Starting phenix.real_space_refine on Sun Mar 10 21:13:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7m_18224/03_2024/8q7m_18224.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7m_18224/03_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_18224/03_2024/8q7m_18224.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7m_18224/03_2024/8q7m_18224.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7m_18224/03_2024/8q7m_18224.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7m_18224/03_2024/8q7m_18224.pdb" } 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-5265/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: 3.12, per 1000 atoms: 0.61 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: 1.79 Conformation dependent library (CDL) restraints added in 949.2 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: 0.78 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: 1.40 Time building geometry restraints manager: 1.96 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 2.440 nonbonded pdb=" OD1 ASP G 314 " pdb=" OG SER G 316 " model vdw 2.510 2.440 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.510 2.440 nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.518 2.440 nonbonded pdb=" OD1 ASP I 314 " pdb=" OG SER I 316 " model vdw 2.528 2.440 ... (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 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: 3.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 11.460 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.010 Find NCS groups from input model: 0.400 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.000 ------------------------------------------------------------------------------- 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 : 0.629 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: 0.2878 time to fit residues: 73.6483 Evaluate side-chains 159 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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: 7.9990 chunk 47 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 0.0670 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN D 330 HIS D 362 HIS E 327 ASN E 362 HIS F 327 ASN F 330 HIS G 368 ASN ** H 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 359 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5190 Z= 0.200 Angle : 0.707 7.874 6945 Z= 0.351 Chirality : 0.052 0.153 783 Planarity : 0.003 0.024 882 Dihedral : 6.111 19.207 684 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.71 % Allowed : 10.43 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 0.004 0.001 HIS B 362 PHE 0.014 0.002 PHE A 378 TYR 0.018 0.003 TYR H 310 ARG 0.005 0.001 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 169 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 159 time to evaluate : 0.628 Fit side-chains REVERT: A 317 LYS cc_start: 0.7750 (pttt) cc_final: 0.7487 (ptpp) REVERT: A 340 LYS cc_start: 0.8126 (tttt) cc_final: 0.7922 (mttp) REVERT: A 373 THR cc_start: 0.8123 (m) cc_final: 0.7749 (p) REVERT: B 317 LYS cc_start: 0.8021 (pttt) cc_final: 0.7738 (ptpp) REVERT: B 340 LYS cc_start: 0.8516 (tttt) cc_final: 0.8234 (ttmm) REVERT: B 347 LYS cc_start: 0.8898 (mttm) cc_final: 0.8402 (mttt) REVERT: B 348 ASP cc_start: 0.8427 (t0) cc_final: 0.7358 (p0) REVERT: C 317 LYS cc_start: 0.7882 (pttt) cc_final: 0.7643 (ptpp) REVERT: C 340 LYS cc_start: 0.8405 (tttt) cc_final: 0.8194 (mttp) REVERT: C 349 ARG cc_start: 0.7600 (mtm180) cc_final: 0.7203 (mtp85) REVERT: C 369 LYS cc_start: 0.6888 (mttt) cc_final: 0.6607 (ttmt) REVERT: C 379 ARG cc_start: 0.6527 (tpp80) cc_final: 0.5840 (ttp-170) REVERT: D 311 LYS cc_start: 0.8327 (pttt) cc_final: 0.7685 (ptmm) REVERT: D 349 ARG cc_start: 0.7670 (ttm110) cc_final: 0.7340 (mtp85) REVERT: E 311 LYS cc_start: 0.8294 (pttt) cc_final: 0.7761 (ptmm) REVERT: E 317 LYS cc_start: 0.7369 (pttt) cc_final: 0.7061 (ptpt) REVERT: E 360 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7518 (mt) REVERT: F 311 LYS cc_start: 0.8326 (ttmt) cc_final: 0.7710 (tttm) REVERT: F 317 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7627 (ptpp) REVERT: F 349 ARG cc_start: 0.7549 (ttm110) cc_final: 0.7219 (mtp85) REVERT: G 374 HIS cc_start: 0.7253 (m-70) cc_final: 0.5700 (p-80) outliers start: 10 outliers final: 8 residues processed: 164 average time/residue: 0.2838 time to fit residues: 53.9657 Evaluate side-chains 143 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 133 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 17 optimal weight: 0.5980 chunk 47 optimal weight: 20.0000 chunk 38 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN C 327 ASN D 327 ASN E 327 ASN G 368 ASN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 ASN ** I 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5190 Z= 0.215 Angle : 0.625 6.466 6945 Z= 0.315 Chirality : 0.051 0.143 783 Planarity : 0.002 0.017 882 Dihedral : 5.430 15.547 684 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.74 % Allowed : 10.43 % Favored : 86.84 % 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: -1.44 (0.27), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (0.20), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 330 PHE 0.010 0.001 PHE A 378 TYR 0.015 0.002 TYR G 310 ARG 0.002 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 153 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 137 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7755 (pttt) cc_final: 0.7496 (ptpp) REVERT: A 373 THR cc_start: 0.8145 (m) cc_final: 0.7780 (p) REVERT: B 317 LYS cc_start: 0.8072 (pttt) cc_final: 0.7808 (ptpp) REVERT: B 340 LYS cc_start: 0.8625 (tttt) cc_final: 0.8291 (ttmm) REVERT: B 347 LYS cc_start: 0.8894 (mttm) cc_final: 0.8490 (mttt) REVERT: B 348 ASP cc_start: 0.8379 (t0) cc_final: 0.7573 (p0) REVERT: C 311 LYS cc_start: 0.8909 (mtmt) cc_final: 0.8255 (mmtt) REVERT: C 317 LYS cc_start: 0.7764 (pttt) cc_final: 0.7548 (ptpp) REVERT: C 340 LYS cc_start: 0.8514 (tttt) cc_final: 0.8215 (mttp) REVERT: C 349 ARG cc_start: 0.7631 (mtm180) cc_final: 0.7252 (mtp85) REVERT: C 369 LYS cc_start: 0.6954 (mttt) cc_final: 0.6646 (ttmt) REVERT: D 311 LYS cc_start: 0.8360 (pttt) cc_final: 0.7766 (ptmt) REVERT: D 349 ARG cc_start: 0.7691 (ttm110) cc_final: 0.7345 (mtp85) REVERT: E 311 LYS cc_start: 0.8271 (pttt) cc_final: 0.7738 (ptmm) REVERT: F 311 LYS cc_start: 0.8311 (ttmt) cc_final: 0.7733 (tttp) REVERT: F 317 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7850 (ptpp) REVERT: F 349 ARG cc_start: 0.7547 (ttm110) cc_final: 0.7279 (mtp85) REVERT: F 370 LYS cc_start: 0.4432 (OUTLIER) cc_final: 0.3585 (pttt) REVERT: G 369 LYS cc_start: 0.8065 (mptt) cc_final: 0.7748 (mttt) REVERT: G 374 HIS cc_start: 0.7251 (m-70) cc_final: 0.5664 (p-80) REVERT: H 311 LYS cc_start: 0.8799 (tttt) cc_final: 0.8583 (ttmt) outliers start: 16 outliers final: 11 residues processed: 146 average time/residue: 0.2798 time to fit residues: 47.7896 Evaluate side-chains 138 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 125 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 G residue 368 ASN 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: 20.0000 chunk 43 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 30 optimal weight: 0.4980 chunk 54 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 overall best weight: 7.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 5190 Z= 0.526 Angle : 0.779 6.635 6945 Z= 0.402 Chirality : 0.057 0.180 783 Planarity : 0.003 0.023 882 Dihedral : 6.022 17.076 684 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.27 % Allowed : 11.97 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.28), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.21), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS A 362 PHE 0.012 0.002 PHE F 378 TYR 0.017 0.004 TYR E 310 ARG 0.004 0.001 ARG B 349 *********************** 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 167 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 142 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8668 (mttt) cc_final: 0.8425 (mttp) REVERT: A 317 LYS cc_start: 0.7792 (pttt) cc_final: 0.7424 (ptpp) REVERT: A 373 THR cc_start: 0.8059 (m) cc_final: 0.7633 (p) REVERT: B 317 LYS cc_start: 0.8191 (pttt) cc_final: 0.7930 (ptpp) REVERT: B 340 LYS cc_start: 0.8729 (tttt) cc_final: 0.8378 (ttmm) REVERT: B 347 LYS cc_start: 0.8940 (mttm) cc_final: 0.8512 (mttt) REVERT: B 348 ASP cc_start: 0.8559 (t0) cc_final: 0.7623 (p0) REVERT: B 349 ARG cc_start: 0.8194 (mtp85) cc_final: 0.7864 (mtp85) REVERT: C 311 LYS cc_start: 0.8744 (mtmt) cc_final: 0.8104 (mmtm) REVERT: C 317 LYS cc_start: 0.7833 (pttt) cc_final: 0.7558 (ptpp) REVERT: C 340 LYS cc_start: 0.8441 (tttt) cc_final: 0.7973 (mttp) REVERT: C 349 ARG cc_start: 0.7571 (mtm180) cc_final: 0.7303 (mtp85) REVERT: C 351 GLN cc_start: 0.7688 (mt0) cc_final: 0.7317 (mt0) REVERT: C 369 LYS cc_start: 0.7067 (mttt) cc_final: 0.6719 (ttmt) REVERT: C 372 GLU cc_start: 0.7891 (pt0) cc_final: 0.7534 (pt0) REVERT: D 311 LYS cc_start: 0.8363 (pttt) cc_final: 0.7857 (ptmt) REVERT: D 349 ARG cc_start: 0.7688 (ttm110) cc_final: 0.7339 (mtp85) REVERT: E 311 LYS cc_start: 0.8351 (pttt) cc_final: 0.7949 (ptmt) REVERT: E 340 LYS cc_start: 0.7565 (tttt) cc_final: 0.7244 (tttm) REVERT: F 311 LYS cc_start: 0.8421 (ttmt) cc_final: 0.7843 (tttm) REVERT: F 340 LYS cc_start: 0.8485 (tttt) cc_final: 0.8115 (tttm) REVERT: F 349 ARG cc_start: 0.7679 (ttm110) cc_final: 0.7393 (mtp85) REVERT: F 370 LYS cc_start: 0.4536 (OUTLIER) cc_final: 0.3266 (mptt) REVERT: G 369 LYS cc_start: 0.8273 (mptt) cc_final: 0.7916 (mttt) REVERT: G 374 HIS cc_start: 0.7327 (m-70) cc_final: 0.5687 (p90) outliers start: 25 outliers final: 18 residues processed: 156 average time/residue: 0.2813 time to fit residues: 51.0931 Evaluate side-chains 154 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 135 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 G residue 306 VAL Chi-restraints excluded: chain G residue 354 ILE Chi-restraints excluded: chain G residue 368 ASN Chi-restraints excluded: chain H residue 305 SER 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 Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 368 ASN 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: 2.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 362 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5190 Z= 0.192 Angle : 0.606 8.287 6945 Z= 0.295 Chirality : 0.050 0.138 783 Planarity : 0.002 0.019 882 Dihedral : 5.262 16.215 684 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.74 % Allowed : 13.85 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.28), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 362 PHE 0.007 0.001 PHE A 378 TYR 0.013 0.002 TYR G 310 ARG 0.002 0.000 ARG F 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 147 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 131 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8532 (mttt) cc_final: 0.8321 (mttp) REVERT: A 317 LYS cc_start: 0.7784 (pttt) cc_final: 0.7399 (ptpp) REVERT: A 373 THR cc_start: 0.8068 (m) cc_final: 0.7735 (p) REVERT: B 317 LYS cc_start: 0.8214 (pttt) cc_final: 0.7950 (ptpp) REVERT: B 340 LYS cc_start: 0.8540 (tttt) cc_final: 0.8151 (mttp) REVERT: B 347 LYS cc_start: 0.8870 (mttm) cc_final: 0.8491 (mttt) REVERT: B 348 ASP cc_start: 0.8475 (t0) cc_final: 0.7615 (p0) REVERT: B 373 THR cc_start: 0.8307 (m) cc_final: 0.7845 (p) REVERT: C 311 LYS cc_start: 0.8777 (mtmt) cc_final: 0.8159 (mmtm) REVERT: C 317 LYS cc_start: 0.7693 (pttt) cc_final: 0.7472 (ptpp) REVERT: C 340 LYS cc_start: 0.8470 (tttt) cc_final: 0.8022 (mttp) REVERT: C 349 ARG cc_start: 0.7606 (mtm180) cc_final: 0.7316 (mtp85) REVERT: C 369 LYS cc_start: 0.7051 (mttt) cc_final: 0.6699 (ttmt) REVERT: D 311 LYS cc_start: 0.8333 (pttt) cc_final: 0.7871 (ptmt) REVERT: D 349 ARG cc_start: 0.7649 (ttm110) cc_final: 0.7349 (mtp85) REVERT: E 360 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7885 (mt) REVERT: F 311 LYS cc_start: 0.8314 (ttmt) cc_final: 0.7770 (tttm) REVERT: F 349 ARG cc_start: 0.7629 (ttm110) cc_final: 0.7385 (mtp85) REVERT: F 370 LYS cc_start: 0.3986 (OUTLIER) cc_final: 0.3255 (tppt) REVERT: G 321 LYS cc_start: 0.5601 (mmmt) cc_final: 0.5228 (mmtt) REVERT: G 374 HIS cc_start: 0.7302 (m-70) cc_final: 0.5693 (p90) REVERT: I 336 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.7336 (tt0) outliers start: 16 outliers final: 12 residues processed: 140 average time/residue: 0.2620 time to fit residues: 43.2961 Evaluate side-chains 142 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 B 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 G residue 368 ASN Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain H residue 341 SER Chi-restraints excluded: chain I residue 336 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 50 optimal weight: 20.0000 chunk 28 optimal weight: 0.1980 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6957 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5190 Z= 0.362 Angle : 0.677 7.842 6945 Z= 0.336 Chirality : 0.053 0.161 783 Planarity : 0.003 0.021 882 Dihedral : 5.383 17.024 684 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.25 % Allowed : 14.53 % 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: -1.73 (0.28), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 374 PHE 0.008 0.002 PHE A 346 TYR 0.013 0.003 TYR A 310 ARG 0.002 0.000 ARG B 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 151 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 0.680 Fit side-chains REVERT: A 311 LYS cc_start: 0.8782 (mttt) cc_final: 0.8540 (mtpp) REVERT: A 317 LYS cc_start: 0.7822 (pttt) cc_final: 0.7410 (ptpp) REVERT: A 373 THR cc_start: 0.8080 (m) cc_final: 0.7685 (p) REVERT: B 311 LYS cc_start: 0.8933 (mtmt) cc_final: 0.8538 (mtpp) REVERT: B 317 LYS cc_start: 0.8272 (pttt) cc_final: 0.7989 (ptpp) REVERT: B 340 LYS cc_start: 0.8519 (tttt) cc_final: 0.8164 (mttp) REVERT: B 347 LYS cc_start: 0.8874 (mttm) cc_final: 0.8527 (mttt) REVERT: B 348 ASP cc_start: 0.8498 (t0) cc_final: 0.7598 (p0) REVERT: B 373 THR cc_start: 0.8283 (m) cc_final: 0.7816 (p) REVERT: C 311 LYS cc_start: 0.8867 (mtmt) cc_final: 0.8100 (mmtt) REVERT: C 317 LYS cc_start: 0.7711 (pttt) cc_final: 0.7467 (ptpp) REVERT: C 340 LYS cc_start: 0.8476 (tttt) cc_final: 0.7956 (mttp) REVERT: C 349 ARG cc_start: 0.7613 (mtm180) cc_final: 0.7298 (mtp85) REVERT: C 369 LYS cc_start: 0.7105 (mttt) cc_final: 0.6722 (ttmt) REVERT: C 372 GLU cc_start: 0.7784 (pt0) cc_final: 0.7349 (pt0) REVERT: D 311 LYS cc_start: 0.8369 (pttt) cc_final: 0.7744 (ptmm) REVERT: D 349 ARG cc_start: 0.7679 (ttm110) cc_final: 0.7354 (mtp85) REVERT: E 360 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.7884 (mt) REVERT: F 311 LYS cc_start: 0.8301 (ttmt) cc_final: 0.7737 (tttm) REVERT: F 340 LYS cc_start: 0.8467 (tttt) cc_final: 0.8116 (tttp) REVERT: F 349 ARG cc_start: 0.7675 (ttm110) cc_final: 0.7399 (mtp85) REVERT: F 370 LYS cc_start: 0.4133 (OUTLIER) cc_final: 0.3361 (tppt) REVERT: G 321 LYS cc_start: 0.5520 (mmmt) cc_final: 0.5284 (mmtt) outliers start: 19 outliers final: 16 residues processed: 144 average time/residue: 0.2697 time to fit residues: 45.5842 Evaluate side-chains 148 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 B 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 G residue 368 ASN Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain H residue 328 ILE Chi-restraints excluded: chain H residue 341 SER Chi-restraints excluded: chain H residue 356 SER Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain I residue 368 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 44 optimal weight: 20.0000 chunk 51 optimal weight: 0.3980 chunk 60 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 37 optimal weight: 0.0470 chunk 28 optimal weight: 0.0980 chunk 24 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 overall best weight: 2.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6924 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5190 Z= 0.198 Angle : 0.589 7.775 6945 Z= 0.287 Chirality : 0.049 0.132 783 Planarity : 0.002 0.017 882 Dihedral : 4.988 15.875 684 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.56 % Allowed : 14.53 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.29), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 374 PHE 0.006 0.001 PHE A 346 TYR 0.011 0.002 TYR G 310 ARG 0.001 0.000 ARG B 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 141 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7874 (pttt) cc_final: 0.7455 (ptpp) REVERT: A 373 THR cc_start: 0.8087 (m) cc_final: 0.7722 (p) REVERT: B 311 LYS cc_start: 0.8882 (mtmt) cc_final: 0.8460 (mtpp) REVERT: B 317 LYS cc_start: 0.8260 (pttt) cc_final: 0.7990 (ptpp) REVERT: B 347 LYS cc_start: 0.8837 (mttm) cc_final: 0.8559 (mttt) REVERT: B 348 ASP cc_start: 0.8468 (t0) cc_final: 0.7600 (p0) REVERT: B 368 ASN cc_start: 0.8109 (t0) cc_final: 0.7691 (m110) REVERT: B 373 THR cc_start: 0.8228 (m) cc_final: 0.7770 (p) REVERT: C 311 LYS cc_start: 0.8813 (mtmt) cc_final: 0.8179 (mmtm) REVERT: C 317 LYS cc_start: 0.7700 (pttt) cc_final: 0.7482 (ptpp) REVERT: C 340 LYS cc_start: 0.8509 (tttt) cc_final: 0.7992 (mttp) REVERT: C 349 ARG cc_start: 0.7615 (mtm180) cc_final: 0.7273 (mtp85) REVERT: C 369 LYS cc_start: 0.7123 (mttt) cc_final: 0.6731 (ttmt) REVERT: D 311 LYS cc_start: 0.8337 (pttt) cc_final: 0.7712 (ptmm) REVERT: D 349 ARG cc_start: 0.7649 (ttm110) cc_final: 0.7343 (mtp85) REVERT: E 360 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.7949 (mt) REVERT: F 349 ARG cc_start: 0.7635 (ttm110) cc_final: 0.7376 (mtp85) REVERT: F 370 LYS cc_start: 0.3893 (OUTLIER) cc_final: 0.3223 (tppt) REVERT: G 374 HIS cc_start: 0.7310 (m-70) cc_final: 0.5729 (p90) outliers start: 15 outliers final: 13 residues processed: 136 average time/residue: 0.2700 time to fit residues: 43.1976 Evaluate side-chains 132 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 117 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 B 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 G residue 368 ASN Chi-restraints excluded: chain H residue 305 SER Chi-restraints excluded: chain H residue 341 SER Chi-restraints excluded: chain H residue 356 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 30 optimal weight: 0.0050 chunk 5 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 53 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN ** G 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 330 HIS H 374 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5190 Z= 0.127 Angle : 0.559 7.854 6945 Z= 0.266 Chirality : 0.049 0.125 783 Planarity : 0.002 0.019 882 Dihedral : 4.530 15.181 684 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % 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: -1.76 (0.29), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 329 PHE 0.006 0.001 PHE B 378 TYR 0.009 0.002 TYR G 310 ARG 0.003 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 134 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7849 (pttt) cc_final: 0.7441 (ptpp) REVERT: A 372 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7203 (mt-10) REVERT: A 373 THR cc_start: 0.8133 (m) cc_final: 0.7746 (p) REVERT: B 311 LYS cc_start: 0.8838 (mtmt) cc_final: 0.8430 (mtpp) REVERT: B 317 LYS cc_start: 0.8194 (pttt) cc_final: 0.7957 (ptpp) REVERT: B 348 ASP cc_start: 0.8401 (t0) cc_final: 0.7617 (p0) REVERT: B 368 ASN cc_start: 0.7987 (OUTLIER) cc_final: 0.7654 (m110) REVERT: C 311 LYS cc_start: 0.8502 (mtmt) cc_final: 0.7796 (mmmt) REVERT: C 340 LYS cc_start: 0.8565 (tttt) cc_final: 0.8053 (mttp) REVERT: C 349 ARG cc_start: 0.7641 (mtm180) cc_final: 0.7326 (mtp85) REVERT: C 369 LYS cc_start: 0.7126 (mttt) cc_final: 0.6753 (ttmt) REVERT: D 311 LYS cc_start: 0.8320 (pttt) cc_final: 0.7744 (ptmm) REVERT: D 349 ARG cc_start: 0.7668 (ttm110) cc_final: 0.7347 (mtp85) REVERT: E 360 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.7988 (mt) REVERT: F 349 ARG cc_start: 0.7640 (ttm110) cc_final: 0.7366 (mtp85) REVERT: F 370 LYS cc_start: 0.3486 (OUTLIER) cc_final: 0.2909 (tppt) REVERT: G 374 HIS cc_start: 0.7278 (m-70) cc_final: 0.5733 (p90) REVERT: H 311 LYS cc_start: 0.8696 (ttmt) cc_final: 0.8459 (ttmt) outliers start: 11 outliers final: 7 residues processed: 129 average time/residue: 0.2512 time to fit residues: 38.5287 Evaluate side-chains 126 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 342 GLU Chi-restraints excluded: chain B residue 368 ASN Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain F residue 375 LYS Chi-restraints excluded: chain G residue 368 ASN Chi-restraints excluded: chain H residue 341 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: 6.9990 chunk 17 optimal weight: 8.9990 chunk 51 optimal weight: 0.3980 chunk 53 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 37 optimal weight: 0.0870 chunk 59 optimal weight: 30.0000 chunk 36 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 overall best weight: 1.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 368 ASN ** 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: 0.6901 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5190 Z= 0.187 Angle : 0.579 7.766 6945 Z= 0.276 Chirality : 0.049 0.127 783 Planarity : 0.002 0.018 882 Dihedral : 4.568 14.363 684 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.05 % Allowed : 16.41 % Favored : 81.54 % 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: -1.75 (0.29), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS H 374 PHE 0.005 0.001 PHE A 378 TYR 0.013 0.002 TYR A 310 ARG 0.003 0.000 ARG H 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 129 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 0.686 Fit side-chains REVERT: A 317 LYS cc_start: 0.7808 (pttt) cc_final: 0.7431 (ptpp) REVERT: A 373 THR cc_start: 0.8130 (m) cc_final: 0.7684 (p) REVERT: B 311 LYS cc_start: 0.8846 (mtmt) cc_final: 0.8454 (mtpp) REVERT: B 317 LYS cc_start: 0.8204 (pttt) cc_final: 0.7918 (ptpp) REVERT: B 318 VAL cc_start: 0.8891 (t) cc_final: 0.8634 (t) REVERT: B 348 ASP cc_start: 0.8404 (t0) cc_final: 0.7608 (p0) REVERT: B 368 ASN cc_start: 0.7958 (t0) cc_final: 0.7756 (m-40) REVERT: C 311 LYS cc_start: 0.8582 (mtmt) cc_final: 0.7865 (mmmt) REVERT: C 318 VAL cc_start: 0.8944 (t) cc_final: 0.8738 (t) REVERT: C 340 LYS cc_start: 0.8536 (tttt) cc_final: 0.8013 (mttp) REVERT: C 349 ARG cc_start: 0.7646 (mtm180) cc_final: 0.7317 (mtp85) REVERT: C 369 LYS cc_start: 0.7137 (mttt) cc_final: 0.6732 (ttmt) REVERT: C 372 GLU cc_start: 0.7627 (pt0) cc_final: 0.7298 (pt0) REVERT: D 311 LYS cc_start: 0.8300 (pttt) cc_final: 0.7716 (ptmm) REVERT: D 349 ARG cc_start: 0.7685 (ttm110) cc_final: 0.7346 (mtp85) REVERT: E 360 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.7986 (mt) REVERT: F 349 ARG cc_start: 0.7657 (ttm110) cc_final: 0.7373 (mtp85) REVERT: F 370 LYS cc_start: 0.3522 (OUTLIER) cc_final: 0.2993 (tppt) REVERT: G 374 HIS cc_start: 0.7288 (m-70) cc_final: 0.5741 (p90) REVERT: H 311 LYS cc_start: 0.8689 (ttmt) cc_final: 0.8463 (ttmt) outliers start: 12 outliers final: 7 residues processed: 125 average time/residue: 0.2613 time to fit residues: 38.6619 Evaluate side-chains 126 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain B 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 370 LYS Chi-restraints excluded: chain F residue 375 LYS Chi-restraints excluded: chain G residue 368 ASN Chi-restraints excluded: chain H residue 341 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 0.2980 chunk 57 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 15 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN ** G 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5190 Z= 0.146 Angle : 0.576 7.586 6945 Z= 0.273 Chirality : 0.049 0.121 783 Planarity : 0.002 0.019 882 Dihedral : 4.457 13.841 684 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.54 % Allowed : 17.09 % Favored : 81.37 % 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 0.003 0.000 HIS H 374 PHE 0.005 0.001 PHE A 378 TYR 0.011 0.001 TYR A 310 ARG 0.003 0.000 ARG H 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 128 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 0.600 Fit side-chains REVERT: A 317 LYS cc_start: 0.7790 (pttt) cc_final: 0.7527 (ptpp) REVERT: A 373 THR cc_start: 0.8141 (m) cc_final: 0.7688 (p) REVERT: B 311 LYS cc_start: 0.8839 (mtmt) cc_final: 0.8447 (mtpp) REVERT: B 317 LYS cc_start: 0.8142 (pttt) cc_final: 0.7874 (ptpp) REVERT: B 318 VAL cc_start: 0.8888 (t) cc_final: 0.8638 (t) REVERT: B 348 ASP cc_start: 0.8308 (t0) cc_final: 0.7616 (p0) REVERT: B 368 ASN cc_start: 0.8040 (OUTLIER) cc_final: 0.7804 (m-40) REVERT: C 311 LYS cc_start: 0.8550 (mtmt) cc_final: 0.7762 (mmmt) REVERT: C 318 VAL cc_start: 0.8942 (t) cc_final: 0.8733 (t) REVERT: C 340 LYS cc_start: 0.8564 (tttt) cc_final: 0.8048 (mttp) REVERT: C 349 ARG cc_start: 0.7649 (mtm180) cc_final: 0.7318 (mtp85) REVERT: C 369 LYS cc_start: 0.7152 (mttt) cc_final: 0.6757 (ttmt) REVERT: C 372 GLU cc_start: 0.7572 (pt0) cc_final: 0.7233 (pt0) REVERT: D 311 LYS cc_start: 0.8288 (pttt) cc_final: 0.7709 (ptmm) REVERT: D 349 ARG cc_start: 0.7652 (ttm110) cc_final: 0.7323 (mtp85) REVERT: E 360 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8001 (mt) REVERT: F 349 ARG cc_start: 0.7669 (ttm110) cc_final: 0.7378 (mtp85) REVERT: F 370 LYS cc_start: 0.3506 (OUTLIER) cc_final: 0.3003 (tppt) REVERT: G 374 HIS cc_start: 0.7256 (m-70) cc_final: 0.5734 (p90) outliers start: 9 outliers final: 6 residues processed: 126 average time/residue: 0.2547 time to fit residues: 38.0302 Evaluate side-chains 130 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 121 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain B residue 342 GLU 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 Chi-restraints excluded: chain F residue 375 LYS Chi-restraints excluded: chain G residue 368 ASN Chi-restraints excluded: chain H residue 341 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 43 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 368 ASN ** 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 = 0.4207 r_free = 0.4207 target = 0.149798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.116429 restraints weight = 6586.907| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 1.94 r_work: 0.3762 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.4858 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= 0.395 Angle : 0.685 6.981 6945 Z= 0.340 Chirality : 0.053 0.166 783 Planarity : 0.003 0.020 882 Dihedral : 5.011 16.066 684 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.71 % Allowed : 16.75 % Favored : 81.54 % 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 0.003 0.001 HIS A 330 PHE 0.009 0.002 PHE C 346 TYR 0.018 0.003 TYR A 310 ARG 0.002 0.000 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1874.91 seconds wall clock time: 34 minutes 35.18 seconds (2075.18 seconds total)