Starting phenix.real_space_refine on Thu Nov 14 02:32:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oti_17180/11_2024/8oti_17180.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oti_17180/11_2024/8oti_17180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oti_17180/11_2024/8oti_17180.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oti_17180/11_2024/8oti_17180.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oti_17180/11_2024/8oti_17180.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oti_17180/11_2024/8oti_17180.cif" } resolution = 2.7 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 6 5.16 5 C 2160 2.51 5 N 636 2.21 5 O 642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 3444 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 3.01, per 1000 atoms: 0.87 Number of scatterers: 3444 At special positions: 0 Unit cell: (98.056, 126.072, 37.08, 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 6 16.00 O 642 8.00 N 636 7.00 C 2160 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: 0.77 Conformation dependent library (CDL) restraints added in 397.3 milliseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 17 sheets defined 0.0% alpha, 54.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.400A pdb=" N GLN A 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N TYR E 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.766A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 319 removed outlier: 6.523A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 322 through 330 removed outlier: 6.737A pdb=" N SER A 324 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU C 325 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLY A 326 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASN C 327 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLY A 323 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 9.808A pdb=" N GLY E 326 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N LEU A 325 " --> pdb=" O GLY E 326 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N ILE E 328 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN A 327 " --> pdb=" O ILE E 328 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N HIS E 330 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N HIS A 329 " --> pdb=" O HIS E 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 346 removed outlier: 6.414A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N LYS C 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL A 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N GLU C 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER A 341 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU C 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LYS A 343 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 10.197A pdb=" N PHE C 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU A 344 " --> pdb=" O LYS E 343 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASP E 345 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N PHE A 346 " --> pdb=" O ASP E 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 350 through 357 removed outlier: 6.211A pdb=" N VAL A 350 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LYS C 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N SER A 352 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N GLY C 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE A 354 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU C 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER A 356 " --> pdb=" O LEU C 357 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.310A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 369 through 373 removed outlier: 6.329A pdb=" N LYS A 370 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N THR C 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU A 372 " --> pdb=" O THR C 373 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 376 through 378 removed outlier: 6.438A pdb=" N LEU A 376 " --> pdb=" O THR C 377 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 307 through 310 removed outlier: 6.504A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.804A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 317 through 319 removed outlier: 6.504A pdb=" N VAL B 318 " --> pdb=" O THR F 319 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 322 through 330 removed outlier: 6.042A pdb=" N CYS B 322 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU D 325 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N SER B 324 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ASN D 327 " --> pdb=" O SER B 324 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N GLY B 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N HIS D 329 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 9.191A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLY B 323 " --> pdb=" O CYS F 322 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE F 328 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N HIS B 329 " --> pdb=" O ILE F 328 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N HIS F 330 " --> pdb=" O HIS B 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 336 through 346 removed outlier: 6.805A pdb=" N LEU B 344 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASP D 345 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE B 346 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL B 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N LYS F 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL B 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N GLU F 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N SER B 341 " --> pdb=" O GLU F 342 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU F 344 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LYS B 343 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 10.200A pdb=" N PHE F 346 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N ASP B 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 350 through 357 removed outlier: 6.256A pdb=" N VAL B 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N LYS F 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER B 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N GLY F 355 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE B 354 " --> pdb=" O GLY F 355 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU F 357 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N SER B 356 " --> pdb=" O LEU F 357 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.322A pdb=" N THR B 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 369 through 378 removed outlier: 6.327A pdb=" N LYS B 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N THR F 373 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLU B 372 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N LYS F 375 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N HIS B 374 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N THR F 377 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU B 376 " --> pdb=" O THR F 377 " (cutoff:3.500A) 67 hydrogen bonds defined for protein. 201 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: 0.80 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 692 1.32 - 1.44: 744 1.44 - 1.56: 2056 1.56 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3498 Sorted by residual: bond pdb=" CG HIS D 329 " pdb=" CD2 HIS D 329 " ideal model delta sigma weight residual 1.354 1.300 0.054 1.10e-02 8.26e+03 2.39e+01 bond pdb=" CG HIS F 329 " pdb=" CD2 HIS F 329 " ideal model delta sigma weight residual 1.354 1.300 0.054 1.10e-02 8.26e+03 2.39e+01 bond pdb=" CG HIS B 329 " pdb=" CD2 HIS B 329 " ideal model delta sigma weight residual 1.354 1.300 0.054 1.10e-02 8.26e+03 2.38e+01 bond pdb=" CA SER D 356 " pdb=" CB SER D 356 " ideal model delta sigma weight residual 1.527 1.467 0.060 1.30e-02 5.92e+03 2.13e+01 bond pdb=" CA SER F 356 " pdb=" CB SER F 356 " ideal model delta sigma weight residual 1.527 1.467 0.060 1.30e-02 5.92e+03 2.12e+01 ... (remaining 3493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 3107 1.37 - 2.75: 1114 2.75 - 4.12: 356 4.12 - 5.49: 79 5.49 - 6.87: 24 Bond angle restraints: 4680 Sorted by residual: angle pdb=" N GLY B 326 " pdb=" CA GLY B 326 " pdb=" C GLY B 326 " ideal model delta sigma weight residual 110.42 117.29 -6.87 1.49e+00 4.50e-01 2.12e+01 angle pdb=" N GLY F 326 " pdb=" CA GLY F 326 " pdb=" C GLY F 326 " ideal model delta sigma weight residual 110.42 117.28 -6.86 1.49e+00 4.50e-01 2.12e+01 angle pdb=" N GLY D 326 " pdb=" CA GLY D 326 " pdb=" C GLY D 326 " ideal model delta sigma weight residual 110.42 117.28 -6.86 1.49e+00 4.50e-01 2.12e+01 angle pdb=" N GLY C 326 " pdb=" CA GLY C 326 " pdb=" C GLY C 326 " ideal model delta sigma weight residual 110.75 116.85 -6.10 1.46e+00 4.69e-01 1.75e+01 angle pdb=" N GLY A 326 " pdb=" CA GLY A 326 " pdb=" C GLY A 326 " ideal model delta sigma weight residual 110.75 116.85 -6.10 1.46e+00 4.69e-01 1.74e+01 ... (remaining 4675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.04: 1803 13.04 - 26.07: 252 26.07 - 39.10: 54 39.10 - 52.13: 18 52.13 - 65.16: 9 Dihedral angle restraints: 2136 sinusoidal: 894 harmonic: 1242 Sorted by residual: dihedral pdb=" CA GLY B 335 " pdb=" C GLY B 335 " pdb=" N GLN B 336 " pdb=" CA GLN B 336 " ideal model delta harmonic sigma weight residual 180.00 158.81 21.19 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA GLY F 335 " pdb=" C GLY F 335 " pdb=" N GLN F 336 " pdb=" CA GLN F 336 " ideal model delta harmonic sigma weight residual 180.00 158.81 21.19 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA GLY D 335 " pdb=" C GLY D 335 " pdb=" N GLN D 336 " pdb=" CA GLN D 336 " ideal model delta harmonic sigma weight residual 180.00 158.83 21.17 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 2133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 250 0.069 - 0.137: 230 0.137 - 0.206: 30 0.206 - 0.274: 9 0.274 - 0.343: 9 Chirality restraints: 528 Sorted by residual: chirality pdb=" CB ILE D 328 " pdb=" CA ILE D 328 " pdb=" CG1 ILE D 328 " pdb=" CG2 ILE D 328 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CB ILE F 328 " pdb=" CA ILE F 328 " pdb=" CG1 ILE F 328 " pdb=" CG2 ILE F 328 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CB ILE B 328 " pdb=" CA ILE B 328 " pdb=" CG1 ILE B 328 " pdb=" CG2 ILE B 328 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 525 not shown) Planarity restraints: 594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 328 " 0.015 2.00e-02 2.50e+03 2.93e-02 8.60e+00 pdb=" C ILE E 328 " -0.051 2.00e-02 2.50e+03 pdb=" O ILE E 328 " 0.019 2.00e-02 2.50e+03 pdb=" N HIS E 329 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 328 " 0.015 2.00e-02 2.50e+03 2.93e-02 8.56e+00 pdb=" C ILE A 328 " -0.051 2.00e-02 2.50e+03 pdb=" O ILE A 328 " 0.019 2.00e-02 2.50e+03 pdb=" N HIS A 329 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 328 " 0.015 2.00e-02 2.50e+03 2.92e-02 8.53e+00 pdb=" C ILE C 328 " -0.051 2.00e-02 2.50e+03 pdb=" O ILE C 328 " 0.019 2.00e-02 2.50e+03 pdb=" N HIS C 329 " 0.017 2.00e-02 2.50e+03 ... (remaining 591 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1162 2.89 - 3.39: 2904 3.39 - 3.89: 5573 3.89 - 4.40: 5962 4.40 - 4.90: 11553 Nonbonded interactions: 27154 Sorted by model distance: nonbonded pdb=" OG SER A 305 " pdb=" N SER C 305 " model vdw 2.388 3.120 nonbonded pdb=" N SER A 305 " pdb=" OG SER E 305 " model vdw 2.388 3.120 nonbonded pdb=" N SER B 305 " pdb=" OG SER D 305 " model vdw 2.399 3.120 nonbonded pdb=" OG SER B 305 " pdb=" N SER F 305 " model vdw 2.399 3.120 nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.409 3.040 ... (remaining 27149 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' } 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: 1.050 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.940 Find NCS groups from input model: 0.120 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:13.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 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 : 0.012 0.101 3498 Z= 0.744 Angle : 1.631 6.866 4680 Z= 1.069 Chirality : 0.097 0.343 528 Planarity : 0.012 0.075 594 Dihedral : 13.672 65.161 1344 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 5.30 % Allowed : 3.03 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.27), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.21), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.007 HIS F 329 PHE 0.036 0.006 PHE B 346 TYR 0.016 0.007 TYR F 310 ARG 0.017 0.003 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.425 Fit side-chains REVERT: A 343 LYS cc_start: 0.8366 (mttm) cc_final: 0.8048 (mtmt) REVERT: A 347 LYS cc_start: 0.8412 (mttt) cc_final: 0.8050 (mptp) REVERT: B 353 LYS cc_start: 0.8991 (mttt) cc_final: 0.8750 (mttp) REVERT: B 369 LYS cc_start: 0.8702 (mttp) cc_final: 0.8486 (mttm) REVERT: C 343 LYS cc_start: 0.8502 (mttm) cc_final: 0.8137 (mtmt) REVERT: D 311 LYS cc_start: 0.8738 (mtmt) cc_final: 0.8339 (ttmt) REVERT: E 343 LYS cc_start: 0.8487 (mttm) cc_final: 0.8209 (mtmt) REVERT: E 347 LYS cc_start: 0.8472 (mttt) cc_final: 0.8137 (mptp) REVERT: F 311 LYS cc_start: 0.8613 (mtmt) cc_final: 0.8183 (ttmt) REVERT: F 349 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8133 (ptp-170) REVERT: F 353 LYS cc_start: 0.9011 (mttt) cc_final: 0.8769 (mttp) outliers start: 21 outliers final: 4 residues processed: 122 average time/residue: 1.5750 time to fit residues: 196.1725 Evaluate side-chains 95 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0470 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN E 362 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3498 Z= 0.265 Angle : 0.655 6.976 4680 Z= 0.333 Chirality : 0.050 0.135 528 Planarity : 0.004 0.032 594 Dihedral : 7.721 57.232 473 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 5.05 % Allowed : 14.90 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 329 PHE 0.007 0.002 PHE A 346 TYR 0.007 0.001 TYR C 310 ARG 0.003 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.477 Fit side-chains REVERT: A 343 LYS cc_start: 0.8449 (mttm) cc_final: 0.8054 (mtmt) REVERT: A 347 LYS cc_start: 0.8394 (mttt) cc_final: 0.7996 (mptp) REVERT: B 311 LYS cc_start: 0.8436 (mtmt) cc_final: 0.7580 (tttt) REVERT: B 372 GLU cc_start: 0.8564 (tt0) cc_final: 0.8329 (tt0) REVERT: C 311 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8168 (mttt) REVERT: C 343 LYS cc_start: 0.8629 (mttm) cc_final: 0.8255 (mtmt) REVERT: C 347 LYS cc_start: 0.8627 (mttp) cc_final: 0.8196 (mptp) REVERT: D 311 LYS cc_start: 0.8669 (mtmt) cc_final: 0.7950 (tttt) REVERT: E 329 HIS cc_start: 0.8795 (t70) cc_final: 0.7788 (m-70) REVERT: E 343 LYS cc_start: 0.8577 (mttm) cc_final: 0.8332 (mtmm) REVERT: E 347 LYS cc_start: 0.8533 (mttt) cc_final: 0.8177 (mptp) REVERT: F 311 LYS cc_start: 0.8596 (mtmt) cc_final: 0.7830 (tttt) REVERT: F 349 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.8116 (ptp-170) REVERT: F 353 LYS cc_start: 0.9102 (mttt) cc_final: 0.8866 (mttp) REVERT: F 369 LYS cc_start: 0.8662 (mttp) cc_final: 0.8374 (mttm) outliers start: 20 outliers final: 9 residues processed: 122 average time/residue: 1.4652 time to fit residues: 182.7535 Evaluate side-chains 108 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 0.3980 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 HIS D 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3498 Z= 0.209 Angle : 0.581 6.616 4680 Z= 0.292 Chirality : 0.048 0.128 528 Planarity : 0.003 0.019 594 Dihedral : 6.514 58.268 469 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 4.04 % Allowed : 18.94 % Favored : 77.02 % 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: -2.06 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.005 0.001 PHE A 346 TYR 0.007 0.002 TYR A 310 ARG 0.003 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.412 Fit side-chains REVERT: A 329 HIS cc_start: 0.8661 (t70) cc_final: 0.7722 (m-70) REVERT: A 343 LYS cc_start: 0.8440 (mttm) cc_final: 0.8083 (mtmt) REVERT: A 347 LYS cc_start: 0.8400 (mttt) cc_final: 0.7972 (mptp) REVERT: A 370 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8494 (ttmp) REVERT: B 311 LYS cc_start: 0.8389 (mtmt) cc_final: 0.7567 (tttt) REVERT: B 317 LYS cc_start: 0.8263 (pttt) cc_final: 0.7886 (ptpp) REVERT: B 372 GLU cc_start: 0.8546 (tt0) cc_final: 0.8282 (tt0) REVERT: C 311 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8144 (mttt) REVERT: C 329 HIS cc_start: 0.8749 (t-90) cc_final: 0.7745 (m90) REVERT: C 343 LYS cc_start: 0.8648 (mttm) cc_final: 0.8272 (mtmt) REVERT: C 347 LYS cc_start: 0.8669 (mttp) cc_final: 0.8206 (mptp) REVERT: D 311 LYS cc_start: 0.8602 (mtmt) cc_final: 0.7927 (tttt) REVERT: E 329 HIS cc_start: 0.8757 (t70) cc_final: 0.7827 (m-70) REVERT: E 343 LYS cc_start: 0.8583 (mttm) cc_final: 0.8330 (mtmm) REVERT: E 347 LYS cc_start: 0.8558 (mttt) cc_final: 0.8179 (mptp) REVERT: F 311 LYS cc_start: 0.8501 (mtmt) cc_final: 0.7764 (tttt) REVERT: F 349 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.8114 (ptp-170) REVERT: F 353 LYS cc_start: 0.9115 (mttt) cc_final: 0.8897 (mttp) REVERT: F 369 LYS cc_start: 0.8650 (mttp) cc_final: 0.8377 (mttm) REVERT: F 379 ARG cc_start: 0.7188 (mpt180) cc_final: 0.6727 (mmt-90) outliers start: 16 outliers final: 9 residues processed: 116 average time/residue: 1.5149 time to fit residues: 179.7367 Evaluate side-chains 107 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 HIS D 351 GLN F 330 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3498 Z= 0.330 Angle : 0.629 6.759 4680 Z= 0.318 Chirality : 0.049 0.128 528 Planarity : 0.003 0.024 594 Dihedral : 6.937 59.813 469 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 5.05 % Allowed : 18.43 % Favored : 76.52 % 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: -2.02 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 329 PHE 0.007 0.002 PHE A 346 TYR 0.011 0.002 TYR E 310 ARG 0.001 0.000 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.426 Fit side-chains REVERT: A 329 HIS cc_start: 0.8629 (t70) cc_final: 0.7681 (m-70) REVERT: A 343 LYS cc_start: 0.8474 (mttm) cc_final: 0.8117 (mtmt) REVERT: A 347 LYS cc_start: 0.8408 (mttt) cc_final: 0.7976 (mptp) REVERT: A 370 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8544 (ttmp) REVERT: B 311 LYS cc_start: 0.8442 (mtmt) cc_final: 0.7614 (tttt) REVERT: B 317 LYS cc_start: 0.8251 (pttt) cc_final: 0.7870 (ptpp) REVERT: B 372 GLU cc_start: 0.8579 (tt0) cc_final: 0.8313 (tt0) REVERT: C 311 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8170 (mttt) REVERT: C 329 HIS cc_start: 0.8734 (t-90) cc_final: 0.7758 (m90) REVERT: C 343 LYS cc_start: 0.8628 (mttm) cc_final: 0.8242 (mtmt) REVERT: C 347 LYS cc_start: 0.8642 (mttp) cc_final: 0.8161 (mptp) REVERT: D 311 LYS cc_start: 0.8677 (mtmt) cc_final: 0.7965 (tttt) REVERT: E 329 HIS cc_start: 0.8804 (t70) cc_final: 0.7868 (m-70) REVERT: E 343 LYS cc_start: 0.8583 (mttm) cc_final: 0.8347 (mtmm) REVERT: E 347 LYS cc_start: 0.8610 (mttt) cc_final: 0.8202 (mptp) REVERT: F 311 LYS cc_start: 0.8538 (mtmt) cc_final: 0.7792 (tttt) REVERT: F 349 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8193 (ptp-170) REVERT: F 379 ARG cc_start: 0.7137 (mpt180) cc_final: 0.6675 (mmt-90) outliers start: 20 outliers final: 12 residues processed: 102 average time/residue: 1.6043 time to fit residues: 167.2216 Evaluate side-chains 107 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 13 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 3498 Z= 0.396 Angle : 0.659 7.078 4680 Z= 0.335 Chirality : 0.049 0.128 528 Planarity : 0.003 0.021 594 Dihedral : 7.164 59.321 469 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 5.05 % Allowed : 18.69 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 329 PHE 0.009 0.002 PHE A 346 TYR 0.011 0.003 TYR E 310 ARG 0.002 0.000 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.408 Fit side-chains REVERT: A 329 HIS cc_start: 0.8668 (t70) cc_final: 0.7686 (m-70) REVERT: A 343 LYS cc_start: 0.8498 (mttm) cc_final: 0.8157 (mtmt) REVERT: A 347 LYS cc_start: 0.8446 (mttt) cc_final: 0.7976 (mptp) REVERT: A 370 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8531 (ttmp) REVERT: B 317 LYS cc_start: 0.8241 (pttt) cc_final: 0.7867 (ptpp) REVERT: B 372 GLU cc_start: 0.8601 (tt0) cc_final: 0.8340 (tt0) REVERT: C 311 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8168 (mttt) REVERT: C 329 HIS cc_start: 0.8712 (t-90) cc_final: 0.7727 (m90) REVERT: C 343 LYS cc_start: 0.8641 (mttm) cc_final: 0.8270 (mtmt) REVERT: C 347 LYS cc_start: 0.8653 (mttp) cc_final: 0.8164 (mptp) REVERT: D 328 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8974 (mp) REVERT: E 329 HIS cc_start: 0.8804 (t70) cc_final: 0.7877 (m-70) REVERT: E 343 LYS cc_start: 0.8590 (mttm) cc_final: 0.8355 (mtmm) REVERT: E 347 LYS cc_start: 0.8607 (mttt) cc_final: 0.8205 (mptp) REVERT: F 311 LYS cc_start: 0.8569 (mtmt) cc_final: 0.7862 (tttt) outliers start: 20 outliers final: 12 residues processed: 106 average time/residue: 1.5367 time to fit residues: 166.5901 Evaluate side-chains 108 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS B 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3498 Z= 0.230 Angle : 0.561 6.082 4680 Z= 0.283 Chirality : 0.047 0.127 528 Planarity : 0.003 0.018 594 Dihedral : 6.027 42.953 465 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 4.55 % Allowed : 18.94 % Favored : 76.52 % 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: -2.00 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.005 0.001 PHE A 346 TYR 0.008 0.002 TYR E 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.612 Fit side-chains REVERT: A 329 HIS cc_start: 0.8684 (t70) cc_final: 0.7711 (m-70) REVERT: A 343 LYS cc_start: 0.8513 (mttm) cc_final: 0.8177 (mtmt) REVERT: A 347 LYS cc_start: 0.8416 (mttt) cc_final: 0.7958 (mptp) REVERT: A 370 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8520 (ttmp) REVERT: B 311 LYS cc_start: 0.8390 (mtmt) cc_final: 0.7600 (tttt) REVERT: B 317 LYS cc_start: 0.8264 (pttt) cc_final: 0.7898 (ptpp) REVERT: B 372 GLU cc_start: 0.8613 (tt0) cc_final: 0.8349 (tt0) REVERT: C 311 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8145 (mttt) REVERT: C 329 HIS cc_start: 0.8667 (t-90) cc_final: 0.7713 (m90) REVERT: C 343 LYS cc_start: 0.8652 (mttm) cc_final: 0.8278 (mtmt) REVERT: D 311 LYS cc_start: 0.8602 (mtmt) cc_final: 0.7889 (tttt) REVERT: D 317 LYS cc_start: 0.8574 (pttp) cc_final: 0.8206 (ptpp) REVERT: D 328 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8964 (mp) REVERT: E 329 HIS cc_start: 0.8792 (t70) cc_final: 0.7865 (m-70) REVERT: E 343 LYS cc_start: 0.8599 (mttm) cc_final: 0.8366 (mtmm) REVERT: E 347 LYS cc_start: 0.8617 (mttt) cc_final: 0.8200 (mptp) REVERT: F 311 LYS cc_start: 0.8494 (mtmt) cc_final: 0.7769 (tttt) REVERT: F 316 SER cc_start: 0.9236 (OUTLIER) cc_final: 0.8981 (p) outliers start: 18 outliers final: 11 residues processed: 107 average time/residue: 1.5207 time to fit residues: 166.3797 Evaluate side-chains 110 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 0.0770 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 0.3980 chunk 16 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 overall best weight: 1.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3498 Z= 0.131 Angle : 0.499 5.129 4680 Z= 0.250 Chirality : 0.047 0.125 528 Planarity : 0.002 0.017 594 Dihedral : 5.263 32.715 465 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 4.04 % Allowed : 19.95 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 362 PHE 0.004 0.001 PHE E 346 TYR 0.006 0.001 TYR A 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.425 Fit side-chains REVERT: A 329 HIS cc_start: 0.8714 (t70) cc_final: 0.7732 (m90) REVERT: A 343 LYS cc_start: 0.8524 (mttm) cc_final: 0.8171 (mtmt) REVERT: A 347 LYS cc_start: 0.8417 (mttt) cc_final: 0.7967 (mptp) REVERT: B 311 LYS cc_start: 0.8300 (mtmt) cc_final: 0.7604 (tttt) REVERT: B 317 LYS cc_start: 0.8265 (pttt) cc_final: 0.7895 (ptpp) REVERT: B 372 GLU cc_start: 0.8568 (tt0) cc_final: 0.8296 (tt0) REVERT: C 311 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8115 (mttt) REVERT: C 329 HIS cc_start: 0.8631 (t-90) cc_final: 0.7698 (m90) REVERT: C 343 LYS cc_start: 0.8658 (mttm) cc_final: 0.8299 (mtmt) REVERT: C 347 LYS cc_start: 0.8665 (mttp) cc_final: 0.8342 (mptt) REVERT: D 311 LYS cc_start: 0.8556 (mtmt) cc_final: 0.7902 (tttt) REVERT: D 317 LYS cc_start: 0.8551 (pttp) cc_final: 0.8205 (ptpp) REVERT: D 328 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8995 (mp) REVERT: E 329 HIS cc_start: 0.8744 (t70) cc_final: 0.7815 (m-70) REVERT: E 343 LYS cc_start: 0.8605 (mttm) cc_final: 0.8385 (mtmm) REVERT: E 347 LYS cc_start: 0.8624 (mttt) cc_final: 0.8218 (mptp) REVERT: F 311 LYS cc_start: 0.8466 (mtmt) cc_final: 0.7793 (tttt) REVERT: F 316 SER cc_start: 0.9220 (OUTLIER) cc_final: 0.8976 (p) outliers start: 16 outliers final: 8 residues processed: 105 average time/residue: 1.3901 time to fit residues: 149.5093 Evaluate side-chains 105 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 3498 Z= 0.409 Angle : 0.642 6.842 4680 Z= 0.328 Chirality : 0.049 0.128 528 Planarity : 0.003 0.020 594 Dihedral : 6.323 44.806 465 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 4.04 % Allowed : 19.19 % Favored : 76.77 % 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: -2.00 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 329 PHE 0.009 0.002 PHE A 346 TYR 0.012 0.003 TYR A 310 ARG 0.001 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.448 Fit side-chains REVERT: A 329 HIS cc_start: 0.8682 (t70) cc_final: 0.7694 (m-70) REVERT: A 343 LYS cc_start: 0.8514 (mttm) cc_final: 0.8182 (mtmt) REVERT: A 347 LYS cc_start: 0.8454 (mttt) cc_final: 0.7976 (mptp) REVERT: A 370 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8520 (ttmp) REVERT: B 311 LYS cc_start: 0.8425 (mtmt) cc_final: 0.7661 (tttt) REVERT: B 317 LYS cc_start: 0.8286 (pttt) cc_final: 0.7914 (ptpp) REVERT: B 372 GLU cc_start: 0.8594 (tt0) cc_final: 0.8324 (tt0) REVERT: C 311 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8141 (mttt) REVERT: C 329 HIS cc_start: 0.8656 (t-90) cc_final: 0.7711 (m90) REVERT: C 343 LYS cc_start: 0.8620 (mttm) cc_final: 0.8245 (mtmt) REVERT: C 347 LYS cc_start: 0.8672 (mttp) cc_final: 0.8327 (mptt) REVERT: D 328 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8972 (mp) REVERT: E 329 HIS cc_start: 0.8830 (t70) cc_final: 0.7887 (m-70) REVERT: E 343 LYS cc_start: 0.8577 (mttm) cc_final: 0.8353 (mtmm) REVERT: E 347 LYS cc_start: 0.8612 (mttt) cc_final: 0.8182 (mptp) REVERT: F 311 LYS cc_start: 0.8555 (mtmt) cc_final: 0.7808 (tttt) REVERT: F 316 SER cc_start: 0.9245 (OUTLIER) cc_final: 0.8987 (p) outliers start: 16 outliers final: 11 residues processed: 104 average time/residue: 1.4790 time to fit residues: 157.2614 Evaluate side-chains 110 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 41 optimal weight: 0.1980 chunk 38 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 overall best weight: 6.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 3498 Z= 0.410 Angle : 0.648 6.680 4680 Z= 0.333 Chirality : 0.050 0.129 528 Planarity : 0.003 0.016 594 Dihedral : 6.457 48.183 465 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 4.55 % Allowed : 18.94 % Favored : 76.52 % 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: -2.09 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 329 PHE 0.008 0.002 PHE A 346 TYR 0.012 0.003 TYR A 310 ARG 0.001 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.449 Fit side-chains REVERT: A 329 HIS cc_start: 0.8675 (t70) cc_final: 0.7674 (m-70) REVERT: A 343 LYS cc_start: 0.8515 (mttm) cc_final: 0.8182 (mtmt) REVERT: A 347 LYS cc_start: 0.8425 (mttt) cc_final: 0.7956 (mptp) REVERT: A 370 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8531 (ttmp) REVERT: B 317 LYS cc_start: 0.8288 (pttt) cc_final: 0.7923 (ptpp) REVERT: B 372 GLU cc_start: 0.8599 (tt0) cc_final: 0.8333 (tt0) REVERT: C 311 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8160 (mttt) REVERT: C 329 HIS cc_start: 0.8660 (t-90) cc_final: 0.7714 (m90) REVERT: C 343 LYS cc_start: 0.8625 (mttm) cc_final: 0.8248 (mtmt) REVERT: C 347 LYS cc_start: 0.8667 (mttp) cc_final: 0.8303 (mptt) REVERT: D 328 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8964 (mp) REVERT: E 329 HIS cc_start: 0.8836 (t70) cc_final: 0.7890 (m-70) REVERT: E 343 LYS cc_start: 0.8569 (mttm) cc_final: 0.8344 (mtmm) REVERT: E 347 LYS cc_start: 0.8611 (mttt) cc_final: 0.8189 (mptp) REVERT: F 311 LYS cc_start: 0.8549 (mtmt) cc_final: 0.7827 (tttt) outliers start: 18 outliers final: 12 residues processed: 103 average time/residue: 1.4596 time to fit residues: 153.8056 Evaluate side-chains 108 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3498 Z= 0.194 Angle : 0.538 5.849 4680 Z= 0.273 Chirality : 0.047 0.127 528 Planarity : 0.002 0.015 594 Dihedral : 5.817 41.354 465 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 3.28 % Allowed : 20.45 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.005 0.001 PHE A 346 TYR 0.008 0.002 TYR A 310 ARG 0.000 0.000 ARG D 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.384 Fit side-chains REVERT: A 329 HIS cc_start: 0.8690 (t70) cc_final: 0.7680 (m90) REVERT: A 343 LYS cc_start: 0.8521 (mttm) cc_final: 0.8165 (mtmt) REVERT: A 347 LYS cc_start: 0.8409 (mttt) cc_final: 0.7944 (mptp) REVERT: B 311 LYS cc_start: 0.8351 (mtmt) cc_final: 0.7600 (tttt) REVERT: B 317 LYS cc_start: 0.8279 (pttt) cc_final: 0.7924 (ptpp) REVERT: B 372 GLU cc_start: 0.8607 (tt0) cc_final: 0.8346 (tt0) REVERT: C 311 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8143 (mttt) REVERT: C 329 HIS cc_start: 0.8639 (t-90) cc_final: 0.7700 (m90) REVERT: C 343 LYS cc_start: 0.8666 (mttm) cc_final: 0.8295 (mtmt) REVERT: C 347 LYS cc_start: 0.8659 (mttp) cc_final: 0.8303 (mptt) REVERT: D 311 LYS cc_start: 0.8600 (mtmt) cc_final: 0.7911 (tttt) REVERT: D 317 LYS cc_start: 0.8563 (pttp) cc_final: 0.8198 (ptpp) REVERT: D 328 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8962 (mp) REVERT: E 329 HIS cc_start: 0.8794 (t70) cc_final: 0.7873 (m-70) REVERT: E 343 LYS cc_start: 0.8572 (mttm) cc_final: 0.8356 (mtmm) REVERT: E 347 LYS cc_start: 0.8603 (mttt) cc_final: 0.8195 (mptp) REVERT: F 311 LYS cc_start: 0.8506 (mtmt) cc_final: 0.7795 (tttt) REVERT: F 316 SER cc_start: 0.9227 (OUTLIER) cc_final: 0.8986 (p) REVERT: F 379 ARG cc_start: 0.7099 (mpt180) cc_final: 0.6587 (mmt-90) outliers start: 13 outliers final: 11 residues processed: 104 average time/residue: 1.4207 time to fit residues: 151.1951 Evaluate side-chains 110 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 0.3980 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.122846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.094378 restraints weight = 3857.398| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.96 r_work: 0.3275 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3498 Z= 0.269 Angle : 0.569 6.094 4680 Z= 0.289 Chirality : 0.048 0.127 528 Planarity : 0.002 0.016 594 Dihedral : 5.918 41.074 465 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.29 % Allowed : 19.44 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 329 PHE 0.006 0.001 PHE A 346 TYR 0.010 0.002 TYR A 310 ARG 0.001 0.000 ARG D 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2729.22 seconds wall clock time: 49 minutes 11.25 seconds (2951.25 seconds total)