Starting phenix.real_space_refine on Fri Aug 22 16:01:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8seh_40411/08_2025/8seh_40411_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8seh_40411/08_2025/8seh_40411.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8seh_40411/08_2025/8seh_40411.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8seh_40411/08_2025/8seh_40411.map" model { file = "/net/cci-nas-00/data/ceres_data/8seh_40411/08_2025/8seh_40411_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8seh_40411/08_2025/8seh_40411_neut.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 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 10 5.16 5 C 3510 2.51 5 N 1010 2.21 5 O 1040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5570 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 0.77, per 1000 atoms: 0.14 Number of scatterers: 5570 At special positions: 0 Unit cell: (79.05, 144.398, 44.268, 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 10 16.00 O 1040 8.00 N 1010 7.00 C 3510 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 - 3.00 Amino acid : True - 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: 0.29 Conformation dependent library (CDL) restraints added in 175.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1280 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 54.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 307 through 310 removed outlier: 6.485A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLN C 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N TYR E 310 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL C 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLN E 307 " --> pdb=" O ILE G 308 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N TYR G 310 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL E 309 " --> pdb=" O TYR G 310 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLN G 307 " --> pdb=" O ILE I 308 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N TYR I 310 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL G 309 " --> pdb=" O TYR I 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 314 through 324 removed outlier: 6.734A pdb=" N SER C 324 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER E 324 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER G 324 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER I 324 " --> pdb=" O GLY G 323 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 328 through 330 removed outlier: 6.416A pdb=" N HIS A 329 " --> pdb=" O HIS C 330 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N HIS C 329 " --> pdb=" O HIS E 330 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N HIS E 329 " --> pdb=" O HIS G 330 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N HIS G 329 " --> pdb=" O HIS I 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 340 Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 347 removed outlier: 6.187A pdb=" N LYS A 343 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE C 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LYS C 343 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE E 346 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP C 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LYS E 343 " --> pdb=" O LEU G 344 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE G 346 " --> pdb=" O LYS E 343 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP E 345 " --> pdb=" O PHE G 346 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LYS G 343 " --> pdb=" O LEU I 344 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE I 346 " --> pdb=" O LYS G 343 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASP G 345 " --> pdb=" O PHE I 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 350 through 356 removed outlier: 6.623A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ILE C 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS A 353 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER C 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N GLY A 355 " --> pdb=" O SER C 356 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN C 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ILE E 354 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS C 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N SER E 356 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N GLY C 355 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN E 351 " --> pdb=" O SER G 352 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ILE G 354 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LYS E 353 " --> pdb=" O ILE G 354 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N SER G 356 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N GLY E 355 " --> pdb=" O SER G 356 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN G 351 " --> pdb=" O SER I 352 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ILE I 354 " --> pdb=" O GLN G 351 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS G 353 " --> pdb=" O ILE I 354 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N SER I 356 " --> pdb=" O LYS G 353 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N GLY G 355 " --> pdb=" O SER I 356 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 359 through 362 Processing sheet with id=AA8, first strand: chain 'A' and resid 369 through 377 Processing sheet with id=AA9, first strand: chain 'B' and resid 307 through 310 removed outlier: 6.485A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLN D 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N TYR F 310 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL D 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLN F 307 " --> pdb=" O ILE H 308 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N TYR H 310 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL F 309 " --> pdb=" O TYR H 310 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLN H 307 " --> pdb=" O ILE J 308 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N TYR J 310 " --> pdb=" O GLN H 307 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL H 309 " --> pdb=" O TYR J 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 314 through 324 removed outlier: 6.734A pdb=" N SER D 324 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER F 324 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER H 324 " --> pdb=" O GLY F 323 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER J 324 " --> pdb=" O GLY H 323 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.416A pdb=" N HIS B 329 " --> pdb=" O HIS D 330 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N HIS D 329 " --> pdb=" O HIS F 330 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N HIS F 329 " --> pdb=" O HIS H 330 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N HIS H 329 " --> pdb=" O HIS J 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 336 through 340 Processing sheet with id=AB4, first strand: chain 'B' and resid 343 through 347 removed outlier: 6.187A pdb=" N LYS B 343 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE D 346 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LYS D 343 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N PHE F 346 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP D 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LYS F 343 " --> pdb=" O LEU H 344 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N PHE H 346 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP F 345 " --> pdb=" O PHE H 346 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LYS H 343 " --> pdb=" O LEU J 344 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N PHE J 346 " --> pdb=" O LYS H 343 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP H 345 " --> pdb=" O PHE J 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 350 through 356 removed outlier: 6.624A pdb=" N GLN B 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ILE D 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS B 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N SER D 356 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N GLY B 355 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLN D 351 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ILE F 354 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LYS D 353 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER F 356 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N GLY D 355 " --> pdb=" O SER F 356 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN F 351 " --> pdb=" O SER H 352 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ILE H 354 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS F 353 " --> pdb=" O ILE H 354 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER H 356 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N GLY F 355 " --> pdb=" O SER H 356 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN H 351 " --> pdb=" O SER J 352 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ILE J 354 " --> pdb=" O GLN H 351 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LYS H 353 " --> pdb=" O ILE J 354 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER J 356 " --> pdb=" O LYS H 353 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N GLY H 355 " --> pdb=" O SER J 356 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 359 through 362 Processing sheet with id=AB7, first strand: chain 'B' and resid 369 through 377 192 hydrogen bonds defined for protein. 576 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: 0.96 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.31: 1358 1.31 - 1.43: 1055 1.43 - 1.55: 3207 1.55 - 1.67: 30 1.67 - 1.79: 10 Bond restraints: 5660 Sorted by residual: bond pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " ideal model delta sigma weight residual 1.497 1.419 0.078 1.40e-02 5.10e+03 3.11e+01 bond pdb=" CB HIS H 374 " pdb=" CG HIS H 374 " ideal model delta sigma weight residual 1.497 1.419 0.078 1.40e-02 5.10e+03 3.08e+01 bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.420 0.077 1.40e-02 5.10e+03 3.06e+01 bond pdb=" CB HIS D 374 " pdb=" CG HIS D 374 " ideal model delta sigma weight residual 1.497 1.420 0.077 1.40e-02 5.10e+03 3.03e+01 bond pdb=" CB HIS F 374 " pdb=" CG HIS F 374 " ideal model delta sigma weight residual 1.497 1.420 0.077 1.40e-02 5.10e+03 3.03e+01 ... (remaining 5655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 5357 1.82 - 3.64: 1565 3.64 - 5.47: 468 5.47 - 7.29: 140 7.29 - 9.11: 50 Bond angle restraints: 7580 Sorted by residual: angle pdb=" CA PHE H 346 " pdb=" CB PHE H 346 " pdb=" CG PHE H 346 " ideal model delta sigma weight residual 113.80 122.53 -8.73 1.00e+00 1.00e+00 7.63e+01 angle pdb=" CA PHE C 346 " pdb=" CB PHE C 346 " pdb=" CG PHE C 346 " ideal model delta sigma weight residual 113.80 122.53 -8.73 1.00e+00 1.00e+00 7.62e+01 angle pdb=" CA PHE D 346 " pdb=" CB PHE D 346 " pdb=" CG PHE D 346 " ideal model delta sigma weight residual 113.80 122.53 -8.73 1.00e+00 1.00e+00 7.62e+01 angle pdb=" CA PHE B 346 " pdb=" CB PHE B 346 " pdb=" CG PHE B 346 " ideal model delta sigma weight residual 113.80 122.52 -8.72 1.00e+00 1.00e+00 7.60e+01 angle pdb=" CA PHE E 346 " pdb=" CB PHE E 346 " pdb=" CG PHE E 346 " ideal model delta sigma weight residual 113.80 122.49 -8.69 1.00e+00 1.00e+00 7.54e+01 ... (remaining 7575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.66: 3280 15.66 - 31.31: 110 31.31 - 46.96: 20 46.96 - 62.62: 20 62.62 - 78.27: 10 Dihedral angle restraints: 3440 sinusoidal: 1430 harmonic: 2010 Sorted by residual: dihedral pdb=" C PHE A 346 " pdb=" N PHE A 346 " pdb=" CA PHE A 346 " pdb=" CB PHE A 346 " ideal model delta harmonic sigma weight residual -122.60 -133.33 10.73 0 2.50e+00 1.60e-01 1.84e+01 dihedral pdb=" C PHE F 346 " pdb=" N PHE F 346 " pdb=" CA PHE F 346 " pdb=" CB PHE F 346 " ideal model delta harmonic sigma weight residual -122.60 -133.33 10.73 0 2.50e+00 1.60e-01 1.84e+01 dihedral pdb=" C PHE E 346 " pdb=" N PHE E 346 " pdb=" CA PHE E 346 " pdb=" CB PHE E 346 " ideal model delta harmonic sigma weight residual -122.60 -133.30 10.70 0 2.50e+00 1.60e-01 1.83e+01 ... (remaining 3437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 590 0.103 - 0.206: 238 0.206 - 0.309: 22 0.309 - 0.412: 0 0.412 - 0.515: 10 Chirality restraints: 860 Sorted by residual: chirality pdb=" CA PHE F 346 " pdb=" N PHE F 346 " pdb=" C PHE F 346 " pdb=" CB PHE F 346 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.63e+00 chirality pdb=" CA PHE E 346 " pdb=" N PHE E 346 " pdb=" C PHE E 346 " pdb=" CB PHE E 346 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.62e+00 chirality pdb=" CA PHE D 346 " pdb=" N PHE D 346 " pdb=" C PHE D 346 " pdb=" CB PHE D 346 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.61e+00 ... (remaining 857 not shown) Planarity restraints: 960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 346 " 0.048 2.00e-02 2.50e+03 2.97e-02 1.54e+01 pdb=" CG PHE G 346 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE G 346 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE G 346 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE G 346 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE G 346 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE G 346 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 346 " 0.048 2.00e-02 2.50e+03 2.97e-02 1.54e+01 pdb=" CG PHE I 346 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE I 346 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE I 346 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE I 346 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE I 346 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE I 346 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 346 " -0.048 2.00e-02 2.50e+03 2.96e-02 1.53e+01 pdb=" CG PHE F 346 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE F 346 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE F 346 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE F 346 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE F 346 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE F 346 " -0.021 2.00e-02 2.50e+03 ... (remaining 957 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 3119 2.99 - 3.46: 4765 3.46 - 3.94: 8642 3.94 - 4.42: 10487 4.42 - 4.90: 20246 Nonbonded interactions: 47259 Sorted by model distance: nonbonded pdb=" CB GLU E 372 " pdb=" OE1 GLU E 372 " model vdw 2.507 2.752 nonbonded pdb=" CB GLU J 372 " pdb=" OE1 GLU J 372 " model vdw 2.507 2.752 nonbonded pdb=" CB GLU G 372 " pdb=" OE1 GLU G 372 " model vdw 2.507 2.752 nonbonded pdb=" CB GLU B 372 " pdb=" OE1 GLU B 372 " model vdw 2.507 2.752 nonbonded pdb=" CB GLU H 372 " pdb=" OE1 GLU H 372 " model vdw 2.507 2.752 ... (remaining 47254 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.710 Find NCS groups from input model: 0.060 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:7.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 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 : 0.026 0.138 5660 Z= 1.395 Angle : 2.088 9.108 7580 Z= 1.335 Chirality : 0.117 0.515 860 Planarity : 0.010 0.035 960 Dihedral : 10.929 78.268 2160 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 1.56 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.29 (0.26), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 349 TYR 0.013 0.008 TYR A 310 PHE 0.051 0.015 PHE G 346 HIS 0.012 0.004 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.02608 ( 5660) covalent geometry : angle 2.08847 ( 7580) hydrogen bonds : bond 0.09730 ( 192) hydrogen bonds : angle 9.12133 ( 576) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: C 342 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7075 (mt-10) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.8000 time to fit residues: 117.1304 Evaluate side-chains 88 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN C 327 ASN C 368 ASN D 368 ASN F 336 GLN ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 ASN J 368 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.146612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.123734 restraints weight = 5803.731| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.05 r_work: 0.3805 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3687 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5660 Z= 0.170 Angle : 0.693 5.800 7580 Z= 0.358 Chirality : 0.051 0.136 860 Planarity : 0.004 0.029 960 Dihedral : 5.879 17.576 740 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.03 % Allowed : 12.03 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.20 (0.28), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 349 TYR 0.012 0.003 TYR H 310 PHE 0.023 0.003 PHE F 346 HIS 0.002 0.001 HIS I 362 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 5660) covalent geometry : angle 0.69305 ( 7580) hydrogen bonds : bond 0.03509 ( 192) hydrogen bonds : angle 6.64280 ( 576) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8322 (tt0) cc_final: 0.7747 (tm-30) REVERT: A 340 LYS cc_start: 0.8376 (ttmm) cc_final: 0.8078 (ttmm) REVERT: A 375 LYS cc_start: 0.8024 (ttmt) cc_final: 0.7517 (ttmp) REVERT: B 331 LYS cc_start: 0.8314 (mtmt) cc_final: 0.7911 (mtpm) REVERT: B 338 GLU cc_start: 0.8451 (tt0) cc_final: 0.8084 (tm-30) REVERT: B 343 LYS cc_start: 0.7243 (mptt) cc_final: 0.6973 (mtmt) REVERT: B 369 LYS cc_start: 0.8155 (ttmt) cc_final: 0.7785 (ttmm) REVERT: B 375 LYS cc_start: 0.8235 (ttmt) cc_final: 0.7641 (ttmp) REVERT: C 340 LYS cc_start: 0.7974 (tttt) cc_final: 0.7608 (ttmm) REVERT: D 343 LYS cc_start: 0.7445 (mptt) cc_final: 0.6984 (ttpp) REVERT: F 336 GLN cc_start: 0.8591 (tt0) cc_final: 0.8326 (mt0) REVERT: F 343 LYS cc_start: 0.7388 (mptt) cc_final: 0.6783 (mtpp) REVERT: F 369 LYS cc_start: 0.8476 (ttmt) cc_final: 0.8248 (ttmm) REVERT: I 308 ILE cc_start: 0.7722 (mt) cc_final: 0.7515 (mp) REVERT: J 319 THR cc_start: 0.8736 (p) cc_final: 0.8416 (t) REVERT: J 321 LYS cc_start: 0.8398 (mttt) cc_final: 0.7758 (tmtt) REVERT: J 331 LYS cc_start: 0.8709 (mtmt) cc_final: 0.8417 (mtpm) outliers start: 13 outliers final: 3 residues processed: 123 average time/residue: 0.6969 time to fit residues: 88.8929 Evaluate side-chains 101 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain G residue 357 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 55 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 67 optimal weight: 0.0770 chunk 40 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN C 362 HIS F 336 GLN ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.138519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.115083 restraints weight = 6032.060| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 1.99 r_work: 0.3708 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 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 : 0.004 0.030 5660 Z= 0.177 Angle : 0.632 4.809 7580 Z= 0.331 Chirality : 0.050 0.127 860 Planarity : 0.004 0.040 960 Dihedral : 5.747 15.754 740 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.97 % Allowed : 15.78 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.45 (0.27), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 349 TYR 0.011 0.002 TYR D 310 PHE 0.023 0.004 PHE H 346 HIS 0.002 0.000 HIS H 362 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 5660) covalent geometry : angle 0.63163 ( 7580) hydrogen bonds : bond 0.03617 ( 192) hydrogen bonds : angle 6.04808 ( 576) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8380 (tt0) cc_final: 0.7894 (tm-30) REVERT: A 340 LYS cc_start: 0.8414 (ttmm) cc_final: 0.7951 (ttmt) REVERT: A 375 LYS cc_start: 0.8130 (ttmt) cc_final: 0.7684 (ttmp) REVERT: B 311 LYS cc_start: 0.7729 (mttt) cc_final: 0.7185 (mmtm) REVERT: B 331 LYS cc_start: 0.8273 (mtmt) cc_final: 0.7969 (mtpm) REVERT: B 338 GLU cc_start: 0.8495 (tt0) cc_final: 0.8102 (tm-30) REVERT: B 343 LYS cc_start: 0.7376 (mptt) cc_final: 0.6949 (ttpp) REVERT: B 352 SER cc_start: 0.8852 (p) cc_final: 0.8566 (t) REVERT: B 369 LYS cc_start: 0.8016 (ttmt) cc_final: 0.7700 (ttmm) REVERT: C 340 LYS cc_start: 0.7977 (tttt) cc_final: 0.7731 (ttmm) REVERT: D 343 LYS cc_start: 0.7569 (mptt) cc_final: 0.6994 (tttm) REVERT: D 369 LYS cc_start: 0.8515 (ttmm) cc_final: 0.8044 (mtpt) REVERT: E 343 LYS cc_start: 0.7721 (tptm) cc_final: 0.7509 (tptp) REVERT: E 378 PHE cc_start: 0.7173 (t80) cc_final: 0.6833 (t80) REVERT: F 343 LYS cc_start: 0.7736 (mptt) cc_final: 0.6989 (mtpp) REVERT: F 347 LYS cc_start: 0.7481 (pttt) cc_final: 0.7015 (pttm) REVERT: G 317 LYS cc_start: 0.7821 (ptmt) cc_final: 0.7425 (pttt) REVERT: G 321 LYS cc_start: 0.8618 (mttp) cc_final: 0.8308 (mttm) REVERT: G 338 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8086 (tt0) REVERT: G 370 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7971 (tttp) REVERT: H 369 LYS cc_start: 0.8190 (ttmt) cc_final: 0.7691 (mtmm) REVERT: I 308 ILE cc_start: 0.7930 (mt) cc_final: 0.7701 (mp) REVERT: I 311 LYS cc_start: 0.7939 (ttpp) cc_final: 0.7734 (ttpt) REVERT: J 331 LYS cc_start: 0.8754 (mtmt) cc_final: 0.8489 (mtpm) REVERT: J 357 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8579 (tt) outliers start: 19 outliers final: 9 residues processed: 118 average time/residue: 0.7435 time to fit residues: 90.7450 Evaluate side-chains 110 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 370 LYS Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain J residue 357 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 chunk 6 optimal weight: 0.0030 chunk 7 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.141199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.118022 restraints weight = 5949.844| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 1.94 r_work: 0.3728 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5660 Z= 0.148 Angle : 0.575 4.433 7580 Z= 0.300 Chirality : 0.049 0.126 860 Planarity : 0.004 0.039 960 Dihedral : 5.560 15.058 740 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.97 % Allowed : 17.66 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.63 (0.27), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 349 TYR 0.011 0.002 TYR H 310 PHE 0.017 0.003 PHE G 346 HIS 0.002 0.000 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 5660) covalent geometry : angle 0.57460 ( 7580) hydrogen bonds : bond 0.03111 ( 192) hydrogen bonds : angle 5.82358 ( 576) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8330 (tt0) cc_final: 0.7828 (tm-30) REVERT: A 340 LYS cc_start: 0.8465 (ttmm) cc_final: 0.8001 (ttmt) REVERT: B 311 LYS cc_start: 0.7815 (mttt) cc_final: 0.7199 (mttm) REVERT: B 331 LYS cc_start: 0.8311 (mtmt) cc_final: 0.7981 (mtpm) REVERT: B 338 GLU cc_start: 0.8483 (tt0) cc_final: 0.8115 (tm-30) REVERT: B 343 LYS cc_start: 0.7403 (mptt) cc_final: 0.6993 (ttpp) REVERT: B 352 SER cc_start: 0.8849 (p) cc_final: 0.8591 (t) REVERT: C 340 LYS cc_start: 0.7976 (tttt) cc_final: 0.7656 (ttmm) REVERT: D 343 LYS cc_start: 0.7466 (mptt) cc_final: 0.7118 (mmmt) REVERT: D 369 LYS cc_start: 0.8501 (ttmm) cc_final: 0.8072 (mtpt) REVERT: E 343 LYS cc_start: 0.7806 (tptm) cc_final: 0.7600 (tptp) REVERT: E 369 LYS cc_start: 0.8508 (ttmm) cc_final: 0.8206 (mtpt) REVERT: E 378 PHE cc_start: 0.7067 (t80) cc_final: 0.6806 (t80) REVERT: F 343 LYS cc_start: 0.7900 (mptt) cc_final: 0.7090 (mtpp) REVERT: F 357 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8605 (tt) REVERT: G 338 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8088 (tt0) REVERT: G 370 LYS cc_start: 0.8454 (ttpt) cc_final: 0.8166 (tttp) REVERT: I 342 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7333 (mp0) REVERT: J 308 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7790 (mp) REVERT: J 331 LYS cc_start: 0.8745 (mtmt) cc_final: 0.8512 (mtpm) REVERT: J 340 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8360 (mtpp) REVERT: J 342 GLU cc_start: 0.7496 (mt-10) cc_final: 0.6955 (mm-30) outliers start: 19 outliers final: 8 residues processed: 110 average time/residue: 0.7384 time to fit residues: 84.1501 Evaluate side-chains 111 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain J residue 308 ILE Chi-restraints excluded: chain J residue 340 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 7 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 17 optimal weight: 0.0980 chunk 37 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS D 362 HIS F 327 ASN ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 362 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.133154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.109881 restraints weight = 6129.544| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 1.97 r_work: 0.3628 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 5660 Z= 0.253 Angle : 0.687 5.494 7580 Z= 0.363 Chirality : 0.052 0.152 860 Planarity : 0.005 0.047 960 Dihedral : 6.168 17.100 740 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 5.31 % Allowed : 17.19 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.92 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 349 TYR 0.013 0.003 TYR D 310 PHE 0.027 0.005 PHE G 346 HIS 0.003 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00591 ( 5660) covalent geometry : angle 0.68721 ( 7580) hydrogen bonds : bond 0.04025 ( 192) hydrogen bonds : angle 6.01033 ( 576) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8365 (tt0) cc_final: 0.7907 (tm-30) REVERT: A 340 LYS cc_start: 0.8589 (ttmm) cc_final: 0.8150 (ttmt) REVERT: B 311 LYS cc_start: 0.7830 (mttt) cc_final: 0.7166 (mttm) REVERT: B 338 GLU cc_start: 0.8568 (tt0) cc_final: 0.8287 (tm-30) REVERT: B 343 LYS cc_start: 0.7423 (mptt) cc_final: 0.6976 (ttpp) REVERT: C 346 PHE cc_start: 0.7348 (OUTLIER) cc_final: 0.6683 (p90) REVERT: D 343 LYS cc_start: 0.7406 (mptt) cc_final: 0.6999 (mmmt) REVERT: D 369 LYS cc_start: 0.8543 (ttmm) cc_final: 0.8107 (mtpt) REVERT: E 342 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7538 (mp0) REVERT: E 369 LYS cc_start: 0.8670 (ttmm) cc_final: 0.8365 (mtpt) REVERT: E 378 PHE cc_start: 0.6948 (t80) cc_final: 0.6667 (t80) REVERT: F 343 LYS cc_start: 0.7843 (mptt) cc_final: 0.6987 (mtpp) REVERT: G 311 LYS cc_start: 0.7971 (tmtp) cc_final: 0.7717 (tptt) REVERT: G 340 LYS cc_start: 0.7793 (tttt) cc_final: 0.6974 (mppt) REVERT: G 343 LYS cc_start: 0.7810 (mptt) cc_final: 0.7073 (mmmm) REVERT: G 369 LYS cc_start: 0.8419 (ttmt) cc_final: 0.8107 (ttmm) REVERT: G 375 LYS cc_start: 0.7811 (ttmt) cc_final: 0.7567 (ttmt) REVERT: H 321 LYS cc_start: 0.8745 (mttp) cc_final: 0.8413 (mttp) REVERT: H 340 LYS cc_start: 0.7993 (tttt) cc_final: 0.7650 (mtpm) REVERT: H 343 LYS cc_start: 0.7836 (mptt) cc_final: 0.6883 (ttmm) REVERT: H 347 LYS cc_start: 0.7377 (pttt) cc_final: 0.7030 (pttt) REVERT: H 352 SER cc_start: 0.8849 (OUTLIER) cc_final: 0.8483 (t) REVERT: H 375 LYS cc_start: 0.7620 (ttmt) cc_final: 0.7334 (ttpt) REVERT: I 342 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7941 (mt-10) REVERT: J 308 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8011 (mp) REVERT: J 331 LYS cc_start: 0.8785 (mtmt) cc_final: 0.8500 (mtpm) REVERT: J 340 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8545 (mtpp) REVERT: J 342 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7065 (mm-30) REVERT: J 352 SER cc_start: 0.8886 (OUTLIER) cc_final: 0.8641 (p) REVERT: J 357 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8598 (tt) outliers start: 34 outliers final: 18 residues processed: 129 average time/residue: 0.7809 time to fit residues: 104.0314 Evaluate side-chains 128 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain C residue 346 PHE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 346 PHE Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 357 LEU Chi-restraints excluded: chain I residue 331 LYS Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain J residue 308 ILE Chi-restraints excluded: chain J residue 340 LYS Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain J residue 356 SER Chi-restraints excluded: chain J residue 357 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 43 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 63 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 58 optimal weight: 0.0970 chunk 35 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 327 ASN ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.141070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.117651 restraints weight = 6002.632| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.97 r_work: 0.3720 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.5217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5660 Z= 0.134 Angle : 0.567 6.265 7580 Z= 0.298 Chirality : 0.049 0.125 860 Planarity : 0.004 0.040 960 Dihedral : 5.581 15.134 740 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.59 % Allowed : 19.06 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.88 (0.26), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 349 TYR 0.010 0.002 TYR H 310 PHE 0.014 0.003 PHE G 346 HIS 0.002 0.000 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 5660) covalent geometry : angle 0.56692 ( 7580) hydrogen bonds : bond 0.03009 ( 192) hydrogen bonds : angle 5.72071 ( 576) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8349 (tt0) cc_final: 0.7902 (tm-30) REVERT: A 340 LYS cc_start: 0.8605 (ttmm) cc_final: 0.8127 (ttmt) REVERT: B 331 LYS cc_start: 0.8392 (mtmt) cc_final: 0.8047 (mtpm) REVERT: B 338 GLU cc_start: 0.8559 (tt0) cc_final: 0.8122 (tm-30) REVERT: B 343 LYS cc_start: 0.7439 (mptt) cc_final: 0.7069 (ttpp) REVERT: B 352 SER cc_start: 0.8860 (p) cc_final: 0.8562 (t) REVERT: C 340 LYS cc_start: 0.7960 (tttt) cc_final: 0.7705 (ttmt) REVERT: C 346 PHE cc_start: 0.7056 (OUTLIER) cc_final: 0.6666 (p90) REVERT: C 357 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8644 (tt) REVERT: D 314 ASP cc_start: 0.8311 (t0) cc_final: 0.8078 (t0) REVERT: D 343 LYS cc_start: 0.7411 (mptt) cc_final: 0.7044 (mmmt) REVERT: D 369 LYS cc_start: 0.8549 (ttmm) cc_final: 0.8097 (mtpt) REVERT: E 371 ILE cc_start: 0.8755 (mt) cc_final: 0.8554 (mp) REVERT: F 317 LYS cc_start: 0.8083 (ptmt) cc_final: 0.7781 (pttt) REVERT: F 343 LYS cc_start: 0.7872 (mptt) cc_final: 0.7031 (mtpp) REVERT: F 357 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8567 (tt) REVERT: G 317 LYS cc_start: 0.7900 (ptmt) cc_final: 0.7603 (pttt) REVERT: H 321 LYS cc_start: 0.8779 (mttp) cc_final: 0.8433 (mttp) REVERT: H 352 SER cc_start: 0.8909 (OUTLIER) cc_final: 0.8539 (t) REVERT: I 342 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7929 (mt-10) REVERT: J 308 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.7965 (mp) REVERT: J 331 LYS cc_start: 0.8713 (mtmt) cc_final: 0.8488 (mtpm) REVERT: J 342 GLU cc_start: 0.7592 (mt-10) cc_final: 0.6986 (mm-30) REVERT: J 352 SER cc_start: 0.8838 (OUTLIER) cc_final: 0.8614 (p) REVERT: J 357 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8568 (tt) outliers start: 23 outliers final: 9 residues processed: 114 average time/residue: 0.6601 time to fit residues: 78.1886 Evaluate side-chains 112 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain C residue 346 PHE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 346 PHE Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain I residue 331 LYS Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain J residue 308 ILE Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain J residue 357 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 36 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 6 optimal weight: 0.0370 chunk 27 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 4 optimal weight: 0.2980 overall best weight: 1.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 327 ASN ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.135645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.112116 restraints weight = 6114.934| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.96 r_work: 0.3648 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5660 Z= 0.215 Angle : 0.646 7.331 7580 Z= 0.341 Chirality : 0.050 0.134 860 Planarity : 0.005 0.046 960 Dihedral : 5.946 16.050 740 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 4.69 % Allowed : 19.22 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.03 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 349 TYR 0.012 0.003 TYR D 310 PHE 0.022 0.004 PHE G 346 HIS 0.003 0.001 HIS I 362 Details of bonding type rmsd covalent geometry : bond 0.00503 ( 5660) covalent geometry : angle 0.64561 ( 7580) hydrogen bonds : bond 0.03611 ( 192) hydrogen bonds : angle 5.77400 ( 576) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8329 (tt0) cc_final: 0.7794 (tm-30) REVERT: A 340 LYS cc_start: 0.8614 (ttmm) cc_final: 0.8186 (ttmt) REVERT: B 311 LYS cc_start: 0.7817 (mttt) cc_final: 0.7177 (mttm) REVERT: B 338 GLU cc_start: 0.8593 (tt0) cc_final: 0.8274 (tm-30) REVERT: B 343 LYS cc_start: 0.7501 (mptt) cc_final: 0.7098 (ttpp) REVERT: C 346 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.6732 (p90) REVERT: D 343 LYS cc_start: 0.7389 (mptt) cc_final: 0.6992 (mmmt) REVERT: D 347 LYS cc_start: 0.7180 (pttm) cc_final: 0.6893 (ptpt) REVERT: D 369 LYS cc_start: 0.8545 (ttmm) cc_final: 0.8099 (mtpt) REVERT: E 375 LYS cc_start: 0.8293 (ttmm) cc_final: 0.7981 (ttmp) REVERT: F 343 LYS cc_start: 0.7871 (mptt) cc_final: 0.7035 (mtpp) REVERT: H 321 LYS cc_start: 0.8774 (mttp) cc_final: 0.8440 (mttp) REVERT: H 352 SER cc_start: 0.8915 (OUTLIER) cc_final: 0.8535 (t) REVERT: H 369 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8069 (mtmt) REVERT: I 342 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7887 (mt-10) REVERT: I 369 LYS cc_start: 0.8766 (ttmt) cc_final: 0.8468 (ttmm) REVERT: I 378 PHE cc_start: 0.6957 (m-80) cc_final: 0.6597 (m-80) REVERT: J 308 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.8081 (mp) REVERT: J 331 LYS cc_start: 0.8774 (mtmt) cc_final: 0.8471 (mtpm) REVERT: J 342 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7054 (mm-30) REVERT: J 352 SER cc_start: 0.8862 (OUTLIER) cc_final: 0.8612 (p) REVERT: J 357 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8607 (tt) outliers start: 30 outliers final: 17 residues processed: 112 average time/residue: 0.7242 time to fit residues: 84.0392 Evaluate side-chains 114 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain C residue 346 PHE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 346 PHE Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 357 LEU Chi-restraints excluded: chain H residue 369 LYS Chi-restraints excluded: chain I residue 331 LYS Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain J residue 308 ILE Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain J residue 356 SER Chi-restraints excluded: chain J residue 357 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 42 optimal weight: 0.2980 chunk 62 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS C 362 HIS ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.136686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.113229 restraints weight = 6015.112| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.95 r_work: 0.3662 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5660 Z= 0.193 Angle : 0.629 6.867 7580 Z= 0.332 Chirality : 0.050 0.126 860 Planarity : 0.005 0.043 960 Dihedral : 5.898 17.011 740 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 4.69 % Allowed : 19.53 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.09 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 349 TYR 0.011 0.002 TYR D 310 PHE 0.020 0.004 PHE C 346 HIS 0.002 0.000 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 5660) covalent geometry : angle 0.62939 ( 7580) hydrogen bonds : bond 0.03431 ( 192) hydrogen bonds : angle 5.69568 ( 576) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8347 (tt0) cc_final: 0.7690 (tm-30) REVERT: A 340 LYS cc_start: 0.8615 (ttmm) cc_final: 0.8112 (ttmt) REVERT: B 338 GLU cc_start: 0.8589 (tt0) cc_final: 0.8163 (tm-30) REVERT: B 343 LYS cc_start: 0.7492 (mptt) cc_final: 0.7103 (ttpp) REVERT: B 347 LYS cc_start: 0.7319 (pttt) cc_final: 0.6707 (ptpt) REVERT: C 346 PHE cc_start: 0.7192 (OUTLIER) cc_final: 0.6711 (p90) REVERT: D 343 LYS cc_start: 0.7401 (mptt) cc_final: 0.7002 (mmmt) REVERT: D 347 LYS cc_start: 0.7153 (pttm) cc_final: 0.6880 (ptpt) REVERT: D 369 LYS cc_start: 0.8541 (ttmm) cc_final: 0.8109 (mtpt) REVERT: E 375 LYS cc_start: 0.8281 (ttmm) cc_final: 0.7987 (ttmp) REVERT: F 317 LYS cc_start: 0.8075 (ptmt) cc_final: 0.7722 (pttt) REVERT: F 343 LYS cc_start: 0.7872 (mptt) cc_final: 0.7048 (mtpp) REVERT: F 347 LYS cc_start: 0.7222 (pttt) cc_final: 0.6855 (pttm) REVERT: F 357 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8608 (tt) REVERT: G 346 PHE cc_start: 0.7161 (OUTLIER) cc_final: 0.6803 (p90) REVERT: H 321 LYS cc_start: 0.8793 (mttp) cc_final: 0.8453 (mttp) REVERT: H 352 SER cc_start: 0.8862 (OUTLIER) cc_final: 0.8461 (t) REVERT: H 369 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8068 (mtmt) REVERT: I 342 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7902 (mt-10) REVERT: I 369 LYS cc_start: 0.8758 (ttmt) cc_final: 0.8458 (ttmm) REVERT: I 378 PHE cc_start: 0.6970 (m-80) cc_final: 0.6623 (m-80) REVERT: J 308 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8090 (mp) REVERT: J 331 LYS cc_start: 0.8791 (mtmt) cc_final: 0.8496 (mtpm) REVERT: J 342 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7064 (mm-30) REVERT: J 352 SER cc_start: 0.8847 (OUTLIER) cc_final: 0.8601 (p) REVERT: J 357 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8562 (tt) outliers start: 30 outliers final: 17 residues processed: 109 average time/residue: 0.6820 time to fit residues: 77.1073 Evaluate side-chains 111 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain C residue 346 PHE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 346 PHE Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain G residue 346 PHE Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 369 LYS Chi-restraints excluded: chain I residue 331 LYS Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain J residue 308 ILE Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain J residue 356 SER Chi-restraints excluded: chain J residue 357 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 29 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 2 optimal weight: 0.1980 chunk 31 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 327 ASN ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.137878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.114348 restraints weight = 6032.001| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 1.95 r_work: 0.3677 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3556 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5660 Z= 0.167 Angle : 0.603 6.934 7580 Z= 0.318 Chirality : 0.049 0.125 860 Planarity : 0.004 0.044 960 Dihedral : 5.755 17.621 740 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 4.53 % Allowed : 20.00 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.06 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 349 TYR 0.011 0.002 TYR D 310 PHE 0.018 0.003 PHE C 346 HIS 0.002 0.000 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 5660) covalent geometry : angle 0.60322 ( 7580) hydrogen bonds : bond 0.03170 ( 192) hydrogen bonds : angle 5.57366 ( 576) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 90 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8341 (tt0) cc_final: 0.7784 (tm-30) REVERT: A 340 LYS cc_start: 0.8604 (ttmm) cc_final: 0.8113 (ttmt) REVERT: B 338 GLU cc_start: 0.8588 (tt0) cc_final: 0.8157 (tm-30) REVERT: B 343 LYS cc_start: 0.7482 (mptt) cc_final: 0.7213 (ttpp) REVERT: C 340 LYS cc_start: 0.8384 (ttmm) cc_final: 0.7928 (ttmt) REVERT: C 346 PHE cc_start: 0.7115 (OUTLIER) cc_final: 0.6575 (p90) REVERT: D 343 LYS cc_start: 0.7403 (mptt) cc_final: 0.7017 (mmmt) REVERT: D 347 LYS cc_start: 0.7091 (pttm) cc_final: 0.6827 (ptpt) REVERT: D 369 LYS cc_start: 0.8561 (ttmm) cc_final: 0.8115 (mtpt) REVERT: E 375 LYS cc_start: 0.8276 (ttmm) cc_final: 0.7983 (ttmp) REVERT: F 317 LYS cc_start: 0.8084 (ptmt) cc_final: 0.7721 (ptmt) REVERT: F 343 LYS cc_start: 0.7858 (mptt) cc_final: 0.7047 (mtpp) REVERT: F 357 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8627 (tt) REVERT: G 317 LYS cc_start: 0.7746 (ptmt) cc_final: 0.7466 (pttt) REVERT: H 314 ASP cc_start: 0.8070 (t0) cc_final: 0.7801 (t0) REVERT: H 321 LYS cc_start: 0.8789 (mttp) cc_final: 0.8446 (mttp) REVERT: H 369 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8054 (mtmt) REVERT: I 342 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7970 (mt-10) REVERT: I 369 LYS cc_start: 0.8723 (ttmt) cc_final: 0.8441 (ttmm) REVERT: I 378 PHE cc_start: 0.6871 (m-80) cc_final: 0.6541 (m-80) REVERT: J 308 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.8118 (mp) REVERT: J 331 LYS cc_start: 0.8789 (mtmt) cc_final: 0.8488 (mtpm) REVERT: J 342 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7053 (mm-30) REVERT: J 352 SER cc_start: 0.8836 (OUTLIER) cc_final: 0.8581 (p) REVERT: J 357 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8597 (tt) outliers start: 29 outliers final: 17 residues processed: 110 average time/residue: 0.7028 time to fit residues: 80.1403 Evaluate side-chains 112 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain C residue 346 PHE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 346 PHE Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 357 LEU Chi-restraints excluded: chain H residue 369 LYS Chi-restraints excluded: chain I residue 331 LYS Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain J residue 308 ILE Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain J residue 356 SER Chi-restraints excluded: chain J residue 357 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 22 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 58 optimal weight: 0.0570 chunk 17 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 327 ASN ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.137618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.114043 restraints weight = 6083.616| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 1.96 r_work: 0.3681 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.5451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5660 Z= 0.165 Angle : 0.610 7.080 7580 Z= 0.319 Chirality : 0.049 0.125 860 Planarity : 0.004 0.042 960 Dihedral : 5.756 17.650 740 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 4.22 % Allowed : 20.47 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.07 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 349 TYR 0.010 0.002 TYR H 310 PHE 0.018 0.003 PHE C 346 HIS 0.002 0.000 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 5660) covalent geometry : angle 0.61014 ( 7580) hydrogen bonds : bond 0.03135 ( 192) hydrogen bonds : angle 5.53300 ( 576) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8335 (tt0) cc_final: 0.7785 (tm-30) REVERT: A 340 LYS cc_start: 0.8611 (ttmm) cc_final: 0.8123 (ttmt) REVERT: A 343 LYS cc_start: 0.8142 (mtpp) cc_final: 0.7836 (ttpp) REVERT: B 338 GLU cc_start: 0.8596 (tt0) cc_final: 0.8155 (tm-30) REVERT: B 343 LYS cc_start: 0.7522 (mptt) cc_final: 0.7207 (ttpp) REVERT: C 340 LYS cc_start: 0.8377 (ttmm) cc_final: 0.7887 (ttmt) REVERT: C 346 PHE cc_start: 0.7116 (OUTLIER) cc_final: 0.6575 (p90) REVERT: D 343 LYS cc_start: 0.7457 (mptt) cc_final: 0.7032 (mmmt) REVERT: D 347 LYS cc_start: 0.7081 (pttm) cc_final: 0.6815 (ptpt) REVERT: D 369 LYS cc_start: 0.8562 (ttmm) cc_final: 0.8117 (mtpt) REVERT: E 375 LYS cc_start: 0.8284 (ttmm) cc_final: 0.7989 (ttmp) REVERT: F 317 LYS cc_start: 0.8080 (ptmt) cc_final: 0.7786 (ptmt) REVERT: F 343 LYS cc_start: 0.7853 (mptt) cc_final: 0.7047 (mtpp) REVERT: F 357 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8593 (tt) REVERT: G 317 LYS cc_start: 0.7748 (ptmt) cc_final: 0.7426 (tttt) REVERT: H 314 ASP cc_start: 0.8034 (t0) cc_final: 0.7767 (t0) REVERT: H 317 LYS cc_start: 0.7742 (ptmt) cc_final: 0.7491 (ptmm) REVERT: H 321 LYS cc_start: 0.8789 (mttp) cc_final: 0.8453 (mttp) REVERT: H 369 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8053 (mtmt) REVERT: I 342 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7817 (mt-10) REVERT: I 378 PHE cc_start: 0.6791 (m-80) cc_final: 0.6452 (m-80) REVERT: J 331 LYS cc_start: 0.8795 (mtmt) cc_final: 0.8494 (mtpm) REVERT: J 342 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7093 (mm-30) REVERT: J 352 SER cc_start: 0.8832 (OUTLIER) cc_final: 0.8575 (p) REVERT: J 357 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8579 (tt) outliers start: 27 outliers final: 17 residues processed: 107 average time/residue: 0.7260 time to fit residues: 80.3558 Evaluate side-chains 108 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain C residue 346 PHE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 346 PHE Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 357 LEU Chi-restraints excluded: chain H residue 369 LYS Chi-restraints excluded: chain I residue 331 LYS Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain J residue 356 SER Chi-restraints excluded: chain J residue 357 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 8 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 327 ASN ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.134710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.111146 restraints weight = 6053.336| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 1.95 r_work: 0.3638 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5660 Z= 0.218 Angle : 0.657 7.113 7580 Z= 0.347 Chirality : 0.051 0.136 860 Planarity : 0.005 0.046 960 Dihedral : 6.051 21.115 740 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 4.38 % Allowed : 20.16 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.15 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.011 0.002 TYR D 310 PHE 0.022 0.004 PHE C 346 HIS 0.003 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00509 ( 5660) covalent geometry : angle 0.65743 ( 7580) hydrogen bonds : bond 0.03642 ( 192) hydrogen bonds : angle 5.69441 ( 576) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2462.02 seconds wall clock time: 43 minutes 6.78 seconds (2586.78 seconds total)