Starting phenix.real_space_refine on Fri Aug 22 13:40:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oti_17180/08_2025/8oti_17180.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oti_17180/08_2025/8oti_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 { model { file = "/net/cci-nas-00/data/ceres_data/8oti_17180/08_2025/8oti_17180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oti_17180/08_2025/8oti_17180.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oti_17180/08_2025/8oti_17180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oti_17180/08_2025/8oti_17180.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.07, per 1000 atoms: 0.31 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: 0.27 Conformation dependent library (CDL) restraints added in 138.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.17 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: 0.53 Time building geometry restraints manager: 0.37 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.230 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:9.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.770 ------------------------------------------------------------------------------- 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= 0.786 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 : 3.70 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.63 (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 ARG 0.017 0.003 ARG F 349 TYR 0.016 0.007 TYR F 310 PHE 0.036 0.006 PHE B 346 HIS 0.017 0.007 HIS F 329 Details of bonding type rmsd covalent geometry : bond 0.01198 ( 3498) covalent geometry : angle 1.63061 ( 4680) hydrogen bonds : bond 0.13718 ( 67) hydrogen bonds : angle 6.72720 ( 201) *********************** 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 : 0.106 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: 0.8032 (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: C 347 LYS cc_start: 0.8482 (mttt) cc_final: 0.8195 (mptp) 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: 0.7702 time to fit residues: 95.7200 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 : 0.127 ------------------------------------------------------------------------------- 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 24 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.129908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.100594 restraints weight = 3642.673| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.96 r_work: 0.3280 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2084 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= 0.167 Angle : 0.650 6.868 4680 Z= 0.331 Chirality : 0.050 0.134 528 Planarity : 0.004 0.031 594 Dihedral : 7.678 56.981 473 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 : 5.30 % Allowed : 14.39 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.52 (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 ARG 0.003 0.000 ARG D 349 TYR 0.006 0.001 TYR C 310 PHE 0.006 0.001 PHE A 346 HIS 0.003 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 3498) covalent geometry : angle 0.64980 ( 4680) hydrogen bonds : bond 0.02414 ( 67) hydrogen bonds : angle 5.29005 ( 201) *********************** 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 131 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.166 Fit side-chains REVERT: A 343 LYS cc_start: 0.8279 (mttm) cc_final: 0.7765 (mtmt) REVERT: A 347 LYS cc_start: 0.8094 (mttt) cc_final: 0.7630 (mptp) REVERT: B 311 LYS cc_start: 0.8178 (mtmt) cc_final: 0.7330 (tttt) REVERT: B 372 GLU cc_start: 0.7873 (tt0) cc_final: 0.7573 (tt0) REVERT: C 343 LYS cc_start: 0.8436 (mttm) cc_final: 0.7947 (mtmt) REVERT: C 347 LYS cc_start: 0.8172 (mttt) cc_final: 0.7789 (mptp) REVERT: D 311 LYS cc_start: 0.8431 (mtmt) cc_final: 0.7769 (tttt) REVERT: D 347 LYS cc_start: 0.8535 (mptp) cc_final: 0.8271 (mptm) REVERT: E 329 HIS cc_start: 0.8557 (t70) cc_final: 0.7757 (m-70) REVERT: E 343 LYS cc_start: 0.8515 (mttm) cc_final: 0.8119 (mtmt) REVERT: E 347 LYS cc_start: 0.8117 (mttt) cc_final: 0.7803 (mptp) REVERT: F 311 LYS cc_start: 0.8344 (mtmt) cc_final: 0.7610 (tttt) REVERT: F 349 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7791 (ptp-170) REVERT: F 353 LYS cc_start: 0.8856 (mttt) cc_final: 0.8507 (mttp) REVERT: F 369 LYS cc_start: 0.8529 (mttp) cc_final: 0.8155 (mttm) outliers start: 21 outliers final: 9 residues processed: 122 average time/residue: 0.7171 time to fit residues: 89.3291 Evaluate side-chains 107 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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 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 0 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 11 optimal weight: 8.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- 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 D 351 GLN F 330 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.122534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.093752 restraints weight = 3831.361| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.93 r_work: 0.3245 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2499 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= 0.251 Angle : 0.681 7.679 4680 Z= 0.345 Chirality : 0.050 0.129 528 Planarity : 0.003 0.022 594 Dihedral : 7.305 58.849 469 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 4.55 % Allowed : 18.18 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.20 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 379 TYR 0.010 0.002 TYR A 310 PHE 0.008 0.002 PHE A 346 HIS 0.004 0.001 HIS E 329 Details of bonding type rmsd covalent geometry : bond 0.00585 ( 3498) covalent geometry : angle 0.68085 ( 4680) hydrogen bonds : bond 0.02569 ( 67) hydrogen bonds : angle 5.46933 ( 201) *********************** 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 111 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.150 Fit side-chains REVERT: A 329 HIS cc_start: 0.8370 (t70) cc_final: 0.7424 (m90) REVERT: A 343 LYS cc_start: 0.8193 (mttm) cc_final: 0.7698 (mtmt) REVERT: A 347 LYS cc_start: 0.8074 (mttt) cc_final: 0.7612 (mptp) REVERT: A 370 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8256 (ttmp) REVERT: B 311 LYS cc_start: 0.8205 (mtmt) cc_final: 0.7256 (tttt) REVERT: B 317 LYS cc_start: 0.8035 (pttt) cc_final: 0.7493 (ptpp) REVERT: B 372 GLU cc_start: 0.7975 (tt0) cc_final: 0.7640 (tt0) REVERT: C 311 LYS cc_start: 0.8510 (mtmt) cc_final: 0.7674 (mttt) REVERT: C 329 HIS cc_start: 0.8507 (t70) cc_final: 0.7608 (m90) REVERT: C 343 LYS cc_start: 0.8385 (mttm) cc_final: 0.7860 (mtmt) REVERT: C 347 LYS cc_start: 0.8203 (mttt) cc_final: 0.7791 (mptp) REVERT: D 311 LYS cc_start: 0.8493 (mtmt) cc_final: 0.7717 (tttt) REVERT: E 329 HIS cc_start: 0.8582 (t70) cc_final: 0.7751 (m-70) REVERT: E 343 LYS cc_start: 0.8427 (mttm) cc_final: 0.8016 (mtmm) REVERT: E 347 LYS cc_start: 0.8196 (mttt) cc_final: 0.7756 (mptp) REVERT: F 311 LYS cc_start: 0.8294 (mtmt) cc_final: 0.7505 (tttt) REVERT: F 316 SER cc_start: 0.9224 (OUTLIER) cc_final: 0.8925 (p) REVERT: F 349 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7821 (ptp-170) outliers start: 18 outliers final: 11 residues processed: 104 average time/residue: 0.7347 time to fit residues: 78.0180 Evaluate side-chains 105 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.159 ------------------------------------------------------------------------------- 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 319 THR Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 373 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 330 HIS D 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.123259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.094610 restraints weight = 3821.680| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.93 r_work: 0.3235 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 3498 Z= 0.241 Angle : 0.645 6.994 4680 Z= 0.328 Chirality : 0.049 0.129 528 Planarity : 0.003 0.024 594 Dihedral : 7.158 59.620 469 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 5.30 % Allowed : 17.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.11 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 379 TYR 0.010 0.002 TYR E 310 PHE 0.007 0.002 PHE A 346 HIS 0.004 0.001 HIS E 329 Details of bonding type rmsd covalent geometry : bond 0.00561 ( 3498) covalent geometry : angle 0.64513 ( 4680) hydrogen bonds : bond 0.02417 ( 67) hydrogen bonds : angle 5.48711 ( 201) *********************** 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 113 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.153 Fit side-chains REVERT: A 329 HIS cc_start: 0.8346 (t70) cc_final: 0.7427 (m-70) REVERT: A 343 LYS cc_start: 0.8229 (mttm) cc_final: 0.7735 (mtmt) REVERT: A 347 LYS cc_start: 0.8182 (mttt) cc_final: 0.7623 (mptp) REVERT: A 370 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8238 (ttmp) REVERT: B 311 LYS cc_start: 0.8215 (mtmt) cc_final: 0.7300 (tttt) REVERT: B 317 LYS cc_start: 0.8102 (pttt) cc_final: 0.7577 (ptpp) REVERT: B 372 GLU cc_start: 0.7997 (tt0) cc_final: 0.7639 (tt0) REVERT: C 311 LYS cc_start: 0.8497 (mtmt) cc_final: 0.7619 (mttt) REVERT: C 329 HIS cc_start: 0.8501 (t70) cc_final: 0.7623 (m90) REVERT: C 343 LYS cc_start: 0.8404 (mttm) cc_final: 0.7867 (mtmt) REVERT: C 347 LYS cc_start: 0.8269 (mttt) cc_final: 0.7796 (mptp) REVERT: D 311 LYS cc_start: 0.8473 (mtmt) cc_final: 0.7699 (tttt) REVERT: E 329 HIS cc_start: 0.8584 (t70) cc_final: 0.7772 (m-70) REVERT: E 343 LYS cc_start: 0.8422 (mttm) cc_final: 0.8006 (mtmm) REVERT: E 347 LYS cc_start: 0.8225 (mttt) cc_final: 0.7800 (mptp) REVERT: F 311 LYS cc_start: 0.8294 (mtmt) cc_final: 0.7536 (tttt) REVERT: F 316 SER cc_start: 0.9203 (OUTLIER) cc_final: 0.8924 (p) REVERT: F 349 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7829 (ptp-170) outliers start: 21 outliers final: 11 residues processed: 102 average time/residue: 0.7917 time to fit residues: 82.3810 Evaluate side-chains 106 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.159 ------------------------------------------------------------------------------- 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 319 THR Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 373 THR 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 21 optimal weight: 20.0000 chunk 17 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 6 optimal weight: 0.0570 chunk 36 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 overall best weight: 3.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.124952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.096544 restraints weight = 3847.763| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.94 r_work: 0.3273 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3498 Z= 0.162 Angle : 0.570 6.336 4680 Z= 0.287 Chirality : 0.047 0.127 528 Planarity : 0.003 0.017 594 Dihedral : 6.650 55.883 469 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 4.55 % Allowed : 19.70 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.02 (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 ARG 0.001 0.000 ARG B 379 TYR 0.009 0.002 TYR E 310 PHE 0.006 0.001 PHE A 346 HIS 0.003 0.001 HIS E 329 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 3498) covalent geometry : angle 0.56975 ( 4680) hydrogen bonds : bond 0.02076 ( 67) hydrogen bonds : angle 5.35371 ( 201) *********************** 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 118 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.159 Fit side-chains REVERT: A 329 HIS cc_start: 0.8377 (t70) cc_final: 0.7490 (m-70) REVERT: A 343 LYS cc_start: 0.8261 (mttm) cc_final: 0.7773 (mtmt) REVERT: A 347 LYS cc_start: 0.8171 (mttt) cc_final: 0.7605 (mptp) REVERT: A 370 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8249 (ttmp) REVERT: B 311 LYS cc_start: 0.8137 (mtmt) cc_final: 0.7281 (tttt) REVERT: B 317 LYS cc_start: 0.8097 (pttt) cc_final: 0.7597 (ptpp) REVERT: B 372 GLU cc_start: 0.8019 (tt0) cc_final: 0.7647 (tt0) REVERT: C 311 LYS cc_start: 0.8475 (mtmt) cc_final: 0.7578 (mttt) REVERT: C 329 HIS cc_start: 0.8460 (t70) cc_final: 0.7606 (m90) REVERT: C 343 LYS cc_start: 0.8426 (mttm) cc_final: 0.7893 (mtmt) REVERT: C 347 LYS cc_start: 0.8258 (mttt) cc_final: 0.7798 (mptp) REVERT: D 311 LYS cc_start: 0.8410 (mtmt) cc_final: 0.7654 (tttt) REVERT: D 328 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.8966 (mp) REVERT: E 329 HIS cc_start: 0.8546 (t70) cc_final: 0.7765 (m-70) REVERT: E 343 LYS cc_start: 0.8425 (mttm) cc_final: 0.8007 (mtmm) REVERT: E 347 LYS cc_start: 0.8254 (mttt) cc_final: 0.7818 (mptp) REVERT: F 311 LYS cc_start: 0.8243 (mtmt) cc_final: 0.7489 (tttt) REVERT: F 316 SER cc_start: 0.9200 (OUTLIER) cc_final: 0.8930 (p) REVERT: F 349 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7824 (ptp-170) REVERT: F 379 ARG cc_start: 0.7116 (mpt180) cc_final: 0.6643 (mmt-90) outliers start: 18 outliers final: 9 residues processed: 111 average time/residue: 0.7238 time to fit residues: 82.0775 Evaluate side-chains 112 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.145 ------------------------------------------------------------------------------- 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 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 349 ARG 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 33 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 7 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 362 HIS E 330 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.119664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.090656 restraints weight = 3838.807| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.96 r_work: 0.3195 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 3498 Z= 0.353 Angle : 0.722 8.143 4680 Z= 0.371 Chirality : 0.052 0.144 528 Planarity : 0.003 0.023 594 Dihedral : 7.423 57.776 469 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 4.80 % Allowed : 19.44 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.18 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 379 TYR 0.012 0.003 TYR E 310 PHE 0.010 0.002 PHE A 346 HIS 0.006 0.002 HIS E 329 Details of bonding type rmsd covalent geometry : bond 0.00827 ( 3498) covalent geometry : angle 0.72160 ( 4680) hydrogen bonds : bond 0.02798 ( 67) hydrogen bonds : angle 5.62980 ( 201) *********************** 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 117 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.151 Fit side-chains REVERT: A 329 HIS cc_start: 0.8393 (t70) cc_final: 0.7434 (m-70) REVERT: A 343 LYS cc_start: 0.8244 (mttm) cc_final: 0.7749 (mtmt) REVERT: A 347 LYS cc_start: 0.8210 (mttt) cc_final: 0.7632 (mptp) REVERT: A 370 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8327 (ttmp) REVERT: B 317 LYS cc_start: 0.8086 (pttt) cc_final: 0.7536 (ptpp) REVERT: B 347 LYS cc_start: 0.8121 (mptm) cc_final: 0.7839 (mptm) REVERT: B 372 GLU cc_start: 0.8028 (tt0) cc_final: 0.7665 (tt0) REVERT: C 311 LYS cc_start: 0.8520 (mtmt) cc_final: 0.7662 (mttt) REVERT: C 329 HIS cc_start: 0.8508 (t70) cc_final: 0.7604 (m90) REVERT: C 343 LYS cc_start: 0.8368 (mttm) cc_final: 0.7835 (mtmt) REVERT: C 347 LYS cc_start: 0.8348 (mttt) cc_final: 0.7856 (mptp) REVERT: D 328 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.8951 (mp) REVERT: E 329 HIS cc_start: 0.8605 (t70) cc_final: 0.7764 (m-70) REVERT: E 343 LYS cc_start: 0.8378 (mttm) cc_final: 0.7950 (mtmm) REVERT: E 347 LYS cc_start: 0.8280 (mttt) cc_final: 0.7807 (mptp) REVERT: F 349 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7911 (ptp-170) outliers start: 19 outliers final: 12 residues processed: 109 average time/residue: 0.7444 time to fit residues: 82.8528 Evaluate side-chains 111 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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 319 THR Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 373 THR 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 349 ARG 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 21 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 6 optimal weight: 0.0270 chunk 11 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 overall best weight: 3.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS F 362 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.125438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.097108 restraints weight = 3868.239| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.94 r_work: 0.3269 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3498 Z= 0.165 Angle : 0.576 6.292 4680 Z= 0.291 Chirality : 0.048 0.129 528 Planarity : 0.002 0.018 594 Dihedral : 6.811 57.463 469 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 3.79 % Allowed : 20.96 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.05 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 349 TYR 0.007 0.002 TYR A 310 PHE 0.005 0.001 PHE E 346 HIS 0.003 0.001 HIS E 329 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 3498) covalent geometry : angle 0.57633 ( 4680) hydrogen bonds : bond 0.02081 ( 67) hydrogen bonds : angle 5.33077 ( 201) *********************** 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: 15 poor density : 97 time to evaluate : 0.172 Fit side-chains REVERT: A 329 HIS cc_start: 0.8356 (t70) cc_final: 0.7515 (m-70) REVERT: A 343 LYS cc_start: 0.8330 (mttm) cc_final: 0.7859 (mtmt) REVERT: A 347 LYS cc_start: 0.8211 (mttt) cc_final: 0.7680 (mptp) REVERT: A 370 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8273 (ttmp) REVERT: B 311 LYS cc_start: 0.8201 (mtmt) cc_final: 0.7410 (tttt) REVERT: B 317 LYS cc_start: 0.8203 (pttt) cc_final: 0.7725 (ptpp) REVERT: B 347 LYS cc_start: 0.8189 (mptm) cc_final: 0.7717 (mptp) REVERT: B 372 GLU cc_start: 0.8036 (tt0) cc_final: 0.7682 (tt0) REVERT: C 311 LYS cc_start: 0.8479 (mtmt) cc_final: 0.7629 (mttt) REVERT: C 329 HIS cc_start: 0.8427 (t70) cc_final: 0.7655 (m90) REVERT: C 343 LYS cc_start: 0.8463 (mttm) cc_final: 0.7958 (mtmt) REVERT: C 347 LYS cc_start: 0.8314 (mttt) cc_final: 0.7883 (mptp) REVERT: D 328 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.8974 (mp) REVERT: E 329 HIS cc_start: 0.8531 (t70) cc_final: 0.7797 (m-70) REVERT: E 343 LYS cc_start: 0.8477 (mttm) cc_final: 0.8116 (mtmm) REVERT: E 347 LYS cc_start: 0.8290 (mttt) cc_final: 0.7879 (mptp) REVERT: F 311 LYS cc_start: 0.8286 (mtmt) cc_final: 0.7556 (tttt) REVERT: F 316 SER cc_start: 0.9189 (OUTLIER) cc_final: 0.8932 (p) REVERT: F 349 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7872 (ptp-170) REVERT: F 379 ARG cc_start: 0.7142 (mpt180) cc_final: 0.6609 (mmt-90) outliers start: 15 outliers final: 10 residues processed: 105 average time/residue: 0.7570 time to fit residues: 81.1625 Evaluate side-chains 109 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.149 ------------------------------------------------------------------------------- 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 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 349 ARG 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 13 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 7 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 overall best weight: 5.9188 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.123670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.094997 restraints weight = 3895.016| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.94 r_work: 0.3237 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 3498 Z= 0.250 Angle : 0.638 7.025 4680 Z= 0.325 Chirality : 0.049 0.128 528 Planarity : 0.003 0.019 594 Dihedral : 7.086 59.194 469 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 5.30 % Allowed : 19.19 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.11 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 379 TYR 0.011 0.003 TYR A 310 PHE 0.007 0.002 PHE A 346 HIS 0.005 0.001 HIS E 329 Details of bonding type rmsd covalent geometry : bond 0.00582 ( 3498) covalent geometry : angle 0.63770 ( 4680) hydrogen bonds : bond 0.02403 ( 67) hydrogen bonds : angle 5.38627 ( 201) *********************** 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 116 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.158 Fit side-chains REVERT: A 329 HIS cc_start: 0.8367 (t70) cc_final: 0.7493 (m-70) REVERT: A 343 LYS cc_start: 0.8308 (mttm) cc_final: 0.7837 (mtmt) REVERT: A 347 LYS cc_start: 0.8223 (mttt) cc_final: 0.7691 (mptp) REVERT: A 370 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8288 (ttmp) REVERT: B 317 LYS cc_start: 0.8155 (pttt) cc_final: 0.7697 (ptpp) REVERT: B 347 LYS cc_start: 0.8194 (mptm) cc_final: 0.7738 (mptp) REVERT: B 372 GLU cc_start: 0.8030 (tt0) cc_final: 0.7678 (tt0) REVERT: C 311 LYS cc_start: 0.8518 (mtmt) cc_final: 0.7686 (mttt) REVERT: C 329 HIS cc_start: 0.8444 (t70) cc_final: 0.7662 (m90) REVERT: C 340 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8052 (mtmm) REVERT: C 343 LYS cc_start: 0.8440 (mttm) cc_final: 0.7920 (mtmt) REVERT: C 347 LYS cc_start: 0.8377 (mttt) cc_final: 0.7909 (mptp) REVERT: D 328 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.8975 (mp) REVERT: E 329 HIS cc_start: 0.8592 (t70) cc_final: 0.7859 (m-70) REVERT: E 343 LYS cc_start: 0.8427 (mttm) cc_final: 0.8059 (mtmm) REVERT: E 347 LYS cc_start: 0.8285 (mttt) cc_final: 0.7862 (mptp) REVERT: F 311 LYS cc_start: 0.8371 (mtmt) cc_final: 0.7623 (tttt) REVERT: F 316 SER cc_start: 0.9205 (OUTLIER) cc_final: 0.8936 (p) REVERT: F 349 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7906 (ptp-170) outliers start: 21 outliers final: 11 residues processed: 106 average time/residue: 0.7882 time to fit residues: 85.2488 Evaluate side-chains 111 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.150 ------------------------------------------------------------------------------- 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 340 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 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 349 ARG 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 33 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.122797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.094085 restraints weight = 3852.040| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.95 r_work: 0.3227 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.3101 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= 0.261 Angle : 0.653 7.022 4680 Z= 0.332 Chirality : 0.049 0.128 528 Planarity : 0.003 0.018 594 Dihedral : 7.170 59.444 469 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.29 % Allowed : 20.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.15 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 379 TYR 0.011 0.003 TYR A 310 PHE 0.007 0.002 PHE A 346 HIS 0.005 0.001 HIS E 329 Details of bonding type rmsd covalent geometry : bond 0.00607 ( 3498) covalent geometry : angle 0.65257 ( 4680) hydrogen bonds : bond 0.02462 ( 67) hydrogen bonds : angle 5.38621 ( 201) *********************** 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 112 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.156 Fit side-chains REVERT: A 329 HIS cc_start: 0.8385 (t70) cc_final: 0.7441 (m-70) REVERT: A 343 LYS cc_start: 0.8266 (mttm) cc_final: 0.7787 (mtmt) REVERT: A 347 LYS cc_start: 0.8217 (mttt) cc_final: 0.7651 (mptp) REVERT: A 370 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8267 (ttmp) REVERT: B 317 LYS cc_start: 0.8092 (pttt) cc_final: 0.7610 (ptpp) REVERT: B 372 GLU cc_start: 0.8020 (tt0) cc_final: 0.7648 (tt0) REVERT: C 311 LYS cc_start: 0.8495 (mtmt) cc_final: 0.7638 (mttt) REVERT: C 329 HIS cc_start: 0.8428 (t70) cc_final: 0.7588 (m90) REVERT: C 340 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7994 (mtmm) REVERT: C 343 LYS cc_start: 0.8395 (mttm) cc_final: 0.7866 (mtmt) REVERT: C 347 LYS cc_start: 0.8365 (mttt) cc_final: 0.7866 (mptp) REVERT: D 328 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.8963 (mp) REVERT: E 329 HIS cc_start: 0.8616 (t70) cc_final: 0.7804 (m-70) REVERT: E 343 LYS cc_start: 0.8397 (mttm) cc_final: 0.8027 (mtmm) REVERT: E 347 LYS cc_start: 0.8285 (mttt) cc_final: 0.7813 (mptp) REVERT: F 311 LYS cc_start: 0.8319 (mtmt) cc_final: 0.7533 (tttt) REVERT: F 316 SER cc_start: 0.9192 (OUTLIER) cc_final: 0.8902 (p) REVERT: F 349 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7900 (ptp-170) outliers start: 17 outliers final: 12 residues processed: 104 average time/residue: 0.7683 time to fit residues: 81.5231 Evaluate side-chains 112 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.159 ------------------------------------------------------------------------------- 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 319 THR Chi-restraints excluded: chain C residue 340 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 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 349 ARG 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 34 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 35 optimal weight: 0.4980 chunk 32 optimal weight: 10.0000 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN D 362 HIS F 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.126243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.098007 restraints weight = 3861.590| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.94 r_work: 0.3285 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3498 Z= 0.129 Angle : 0.545 6.045 4680 Z= 0.274 Chirality : 0.047 0.129 528 Planarity : 0.003 0.020 594 Dihedral : 6.528 55.154 469 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.28 % Allowed : 21.46 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.99 (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 ARG 0.001 0.000 ARG F 349 TYR 0.008 0.002 TYR E 310 PHE 0.004 0.001 PHE E 346 HIS 0.002 0.001 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 3498) covalent geometry : angle 0.54450 ( 4680) hydrogen bonds : bond 0.01921 ( 67) hydrogen bonds : angle 5.18784 ( 201) ********************** 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 108 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.138 Fit side-chains REVERT: A 329 HIS cc_start: 0.8374 (t70) cc_final: 0.7532 (m-70) REVERT: A 343 LYS cc_start: 0.8336 (mttm) cc_final: 0.7867 (mtmt) REVERT: A 347 LYS cc_start: 0.8224 (mttt) cc_final: 0.7690 (mptp) REVERT: A 370 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8303 (ttmp) REVERT: B 311 LYS cc_start: 0.8165 (mtmt) cc_final: 0.7382 (tttt) REVERT: B 317 LYS cc_start: 0.8200 (pttt) cc_final: 0.7737 (ptpp) REVERT: B 347 LYS cc_start: 0.8182 (mptm) cc_final: 0.7699 (mptp) REVERT: B 372 GLU cc_start: 0.8050 (tt0) cc_final: 0.7701 (tt0) REVERT: C 311 LYS cc_start: 0.8457 (mtmt) cc_final: 0.8173 (pttt) REVERT: C 329 HIS cc_start: 0.8399 (t70) cc_final: 0.7628 (m90) REVERT: C 343 LYS cc_start: 0.8442 (mttm) cc_final: 0.7937 (mtmt) REVERT: C 347 LYS cc_start: 0.8333 (mttt) cc_final: 0.7881 (mptp) REVERT: D 311 LYS cc_start: 0.8416 (mtmt) cc_final: 0.7742 (tttt) REVERT: D 328 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.9007 (mp) REVERT: E 329 HIS cc_start: 0.8510 (t70) cc_final: 0.7779 (m-70) REVERT: E 343 LYS cc_start: 0.8448 (mttm) cc_final: 0.8099 (mtmm) REVERT: E 347 LYS cc_start: 0.8280 (mttt) cc_final: 0.7862 (mptp) REVERT: F 311 LYS cc_start: 0.8279 (mtmt) cc_final: 0.7565 (tttt) REVERT: F 316 SER cc_start: 0.9193 (OUTLIER) cc_final: 0.8939 (p) REVERT: F 349 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7862 (ptp-170) outliers start: 13 outliers final: 9 residues processed: 103 average time/residue: 0.7775 time to fit residues: 81.7597 Evaluate side-chains 108 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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 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 349 ARG 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 1 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.123817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.095095 restraints weight = 3890.329| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.95 r_work: 0.3237 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 3498 Z= 0.244 Angle : 0.634 7.056 4680 Z= 0.323 Chirality : 0.049 0.129 528 Planarity : 0.003 0.020 594 Dihedral : 6.978 57.619 469 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.04 % Allowed : 20.20 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.08 (0.32), 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 ARG 0.001 0.000 ARG F 379 TYR 0.011 0.003 TYR A 310 PHE 0.008 0.002 PHE A 346 HIS 0.005 0.001 HIS E 329 Details of bonding type rmsd covalent geometry : bond 0.00569 ( 3498) covalent geometry : angle 0.63404 ( 4680) hydrogen bonds : bond 0.02391 ( 67) hydrogen bonds : angle 5.31099 ( 201) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2074.22 seconds wall clock time: 36 minutes 10.42 seconds (2170.42 seconds total)