Starting phenix.real_space_refine on Mon Nov 13 20:50:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7m_18224/11_2023/8q7m_18224.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7m_18224/11_2023/8q7m_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_18224/11_2023/8q7m_18224.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7m_18224/11_2023/8q7m_18224.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7m_18224/11_2023/8q7m_18224.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7m_18224/11_2023/8q7m_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-1.21rc1-5144/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: 3.19, per 1000 atoms: 0.62 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: 1.84 Conformation dependent library (CDL) restraints added in 931.1 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: 0.73 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: 1.32 Time building geometry restraints manager: 2.02 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: 3.140 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: 11.390 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 18.130 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.130 ------------------------------------------------------------------------------- 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 *********************** 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 : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 222 average time/residue: 0.2800 time to fit residues: 71.9347 Evaluate side-chains 142 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.623 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8663 ------------------------------------------------------------------------------- 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: 5.9990 chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 0.0670 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- 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 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 359 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5190 Z= 0.249 Angle : 0.724 7.905 6945 Z= 0.362 Chirality : 0.053 0.165 783 Planarity : 0.003 0.025 882 Dihedral : 6.229 19.796 684 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.22 % Allowed : 10.43 % Favored : 87.35 % 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: -1.51 (0.26), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.20), residues: 651 *********************** 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 160 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 147 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 153 average time/residue: 0.2535 time to fit residues: 45.7927 Evaluate side-chains 130 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 120 time to evaluate : 0.615 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0794 time to fit residues: 2.0464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 47 optimal weight: 20.0000 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 57 optimal weight: 30.0000 chunk 61 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 56 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN D 327 ASN E 327 ASN G 374 HIS ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 ASN ** I 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 5190 Z= 0.460 Angle : 0.738 7.201 6945 Z= 0.378 Chirality : 0.055 0.160 783 Planarity : 0.004 0.037 882 Dihedral : 5.946 17.105 684 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.20 % Allowed : 13.33 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.27), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.21), residues: 651 *********************** 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 134 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 127 time to evaluate : 0.634 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 131 average time/residue: 0.2509 time to fit residues: 39.0107 Evaluate side-chains 125 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 0.645 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1239 time to fit residues: 1.5563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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** ** 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: 0.6909 moved from start: 0.4411 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= 0.237 Angle : 0.634 6.380 6945 Z= 0.312 Chirality : 0.050 0.131 783 Planarity : 0.003 0.028 882 Dihedral : 5.402 16.780 684 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.68 % Allowed : 15.90 % 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: -1.67 (0.28), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.21), residues: 651 *********************** 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 128 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 124 time to evaluate : 0.671 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 126 average time/residue: 0.2624 time to fit residues: 39.2238 Evaluate side-chains 116 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 113 time to evaluate : 0.587 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1317 time to fit residues: 1.3895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 359 ASN H 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 5190 Z= 0.451 Angle : 0.699 7.012 6945 Z= 0.354 Chirality : 0.054 0.158 783 Planarity : 0.004 0.040 882 Dihedral : 5.615 17.169 684 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.88 % Allowed : 15.21 % 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: -1.86 (0.28), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.22), residues: 651 *********************** 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 124 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 0.635 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 117 average time/residue: 0.2597 time to fit residues: 36.1602 Evaluate side-chains 124 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 0.575 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0697 time to fit residues: 1.7912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 15 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 28 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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: 0.6913 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5190 Z= 0.162 Angle : 0.591 6.956 6945 Z= 0.290 Chirality : 0.049 0.126 783 Planarity : 0.003 0.039 882 Dihedral : 5.095 16.565 684 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.34 % Allowed : 15.90 % 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: -1.81 (0.29), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.22), residues: 651 *********************** 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 113 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 0.628 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 112 average time/residue: 0.2366 time to fit residues: 32.0518 Evaluate side-chains 103 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.612 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0451 time to fit residues: 0.9059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 51 optimal weight: 0.0270 chunk 60 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 overall best weight: 6.2046 ------------------------------------------------------------------------------- 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: 0.6971 moved from start: 0.5161 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= 0.462 Angle : 0.702 6.964 6945 Z= 0.356 Chirality : 0.054 0.153 783 Planarity : 0.004 0.050 882 Dihedral : 5.469 17.732 684 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.85 % Allowed : 16.75 % Favored : 82.39 % 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: -1.95 (0.29), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.22), residues: 651 *********************** 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 116 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 111 time to evaluate : 0.558 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 114 average time/residue: 0.2598 time to fit residues: 35.0322 Evaluate side-chains 109 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 0.625 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1140 time to fit residues: 1.4760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 0.0670 chunk 5 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 53 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 overall best weight: 1.9324 ------------------------------------------------------------------------------- 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: 0.6927 moved from start: 0.5320 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= 0.186 Angle : 0.598 6.776 6945 Z= 0.294 Chirality : 0.049 0.125 783 Planarity : 0.003 0.045 882 Dihedral : 5.034 15.700 684 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.34 % Allowed : 17.78 % 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: -1.94 (0.29), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.22), residues: 651 *********************** 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 113 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 0.630 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 113 average time/residue: 0.2432 time to fit residues: 33.0282 Evaluate side-chains 105 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 0.625 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0475 time to fit residues: 0.9511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 17 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 overall best weight: 7.1788 ------------------------------------------------------------------------------- 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 359 ASN H 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.5471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 5190 Z= 0.511 Angle : 0.730 6.790 6945 Z= 0.371 Chirality : 0.055 0.160 783 Planarity : 0.004 0.055 882 Dihedral : 5.567 18.056 684 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.85 % Allowed : 18.63 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.29), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.22), residues: 651 *********************** 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 121 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 116 time to evaluate : 0.660 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 119 average time/residue: 0.2727 time to fit residues: 38.2649 Evaluate side-chains 120 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 118 time to evaluate : 0.558 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0479 time to fit residues: 0.9922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 5 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 0.0980 chunk 39 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 359 ASN H 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5190 Z= 0.193 Angle : 0.619 7.118 6945 Z= 0.303 Chirality : 0.050 0.125 783 Planarity : 0.003 0.046 882 Dihedral : 5.138 16.394 684 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.17 % Allowed : 18.97 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.29), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.22), residues: 651 ********************** 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 108 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 0.649 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 107 average time/residue: 0.2383 time to fit residues: 30.9289 Evaluate side-chains 103 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.634 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 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 336 GLN ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.147279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.114578 restraints weight = 6596.851| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 1.89 r_work: 0.3742 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.5692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 5190 Z= 0.478 Angle : 0.728 6.798 6945 Z= 0.368 Chirality : 0.054 0.155 783 Planarity : 0.004 0.056 882 Dihedral : 5.522 17.932 684 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.85 % Allowed : 18.29 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.29), residues: 651 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.22), residues: 651 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1700.07 seconds wall clock time: 31 minutes 28.34 seconds (1888.34 seconds total)