttt) REVERT: B 342 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7760 (mm-30) REVERT: D 340 LYS cc_start: 0.8104 (mtpt) cc_final: 0.7692 (mttt) REVERT: D 342 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7694 (mm-30) REVERT: D 345 ASP cc_start: 0.8312 (t0) cc_final: 0.7966 (t0) REVERT: D 375 LYS cc_start: 0.5985 (tttt) cc_final: 0.5583 (tppt) REVERT: F 310 TYR cc_start: 0.5171 (t80) cc_final: 0.4884 (t80) REVERT: F 311 LYS cc_start: 0.6919 (ttpt) cc_final: 0.6600 (mttt) REVERT: F 338 GLU cc_start: 0.7525 (tt0) cc_final: 0.7293 (tt0) REVERT: F 340 LYS cc_start: 0.8497 (mtpt) cc_final: 0.8168 (mttt) REVERT: F 342 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8001 (mm-30) REVERT: F 347 LYS cc_start: 0.8646 (mttt) cc_final: 0.7873 (mppt) REVERT: F 375 LYS cc_start: 0.7539 (tttt) cc_final: 0.6472 (tmmt) REVERT: G 342 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7690 (mm-30) REVERT: H 340 LYS cc_start: 0.8219 (mtpt) cc_final: 0.7793 (mttt) REVERT: H 342 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7849 (mm-30) REVERT: H 375 LYS cc_start: 0.5928 (tttt) cc_final: 0.5514 (tppt) REVERT: I 311 LYS cc_start: 0.6985 (ttpt) cc_final: 0.6660 (mttt) REVERT: I 314 ASP cc_start: 0.5828 (t0) cc_final: 0.5396 (t0) REVERT: I 340 LYS cc_start: 0.8544 (mtpt) cc_final: 0.8243 (mttt) REVERT: I 342 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8058 (mm-30) REVERT: I 347 LYS cc_start: 0.8664 (mttt) cc_final: 0.7886 (mppt) REVERT: I 369 LYS cc_start: 0.8069 (mttt) cc_final: 0.7591 (ttmp) REVERT: I 375 LYS cc_start: 0.7488 (tttt) cc_final: 0.6051 (pptt) outliers start: 9 outliers final: 6 residues processed: 154 average time/residue: 3.1018 time to fit residues: 493.0043 Evaluate side-chains 150 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 144 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain G residue 309 VAL Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain I residue 309 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.5315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5094 Z= 0.262 Angle : 0.525 4.728 6822 Z= 0.274 Chirality : 0.051 0.142 774 Planarity : 0.003 0.022 864 Dihedral : 5.210 16.655 666 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.26 % Allowed : 17.71 % Favored : 80.03 % 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: -2.24 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.20), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.008 0.001 PHE C 346 TYR 0.010 0.002 TYR G 310 ARG 0.003 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 149 time to evaluate : 0.900 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: A 309 VAL cc_start: 0.5690 (t) cc_final: 0.5490 (t) REVERT: A 342 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7639 (mm-30) REVERT: C 311 LYS cc_start: 0.6293 (mtpt) cc_final: 0.5592 (mmpt) REVERT: C 340 LYS cc_start: 0.8186 (mtpt) cc_final: 0.7795 (mttt) REVERT: C 342 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7751 (mm-30) REVERT: C 375 LYS cc_start: 0.5937 (tttt) cc_final: 0.5536 (tppt) REVERT: C 378 PHE cc_start: 0.5646 (t80) cc_final: 0.5399 (t80) REVERT: E 311 LYS cc_start: 0.7052 (ttpt) cc_final: 0.6711 (mttt) REVERT: E 338 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7758 (tm-30) REVERT: E 342 GLU cc_start: 0.8424 (mt-10) cc_final: 0.7971 (mm-30) REVERT: E 347 LYS cc_start: 0.8650 (mttt) cc_final: 0.7951 (mppt) REVERT: E 369 LYS cc_start: 0.8132 (mttt) cc_final: 0.7645 (ttmp) REVERT: E 375 LYS cc_start: 0.7479 (tttt) cc_final: 0.6402 (tmmt) REVERT: E 378 PHE cc_start: 0.4684 (t80) cc_final: 0.4475 (t80) REVERT: B 340 LYS cc_start: 0.8165 (mtpt) cc_final: 0.7719 (mttt) REVERT: B 342 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7760 (mm-30) REVERT: D 340 LYS cc_start: 0.8117 (mtpt) cc_final: 0.7691 (mttt) REVERT: D 342 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7697 (mm-30) REVERT: D 345 ASP cc_start: 0.8291 (t0) cc_final: 0.7943 (t0) REVERT: D 375 LYS cc_start: 0.5954 (tttt) cc_final: 0.5561 (tppt) REVERT: F 310 TYR cc_start: 0.5179 (t80) cc_final: 0.4909 (t80) REVERT: F 311 LYS cc_start: 0.6936 (ttpt) cc_final: 0.6637 (mttt) REVERT: F 338 GLU cc_start: 0.7578 (tt0) cc_final: 0.7319 (tt0) REVERT: F 340 LYS cc_start: 0.8511 (mtpt) cc_final: 0.8186 (mttt) REVERT: F 342 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8021 (mm-30) REVERT: F 347 LYS cc_start: 0.8658 (mttt) cc_final: 0.7892 (mppt) REVERT: F 375 LYS cc_start: 0.7593 (tttt) cc_final: 0.6490 (tmmt) REVERT: G 342 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7686 (mm-30) REVERT: H 340 LYS cc_start: 0.8210 (mtpt) cc_final: 0.7782 (mttt) REVERT: H 342 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7854 (mm-30) REVERT: H 375 LYS cc_start: 0.5914 (tttt) cc_final: 0.5548 (tppt) REVERT: I 311 LYS cc_start: 0.6933 (ttpt) cc_final: 0.6630 (mttt) REVERT: I 340 LYS cc_start: 0.8552 (mtpt) cc_final: 0.8251 (mttt) REVERT: I 342 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8071 (mm-30) REVERT: I 347 LYS cc_start: 0.8673 (mttt) cc_final: 0.7882 (mppt) REVERT: I 369 LYS cc_start: 0.8149 (mttt) cc_final: 0.7643 (ttmp) REVERT: I 375 LYS cc_start: 0.7534 (tttt) cc_final: 0.6464 (tmmt) outliers start: 13 outliers final: 8 residues processed: 155 average time/residue: 2.8666 time to fit residues: 459.2637 Evaluate side-chains 154 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 145 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain G residue 309 VAL Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain I residue 309 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5094 Z= 0.284 Angle : 0.539 5.565 6822 Z= 0.281 Chirality : 0.051 0.142 774 Planarity : 0.003 0.019 864 Dihedral : 5.229 16.727 666 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.26 % Allowed : 18.40 % Favored : 79.34 % 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: -2.32 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.20), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.007 0.001 PHE C 346 TYR 0.014 0.002 TYR D 310 ARG 0.003 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 148 time to evaluate : 0.957 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: A 309 VAL cc_start: 0.5699 (t) cc_final: 0.5498 (t) REVERT: A 320 SER cc_start: 0.8812 (t) cc_final: 0.8360 (p) REVERT: A 342 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7661 (mm-30) REVERT: C 311 LYS cc_start: 0.6305 (mtpt) cc_final: 0.5597 (mmpt) REVERT: C 340 LYS cc_start: 0.8191 (mtpt) cc_final: 0.7759 (mttt) REVERT: C 342 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7730 (mm-30) REVERT: C 375 LYS cc_start: 0.5999 (tttt) cc_final: 0.5625 (tppt) REVERT: C 378 PHE cc_start: 0.5523 (t80) cc_final: 0.5279 (t80) REVERT: E 311 LYS cc_start: 0.7054 (ttpt) cc_final: 0.6714 (mttt) REVERT: E 340 LYS cc_start: 0.8567 (mtpt) cc_final: 0.8247 (mttp) REVERT: E 342 GLU cc_start: 0.8420 (mt-10) cc_final: 0.7972 (mm-30) REVERT: E 347 LYS cc_start: 0.8656 (mttt) cc_final: 0.7886 (mtmt) REVERT: E 369 LYS cc_start: 0.8136 (mttt) cc_final: 0.7634 (ttmp) REVERT: E 375 LYS cc_start: 0.7515 (tttt) cc_final: 0.6450 (tmmt) REVERT: E 378 PHE cc_start: 0.4525 (t80) cc_final: 0.4184 (t80) REVERT: B 340 LYS cc_start: 0.8161 (mtpt) cc_final: 0.7718 (mttt) REVERT: B 342 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7764 (mm-30) REVERT: D 340 LYS cc_start: 0.8117 (mtpt) cc_final: 0.7679 (mttt) REVERT: D 342 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7727 (mm-30) REVERT: D 345 ASP cc_start: 0.8270 (t0) cc_final: 0.7928 (t0) REVERT: D 375 LYS cc_start: 0.5943 (tttt) cc_final: 0.5590 (tppt) REVERT: F 311 LYS cc_start: 0.6880 (ttpt) cc_final: 0.6592 (mttt) REVERT: F 338 GLU cc_start: 0.7597 (tt0) cc_final: 0.7337 (tt0) REVERT: F 340 LYS cc_start: 0.8532 (mtpt) cc_final: 0.8193 (mttt) REVERT: F 342 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8024 (mm-30) REVERT: F 347 LYS cc_start: 0.8644 (mttt) cc_final: 0.7803 (mtmm) REVERT: F 375 LYS cc_start: 0.7614 (tttt) cc_final: 0.6524 (tmmt) REVERT: G 342 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7685 (mm-30) REVERT: H 340 LYS cc_start: 0.8197 (mtpt) cc_final: 0.7776 (mttt) REVERT: H 342 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7861 (mm-30) REVERT: H 375 LYS cc_start: 0.5914 (tttt) cc_final: 0.5511 (tppt) REVERT: I 311 LYS cc_start: 0.6961 (ttpt) cc_final: 0.6650 (mttt) REVERT: I 340 LYS cc_start: 0.8591 (mtpt) cc_final: 0.8272 (mttt) REVERT: I 342 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8058 (mm-30) REVERT: I 347 LYS cc_start: 0.8661 (mttt) cc_final: 0.7863 (mppt) REVERT: I 369 LYS cc_start: 0.8151 (mttt) cc_final: 0.7268 (tttt) REVERT: I 375 LYS cc_start: 0.7561 (tttt) cc_final: 0.6484 (tmmt) outliers start: 13 outliers final: 8 residues processed: 154 average time/residue: 2.8839 time to fit residues: 459.0288 Evaluate side-chains 155 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 147 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain G residue 309 VAL Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain I residue 309 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5094 Z= 0.324 Angle : 0.558 5.725 6822 Z= 0.292 Chirality : 0.051 0.143 774 Planarity : 0.003 0.020 864 Dihedral : 5.324 17.003 666 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.43 % Allowed : 19.10 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.26), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.20), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 374 PHE 0.008 0.001 PHE C 346 TYR 0.009 0.002 TYR G 310 ARG 0.003 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 150 time to evaluate : 0.949 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: A 309 VAL cc_start: 0.5703 (t) cc_final: 0.5120 (p) REVERT: A 320 SER cc_start: 0.8822 (t) cc_final: 0.8374 (p) REVERT: A 342 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7697 (mm-30) REVERT: C 311 LYS cc_start: 0.6268 (mtpt) cc_final: 0.5594 (mmpt) REVERT: C 331 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8521 (mtmt) REVERT: C 340 LYS cc_start: 0.8162 (mtpt) cc_final: 0.7726 (mttt) REVERT: C 342 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7725 (mm-30) REVERT: C 375 LYS cc_start: 0.6025 (tttt) cc_final: 0.5663 (tppt) REVERT: C 378 PHE cc_start: 0.5514 (t80) cc_final: 0.5257 (t80) REVERT: E 311 LYS cc_start: 0.7053 (ttpt) cc_final: 0.6705 (mttt) REVERT: E 340 LYS cc_start: 0.8573 (mtpt) cc_final: 0.8270 (mttt) REVERT: E 342 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7975 (mm-30) REVERT: E 347 LYS cc_start: 0.8655 (mttt) cc_final: 0.7871 (mtmt) REVERT: E 369 LYS cc_start: 0.8161 (mttt) cc_final: 0.7662 (ttmp) REVERT: E 375 LYS cc_start: 0.7521 (tttt) cc_final: 0.6439 (tmmt) REVERT: B 340 LYS cc_start: 0.8154 (mtpt) cc_final: 0.7711 (mttt) REVERT: B 342 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7759 (mm-30) REVERT: D 340 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7671 (mttt) REVERT: D 342 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7733 (mm-30) REVERT: D 345 ASP cc_start: 0.8271 (t0) cc_final: 0.7942 (t0) REVERT: D 375 LYS cc_start: 0.5925 (tttt) cc_final: 0.5521 (tppt) REVERT: F 311 LYS cc_start: 0.6860 (ttpt) cc_final: 0.6565 (mttt) REVERT: F 338 GLU cc_start: 0.7606 (tt0) cc_final: 0.7346 (tt0) REVERT: F 340 LYS cc_start: 0.8523 (mtpt) cc_final: 0.8184 (mttt) REVERT: F 342 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8021 (mm-30) REVERT: F 347 LYS cc_start: 0.8625 (mttt) cc_final: 0.7798 (mtmm) REVERT: F 375 LYS cc_start: 0.7601 (tttt) cc_final: 0.6498 (tmmt) REVERT: G 342 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7678 (mm-30) REVERT: H 340 LYS cc_start: 0.8214 (mtpt) cc_final: 0.7784 (mttt) REVERT: H 342 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7877 (mm-30) REVERT: H 375 LYS cc_start: 0.5874 (tttt) cc_final: 0.5535 (tppt) REVERT: I 311 LYS cc_start: 0.6929 (ttpt) cc_final: 0.6617 (mttp) REVERT: I 340 LYS cc_start: 0.8591 (mtpt) cc_final: 0.8256 (mttp) REVERT: I 342 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8093 (mm-30) REVERT: I 347 LYS cc_start: 0.8667 (mttt) cc_final: 0.7878 (mppt) REVERT: I 369 LYS cc_start: 0.8158 (mttt) cc_final: 0.7267 (tttt) REVERT: I 375 LYS cc_start: 0.7677 (tttt) cc_final: 0.6573 (tmmt) outliers start: 14 outliers final: 8 residues processed: 155 average time/residue: 2.9632 time to fit residues: 474.5532 Evaluate side-chains 156 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 147 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain G residue 309 VAL Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain I residue 309 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5094 Z= 0.254 Angle : 0.529 5.793 6822 Z= 0.276 Chirality : 0.051 0.141 774 Planarity : 0.003 0.018 864 Dihedral : 5.164 16.221 666 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.22 % Allowed : 20.31 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.20), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 374 PHE 0.008 0.001 PHE C 346 TYR 0.010 0.002 TYR C 310 ARG 0.003 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 151 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 VAL cc_start: 0.5655 (t) cc_final: 0.5434 (t) REVERT: A 320 SER cc_start: 0.8814 (t) cc_final: 0.8360 (p) REVERT: A 342 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7690 (mm-30) REVERT: C 311 LYS cc_start: 0.6272 (mtpt) cc_final: 0.5575 (mmpt) REVERT: C 340 LYS cc_start: 0.8176 (mtpt) cc_final: 0.7743 (mttt) REVERT: C 342 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7705 (mm-30) REVERT: C 375 LYS cc_start: 0.5940 (tttt) cc_final: 0.5646 (tppt) REVERT: E 311 LYS cc_start: 0.7051 (ttpt) cc_final: 0.6700 (mttt) REVERT: E 340 LYS cc_start: 0.8553 (mtpt) cc_final: 0.8245 (mttp) REVERT: E 342 GLU cc_start: 0.8430 (mt-10) cc_final: 0.7973 (mm-30) REVERT: E 347 LYS cc_start: 0.8657 (mttt) cc_final: 0.7877 (mtmt) REVERT: E 369 LYS cc_start: 0.8154 (mttt) cc_final: 0.7668 (ttmp) REVERT: E 375 LYS cc_start: 0.7502 (tttt) cc_final: 0.6436 (tmmt) REVERT: B 340 LYS cc_start: 0.8158 (mtpt) cc_final: 0.7713 (mttp) REVERT: B 342 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7754 (mm-30) REVERT: B 375 LYS cc_start: 0.6583 (tttt) cc_final: 0.6228 (tptt) REVERT: D 340 LYS cc_start: 0.8131 (mtpt) cc_final: 0.7680 (mttt) REVERT: D 342 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7689 (mm-30) REVERT: D 345 ASP cc_start: 0.8270 (t0) cc_final: 0.7945 (t0) REVERT: D 375 LYS cc_start: 0.6067 (tttt) cc_final: 0.5692 (tppt) REVERT: F 310 TYR cc_start: 0.5082 (t80) cc_final: 0.4812 (t80) REVERT: F 311 LYS cc_start: 0.6860 (ttpt) cc_final: 0.6564 (mttt) REVERT: F 338 GLU cc_start: 0.7591 (tt0) cc_final: 0.7331 (tt0) REVERT: F 340 LYS cc_start: 0.8520 (mtpt) cc_final: 0.8187 (mttt) REVERT: F 342 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8015 (mm-30) REVERT: F 347 LYS cc_start: 0.8606 (mttt) cc_final: 0.7713 (mtmm) REVERT: F 375 LYS cc_start: 0.7599 (tttt) cc_final: 0.6488 (tmmt) REVERT: G 342 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7696 (mm-30) REVERT: H 340 LYS cc_start: 0.8194 (mtpt) cc_final: 0.7784 (mttt) REVERT: H 342 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7876 (mm-30) REVERT: H 375 LYS cc_start: 0.5899 (tttt) cc_final: 0.5512 (tppt) REVERT: I 311 LYS cc_start: 0.6932 (ttpt) cc_final: 0.6608 (mttp) REVERT: I 340 LYS cc_start: 0.8590 (mtpt) cc_final: 0.8261 (mttp) REVERT: I 342 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8059 (mm-30) REVERT: I 347 LYS cc_start: 0.8662 (mttt) cc_final: 0.7869 (mppt) REVERT: I 369 LYS cc_start: 0.8145 (mttt) cc_final: 0.7645 (ttmp) REVERT: I 375 LYS cc_start: 0.7532 (tttt) cc_final: 0.6430 (tmmt) outliers start: 7 outliers final: 7 residues processed: 153 average time/residue: 3.0601 time to fit residues: 483.5404 Evaluate side-chains 154 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 147 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain G residue 309 VAL Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain I residue 309 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 38 optimal weight: 0.3980 chunk 30 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.5512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5094 Z= 0.178 Angle : 0.492 5.814 6822 Z= 0.255 Chirality : 0.051 0.139 774 Planarity : 0.002 0.018 864 Dihedral : 4.849 15.000 666 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.39 % Allowed : 20.31 % Favored : 78.30 % 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: -2.33 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.20), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 374 PHE 0.006 0.000 PHE C 346 TYR 0.010 0.001 TYR H 310 ARG 0.002 0.000 ARG E 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 149 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 VAL cc_start: 0.5662 (t) cc_final: 0.5436 (t) REVERT: A 320 SER cc_start: 0.8770 (t) cc_final: 0.8338 (p) REVERT: A 342 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7658 (mm-30) REVERT: C 311 LYS cc_start: 0.6299 (mtpt) cc_final: 0.5567 (mmpt) REVERT: C 340 LYS cc_start: 0.8197 (mtpt) cc_final: 0.7767 (mttt) REVERT: C 342 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7696 (mm-30) REVERT: C 375 LYS cc_start: 0.5918 (tttt) cc_final: 0.5574 (tppt) REVERT: E 311 LYS cc_start: 0.7047 (ttpt) cc_final: 0.6695 (mttm) REVERT: E 340 LYS cc_start: 0.8570 (mtpt) cc_final: 0.8269 (mttp) REVERT: E 342 GLU cc_start: 0.8424 (mt-10) cc_final: 0.7971 (mm-30) REVERT: E 347 LYS cc_start: 0.8649 (mttt) cc_final: 0.7832 (mtmm) REVERT: E 369 LYS cc_start: 0.8089 (mttt) cc_final: 0.7610 (ttmp) REVERT: E 375 LYS cc_start: 0.7492 (tttt) cc_final: 0.6441 (tmmt) REVERT: B 340 LYS cc_start: 0.8180 (mtpt) cc_final: 0.7732 (mttp) REVERT: B 342 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7765 (mm-30) REVERT: B 375 LYS cc_start: 0.6655 (tttt) cc_final: 0.6297 (tptt) REVERT: D 340 LYS cc_start: 0.8136 (mtpt) cc_final: 0.7680 (mttt) REVERT: D 342 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7650 (mm-30) REVERT: D 345 ASP cc_start: 0.8292 (t0) cc_final: 0.7952 (t0) REVERT: D 375 LYS cc_start: 0.6113 (tttt) cc_final: 0.5749 (tppt) REVERT: F 311 LYS cc_start: 0.6877 (ttpt) cc_final: 0.6588 (mtpt) REVERT: F 314 ASP cc_start: 0.6045 (t0) cc_final: 0.5797 (t0) REVERT: F 338 GLU cc_start: 0.7573 (tt0) cc_final: 0.7340 (tt0) REVERT: F 340 LYS cc_start: 0.8510 (mtpt) cc_final: 0.8180 (mttt) REVERT: F 342 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7997 (mm-30) REVERT: F 347 LYS cc_start: 0.8596 (mttt) cc_final: 0.7700 (mtmm) REVERT: F 375 LYS cc_start: 0.7610 (tttt) cc_final: 0.6503 (tmmt) REVERT: G 342 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7682 (mm-30) REVERT: H 340 LYS cc_start: 0.8201 (mtpt) cc_final: 0.7793 (mttt) REVERT: H 342 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7878 (mm-30) REVERT: H 375 LYS cc_start: 0.5900 (tttt) cc_final: 0.5507 (tppt) REVERT: I 310 TYR cc_start: 0.5442 (t80) cc_final: 0.5233 (t80) REVERT: I 311 LYS cc_start: 0.6953 (ttpt) cc_final: 0.6610 (mttp) REVERT: I 340 LYS cc_start: 0.8577 (mtpt) cc_final: 0.8269 (mttt) REVERT: I 342 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8047 (mm-30) REVERT: I 347 LYS cc_start: 0.8645 (mttt) cc_final: 0.7849 (mppt) REVERT: I 369 LYS cc_start: 0.8077 (mttt) cc_final: 0.7596 (ttmp) REVERT: I 375 LYS cc_start: 0.7489 (tttt) cc_final: 0.6417 (tmmt) outliers start: 8 outliers final: 6 residues processed: 151 average time/residue: 2.9549 time to fit residues: 460.8802 Evaluate side-chains 150 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 144 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain G residue 309 VAL Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain I residue 309 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.157582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.134462 restraints weight = 18407.449| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 1.73 r_work: 0.3678 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.5576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5094 Z= 0.189 Angle : 0.496 5.809 6822 Z= 0.257 Chirality : 0.051 0.140 774 Planarity : 0.002 0.018 864 Dihedral : 4.818 14.679 666 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.39 % Allowed : 20.83 % Favored : 77.78 % 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: -2.32 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.20), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 374 PHE 0.006 0.000 PHE C 346 TYR 0.013 0.002 TYR E 310 ARG 0.002 0.000 ARG E 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7882.52 seconds wall clock time: 137 minutes 9.96 seconds (8229.96 seconds total)