Starting phenix.real_space_refine on Fri Aug 2 20:42:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7m_18224/08_2024/8q7m_18224.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7m_18224/08_2024/8q7m_18224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7m_18224/08_2024/8q7m_18224.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7m_18224/08_2024/8q7m_18224.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7m_18224/08_2024/8q7m_18224.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7m_18224/08_2024/8q7m_18224.cif" } resolution = 3.26 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: 4 Type Number sf(0) Gaussians S 9 5.16 5 C 3210 2.51 5 N 939 2.21 5 O 951 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 338": "OE1" <-> "OE2" Residue "A ASP 358": "OD1" <-> "OD2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B ASP 348": "OD1" <-> "OD2" Residue "B ASP 358": "OD1" <-> "OD2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C ASP 358": "OD1" <-> "OD2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E GLU 372": "OE1" <-> "OE2" Residue "F GLU 338": "OE1" <-> "OE2" Residue "F GLU 372": "OE1" <-> "OE2" Residue "G GLU 342": "OE1" <-> "OE2" Residue "H GLU 338": "OE1" <-> "OE2" Residue "H GLU 342": "OE1" <-> "OE2" Residue "I GLU 342": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 5109 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 568 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "B" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 568 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "C" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 568 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "D" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "E" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "F" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "G" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "H" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "I" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Time building chain proxies: 3.83, per 1000 atoms: 0.75 Number of scatterers: 5109 At special positions: 0 Unit cell: (161.504, 161.504, 50.264, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 9 16.00 O 951 8.00 N 939 7.00 C 3210 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 961.9 milliseconds 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1170 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 28 sheets defined 0.0% alpha, 52.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 307 through 310 Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.878A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 325 removed outlier: 6.471A pdb=" N LYS A 317 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N SER B 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR A 319 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N CYS B 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS A 321 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N SER B 324 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLY A 323 " --> pdb=" O SER B 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 328 through 330 Processing sheet with id=AA5, first strand: chain 'B' and resid 336 through 339 Processing sheet with id=AA6, first strand: chain 'B' and resid 342 through 346 removed outlier: 7.031A pdb=" N LYS A 343 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N PHE B 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASP A 345 " --> pdb=" O PHE B 346 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LYS C 343 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 350 through 354 removed outlier: 6.447A pdb=" N GLN A 351 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE B 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LYS A 353 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 357 through 362 removed outlier: 6.609A pdb=" N LEU A 357 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ILE C 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASN A 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N HIS C 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 368 through 373 removed outlier: 6.539A pdb=" N LYS A 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N GLU B 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE A 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 376 through 378 removed outlier: 6.557A pdb=" N THR A 377 " --> pdb=" O PHE B 378 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU A 376 " --> pdb=" O THR C 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 307 through 310 Processing sheet with id=AB3, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.824A pdb=" N VAL D 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 317 through 325 Processing sheet with id=AB5, first strand: chain 'E' and resid 328 through 330 removed outlier: 6.487A pdb=" N ILE D 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 336 through 340 removed outlier: 6.351A pdb=" N GLN D 336 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N VAL F 339 " --> pdb=" O GLN D 336 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU D 338 " --> pdb=" O VAL F 339 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 343 through 346 removed outlier: 6.431A pdb=" N LYS D 343 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N PHE F 346 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ASP D 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 351 through 354 removed outlier: 6.461A pdb=" N GLN D 351 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ILE F 354 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LYS D 353 " --> pdb=" O ILE F 354 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 357 through 362 removed outlier: 6.696A pdb=" N LEU D 357 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ILE E 360 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASN D 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N HIS E 362 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N THR D 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 368 through 377 removed outlier: 6.550A pdb=" N LYS D 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N GLU F 372 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE D 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N HIS F 374 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N THR D 373 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU F 376 " --> pdb=" O THR D 373 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS D 375 " --> pdb=" O LEU F 376 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 306 through 310 removed outlier: 6.547A pdb=" N GLN G 307 " --> pdb=" O ILE I 308 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N TYR I 310 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL G 309 " --> pdb=" O TYR I 310 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 313 through 314 removed outlier: 6.826A pdb=" N VAL G 313 " --> pdb=" O ASP I 314 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 317 through 322 removed outlier: 6.386A pdb=" N VAL H 318 " --> pdb=" O THR I 319 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N LYS I 321 " --> pdb=" O VAL H 318 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER H 320 " --> pdb=" O LYS I 321 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 325 through 330 removed outlier: 7.010A pdb=" N GLY I 326 " --> pdb=" O LEU G 325 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN G 327 " --> pdb=" O GLY I 326 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLY H 326 " --> pdb=" O ASN I 327 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N HIS I 329 " --> pdb=" O GLY H 326 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE H 328 " --> pdb=" O HIS I 329 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 336 through 340 removed outlier: 6.590A pdb=" N GLN G 336 " --> pdb=" O VAL I 337 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N VAL I 339 " --> pdb=" O GLN G 336 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLU G 338 " --> pdb=" O VAL I 339 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 343 through 348 removed outlier: 6.861A pdb=" N LEU G 344 " --> pdb=" O LYS I 343 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASP I 345 " --> pdb=" O LEU G 344 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N PHE G 346 " --> pdb=" O ASP I 345 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LYS I 347 " --> pdb=" O PHE G 346 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU H 344 " --> pdb=" O ASP I 345 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N LYS I 347 " --> pdb=" O LEU H 344 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N PHE H 346 " --> pdb=" O LYS I 347 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 351 through 354 removed outlier: 6.685A pdb=" N GLN G 351 " --> pdb=" O SER I 352 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N ILE I 354 " --> pdb=" O GLN G 351 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LYS G 353 " --> pdb=" O ILE I 354 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 357 through 362 Processing sheet with id=AD1, first strand: chain 'G' and resid 369 through 378 removed outlier: 6.509A pdb=" N LYS G 369 " --> pdb=" O LYS I 370 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N GLU I 372 " --> pdb=" O LYS G 369 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE G 371 " --> pdb=" O GLU I 372 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N HIS I 374 " --> pdb=" O ILE G 371 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR G 373 " --> pdb=" O HIS I 374 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N LEU I 376 " --> pdb=" O THR G 373 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LYS G 375 " --> pdb=" O LEU I 376 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N PHE I 378 " --> pdb=" O LYS G 375 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N THR G 377 " --> pdb=" O PHE I 378 " (cutoff:3.500A) 131 hydrogen bonds defined for protein. 393 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: 1.37 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1374 1.33 - 1.45: 692 1.45 - 1.57: 3115 1.57 - 1.69: 0 1.69 - 1.81: 9 Bond restraints: 5190 Sorted by residual: bond pdb=" CZ ARG I 349 " pdb=" NH2 ARG I 349 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 7.89e+00 bond pdb=" CZ ARG G 349 " pdb=" NH2 ARG G 349 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.76e+00 bond pdb=" CZ ARG H 349 " pdb=" NH2 ARG H 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.24e+00 bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.12e+00 bond pdb=" CZ ARG C 379 " pdb=" NH2 ARG C 379 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.05e+00 ... (remaining 5185 not shown) Histogram of bond angle deviations from ideal: 101.36 - 107.04: 310 107.04 - 112.71: 2402 112.71 - 118.39: 1411 118.39 - 124.07: 2417 124.07 - 129.75: 405 Bond angle restraints: 6945 Sorted by residual: angle pdb=" CA ASP B 358 " pdb=" CB ASP B 358 " pdb=" CG ASP B 358 " ideal model delta sigma weight residual 112.60 119.33 -6.73 1.00e+00 1.00e+00 4.54e+01 angle pdb=" CA PHE D 346 " pdb=" CB PHE D 346 " pdb=" CG PHE D 346 " ideal model delta sigma weight residual 113.80 120.52 -6.72 1.00e+00 1.00e+00 4.51e+01 angle pdb=" C LYS F 370 " pdb=" CA LYS F 370 " pdb=" CB LYS F 370 " ideal model delta sigma weight residual 109.65 121.15 -11.50 1.75e+00 3.27e-01 4.32e+01 angle pdb=" N LYS E 347 " pdb=" CA LYS E 347 " pdb=" C LYS E 347 " ideal model delta sigma weight residual 113.19 122.72 -9.53 1.58e+00 4.01e-01 3.64e+01 angle pdb=" CA PHE E 346 " pdb=" CB PHE E 346 " pdb=" CG PHE E 346 " ideal model delta sigma weight residual 113.80 119.53 -5.73 1.00e+00 1.00e+00 3.28e+01 ... (remaining 6940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 2973 16.98 - 33.95: 143 33.95 - 50.93: 27 50.93 - 67.91: 8 67.91 - 84.88: 8 Dihedral angle restraints: 3159 sinusoidal: 1320 harmonic: 1839 Sorted by residual: dihedral pdb=" C LYS F 370 " pdb=" N LYS F 370 " pdb=" CA LYS F 370 " pdb=" CB LYS F 370 " ideal model delta harmonic sigma weight residual -122.60 -139.39 16.79 0 2.50e+00 1.60e-01 4.51e+01 dihedral pdb=" CA GLY D 334 " pdb=" C GLY D 334 " pdb=" N GLY D 335 " pdb=" CA GLY D 335 " ideal model delta harmonic sigma weight residual 180.00 -151.00 -29.00 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" N LYS F 370 " pdb=" C LYS F 370 " pdb=" CA LYS F 370 " pdb=" CB LYS F 370 " ideal model delta harmonic sigma weight residual 122.80 136.21 -13.41 0 2.50e+00 1.60e-01 2.88e+01 ... (remaining 3156 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 599 0.111 - 0.221: 154 0.221 - 0.332: 18 0.332 - 0.442: 11 0.442 - 0.553: 1 Chirality restraints: 783 Sorted by residual: chirality pdb=" CA LYS F 370 " pdb=" N LYS F 370 " pdb=" C LYS F 370 " pdb=" CB LYS F 370 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.63e+00 chirality pdb=" CA LYS E 347 " pdb=" N LYS E 347 " pdb=" C LYS E 347 " pdb=" CB LYS E 347 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" CA LYS D 347 " pdb=" N LYS D 347 " pdb=" C LYS D 347 " pdb=" CB LYS D 347 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.62e+00 ... (remaining 780 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 310 " 0.080 2.00e-02 2.50e+03 4.50e-02 4.05e+01 pdb=" CG TYR I 310 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR I 310 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR I 310 " -0.040 2.00e-02 2.50e+03 pdb=" CE1 TYR I 310 " -0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR I 310 " -0.023 2.00e-02 2.50e+03 pdb=" CZ TYR I 310 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR I 310 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 310 " 0.079 2.00e-02 2.50e+03 4.44e-02 3.95e+01 pdb=" CG TYR G 310 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR G 310 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR G 310 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR G 310 " -0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR G 310 " -0.022 2.00e-02 2.50e+03 pdb=" CZ TYR G 310 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR G 310 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 378 " 0.060 2.00e-02 2.50e+03 3.71e-02 2.41e+01 pdb=" CG PHE H 378 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE H 378 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE H 378 " -0.030 2.00e-02 2.50e+03 pdb=" CE1 PHE H 378 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE H 378 " 0.016 2.00e-02 2.50e+03 pdb=" CZ PHE H 378 " 0.026 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 2245 2.97 - 3.45: 4035 3.45 - 3.94: 8195 3.94 - 4.42: 7979 4.42 - 4.90: 15876 Nonbonded interactions: 38330 Sorted by model distance: nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.490 3.040 nonbonded pdb=" OD1 ASP G 314 " pdb=" OG SER G 316 " model vdw 2.510 3.040 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.510 3.040 nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.518 3.040 nonbonded pdb=" OD1 ASP I 314 " pdb=" OG SER I 316 " model vdw 2.528 3.040 ... (remaining 38325 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 306 through 378) selection = (chain 'B' and resid 306 through 378) selection = (chain 'C' and resid 306 through 378) selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = (chain 'G' and resid 306 through 378) selection = (chain 'H' and resid 306 through 378) selection = (chain 'I' and resid 306 through 378) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.560 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: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.920 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 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 0.047 5190 Z= 0.760 Angle : 1.958 11.497 6945 Z= 1.286 Chirality : 0.105 0.553 783 Planarity : 0.009 0.052 882 Dihedral : 11.701 84.883 1989 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 0.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.17 % Allowed : 3.08 % Favored : 96.75 % Cbeta Deviations : 0.68 % 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: -1.88 (0.26), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.20), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.021 0.004 HIS H 330 PHE 0.060 0.014 PHE H 378 TYR 0.080 0.019 TYR I 310 ARG 0.008 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 222 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8826 (ttmt) cc_final: 0.8376 (tmtt) REVERT: A 317 LYS cc_start: 0.7605 (pttt) cc_final: 0.7308 (ptpp) REVERT: A 340 LYS cc_start: 0.8392 (tttt) cc_final: 0.7937 (ttmm) REVERT: A 351 GLN cc_start: 0.7835 (mt0) cc_final: 0.6647 (mp10) REVERT: A 369 LYS cc_start: 0.6831 (mttt) cc_final: 0.6541 (mtpp) REVERT: A 373 THR cc_start: 0.8088 (m) cc_final: 0.7469 (p) REVERT: B 317 LYS cc_start: 0.8038 (pttt) cc_final: 0.7692 (ptpp) REVERT: B 340 LYS cc_start: 0.8492 (tttt) cc_final: 0.8182 (ttmm) REVERT: B 348 ASP cc_start: 0.8213 (t0) cc_final: 0.7459 (p0) REVERT: C 311 LYS cc_start: 0.8731 (ttmt) cc_final: 0.8392 (mttm) REVERT: C 317 LYS cc_start: 0.7892 (pttt) cc_final: 0.7593 (ptpp) REVERT: C 349 ARG cc_start: 0.7549 (mtm180) cc_final: 0.6645 (mtt-85) REVERT: C 351 GLN cc_start: 0.7773 (mt0) cc_final: 0.7386 (mt0) REVERT: C 369 LYS cc_start: 0.7251 (mttt) cc_final: 0.6976 (ttmt) REVERT: C 373 THR cc_start: 0.7944 (m) cc_final: 0.7208 (p) REVERT: C 379 ARG cc_start: 0.6470 (tpp80) cc_final: 0.6239 (ttp-170) REVERT: D 311 LYS cc_start: 0.8444 (pttt) cc_final: 0.7822 (ptmm) REVERT: D 360 ILE cc_start: 0.8031 (tt) cc_final: 0.7737 (mt) REVERT: E 311 LYS cc_start: 0.8458 (pttt) cc_final: 0.7905 (ptmm) REVERT: E 317 LYS cc_start: 0.7466 (pttt) cc_final: 0.7115 (ptpt) REVERT: F 311 LYS cc_start: 0.8424 (ttmt) cc_final: 0.7840 (tttm) REVERT: F 372 GLU cc_start: 0.7279 (pt0) cc_final: 0.6987 (pt0) REVERT: G 378 PHE cc_start: 0.7351 (t80) cc_final: 0.6999 (t80) outliers start: 1 outliers final: 0 residues processed: 222 average time/residue: 0.2774 time to fit residues: 71.1012 Evaluate side-chains 159 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN B 327 ASN C 327 ASN D 330 HIS D 362 HIS E 327 ASN E 362 HIS F 327 ASN F 330 HIS G 368 ASN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 359 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5190 Z= 0.216 Angle : 0.720 8.034 6945 Z= 0.357 Chirality : 0.053 0.150 783 Planarity : 0.003 0.023 882 Dihedral : 6.206 19.706 684 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.88 % Allowed : 10.43 % Favored : 87.69 % 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: -1.53 (0.26), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.20), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.014 0.002 PHE A 378 TYR 0.018 0.003 TYR H 310 ARG 0.005 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 153 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7738 (pttt) cc_final: 0.7470 (ptpp) REVERT: A 340 LYS cc_start: 0.8301 (tttt) cc_final: 0.8008 (mttp) REVERT: A 373 THR cc_start: 0.8105 (m) cc_final: 0.7731 (p) REVERT: B 317 LYS cc_start: 0.8004 (pttt) cc_final: 0.7718 (ptpp) REVERT: B 340 LYS cc_start: 0.8598 (tttt) cc_final: 0.8277 (ttmm) REVERT: B 347 LYS cc_start: 0.8956 (mttm) cc_final: 0.8458 (mttt) REVERT: B 348 ASP cc_start: 0.8459 (t0) cc_final: 0.7389 (p0) REVERT: C 317 LYS cc_start: 0.7885 (pttt) cc_final: 0.7644 (ptpp) REVERT: C 340 LYS cc_start: 0.8405 (tttt) cc_final: 0.8173 (mttp) REVERT: C 349 ARG cc_start: 0.7606 (mtm180) cc_final: 0.7267 (mtp85) REVERT: C 369 LYS cc_start: 0.6930 (mttt) cc_final: 0.6629 (ttmt) REVERT: C 379 ARG cc_start: 0.6594 (tpp80) cc_final: 0.5932 (ttp-170) REVERT: D 311 LYS cc_start: 0.8337 (pttt) cc_final: 0.7694 (ptmm) REVERT: D 349 ARG cc_start: 0.7676 (ttm110) cc_final: 0.7334 (mtp85) REVERT: E 311 LYS cc_start: 0.8299 (pttt) cc_final: 0.7768 (ptmm) REVERT: E 317 LYS cc_start: 0.7337 (pttt) cc_final: 0.7075 (ptpt) REVERT: E 360 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7577 (mt) REVERT: F 311 LYS cc_start: 0.8352 (ttmt) cc_final: 0.7733 (tttm) REVERT: F 317 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7622 (ptpp) REVERT: F 349 ARG cc_start: 0.7521 (ttm110) cc_final: 0.7221 (mtp85) REVERT: G 374 HIS cc_start: 0.7224 (m-70) cc_final: 0.5623 (p-80) REVERT: H 374 HIS cc_start: 0.7886 (m-70) cc_final: 0.7569 (m-70) outliers start: 11 outliers final: 9 residues processed: 158 average time/residue: 0.3214 time to fit residues: 58.7901 Evaluate side-chains 143 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 132 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 375 LYS Chi-restraints excluded: chain G residue 368 ASN Chi-restraints excluded: chain H residue 305 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 47 optimal weight: 20.0000 chunk 38 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 chunk 51 optimal weight: 0.0020 chunk 56 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 45 optimal weight: 0.0040 overall best weight: 1.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN G 368 ASN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 359 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5190 Z= 0.170 Angle : 0.619 6.775 6945 Z= 0.308 Chirality : 0.050 0.134 783 Planarity : 0.002 0.017 882 Dihedral : 5.476 15.951 684 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.56 % Allowed : 10.77 % Favored : 86.67 % 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: -1.46 (0.27), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.20), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 330 PHE 0.011 0.001 PHE A 378 TYR 0.016 0.002 TYR G 310 ARG 0.003 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 140 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7807 (pttt) cc_final: 0.7536 (ptpp) REVERT: A 340 LYS cc_start: 0.8349 (tttt) cc_final: 0.7994 (mttp) REVERT: A 373 THR cc_start: 0.8107 (m) cc_final: 0.7779 (p) REVERT: B 317 LYS cc_start: 0.7969 (pttt) cc_final: 0.7728 (ptpp) REVERT: B 340 LYS cc_start: 0.8596 (tttt) cc_final: 0.8258 (ttmm) REVERT: B 347 LYS cc_start: 0.8956 (mttm) cc_final: 0.8538 (mttt) REVERT: B 348 ASP cc_start: 0.8377 (t0) cc_final: 0.7543 (p0) REVERT: C 311 LYS cc_start: 0.8938 (pttt) cc_final: 0.8337 (mmtt) REVERT: C 317 LYS cc_start: 0.7796 (pttt) cc_final: 0.7585 (ptpp) REVERT: C 340 LYS cc_start: 0.8509 (tttt) cc_final: 0.8233 (mttp) REVERT: C 349 ARG cc_start: 0.7647 (mtm180) cc_final: 0.7311 (mtp85) REVERT: C 369 LYS cc_start: 0.6996 (mttt) cc_final: 0.6691 (ttmt) REVERT: D 311 LYS cc_start: 0.8329 (pttt) cc_final: 0.7710 (ptmm) REVERT: D 349 ARG cc_start: 0.7636 (ttm110) cc_final: 0.7302 (mtp85) REVERT: E 311 LYS cc_start: 0.8222 (pttt) cc_final: 0.7683 (ptmm) REVERT: E 317 LYS cc_start: 0.7324 (pttt) cc_final: 0.7087 (ptpt) REVERT: F 311 LYS cc_start: 0.8305 (ttmt) cc_final: 0.7773 (tttp) REVERT: F 317 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7795 (ptpp) REVERT: F 349 ARG cc_start: 0.7560 (ttm110) cc_final: 0.7281 (mtp85) REVERT: F 370 LYS cc_start: 0.4235 (OUTLIER) cc_final: 0.3432 (pttt) REVERT: G 311 LYS cc_start: 0.6157 (mmmt) cc_final: 0.5895 (mmmt) REVERT: G 374 HIS cc_start: 0.7098 (m-70) cc_final: 0.5501 (p-80) outliers start: 15 outliers final: 10 residues processed: 147 average time/residue: 0.2584 time to fit residues: 44.7020 Evaluate side-chains 144 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 132 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 375 LYS Chi-restraints excluded: chain H residue 305 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 5.9990 chunk 43 optimal weight: 20.0000 chunk 29 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 57 optimal weight: 9.9990 chunk 60 optimal weight: 20.0000 chunk 30 optimal weight: 0.0980 chunk 54 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 overall best weight: 4.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 ASN H 374 HIS ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 5190 Z= 0.388 Angle : 0.698 6.762 6945 Z= 0.353 Chirality : 0.054 0.152 783 Planarity : 0.003 0.022 882 Dihedral : 5.657 15.847 684 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.25 % Allowed : 12.82 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.28), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.21), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 362 PHE 0.010 0.002 PHE F 378 TYR 0.024 0.004 TYR H 310 ARG 0.002 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 139 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8678 (mtmt) cc_final: 0.8404 (mtpp) REVERT: A 317 LYS cc_start: 0.7755 (pttt) cc_final: 0.7398 (ptpp) REVERT: A 340 LYS cc_start: 0.8353 (tttt) cc_final: 0.7944 (mttp) REVERT: A 373 THR cc_start: 0.8050 (m) cc_final: 0.7667 (p) REVERT: B 317 LYS cc_start: 0.8193 (pttt) cc_final: 0.7887 (ptpp) REVERT: B 340 LYS cc_start: 0.8678 (tttt) cc_final: 0.8336 (ttmm) REVERT: B 347 LYS cc_start: 0.8945 (mttm) cc_final: 0.8539 (mttt) REVERT: B 348 ASP cc_start: 0.8547 (t0) cc_final: 0.7579 (p0) REVERT: C 311 LYS cc_start: 0.8973 (pttt) cc_final: 0.8022 (mmmt) REVERT: C 317 LYS cc_start: 0.7819 (pttt) cc_final: 0.7583 (ptpp) REVERT: C 340 LYS cc_start: 0.8472 (tttt) cc_final: 0.8035 (mttp) REVERT: C 349 ARG cc_start: 0.7581 (mtm180) cc_final: 0.7334 (mtp85) REVERT: C 351 GLN cc_start: 0.7700 (mt0) cc_final: 0.7359 (mt0) REVERT: C 369 LYS cc_start: 0.7093 (mttt) cc_final: 0.6749 (ttmt) REVERT: D 311 LYS cc_start: 0.8375 (pttt) cc_final: 0.7862 (ptmt) REVERT: D 349 ARG cc_start: 0.7674 (ttm110) cc_final: 0.7351 (mtp85) REVERT: E 311 LYS cc_start: 0.8368 (pttt) cc_final: 0.7970 (ptmt) REVERT: F 311 LYS cc_start: 0.8360 (ttmt) cc_final: 0.7833 (tttm) REVERT: F 349 ARG cc_start: 0.7645 (ttm110) cc_final: 0.7401 (mtp85) REVERT: F 370 LYS cc_start: 0.4404 (OUTLIER) cc_final: 0.3457 (mmmt) REVERT: G 311 LYS cc_start: 0.6031 (mmmt) cc_final: 0.5758 (mmmt) REVERT: G 374 HIS cc_start: 0.7214 (m-70) cc_final: 0.5611 (p90) outliers start: 19 outliers final: 13 residues processed: 151 average time/residue: 0.2770 time to fit residues: 48.8277 Evaluate side-chains 144 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 130 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 375 LYS Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 328 ILE Chi-restraints excluded: chain H residue 341 SER Chi-restraints excluded: chain I residue 306 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 20.0000 chunk 34 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 31 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 359 ASN H 374 HIS ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 5190 Z= 0.497 Angle : 0.764 9.930 6945 Z= 0.384 Chirality : 0.055 0.167 783 Planarity : 0.003 0.018 882 Dihedral : 5.863 18.746 684 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.59 % Allowed : 14.19 % Favored : 82.22 % 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: -1.83 (0.28), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.21), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 362 PHE 0.010 0.002 PHE H 378 TYR 0.016 0.003 TYR A 310 ARG 0.004 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 133 time to evaluate : 0.632 Fit side-chains REVERT: A 311 LYS cc_start: 0.8780 (mtmt) cc_final: 0.8191 (mtmt) REVERT: A 317 LYS cc_start: 0.7830 (pttt) cc_final: 0.7425 (ptpp) REVERT: A 340 LYS cc_start: 0.8468 (tttt) cc_final: 0.8093 (mttp) REVERT: A 373 THR cc_start: 0.8099 (m) cc_final: 0.7700 (p) REVERT: B 311 LYS cc_start: 0.9070 (ttmt) cc_final: 0.8267 (mttt) REVERT: B 317 LYS cc_start: 0.8276 (pttt) cc_final: 0.7989 (ptpp) REVERT: B 340 LYS cc_start: 0.8641 (tttt) cc_final: 0.7853 (tmtt) REVERT: B 347 LYS cc_start: 0.8944 (mttm) cc_final: 0.8573 (mttt) REVERT: B 348 ASP cc_start: 0.8559 (t0) cc_final: 0.7620 (p0) REVERT: B 349 ARG cc_start: 0.8185 (mtp85) cc_final: 0.7902 (mtp85) REVERT: C 311 LYS cc_start: 0.8973 (pttt) cc_final: 0.8206 (mmtm) REVERT: C 317 LYS cc_start: 0.7804 (pttt) cc_final: 0.7549 (ptpp) REVERT: C 340 LYS cc_start: 0.8496 (tttt) cc_final: 0.7956 (mttp) REVERT: C 349 ARG cc_start: 0.7620 (mtm180) cc_final: 0.7325 (mtp85) REVERT: C 369 LYS cc_start: 0.7158 (mttt) cc_final: 0.6778 (ttmt) REVERT: C 372 GLU cc_start: 0.7968 (pt0) cc_final: 0.7572 (pt0) REVERT: D 311 LYS cc_start: 0.8384 (pttt) cc_final: 0.7921 (ptmt) REVERT: D 349 ARG cc_start: 0.7688 (ttm110) cc_final: 0.7350 (mtp85) REVERT: F 311 LYS cc_start: 0.8405 (ttmt) cc_final: 0.7862 (tttm) REVERT: F 340 LYS cc_start: 0.8534 (tttt) cc_final: 0.8114 (tttp) REVERT: F 349 ARG cc_start: 0.7694 (ttm110) cc_final: 0.7412 (mtp85) REVERT: F 370 LYS cc_start: 0.4168 (OUTLIER) cc_final: 0.3280 (tppt) REVERT: F 372 GLU cc_start: 0.8363 (pt0) cc_final: 0.7996 (pt0) outliers start: 21 outliers final: 16 residues processed: 145 average time/residue: 0.2924 time to fit residues: 49.7672 Evaluate side-chains 147 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain G residue 354 ILE Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 328 ILE Chi-restraints excluded: chain H residue 341 SER Chi-restraints excluded: chain H residue 354 ILE Chi-restraints excluded: chain I residue 306 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 20.0000 chunk 12 optimal weight: 0.7980 chunk 35 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 50 optimal weight: 20.0000 chunk 28 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 374 HIS ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5190 Z= 0.176 Angle : 0.619 7.964 6945 Z= 0.298 Chirality : 0.050 0.128 783 Planarity : 0.002 0.017 882 Dihedral : 5.185 16.483 684 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.71 % Allowed : 16.24 % Favored : 82.05 % 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: -1.78 (0.29), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 330 PHE 0.006 0.001 PHE A 378 TYR 0.010 0.002 TYR A 310 ARG 0.003 0.000 ARG H 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8751 (mtmt) cc_final: 0.8394 (mtmt) REVERT: A 317 LYS cc_start: 0.7825 (pttt) cc_final: 0.7418 (ptpp) REVERT: A 340 LYS cc_start: 0.8469 (tttt) cc_final: 0.8082 (mttp) REVERT: A 373 THR cc_start: 0.8073 (m) cc_final: 0.7693 (p) REVERT: B 317 LYS cc_start: 0.8260 (pttt) cc_final: 0.7984 (ptpp) REVERT: B 340 LYS cc_start: 0.8581 (tttt) cc_final: 0.8167 (mttp) REVERT: B 347 LYS cc_start: 0.8897 (mttm) cc_final: 0.8567 (mttt) REVERT: B 348 ASP cc_start: 0.8455 (t0) cc_final: 0.7617 (p0) REVERT: B 373 THR cc_start: 0.8235 (m) cc_final: 0.7756 (p) REVERT: C 311 LYS cc_start: 0.8787 (pttt) cc_final: 0.7785 (mmmt) REVERT: C 317 LYS cc_start: 0.7703 (pttt) cc_final: 0.7488 (ptpp) REVERT: C 340 LYS cc_start: 0.8544 (tttt) cc_final: 0.8008 (mttp) REVERT: C 349 ARG cc_start: 0.7621 (mtm180) cc_final: 0.7351 (mtp85) REVERT: C 369 LYS cc_start: 0.7133 (mttt) cc_final: 0.6781 (ttmt) REVERT: D 311 LYS cc_start: 0.8380 (pttt) cc_final: 0.7879 (ptmt) REVERT: D 349 ARG cc_start: 0.7639 (ttm110) cc_final: 0.7340 (mtp85) REVERT: E 311 LYS cc_start: 0.8369 (pttt) cc_final: 0.7900 (ptmm) REVERT: E 360 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.7972 (mt) REVERT: F 311 LYS cc_start: 0.8296 (ttmt) cc_final: 0.7795 (tttm) REVERT: F 340 LYS cc_start: 0.8518 (tttt) cc_final: 0.8070 (tttp) REVERT: F 349 ARG cc_start: 0.7637 (ttm110) cc_final: 0.7384 (mtp85) REVERT: F 370 LYS cc_start: 0.3905 (OUTLIER) cc_final: 0.3370 (mmmt) REVERT: G 374 HIS cc_start: 0.7182 (m-70) cc_final: 0.5559 (p-80) outliers start: 10 outliers final: 8 residues processed: 135 average time/residue: 0.2575 time to fit residues: 40.9950 Evaluate side-chains 137 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 127 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain H residue 341 SER Chi-restraints excluded: chain H residue 356 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 7.9990 chunk 34 optimal weight: 0.0980 chunk 44 optimal weight: 20.0000 chunk 51 optimal weight: 0.0270 chunk 60 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 28 optimal weight: 0.0170 chunk 24 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5190 Z= 0.125 Angle : 0.570 7.771 6945 Z= 0.272 Chirality : 0.049 0.124 783 Planarity : 0.002 0.018 882 Dihedral : 4.692 15.436 684 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.88 % Allowed : 16.07 % Favored : 82.05 % 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: -1.83 (0.29), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 330 PHE 0.006 0.001 PHE B 378 TYR 0.008 0.001 TYR A 310 ARG 0.004 0.000 ARG H 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 135 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8833 (mtmt) cc_final: 0.8517 (mtmt) REVERT: A 317 LYS cc_start: 0.7875 (pttt) cc_final: 0.7460 (ptpp) REVERT: A 340 LYS cc_start: 0.8519 (tttt) cc_final: 0.8083 (mttp) REVERT: A 372 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7342 (mt-10) REVERT: A 373 THR cc_start: 0.8101 (m) cc_final: 0.7663 (p) REVERT: B 317 LYS cc_start: 0.8184 (pttt) cc_final: 0.7941 (ptpp) REVERT: B 340 LYS cc_start: 0.8469 (tttt) cc_final: 0.8054 (mttp) REVERT: B 347 LYS cc_start: 0.8886 (mttm) cc_final: 0.8595 (mttt) REVERT: B 348 ASP cc_start: 0.8351 (t0) cc_final: 0.7602 (p0) REVERT: B 368 ASN cc_start: 0.7990 (OUTLIER) cc_final: 0.7578 (m110) REVERT: C 311 LYS cc_start: 0.8584 (pttt) cc_final: 0.7479 (mmmt) REVERT: C 340 LYS cc_start: 0.8573 (tttt) cc_final: 0.8074 (mttp) REVERT: C 349 ARG cc_start: 0.7643 (mtm180) cc_final: 0.7353 (mtp85) REVERT: C 369 LYS cc_start: 0.7125 (mttt) cc_final: 0.6754 (ttmt) REVERT: D 311 LYS cc_start: 0.8354 (pttt) cc_final: 0.7690 (ptmm) REVERT: D 349 ARG cc_start: 0.7663 (ttm110) cc_final: 0.7346 (mtp85) REVERT: E 311 LYS cc_start: 0.8271 (pttt) cc_final: 0.7802 (ptmm) REVERT: E 360 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8011 (mt) REVERT: F 349 ARG cc_start: 0.7646 (ttm110) cc_final: 0.7373 (mtp85) REVERT: F 370 LYS cc_start: 0.3633 (OUTLIER) cc_final: 0.3055 (tppt) REVERT: F 372 GLU cc_start: 0.8173 (pt0) cc_final: 0.7970 (pt0) REVERT: G 374 HIS cc_start: 0.7102 (m-70) cc_final: 0.5529 (p-80) REVERT: H 311 LYS cc_start: 0.8723 (ttmt) cc_final: 0.8466 (ttmt) outliers start: 11 outliers final: 3 residues processed: 140 average time/residue: 0.2727 time to fit residues: 45.7634 Evaluate side-chains 139 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 132 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 370 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 30 optimal weight: 0.0270 chunk 5 optimal weight: 9.9990 chunk 47 optimal weight: 20.0000 chunk 55 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 overall best weight: 3.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN B 327 ASN ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 374 HIS I 362 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5190 Z= 0.292 Angle : 0.638 7.628 6945 Z= 0.308 Chirality : 0.051 0.133 783 Planarity : 0.002 0.016 882 Dihedral : 4.897 15.517 684 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.71 % Allowed : 16.58 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.29), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 330 PHE 0.006 0.001 PHE F 378 TYR 0.012 0.002 TYR A 310 ARG 0.002 0.000 ARG H 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8769 (mtmt) cc_final: 0.8431 (mtmt) REVERT: A 317 LYS cc_start: 0.7891 (pttt) cc_final: 0.7467 (ptpp) REVERT: A 340 LYS cc_start: 0.8558 (tttt) cc_final: 0.8137 (mttp) REVERT: A 373 THR cc_start: 0.8094 (m) cc_final: 0.7690 (p) REVERT: B 317 LYS cc_start: 0.8283 (pttt) cc_final: 0.7983 (ptpp) REVERT: B 340 LYS cc_start: 0.8529 (tttt) cc_final: 0.8144 (mttp) REVERT: B 347 LYS cc_start: 0.8896 (mttm) cc_final: 0.8612 (mttt) REVERT: B 348 ASP cc_start: 0.8496 (t0) cc_final: 0.7593 (p0) REVERT: B 368 ASN cc_start: 0.8135 (t0) cc_final: 0.7713 (m110) REVERT: C 311 LYS cc_start: 0.8781 (pttt) cc_final: 0.7740 (mmmt) REVERT: C 340 LYS cc_start: 0.8590 (tttt) cc_final: 0.8049 (mttp) REVERT: C 349 ARG cc_start: 0.7611 (mtm180) cc_final: 0.7325 (mtp85) REVERT: C 369 LYS cc_start: 0.7113 (mttt) cc_final: 0.6761 (ttmt) REVERT: D 311 LYS cc_start: 0.8361 (pttt) cc_final: 0.7918 (ptmt) REVERT: D 349 ARG cc_start: 0.7659 (ttm110) cc_final: 0.7344 (mtp85) REVERT: E 360 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.7996 (mt) REVERT: F 311 LYS cc_start: 0.8363 (ttmt) cc_final: 0.7843 (tttm) REVERT: F 349 ARG cc_start: 0.7685 (ttm110) cc_final: 0.7388 (mtp85) REVERT: F 370 LYS cc_start: 0.3930 (OUTLIER) cc_final: 0.3033 (tppt) REVERT: G 374 HIS cc_start: 0.7196 (m-70) cc_final: 0.5588 (p90) REVERT: H 311 LYS cc_start: 0.8728 (ttmt) cc_final: 0.8468 (ttmt) outliers start: 10 outliers final: 8 residues processed: 137 average time/residue: 0.2561 time to fit residues: 41.1857 Evaluate side-chains 140 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain H residue 341 SER Chi-restraints excluded: chain H residue 356 SER 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: 20.0000 chunk 17 optimal weight: 0.8980 chunk 51 optimal weight: 20.0000 chunk 53 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 30.0000 chunk 36 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5190 Z= 0.278 Angle : 0.632 7.473 6945 Z= 0.308 Chirality : 0.051 0.135 783 Planarity : 0.002 0.019 882 Dihedral : 4.993 16.181 684 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.71 % Allowed : 16.41 % Favored : 81.88 % 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: -1.90 (0.29), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.005 0.001 PHE A 346 TYR 0.012 0.002 TYR A 310 ARG 0.004 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 135 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8732 (mtmt) cc_final: 0.8472 (mtmt) REVERT: A 317 LYS cc_start: 0.7838 (pttt) cc_final: 0.7456 (ptpp) REVERT: A 340 LYS cc_start: 0.8547 (tttt) cc_final: 0.8122 (mttp) REVERT: A 373 THR cc_start: 0.8077 (m) cc_final: 0.7681 (p) REVERT: B 311 LYS cc_start: 0.8993 (ttmt) cc_final: 0.8304 (mtpt) REVERT: B 317 LYS cc_start: 0.8282 (pttt) cc_final: 0.7991 (ptpp) REVERT: B 340 LYS cc_start: 0.8538 (tttt) cc_final: 0.7758 (tmtt) REVERT: B 347 LYS cc_start: 0.8893 (mttm) cc_final: 0.8659 (mttt) REVERT: B 348 ASP cc_start: 0.8511 (t0) cc_final: 0.7609 (p0) REVERT: B 349 ARG cc_start: 0.8123 (mtp85) cc_final: 0.7837 (mtp85) REVERT: B 368 ASN cc_start: 0.8090 (t0) cc_final: 0.7597 (m110) REVERT: C 311 LYS cc_start: 0.8829 (pttt) cc_final: 0.7802 (mmmt) REVERT: C 318 VAL cc_start: 0.8985 (t) cc_final: 0.8763 (t) REVERT: C 340 LYS cc_start: 0.8545 (tttt) cc_final: 0.7980 (mttp) REVERT: C 349 ARG cc_start: 0.7632 (mtm180) cc_final: 0.7365 (mtp85) REVERT: C 369 LYS cc_start: 0.7124 (mttt) cc_final: 0.6762 (ttmt) REVERT: D 311 LYS cc_start: 0.8362 (pttt) cc_final: 0.7750 (ptmm) REVERT: D 349 ARG cc_start: 0.7656 (ttm110) cc_final: 0.7334 (mtp85) REVERT: E 360 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8000 (mt) REVERT: F 311 LYS cc_start: 0.8309 (ttmt) cc_final: 0.7763 (tttm) REVERT: F 349 ARG cc_start: 0.7660 (ttm110) cc_final: 0.7381 (mtp85) REVERT: F 370 LYS cc_start: 0.3970 (OUTLIER) cc_final: 0.3197 (tppt) REVERT: F 372 GLU cc_start: 0.8324 (pt0) cc_final: 0.7967 (pt0) REVERT: G 310 TYR cc_start: 0.7238 (t80) cc_final: 0.7010 (t80) REVERT: G 374 HIS cc_start: 0.7189 (m-70) cc_final: 0.5574 (p90) REVERT: H 379 ARG cc_start: 0.5477 (tmt-80) cc_final: 0.4712 (ttm-80) outliers start: 10 outliers final: 8 residues processed: 140 average time/residue: 0.2842 time to fit residues: 46.6536 Evaluate side-chains 139 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 129 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 317 LYS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain H residue 341 SER Chi-restraints excluded: chain H residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5190 Z= 0.284 Angle : 0.653 7.541 6945 Z= 0.315 Chirality : 0.051 0.137 783 Planarity : 0.002 0.022 882 Dihedral : 5.009 16.647 684 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.71 % Allowed : 17.44 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.29), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 374 PHE 0.006 0.001 PHE A 346 TYR 0.012 0.002 TYR A 310 ARG 0.003 0.000 ARG B 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8726 (mtmt) cc_final: 0.8388 (mtmt) REVERT: A 317 LYS cc_start: 0.7821 (pttt) cc_final: 0.7412 (ptpp) REVERT: A 340 LYS cc_start: 0.8545 (tttt) cc_final: 0.8127 (mttp) REVERT: A 373 THR cc_start: 0.8082 (m) cc_final: 0.7687 (p) REVERT: B 317 LYS cc_start: 0.8347 (pttt) cc_final: 0.8034 (ptpp) REVERT: B 340 LYS cc_start: 0.8551 (tttt) cc_final: 0.7762 (tmtt) REVERT: B 347 LYS cc_start: 0.8888 (mttm) cc_final: 0.8644 (mttt) REVERT: B 348 ASP cc_start: 0.8496 (t0) cc_final: 0.7613 (p0) REVERT: B 349 ARG cc_start: 0.8132 (mtp85) cc_final: 0.7834 (mtp85) REVERT: B 368 ASN cc_start: 0.8125 (t0) cc_final: 0.7643 (m110) REVERT: C 311 LYS cc_start: 0.8852 (pttt) cc_final: 0.7825 (mmmt) REVERT: C 318 VAL cc_start: 0.8989 (t) cc_final: 0.8765 (t) REVERT: C 340 LYS cc_start: 0.8534 (tttt) cc_final: 0.7980 (mttp) REVERT: C 349 ARG cc_start: 0.7631 (mtm180) cc_final: 0.7369 (mtp85) REVERT: C 369 LYS cc_start: 0.7157 (mttt) cc_final: 0.6784 (ttmt) REVERT: D 311 LYS cc_start: 0.8360 (pttt) cc_final: 0.7764 (ptmm) REVERT: D 349 ARG cc_start: 0.7658 (ttm110) cc_final: 0.7337 (mtp85) REVERT: E 360 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.7987 (mt) REVERT: F 311 LYS cc_start: 0.8299 (ttmt) cc_final: 0.7749 (tttm) REVERT: F 314 ASP cc_start: 0.7337 (t0) cc_final: 0.7092 (t0) REVERT: F 349 ARG cc_start: 0.7664 (ttm110) cc_final: 0.7385 (mtp85) REVERT: F 370 LYS cc_start: 0.3939 (OUTLIER) cc_final: 0.3170 (tppt) REVERT: G 310 TYR cc_start: 0.7290 (t80) cc_final: 0.7069 (t80) REVERT: G 374 HIS cc_start: 0.7168 (m-70) cc_final: 0.5576 (p90) REVERT: H 311 LYS cc_start: 0.8701 (ttmt) cc_final: 0.8464 (ttmt) outliers start: 10 outliers final: 7 residues processed: 135 average time/residue: 0.2746 time to fit residues: 43.5241 Evaluate side-chains 139 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 130 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain H residue 341 SER Chi-restraints excluded: chain H residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 2 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.152353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.118985 restraints weight = 6355.381| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 1.81 r_work: 0.3791 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5190 Z= 0.313 Angle : 0.664 7.430 6945 Z= 0.323 Chirality : 0.051 0.139 783 Planarity : 0.003 0.050 882 Dihedral : 5.099 16.965 684 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.54 % Allowed : 17.78 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.29), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 374 PHE 0.008 0.001 PHE I 378 TYR 0.012 0.002 TYR A 310 ARG 0.003 0.000 ARG B 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1957.48 seconds wall clock time: 35 minutes 57.66 seconds (2157.66 seconds total)