Starting phenix.real_space_refine on Thu Nov 14 09:46:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seh_40411/11_2024/8seh_40411_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seh_40411/11_2024/8seh_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seh_40411/11_2024/8seh_40411.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seh_40411/11_2024/8seh_40411.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seh_40411/11_2024/8seh_40411_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seh_40411/11_2024/8seh_40411_neut.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: C, B, E, D, G, F, I, H, J Time building chain proxies: 2.28, per 1000 atoms: 0.41 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: 1.33 Conformation dependent library (CDL) restraints added in 737.0 milliseconds 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: 0.94 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: 1.55 Time building geometry restraints manager: 1.56 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: 0.00 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.170 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.850 ------------------------------------------------------------------------------- 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= 1.751 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (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 HIS 0.012 0.004 HIS E 362 PHE 0.051 0.015 PHE G 346 TYR 0.013 0.008 TYR A 310 ARG 0.002 0.001 ARG C 349 *********************** 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 : 0.726 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: 1.6012 time to fit residues: 234.9151 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 : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3410 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= 0.248 Angle : 0.657 5.585 7580 Z= 0.341 Chirality : 0.050 0.132 860 Planarity : 0.004 0.031 960 Dihedral : 5.926 17.325 740 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.03 % Allowed : 12.19 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.28), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 374 PHE 0.019 0.003 PHE F 346 TYR 0.010 0.002 TYR H 310 ARG 0.001 0.000 ARG B 349 *********************** 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 137 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7447 (tt0) cc_final: 0.7240 (tm-30) REVERT: A 340 LYS cc_start: 0.8431 (ttmm) cc_final: 0.8195 (ttmm) REVERT: B 375 LYS cc_start: 0.8041 (ttmt) cc_final: 0.7748 (ttmp) outliers start: 13 outliers final: 2 residues processed: 129 average time/residue: 1.3099 time to fit residues: 175.7074 Evaluate side-chains 103 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 35 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS B 336 GLN B 362 HIS D 362 HIS F 336 GLN ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 336 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 5660 Z= 0.463 Angle : 0.769 5.572 7580 Z= 0.406 Chirality : 0.053 0.169 860 Planarity : 0.005 0.047 960 Dihedral : 6.411 17.514 740 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 4.69 % Allowed : 15.62 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.26), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 329 PHE 0.035 0.006 PHE G 346 TYR 0.015 0.003 TYR D 310 ARG 0.002 0.000 ARG J 349 *********************** 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 142 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8461 (ttmm) cc_final: 0.8076 (ttmt) REVERT: B 338 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7536 (tm-30) REVERT: B 343 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7726 (ttpp) REVERT: D 343 LYS cc_start: 0.7646 (tttm) cc_final: 0.7415 (tptm) REVERT: D 369 LYS cc_start: 0.8311 (ttmm) cc_final: 0.7964 (mtpt) REVERT: H 321 LYS cc_start: 0.8734 (mttp) cc_final: 0.8507 (mttp) REVERT: H 352 SER cc_start: 0.8792 (OUTLIER) cc_final: 0.8431 (t) outliers start: 30 outliers final: 15 residues processed: 131 average time/residue: 1.4928 time to fit residues: 202.4532 Evaluate side-chains 112 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 343 LYS 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 E residue 346 PHE Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 361 THR 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 I residue 331 LYS Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain J residue 352 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 30 optimal weight: 0.1980 chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 0.0370 chunk 67 optimal weight: 1.9990 chunk 60 optimal weight: 0.2980 chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 HIS ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 362 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.5353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5660 Z= 0.154 Angle : 0.549 5.102 7580 Z= 0.283 Chirality : 0.048 0.123 860 Planarity : 0.004 0.037 960 Dihedral : 5.373 13.660 740 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.50 % Allowed : 21.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.27), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 374 PHE 0.008 0.002 PHE G 346 TYR 0.010 0.001 TYR H 310 ARG 0.001 0.000 ARG J 349 *********************** 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 119 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7067 (tm-30) REVERT: A 340 LYS cc_start: 0.8310 (ttmm) cc_final: 0.8084 (mtmt) REVERT: B 338 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7461 (tm-30) REVERT: D 369 LYS cc_start: 0.8184 (ttmm) cc_final: 0.7914 (mtpt) REVERT: F 357 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8667 (tt) REVERT: G 338 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7294 (tt0) outliers start: 16 outliers final: 2 residues processed: 112 average time/residue: 1.2514 time to fit residues: 146.2261 Evaluate side-chains 92 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 338 GLU 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 H residue 357 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 39 optimal weight: 0.0970 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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** G 336 GLN J 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.5416 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= 0.344 Angle : 0.658 5.064 7580 Z= 0.343 Chirality : 0.050 0.134 860 Planarity : 0.005 0.051 960 Dihedral : 5.937 15.578 740 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 5.47 % Allowed : 19.53 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.26), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.024 0.005 PHE E 346 TYR 0.011 0.003 TYR E 310 ARG 0.001 0.000 ARG J 349 *********************** 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 135 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 338 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7471 (tm-30) REVERT: C 346 PHE cc_start: 0.7041 (OUTLIER) cc_final: 0.6476 (p90) REVERT: D 369 LYS cc_start: 0.8328 (ttmm) cc_final: 0.8040 (mtpt) REVERT: E 375 LYS cc_start: 0.8049 (ttmm) cc_final: 0.7837 (ttmm) REVERT: H 342 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6750 (mp0) REVERT: H 352 SER cc_start: 0.8839 (OUTLIER) cc_final: 0.8459 (t) REVERT: I 369 LYS cc_start: 0.8288 (mtmt) cc_final: 0.8045 (mtpp) outliers start: 35 outliers final: 13 residues processed: 121 average time/residue: 1.4006 time to fit residues: 175.9636 Evaluate side-chains 113 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 338 GLU 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 357 LEU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 357 LEU Chi-restraints excluded: chain I residue 352 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.5581 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= 0.351 Angle : 0.673 5.234 7580 Z= 0.351 Chirality : 0.051 0.135 860 Planarity : 0.005 0.043 960 Dihedral : 6.016 15.703 740 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 4.53 % Allowed : 20.62 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (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 HIS 0.002 0.001 HIS A 362 PHE 0.023 0.005 PHE G 346 TYR 0.012 0.003 TYR F 310 ARG 0.001 0.000 ARG J 349 *********************** 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 130 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7246 (tm-30) REVERT: C 346 PHE cc_start: 0.7005 (OUTLIER) cc_final: 0.6609 (p90) REVERT: D 369 LYS cc_start: 0.8370 (ttmm) cc_final: 0.8025 (mtpt) REVERT: E 375 LYS cc_start: 0.8057 (ttmm) cc_final: 0.7852 (ttmm) REVERT: H 342 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6778 (mp0) REVERT: H 352 SER cc_start: 0.8778 (OUTLIER) cc_final: 0.8446 (t) REVERT: I 369 LYS cc_start: 0.8289 (mtmt) cc_final: 0.8056 (mtpp) outliers start: 29 outliers final: 15 residues processed: 120 average time/residue: 1.5239 time to fit residues: 189.3578 Evaluate side-chains 117 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B 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 357 LEU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 346 PHE Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 357 LEU Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain J residue 356 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.5706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5660 Z= 0.241 Angle : 0.609 6.667 7580 Z= 0.316 Chirality : 0.049 0.127 860 Planarity : 0.005 0.042 960 Dihedral : 5.603 15.258 740 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.59 % Allowed : 22.97 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 362 PHE 0.015 0.003 PHE H 346 TYR 0.009 0.002 TYR H 310 ARG 0.001 0.000 ARG J 349 *********************** 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 110 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7141 (tm-30) REVERT: A 340 LYS cc_start: 0.8419 (mtmt) cc_final: 0.8192 (mtmt) REVERT: C 346 PHE cc_start: 0.6700 (OUTLIER) cc_final: 0.6340 (p90) REVERT: D 369 LYS cc_start: 0.8354 (ttmm) cc_final: 0.8033 (mtpt) REVERT: E 375 LYS cc_start: 0.8056 (ttmm) cc_final: 0.7854 (ttmm) REVERT: F 317 LYS cc_start: 0.8168 (ptmt) cc_final: 0.7949 (pttt) REVERT: F 357 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8715 (tt) REVERT: H 342 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6659 (mp0) REVERT: H 352 SER cc_start: 0.8760 (p) cc_final: 0.8426 (t) REVERT: I 369 LYS cc_start: 0.8289 (mtmt) cc_final: 0.8045 (mtpp) REVERT: J 340 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7844 (mtpp) outliers start: 23 outliers final: 10 residues processed: 102 average time/residue: 1.4006 time to fit residues: 148.4333 Evaluate side-chains 97 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU 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 D residue 357 LEU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain H residue 357 LEU Chi-restraints excluded: chain J residue 340 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.3980 chunk 42 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 6 optimal weight: 0.4980 chunk 53 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 64 optimal weight: 0.0970 chunk 58 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.5706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5660 Z= 0.341 Angle : 0.679 6.900 7580 Z= 0.353 Chirality : 0.051 0.136 860 Planarity : 0.005 0.045 960 Dihedral : 5.956 16.505 740 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 5.16 % Allowed : 22.19 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.002 0.001 HIS B 329 PHE 0.029 0.005 PHE A 346 TYR 0.011 0.002 TYR D 310 ARG 0.002 0.000 ARG J 349 *********************** 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 121 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7164 (tm-30) REVERT: C 346 PHE cc_start: 0.6923 (OUTLIER) cc_final: 0.6555 (p90) REVERT: D 347 LYS cc_start: 0.7543 (ptpt) cc_final: 0.7276 (pttm) REVERT: D 369 LYS cc_start: 0.8364 (ttmm) cc_final: 0.8047 (mtpt) REVERT: E 375 LYS cc_start: 0.8081 (ttmm) cc_final: 0.7880 (ttmm) REVERT: F 317 LYS cc_start: 0.8185 (ptmt) cc_final: 0.7841 (pttt) REVERT: H 342 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6683 (mp0) REVERT: H 352 SER cc_start: 0.8762 (OUTLIER) cc_final: 0.8398 (t) REVERT: I 369 LYS cc_start: 0.8295 (mtmt) cc_final: 0.8062 (mtpp) REVERT: J 340 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7919 (mtpp) outliers start: 33 outliers final: 16 residues processed: 111 average time/residue: 1.4159 time to fit residues: 163.3470 Evaluate side-chains 107 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 ASN 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 D residue 357 LEU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain G residue 340 LYS Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 357 LEU Chi-restraints excluded: chain J residue 340 LYS Chi-restraints excluded: chain J residue 356 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.5745 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= 0.292 Angle : 0.650 7.051 7580 Z= 0.338 Chirality : 0.050 0.127 860 Planarity : 0.005 0.044 960 Dihedral : 5.834 17.903 740 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 4.53 % Allowed : 22.97 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.002 0.000 HIS E 374 PHE 0.018 0.004 PHE H 346 TYR 0.010 0.002 TYR H 310 ARG 0.001 0.000 ARG A 349 *********************** 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 114 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7137 (tm-30) REVERT: A 370 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7885 (ttpp) REVERT: D 369 LYS cc_start: 0.8376 (ttmm) cc_final: 0.8057 (mtpt) REVERT: F 317 LYS cc_start: 0.8166 (ptmt) cc_final: 0.7830 (pttt) REVERT: F 357 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8728 (tt) REVERT: H 342 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6705 (mp0) REVERT: H 352 SER cc_start: 0.8728 (OUTLIER) cc_final: 0.8376 (t) REVERT: I 369 LYS cc_start: 0.8303 (mtmt) cc_final: 0.8061 (mtpp) REVERT: J 340 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7951 (mtpp) REVERT: J 342 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6337 (mp0) outliers start: 29 outliers final: 14 residues processed: 103 average time/residue: 1.3581 time to fit residues: 145.7230 Evaluate side-chains 103 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 327 ASN 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 D residue 357 LEU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain G residue 340 LYS Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain J residue 340 LYS Chi-restraints excluded: chain J residue 342 GLU Chi-restraints excluded: chain J residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.5757 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= 0.362 Angle : 0.697 7.160 7580 Z= 0.365 Chirality : 0.051 0.145 860 Planarity : 0.005 0.046 960 Dihedral : 6.108 21.571 740 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 4.22 % Allowed : 23.44 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 329 PHE 0.027 0.005 PHE B 346 TYR 0.011 0.003 TYR D 310 ARG 0.002 0.000 ARG B 349 ********************** 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 115 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7144 (tm-30) REVERT: A 370 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7901 (ttpp) REVERT: D 347 LYS cc_start: 0.7559 (ptpt) cc_final: 0.7295 (pttm) REVERT: H 314 ASP cc_start: 0.7506 (t0) cc_final: 0.7280 (t0) REVERT: H 342 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6405 (mp0) REVERT: H 352 SER cc_start: 0.8744 (OUTLIER) cc_final: 0.8384 (t) REVERT: I 369 LYS cc_start: 0.8312 (mtmt) cc_final: 0.8073 (mtpp) REVERT: J 340 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7916 (mtpp) REVERT: J 342 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6180 (mm-30) outliers start: 27 outliers final: 16 residues processed: 105 average time/residue: 1.3960 time to fit residues: 152.4281 Evaluate side-chains 105 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 327 ASN 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 D residue 357 LEU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain G residue 340 LYS Chi-restraints excluded: chain G residue 347 LYS Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain J residue 340 LYS Chi-restraints excluded: chain J residue 342 GLU Chi-restraints excluded: chain J residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 329 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 = 0.4088 r_free = 0.4088 target = 0.136224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.112828 restraints weight = 5913.369| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 1.93 r_work: 0.3669 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.5787 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= 0.321 Angle : 0.678 7.146 7580 Z= 0.355 Chirality : 0.050 0.128 860 Planarity : 0.005 0.046 960 Dihedral : 6.029 20.755 740 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 4.38 % Allowed : 23.44 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 329 PHE 0.020 0.004 PHE H 346 TYR 0.011 0.002 TYR D 310 ARG 0.001 0.000 ARG H 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3087.22 seconds wall clock time: 55 minutes 56.28 seconds (3356.28 seconds total)