Starting phenix.real_space_refine on Fri Mar 15 00:53:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9l_18285/03_2024/8q9l_18285.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9l_18285/03_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_18285/03_2024/8q9l_18285.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9l_18285/03_2024/8q9l_18285.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9l_18285/03_2024/8q9l_18285.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9l_18285/03_2024/8q9l_18285.pdb" } 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 4.96, per 1000 atoms: 0.48 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: 7.29 Conformation dependent library (CDL) restraints added in 975.4 milliseconds 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: 1.03 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: 3.38 Time building geometry restraints manager: 7.64 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 1.850 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.581 1.850 nonbonded pdb=" OD1 ASP I 314 " pdb=" HG SER I 316 " model vdw 1.587 1.850 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.602 1.850 nonbonded pdb=" OD1 ASP G 314 " pdb=" HG SER G 316 " model vdw 1.605 1.850 ... (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 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.150 Extract box with map and model: 11.880 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 34.600 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:12.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.990 ------------------------------------------------------------------------------- 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 : 0.903 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: 2.4094 time to fit residues: 680.2020 Evaluate side-chains 220 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 219 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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: 1.9990 chunk 32 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3911 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= 0.282 Angle : 0.589 3.915 6822 Z= 0.312 Chirality : 0.052 0.137 774 Planarity : 0.003 0.019 864 Dihedral : 7.962 127.682 668 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 1.74 % Allowed : 13.02 % Favored : 85.24 % 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: -1.56 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.18 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 374 PHE 0.005 0.001 PHE D 346 TYR 0.012 0.002 TYR D 310 ARG 0.003 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 214 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 204 time to evaluate : 0.913 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: 0.5901 (t) cc_final: 0.5452 (p) REVERT: A 342 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7663 (mm-30) REVERT: A 345 ASP cc_start: 0.8379 (t0) cc_final: 0.8013 (t0) REVERT: A 369 LYS cc_start: 0.7311 (OUTLIER) cc_final: 0.7015 (ttmm) REVERT: A 372 GLU cc_start: 0.7043 (tt0) cc_final: 0.6520 (mm-30) REVERT: C 311 LYS cc_start: 0.6337 (mtpt) cc_final: 0.5729 (mmpt) REVERT: C 340 LYS cc_start: 0.8055 (mtpt) cc_final: 0.7640 (mttt) REVERT: C 342 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7844 (mm-30) REVERT: C 345 ASP cc_start: 0.8415 (t0) cc_final: 0.8017 (t0) REVERT: C 347 LYS cc_start: 0.8613 (mttt) cc_final: 0.8412 (mtmt) REVERT: C 372 GLU cc_start: 0.8148 (tt0) cc_final: 0.7710 (mm-30) REVERT: C 374 HIS cc_start: 0.7967 (m-70) cc_final: 0.7624 (m-70) REVERT: C 375 LYS cc_start: 0.5963 (tttt) cc_final: 0.5528 (tppt) REVERT: C 376 LEU cc_start: 0.7501 (tt) cc_final: 0.7296 (tt) REVERT: C 378 PHE cc_start: 0.5600 (t80) cc_final: 0.5328 (t80) REVERT: E 311 LYS cc_start: 0.6970 (ttpt) cc_final: 0.6677 (mtpp) REVERT: E 317 LYS cc_start: 0.5526 (pttt) cc_final: 0.5268 (mtpt) REVERT: E 324 SER cc_start: 0.8525 (p) cc_final: 0.8325 (m) REVERT: E 340 LYS cc_start: 0.8507 (mtpt) cc_final: 0.8178 (mttt) REVERT: E 342 GLU cc_start: 0.8377 (mt-10) cc_final: 0.7910 (mm-30) REVERT: E 347 LYS cc_start: 0.8635 (mttt) cc_final: 0.7612 (ttpt) REVERT: E 349 ARG cc_start: 0.6672 (mtt180) cc_final: 0.5160 (pmt-80) REVERT: E 369 LYS cc_start: 0.8114 (mttt) cc_final: 0.7653 (ttmp) REVERT: E 372 GLU cc_start: 0.7358 (mm-30) cc_final: 0.7056 (mm-30) REVERT: E 375 LYS cc_start: 0.7509 (tttt) cc_final: 0.6189 (pptt) REVERT: E 378 PHE cc_start: 0.4501 (t80) cc_final: 0.4274 (t80) REVERT: B 309 VAL cc_start: 0.5459 (t) cc_final: 0.5113 (p) REVERT: B 310 TYR cc_start: 0.4963 (t80) cc_final: 0.4699 (t80) REVERT: B 324 SER cc_start: 0.8283 (OUTLIER) cc_final: 0.8067 (m) REVERT: B 342 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7814 (mm-30) REVERT: B 372 GLU cc_start: 0.6939 (tt0) cc_final: 0.6541 (mm-30) REVERT: B 375 LYS cc_start: 0.6063 (tttt) cc_final: 0.5835 (tptt) REVERT: D 310 TYR cc_start: 0.6744 (t80) cc_final: 0.6438 (t80) REVERT: D 324 SER cc_start: 0.8432 (OUTLIER) cc_final: 0.8200 (m) REVERT: D 331 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8508 (mtpt) REVERT: D 342 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7751 (mm-30) REVERT: D 345 ASP cc_start: 0.8342 (t0) cc_final: 0.8020 (t0) REVERT: D 372 GLU cc_start: 0.8023 (tt0) cc_final: 0.7567 (mm-30) REVERT: D 373 THR cc_start: 0.5857 (m) cc_final: 0.5558 (m) REVERT: D 375 LYS cc_start: 0.5998 (tttt) cc_final: 0.5610 (tppt) REVERT: F 311 LYS cc_start: 0.6916 (ttpt) cc_final: 0.6596 (mtpp) REVERT: F 317 LYS cc_start: 0.5537 (pttt) cc_final: 0.5324 (mtpp) REVERT: F 324 SER cc_start: 0.8592 (p) cc_final: 0.8353 (m) REVERT: F 338 GLU cc_start: 0.7599 (tt0) cc_final: 0.7358 (tt0) REVERT: F 340 LYS cc_start: 0.8422 (mtpt) cc_final: 0.8151 (mttt) REVERT: F 342 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8006 (mm-30) REVERT: F 347 LYS cc_start: 0.8635 (mttt) cc_final: 0.7661 (ttpt) REVERT: F 349 ARG cc_start: 0.6723 (mtt180) cc_final: 0.5170 (pmt-80) REVERT: F 369 LYS cc_start: 0.8065 (mttt) cc_final: 0.7852 (mtmm) REVERT: F 372 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7246 (mm-30) REVERT: F 375 LYS cc_start: 0.7486 (tttt) cc_final: 0.6387 (tmmt) REVERT: G 310 TYR cc_start: 0.5067 (t80) cc_final: 0.4820 (t80) REVERT: G 340 LYS cc_start: 0.8072 (mtpt) cc_final: 0.7626 (mttt) REVERT: G 342 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7684 (mm-30) REVERT: G 345 ASP cc_start: 0.8460 (t0) cc_final: 0.8210 (t0) REVERT: G 349 ARG cc_start: 0.6680 (mtm180) cc_final: 0.6202 (mtp85) REVERT: G 372 GLU cc_start: 0.7017 (tt0) cc_final: 0.6619 (mm-30) REVERT: H 310 TYR cc_start: 0.6716 (t80) cc_final: 0.6499 (t80) REVERT: H 340 LYS cc_start: 0.8105 (mtpt) cc_final: 0.7694 (mttt) REVERT: H 342 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7870 (mm-30) REVERT: H 345 ASP cc_start: 0.8363 (t0) cc_final: 0.7997 (t0) REVERT: H 372 GLU cc_start: 0.8064 (tt0) cc_final: 0.7676 (mm-30) REVERT: H 374 HIS cc_start: 0.7943 (m-70) cc_final: 0.7715 (m90) REVERT: H 375 LYS cc_start: 0.5964 (tttt) cc_final: 0.5473 (tppt) REVERT: I 311 LYS cc_start: 0.6966 (ttpt) cc_final: 0.6638 (mttt) REVERT: I 317 LYS cc_start: 0.5512 (pttt) cc_final: 0.5275 (mtpt) REVERT: I 324 SER cc_start: 0.8422 (p) cc_final: 0.8202 (m) REVERT: I 340 LYS cc_start: 0.8530 (mtpt) cc_final: 0.8256 (mttt) REVERT: I 342 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7976 (mm-30) REVERT: I 347 LYS cc_start: 0.8651 (mttt) cc_final: 0.7520 (ttpp) REVERT: I 349 ARG cc_start: 0.6726 (mtt180) cc_final: 0.5138 (pmt-80) REVERT: I 369 LYS cc_start: 0.8103 (mttt) cc_final: 0.7623 (ttmp) REVERT: I 372 GLU cc_start: 0.7408 (mm-30) cc_final: 0.6791 (mm-30) REVERT: I 375 LYS cc_start: 0.7304 (tttt) cc_final: 0.5988 (pptt) outliers start: 10 outliers final: 3 residues processed: 205 average time/residue: 2.8687 time to fit residues: 607.2066 Evaluate side-chains 187 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 180 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 331 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 D 374 HIS H 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5094 Z= 0.202 Angle : 0.518 4.200 6822 Z= 0.272 Chirality : 0.051 0.139 774 Planarity : 0.002 0.014 864 Dihedral : 5.457 15.414 666 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 1.74 % Allowed : 15.45 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 374 PHE 0.005 0.001 PHE H 346 TYR 0.010 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: 10 poor density : 173 time to evaluate : 0.928 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: 0.5962 (t) cc_final: 0.5470 (p) REVERT: A 342 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7635 (mm-30) REVERT: A 345 ASP cc_start: 0.8398 (t0) cc_final: 0.7980 (t0) REVERT: A 369 LYS cc_start: 0.7310 (OUTLIER) cc_final: 0.7010 (ttmm) REVERT: A 372 GLU cc_start: 0.7240 (tt0) cc_final: 0.6948 (mm-30) REVERT: C 311 LYS cc_start: 0.6370 (mtpt) cc_final: 0.5718 (mmpt) REVERT: C 340 LYS cc_start: 0.8050 (mtpt) cc_final: 0.7638 (mttt) REVERT: C 342 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7797 (mm-30) REVERT: C 375 LYS cc_start: 0.5935 (tttt) cc_final: 0.5515 (tppt) REVERT: C 378 PHE cc_start: 0.5668 (t80) cc_final: 0.5400 (t80) REVERT: E 311 LYS cc_start: 0.6985 (ttpt) cc_final: 0.6664 (mtpp) REVERT: E 321 LYS cc_start: 0.7914 (mtpt) cc_final: 0.7472 (mtpt) REVERT: E 340 LYS cc_start: 0.8504 (mtpt) cc_final: 0.8173 (mttt) REVERT: E 342 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7936 (mm-30) REVERT: E 347 LYS cc_start: 0.8631 (mttt) cc_final: 0.7590 (ttpt) REVERT: E 349 ARG cc_start: 0.6913 (mtt180) cc_final: 0.5168 (pmt-80) REVERT: E 369 LYS cc_start: 0.8098 (mttt) cc_final: 0.7620 (ttmp) REVERT: E 372 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7167 (mm-30) REVERT: E 375 LYS cc_start: 0.7469 (tttt) cc_final: 0.6160 (pptt) REVERT: E 378 PHE cc_start: 0.4552 (t80) cc_final: 0.4304 (t80) REVERT: B 340 LYS cc_start: 0.8083 (mtpt) cc_final: 0.7665 (mttp) REVERT: B 342 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7756 (mm-30) REVERT: B 375 LYS cc_start: 0.6323 (tttt) cc_final: 0.6051 (tptt) REVERT: D 340 LYS cc_start: 0.8131 (mtpt) cc_final: 0.7730 (mttt) REVERT: D 342 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7660 (mm-30) REVERT: D 345 ASP cc_start: 0.8314 (t0) cc_final: 0.8000 (t0) REVERT: D 375 LYS cc_start: 0.5992 (tttt) cc_final: 0.5609 (tppt) REVERT: F 311 LYS cc_start: 0.6948 (ttpt) cc_final: 0.6660 (mtpp) REVERT: F 338 GLU cc_start: 0.7605 (tt0) cc_final: 0.7381 (tt0) REVERT: F 340 LYS cc_start: 0.8466 (mtpt) cc_final: 0.8173 (mttt) REVERT: F 342 GLU cc_start: 0.8417 (mt-10) cc_final: 0.7988 (mm-30) REVERT: F 347 LYS cc_start: 0.8652 (mttt) cc_final: 0.7692 (ttpt) REVERT: F 349 ARG cc_start: 0.6936 (mtt180) cc_final: 0.5229 (pmt-80) REVERT: F 369 LYS cc_start: 0.8082 (mttt) cc_final: 0.7838 (mtmm) REVERT: F 372 GLU cc_start: 0.7411 (mm-30) cc_final: 0.7193 (mm-30) REVERT: F 375 LYS cc_start: 0.7570 (tttt) cc_final: 0.6471 (tmmt) REVERT: G 342 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7706 (mm-30) REVERT: G 372 GLU cc_start: 0.7169 (tt0) cc_final: 0.6945 (mm-30) REVERT: H 340 LYS cc_start: 0.8156 (mtpt) cc_final: 0.7720 (mttt) REVERT: H 342 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7811 (mm-30) REVERT: H 375 LYS cc_start: 0.5856 (tttt) cc_final: 0.5457 (tppt) REVERT: I 311 LYS cc_start: 0.6965 (ttpt) cc_final: 0.6648 (mttp) REVERT: I 340 LYS cc_start: 0.8520 (mtpt) cc_final: 0.8234 (mttp) REVERT: I 342 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8034 (mm-30) REVERT: I 347 LYS cc_start: 0.8642 (mttt) cc_final: 0.7637 (ttpt) REVERT: I 349 ARG cc_start: 0.6919 (mtt180) cc_final: 0.5186 (pmt-80) REVERT: I 369 LYS cc_start: 0.8125 (mttt) cc_final: 0.7615 (ttmp) REVERT: I 372 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7003 (mm-30) REVERT: I 375 LYS cc_start: 0.7334 (tttt) cc_final: 0.5987 (pptt) outliers start: 10 outliers final: 2 residues processed: 176 average time/residue: 2.9443 time to fit residues: 534.9457 Evaluate side-chains 158 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 155 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain D residue 309 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 overall best weight: 2.7584 ------------------------------------------------------------------------------- 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: 0.7691 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5094 Z= 0.193 Angle : 0.498 4.050 6822 Z= 0.261 Chirality : 0.051 0.139 774 Planarity : 0.002 0.014 864 Dihedral : 5.171 14.866 666 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.87 % Allowed : 16.84 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 374 PHE 0.005 0.001 PHE C 346 TYR 0.014 0.002 TYR B 310 ARG 0.001 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 160 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 155 time to evaluate : 0.908 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: 0.5899 (t) cc_final: 0.5413 (p) REVERT: A 342 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7640 (mm-30) REVERT: C 331 LYS cc_start: 0.8740 (mtmt) cc_final: 0.8468 (mmmm) REVERT: C 340 LYS cc_start: 0.8062 (mtpt) cc_final: 0.7638 (mttt) REVERT: C 342 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7678 (mm-30) REVERT: C 369 LYS cc_start: 0.7155 (OUTLIER) cc_final: 0.6944 (ttmm) REVERT: C 375 LYS cc_start: 0.5956 (tttt) cc_final: 0.5543 (tppt) REVERT: C 378 PHE cc_start: 0.5742 (t80) cc_final: 0.5475 (t80) REVERT: E 311 LYS cc_start: 0.6982 (ttpt) cc_final: 0.6667 (mtpp) REVERT: E 321 LYS cc_start: 0.7813 (mtpt) cc_final: 0.7517 (mtpt) REVERT: E 340 LYS cc_start: 0.8542 (mtpt) cc_final: 0.8221 (mttt) REVERT: E 342 GLU cc_start: 0.8414 (mt-10) cc_final: 0.7969 (mm-30) REVERT: E 347 LYS cc_start: 0.8618 (mttt) cc_final: 0.7613 (ttpt) REVERT: E 349 ARG cc_start: 0.7069 (mtt180) cc_final: 0.5134 (pmt-80) REVERT: E 369 LYS cc_start: 0.8110 (mttt) cc_final: 0.7624 (ttmp) REVERT: E 375 LYS cc_start: 0.7475 (tttt) cc_final: 0.6171 (pptt) REVERT: B 340 LYS cc_start: 0.8096 (mtpt) cc_final: 0.7684 (mttp) REVERT: B 342 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7751 (mm-30) REVERT: D 340 LYS cc_start: 0.8095 (mtpt) cc_final: 0.7711 (mttt) REVERT: D 342 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7658 (mm-30) REVERT: D 345 ASP cc_start: 0.8253 (t0) cc_final: 0.7917 (t0) REVERT: D 375 LYS cc_start: 0.5970 (tttt) cc_final: 0.5560 (tppt) REVERT: F 311 LYS cc_start: 0.6970 (ttpt) cc_final: 0.6677 (mtpp) REVERT: F 338 GLU cc_start: 0.7608 (tt0) cc_final: 0.7374 (tt0) REVERT: F 340 LYS cc_start: 0.8457 (mtpt) cc_final: 0.8147 (mttt) REVERT: F 342 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7998 (mm-30) REVERT: F 347 LYS cc_start: 0.8651 (mttt) cc_final: 0.7635 (ttpt) REVERT: F 369 LYS cc_start: 0.8099 (mttt) cc_final: 0.7838 (mtmm) REVERT: F 375 LYS cc_start: 0.7559 (tttt) cc_final: 0.6492 (tmmt) REVERT: G 342 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7673 (mm-30) REVERT: H 340 LYS cc_start: 0.8158 (mtpt) cc_final: 0.7721 (mttt) REVERT: H 342 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7819 (mm-30) REVERT: H 347 LYS cc_start: 0.8325 (mtmt) cc_final: 0.8110 (mttp) REVERT: H 375 LYS cc_start: 0.5835 (tttt) cc_final: 0.5426 (tppt) REVERT: I 311 LYS cc_start: 0.6959 (ttpt) cc_final: 0.6651 (mttt) REVERT: I 340 LYS cc_start: 0.8550 (mtpt) cc_final: 0.8250 (mttt) REVERT: I 342 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8041 (mm-30) REVERT: I 347 LYS cc_start: 0.8685 (mttt) cc_final: 0.7932 (mppt) REVERT: I 349 ARG cc_start: 0.7120 (mtt180) cc_final: 0.5247 (pmt-80) REVERT: I 369 LYS cc_start: 0.8112 (mttt) cc_final: 0.7602 (ttmp) REVERT: I 375 LYS cc_start: 0.7399 (tttt) cc_final: 0.6034 (pptt) outliers start: 5 outliers final: 2 residues processed: 156 average time/residue: 3.0515 time to fit residues: 491.3721 Evaluate side-chains 153 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 150 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain D residue 309 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN D 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5094 Z= 0.255 Angle : 0.518 4.124 6822 Z= 0.272 Chirality : 0.051 0.140 774 Planarity : 0.003 0.020 864 Dihedral : 5.239 15.630 666 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.56 % Allowed : 18.06 % Favored : 80.38 % 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: -2.06 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.006 0.001 PHE C 346 TYR 0.009 0.002 TYR G 310 ARG 0.002 0.000 ARG I 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 158 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 149 time to evaluate : 0.971 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: 0.5882 (t) cc_final: 0.5391 (p) REVERT: A 342 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7653 (mm-30) REVERT: A 369 LYS cc_start: 0.7375 (OUTLIER) cc_final: 0.7119 (ttmm) REVERT: C 331 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8491 (mmmm) REVERT: C 340 LYS cc_start: 0.8084 (mtpt) cc_final: 0.7643 (mttt) REVERT: C 342 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7685 (mm-30) REVERT: C 369 LYS cc_start: 0.7215 (OUTLIER) cc_final: 0.7002 (ttmm) REVERT: C 375 LYS cc_start: 0.5991 (tttt) cc_final: 0.5594 (tppt) REVERT: C 378 PHE cc_start: 0.5663 (t80) cc_final: 0.5401 (t80) REVERT: E 311 LYS cc_start: 0.6979 (ttpt) cc_final: 0.6677 (mtpp) REVERT: E 338 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7783 (tm-30) REVERT: E 342 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7978 (mm-30) REVERT: E 347 LYS cc_start: 0.8627 (mttt) cc_final: 0.7620 (ttpt) REVERT: E 369 LYS cc_start: 0.8139 (mttt) cc_final: 0.7653 (ttmp) REVERT: E 375 LYS cc_start: 0.7473 (tttt) cc_final: 0.6142 (pptt) REVERT: E 378 PHE cc_start: 0.4591 (t80) cc_final: 0.4387 (t80) REVERT: B 340 LYS cc_start: 0.8085 (mtpt) cc_final: 0.7661 (mttp) REVERT: B 342 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7746 (mm-30) REVERT: D 340 LYS cc_start: 0.8076 (mtpt) cc_final: 0.7663 (mttt) REVERT: D 342 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7630 (mm-30) REVERT: D 345 ASP cc_start: 0.8211 (t0) cc_final: 0.7848 (t0) REVERT: D 375 LYS cc_start: 0.5909 (tttt) cc_final: 0.5540 (tppt) REVERT: F 311 LYS cc_start: 0.6908 (ttpt) cc_final: 0.6639 (mtpp) REVERT: F 338 GLU cc_start: 0.7622 (tt0) cc_final: 0.7363 (tt0) REVERT: F 340 LYS cc_start: 0.8477 (mtpt) cc_final: 0.8170 (mttt) REVERT: F 342 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8017 (mm-30) REVERT: F 347 LYS cc_start: 0.8675 (mttt) cc_final: 0.7692 (ttpt) REVERT: F 369 LYS cc_start: 0.8103 (mttt) cc_final: 0.7820 (mtmm) REVERT: F 375 LYS cc_start: 0.7591 (tttt) cc_final: 0.6489 (tmmt) REVERT: G 342 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7666 (mm-30) REVERT: H 340 LYS cc_start: 0.8164 (mtpt) cc_final: 0.7720 (mttt) REVERT: H 342 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7829 (mm-30) REVERT: H 375 LYS cc_start: 0.5900 (tttt) cc_final: 0.5532 (tppt) REVERT: I 311 LYS cc_start: 0.6971 (ttpt) cc_final: 0.6669 (mttt) REVERT: I 340 LYS cc_start: 0.8576 (mtpt) cc_final: 0.8268 (mttt) REVERT: I 342 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8075 (mm-30) REVERT: I 347 LYS cc_start: 0.8669 (mttt) cc_final: 0.7886 (mppt) REVERT: I 369 LYS cc_start: 0.8145 (mttt) cc_final: 0.7628 (ttmp) REVERT: I 375 LYS cc_start: 0.7556 (tttt) cc_final: 0.6197 (pptt) outliers start: 9 outliers final: 5 residues processed: 151 average time/residue: 2.9832 time to fit residues: 465.2254 Evaluate side-chains 153 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 144 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain E residue 338 GLU 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 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: 4.9990 chunk 12 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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: 0.5271 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= 0.337 Angle : 0.550 4.220 6822 Z= 0.289 Chirality : 0.051 0.141 774 Planarity : 0.003 0.024 864 Dihedral : 5.406 16.331 666 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.43 % Allowed : 18.06 % Favored : 79.51 % 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: -2.23 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 374 PHE 0.006 0.001 PHE C 346 TYR 0.010 0.002 TYR G 310 ARG 0.002 0.001 ARG I 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 167 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 153 time to evaluate : 0.927 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: 0.5796 (t) cc_final: 0.5255 (p) REVERT: A 320 SER cc_start: 0.8540 (OUTLIER) cc_final: 0.8256 (p) REVERT: A 342 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7664 (mm-30) REVERT: C 331 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8494 (mmmm) REVERT: C 340 LYS cc_start: 0.8096 (mtpt) cc_final: 0.7653 (mttt) REVERT: C 342 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7698 (mm-30) REVERT: C 369 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6979 (ttmm) REVERT: C 375 LYS cc_start: 0.6036 (tttt) cc_final: 0.5643 (tppt) REVERT: C 378 PHE cc_start: 0.5513 (t80) cc_final: 0.5256 (t80) REVERT: E 311 LYS cc_start: 0.7008 (ttpt) cc_final: 0.6655 (mttt) REVERT: E 338 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7616 (tm-30) REVERT: E 340 LYS cc_start: 0.8568 (mtpt) cc_final: 0.7975 (mttt) REVERT: E 342 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7985 (mm-30) REVERT: E 347 LYS cc_start: 0.8621 (mttt) cc_final: 0.7811 (mtmm) REVERT: E 369 LYS cc_start: 0.8165 (mttt) cc_final: 0.7648 (ttmp) REVERT: E 375 LYS cc_start: 0.7571 (tttt) cc_final: 0.6174 (pptt) REVERT: B 309 VAL cc_start: 0.5733 (t) cc_final: 0.5361 (p) REVERT: B 340 LYS cc_start: 0.8066 (mtpt) cc_final: 0.7649 (mttp) REVERT: B 342 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7758 (mm-30) REVERT: B 369 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.6868 (ttmm) REVERT: D 340 LYS cc_start: 0.8115 (mtpt) cc_final: 0.7670 (mttt) REVERT: D 342 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7624 (mm-30) REVERT: D 345 ASP cc_start: 0.8192 (t0) cc_final: 0.7919 (t0) REVERT: D 375 LYS cc_start: 0.5867 (tttt) cc_final: 0.5496 (tppt) REVERT: F 309 VAL cc_start: 0.6918 (p) cc_final: 0.6677 (p) REVERT: F 311 LYS cc_start: 0.6906 (ttpt) cc_final: 0.6587 (mtpp) REVERT: F 338 GLU cc_start: 0.7634 (tt0) cc_final: 0.7376 (tt0) REVERT: F 340 LYS cc_start: 0.8503 (mtpt) cc_final: 0.8197 (mttt) REVERT: F 342 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8026 (mm-30) REVERT: F 347 LYS cc_start: 0.8654 (mttt) cc_final: 0.7808 (mtmm) REVERT: F 369 LYS cc_start: 0.8111 (mttt) cc_final: 0.7824 (mtmm) REVERT: F 375 LYS cc_start: 0.7639 (tttt) cc_final: 0.6519 (tmmt) REVERT: G 342 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7699 (mm-30) REVERT: H 340 LYS cc_start: 0.8180 (mtpt) cc_final: 0.7734 (mttt) REVERT: H 342 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7868 (mm-30) REVERT: H 375 LYS cc_start: 0.5938 (tttt) cc_final: 0.5580 (tppt) REVERT: I 311 LYS cc_start: 0.6973 (ttpt) cc_final: 0.6404 (pttp) REVERT: I 340 LYS cc_start: 0.8612 (mtpt) cc_final: 0.8290 (mttt) REVERT: I 342 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8072 (mm-30) REVERT: I 347 LYS cc_start: 0.8658 (mttt) cc_final: 0.7869 (mppt) REVERT: I 369 LYS cc_start: 0.8164 (mttt) cc_final: 0.7914 (mtmm) REVERT: I 375 LYS cc_start: 0.7610 (tttt) cc_final: 0.6232 (pptt) outliers start: 14 outliers final: 5 residues processed: 155 average time/residue: 2.9714 time to fit residues: 475.4775 Evaluate side-chains 161 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 151 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain B residue 369 LYS 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 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: 10.0000 chunk 34 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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: 0.7702 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5094 Z= 0.197 Angle : 0.488 4.035 6822 Z= 0.255 Chirality : 0.050 0.139 774 Planarity : 0.002 0.014 864 Dihedral : 5.067 15.273 666 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.91 % Allowed : 18.58 % Favored : 79.51 % 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: -2.22 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 374 PHE 0.004 0.001 PHE C 346 TYR 0.008 0.001 TYR H 310 ARG 0.001 0.000 ARG I 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 163 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 152 time to evaluate : 0.976 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: 0.5824 (t) cc_final: 0.5262 (p) REVERT: A 320 SER cc_start: 0.8535 (OUTLIER) cc_final: 0.8248 (p) REVERT: A 342 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7645 (mm-30) REVERT: C 331 LYS cc_start: 0.8760 (mtmt) cc_final: 0.8489 (mmmm) REVERT: C 340 LYS cc_start: 0.8093 (mtpt) cc_final: 0.7654 (mttt) REVERT: C 342 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7670 (mm-30) REVERT: C 369 LYS cc_start: 0.7143 (OUTLIER) cc_final: 0.6895 (ttmm) REVERT: C 375 LYS cc_start: 0.6008 (tttt) cc_final: 0.5655 (tppt) REVERT: C 378 PHE cc_start: 0.5476 (t80) cc_final: 0.5218 (t80) REVERT: E 311 LYS cc_start: 0.7049 (ttpt) cc_final: 0.6680 (mttt) REVERT: E 338 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7812 (tm-30) REVERT: E 342 GLU cc_start: 0.8433 (mt-10) cc_final: 0.7992 (mm-30) REVERT: E 347 LYS cc_start: 0.8619 (mttt) cc_final: 0.7798 (mtmm) REVERT: E 369 LYS cc_start: 0.8132 (mttt) cc_final: 0.7641 (ttmp) REVERT: E 375 LYS cc_start: 0.7503 (tttt) cc_final: 0.6177 (pptt) REVERT: B 309 VAL cc_start: 0.5751 (t) cc_final: 0.5397 (p) REVERT: B 340 LYS cc_start: 0.8092 (mtpt) cc_final: 0.7666 (mttp) REVERT: B 342 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7756 (mm-30) REVERT: D 340 LYS cc_start: 0.8114 (mtpt) cc_final: 0.7662 (mttt) REVERT: D 342 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7598 (mm-30) REVERT: D 375 LYS cc_start: 0.5956 (tttt) cc_final: 0.5580 (tppt) REVERT: F 311 LYS cc_start: 0.7011 (ttpt) cc_final: 0.6688 (mtpt) REVERT: F 338 GLU cc_start: 0.7645 (tt0) cc_final: 0.7384 (tt0) REVERT: F 340 LYS cc_start: 0.8499 (mtpt) cc_final: 0.8190 (mttt) REVERT: F 342 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8002 (mm-30) REVERT: F 347 LYS cc_start: 0.8636 (mttt) cc_final: 0.7654 (ttpt) REVERT: F 369 LYS cc_start: 0.8067 (mttt) cc_final: 0.7776 (mtmm) REVERT: F 375 LYS cc_start: 0.7635 (tttt) cc_final: 0.6548 (tmmt) REVERT: G 342 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7676 (mm-30) REVERT: H 340 LYS cc_start: 0.8157 (mtpt) cc_final: 0.7735 (mttt) REVERT: H 342 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7856 (mm-30) REVERT: H 345 ASP cc_start: 0.8277 (t0) cc_final: 0.8004 (t0) REVERT: H 375 LYS cc_start: 0.5860 (tttt) cc_final: 0.5516 (tppt) REVERT: I 311 LYS cc_start: 0.6974 (ttpt) cc_final: 0.6364 (pttp) REVERT: I 340 LYS cc_start: 0.8606 (mtpt) cc_final: 0.8286 (mttt) REVERT: I 342 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8056 (mm-30) REVERT: I 347 LYS cc_start: 0.8647 (mttt) cc_final: 0.7635 (ttpt) REVERT: I 369 LYS cc_start: 0.8161 (mttt) cc_final: 0.7260 (tttt) REVERT: I 375 LYS cc_start: 0.7567 (tttt) cc_final: 0.6199 (pptt) outliers start: 11 outliers final: 7 residues processed: 156 average time/residue: 2.8618 time to fit residues: 461.7104 Evaluate side-chains 157 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 147 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 347 LYS Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain G residue 309 VAL 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: 8.9990 chunk 38 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 56 optimal weight: 0.4980 chunk 34 optimal weight: 10.0000 overall best weight: 3.6988 ------------------------------------------------------------------------------- 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: 0.7708 moved from start: 0.5323 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= 0.240 Angle : 0.504 4.053 6822 Z= 0.263 Chirality : 0.050 0.140 774 Planarity : 0.003 0.018 864 Dihedral : 5.110 15.497 666 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.91 % Allowed : 19.27 % Favored : 78.82 % 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: -2.26 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 374 PHE 0.005 0.001 PHE C 346 TYR 0.008 0.001 TYR G 310 ARG 0.001 0.000 ARG I 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 161 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 150 time to evaluate : 0.977 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: A 309 VAL cc_start: 0.5810 (t) cc_final: 0.5263 (p) REVERT: A 320 SER cc_start: 0.8547 (OUTLIER) cc_final: 0.8265 (p) REVERT: A 342 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7657 (mm-30) REVERT: C 331 LYS cc_start: 0.8760 (mtmt) cc_final: 0.8492 (mmmm) REVERT: C 340 LYS cc_start: 0.8095 (mtpt) cc_final: 0.7655 (mttt) REVERT: C 342 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7673 (mm-30) REVERT: C 369 LYS cc_start: 0.7164 (OUTLIER) cc_final: 0.6928 (ttmm) REVERT: C 375 LYS cc_start: 0.6035 (tttt) cc_final: 0.5625 (tppt) REVERT: E 311 LYS cc_start: 0.7052 (ttpt) cc_final: 0.6710 (mttm) REVERT: E 338 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7791 (tm-30) REVERT: E 342 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7994 (mm-30) REVERT: E 347 LYS cc_start: 0.8642 (mttt) cc_final: 0.7835 (mtmm) REVERT: E 369 LYS cc_start: 0.8152 (mttt) cc_final: 0.7647 (ttmp) REVERT: E 375 LYS cc_start: 0.7578 (tttt) cc_final: 0.6209 (pptt) REVERT: B 309 VAL cc_start: 0.5749 (t) cc_final: 0.5384 (p) REVERT: B 340 LYS cc_start: 0.8097 (mtpt) cc_final: 0.7674 (mttp) REVERT: B 342 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7753 (mm-30) REVERT: D 331 LYS cc_start: 0.8824 (mtmt) cc_final: 0.8612 (mtpt) REVERT: D 340 LYS cc_start: 0.8121 (mtpt) cc_final: 0.7663 (mttt) REVERT: D 342 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7591 (mm-30) REVERT: D 375 LYS cc_start: 0.5935 (tttt) cc_final: 0.5574 (tppt) REVERT: F 311 LYS cc_start: 0.7011 (ttpt) cc_final: 0.6706 (mtpp) REVERT: F 338 GLU cc_start: 0.7650 (tt0) cc_final: 0.7391 (tt0) REVERT: F 340 LYS cc_start: 0.8506 (mtpt) cc_final: 0.8196 (mttt) REVERT: F 342 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7998 (mm-30) REVERT: F 347 LYS cc_start: 0.8631 (mttt) cc_final: 0.7867 (mtmt) REVERT: F 369 LYS cc_start: 0.8082 (mttt) cc_final: 0.7789 (mtmm) REVERT: F 375 LYS cc_start: 0.7663 (tttt) cc_final: 0.6558 (tmmt) REVERT: G 342 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7681 (mm-30) REVERT: H 340 LYS cc_start: 0.8143 (mtpt) cc_final: 0.7714 (mttt) REVERT: H 342 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7865 (mm-30) REVERT: H 375 LYS cc_start: 0.5881 (tttt) cc_final: 0.5455 (tppt) REVERT: I 311 LYS cc_start: 0.6969 (ttpt) cc_final: 0.6368 (pttp) REVERT: I 340 LYS cc_start: 0.8593 (mtpt) cc_final: 0.8265 (mttp) REVERT: I 342 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8060 (mm-30) REVERT: I 347 LYS cc_start: 0.8654 (mttt) cc_final: 0.7653 (ttpt) REVERT: I 369 LYS cc_start: 0.8176 (mttt) cc_final: 0.7267 (tttt) REVERT: I 375 LYS cc_start: 0.7555 (tttt) cc_final: 0.6193 (pptt) outliers start: 11 outliers final: 7 residues processed: 154 average time/residue: 2.8323 time to fit residues: 451.1876 Evaluate side-chains 159 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 149 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 347 LYS Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain G residue 309 VAL 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: 9.9990 chunk 44 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.5395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5094 Z= 0.144 Angle : 0.457 3.923 6822 Z= 0.237 Chirality : 0.051 0.137 774 Planarity : 0.002 0.013 864 Dihedral : 4.693 13.768 666 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.87 % Allowed : 20.66 % 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: -2.19 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 374 PHE 0.005 0.000 PHE H 346 TYR 0.010 0.001 TYR H 310 ARG 0.001 0.000 ARG I 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 154 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 149 time to evaluate : 0.905 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: 0.5765 (t) cc_final: 0.5556 (t) REVERT: A 320 SER cc_start: 0.8461 (t) cc_final: 0.8185 (p) REVERT: A 342 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7640 (mm-30) REVERT: C 331 LYS cc_start: 0.8736 (mtmt) cc_final: 0.8473 (mmmm) REVERT: C 340 LYS cc_start: 0.8082 (mtpt) cc_final: 0.7664 (mttt) REVERT: C 342 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7671 (mm-30) REVERT: C 375 LYS cc_start: 0.6007 (tttt) cc_final: 0.5632 (tppt) REVERT: E 311 LYS cc_start: 0.7044 (ttpt) cc_final: 0.6701 (mttm) REVERT: E 340 LYS cc_start: 0.8574 (mtpt) cc_final: 0.8242 (mttp) REVERT: E 342 GLU cc_start: 0.8427 (mt-10) cc_final: 0.7982 (mm-30) REVERT: E 347 LYS cc_start: 0.8620 (mttt) cc_final: 0.7587 (ttpt) REVERT: E 369 LYS cc_start: 0.8111 (mttt) cc_final: 0.7623 (ttmp) REVERT: E 375 LYS cc_start: 0.7519 (tttt) cc_final: 0.6208 (pptt) REVERT: B 340 LYS cc_start: 0.8102 (mtpt) cc_final: 0.7688 (mttp) REVERT: B 342 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7760 (mm-30) REVERT: D 331 LYS cc_start: 0.8830 (mtmt) cc_final: 0.8626 (mtpt) REVERT: D 340 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7685 (mttt) REVERT: D 342 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7590 (mm-30) REVERT: D 375 LYS cc_start: 0.6025 (tttt) cc_final: 0.5650 (tppt) REVERT: F 311 LYS cc_start: 0.6999 (ttpt) cc_final: 0.6728 (mtpp) REVERT: F 338 GLU cc_start: 0.7636 (tt0) cc_final: 0.7395 (tt0) REVERT: F 340 LYS cc_start: 0.8505 (mtpt) cc_final: 0.8194 (mttt) REVERT: F 342 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7994 (mm-30) REVERT: F 347 LYS cc_start: 0.8607 (mttt) cc_final: 0.7834 (mtmt) REVERT: F 369 LYS cc_start: 0.8061 (mttt) cc_final: 0.7776 (mtmm) REVERT: F 375 LYS cc_start: 0.7656 (tttt) cc_final: 0.6571 (tmmt) REVERT: G 342 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7672 (mm-30) REVERT: G 347 LYS cc_start: 0.8459 (mppt) cc_final: 0.8123 (mtmt) REVERT: H 340 LYS cc_start: 0.8151 (mtpt) cc_final: 0.7731 (mttt) REVERT: H 342 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7825 (mm-30) REVERT: H 375 LYS cc_start: 0.5814 (tttt) cc_final: 0.5438 (tppt) REVERT: I 311 LYS cc_start: 0.6985 (ttpt) cc_final: 0.6393 (pttp) REVERT: I 340 LYS cc_start: 0.8589 (mtpt) cc_final: 0.8270 (mttt) REVERT: I 342 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8043 (mm-30) REVERT: I 347 LYS cc_start: 0.8620 (mttt) cc_final: 0.7621 (ttpt) REVERT: I 369 LYS cc_start: 0.8115 (mttt) cc_final: 0.7613 (ttmp) REVERT: I 375 LYS cc_start: 0.7533 (tttt) cc_final: 0.6201 (pptt) outliers start: 5 outliers final: 5 residues processed: 150 average time/residue: 2.8892 time to fit residues: 447.9908 Evaluate side-chains 151 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 146 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 347 LYS Chi-restraints excluded: chain G 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: 10.0000 chunk 57 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.5502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5094 Z= 0.168 Angle : 0.466 3.927 6822 Z= 0.242 Chirality : 0.050 0.138 774 Planarity : 0.002 0.013 864 Dihedral : 4.719 13.991 666 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.87 % Allowed : 21.53 % Favored : 77.60 % 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: -2.20 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 374 PHE 0.006 0.001 PHE H 346 TYR 0.007 0.001 TYR H 310 ARG 0.001 0.000 ARG F 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 149 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 144 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 SER cc_start: 0.8515 (t) cc_final: 0.8222 (p) REVERT: A 342 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7631 (mm-30) REVERT: C 331 LYS cc_start: 0.8748 (mtmt) cc_final: 0.8486 (mmmm) REVERT: C 340 LYS cc_start: 0.8081 (mtpt) cc_final: 0.7664 (mttt) REVERT: C 342 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7676 (mm-30) REVERT: C 375 LYS cc_start: 0.6066 (tttt) cc_final: 0.5688 (tppt) REVERT: E 311 LYS cc_start: 0.7054 (ttpt) cc_final: 0.6709 (mttt) REVERT: E 340 LYS cc_start: 0.8579 (mtpt) cc_final: 0.8242 (mttp) REVERT: E 342 GLU cc_start: 0.8409 (mt-10) cc_final: 0.7958 (mm-30) REVERT: E 347 LYS cc_start: 0.8614 (mttt) cc_final: 0.7786 (mtmm) REVERT: E 369 LYS cc_start: 0.8143 (mttt) cc_final: 0.7651 (ttmp) REVERT: E 375 LYS cc_start: 0.7578 (tttt) cc_final: 0.6245 (pptt) REVERT: B 340 LYS cc_start: 0.8101 (mtpt) cc_final: 0.7689 (mttp) REVERT: B 342 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7753 (mm-30) REVERT: B 375 LYS cc_start: 0.6621 (tttt) cc_final: 0.6267 (tptt) REVERT: D 331 LYS cc_start: 0.8821 (mtmt) cc_final: 0.8610 (mtpt) REVERT: D 340 LYS cc_start: 0.8136 (mtpt) cc_final: 0.7690 (mttt) REVERT: D 342 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7599 (mm-30) REVERT: D 375 LYS cc_start: 0.5946 (tttt) cc_final: 0.5618 (tppt) REVERT: F 311 LYS cc_start: 0.6938 (ttpt) cc_final: 0.6671 (mtpp) REVERT: F 338 GLU cc_start: 0.7628 (tt0) cc_final: 0.7367 (tt0) REVERT: F 340 LYS cc_start: 0.8513 (mtpt) cc_final: 0.8197 (mttt) REVERT: F 342 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7996 (mm-30) REVERT: F 347 LYS cc_start: 0.8611 (mttt) cc_final: 0.7847 (mtmt) REVERT: F 369 LYS cc_start: 0.8062 (mttt) cc_final: 0.7774 (mtmm) REVERT: F 375 LYS cc_start: 0.7662 (tttt) cc_final: 0.6552 (tmmt) REVERT: G 342 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7670 (mm-30) REVERT: G 347 LYS cc_start: 0.8485 (mppt) cc_final: 0.8159 (mtmt) REVERT: H 340 LYS cc_start: 0.8166 (mtpt) cc_final: 0.7751 (mttt) REVERT: H 342 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7809 (mm-30) REVERT: H 375 LYS cc_start: 0.5826 (tttt) cc_final: 0.5436 (tppt) REVERT: I 311 LYS cc_start: 0.6954 (ttpt) cc_final: 0.6651 (mtpt) REVERT: I 340 LYS cc_start: 0.8598 (mtpt) cc_final: 0.8280 (mttt) REVERT: I 342 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8052 (mm-30) REVERT: I 347 LYS cc_start: 0.8634 (mttt) cc_final: 0.7614 (ttpt) REVERT: I 369 LYS cc_start: 0.8131 (mttt) cc_final: 0.7227 (tttt) REVERT: I 375 LYS cc_start: 0.7518 (tttt) cc_final: 0.6167 (pptt) outliers start: 5 outliers final: 5 residues processed: 145 average time/residue: 2.9283 time to fit residues: 440.8108 Evaluate side-chains 149 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 144 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 347 LYS Chi-restraints excluded: chain G 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: 0.9990 chunk 50 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 0.3980 chunk 33 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.162779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.139562 restraints weight = 18174.468| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 1.71 r_work: 0.3696 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.5534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5094 Z= 0.133 Angle : 0.443 3.828 6822 Z= 0.228 Chirality : 0.051 0.136 774 Planarity : 0.002 0.013 864 Dihedral : 4.458 12.843 666 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.52 % Allowed : 22.05 % Favored : 77.43 % 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: -2.16 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 374 PHE 0.006 0.000 PHE H 346 TYR 0.008 0.001 TYR H 310 ARG 0.001 0.000 ARG I 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7583.12 seconds wall clock time: 131 minutes 47.07 seconds (7907.07 seconds total)