Starting phenix.real_space_refine on Tue Mar 3 14:10:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nrv_12551/03_2026/7nrv_12551.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nrv_12551/03_2026/7nrv_12551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nrv_12551/03_2026/7nrv_12551.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nrv_12551/03_2026/7nrv_12551.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nrv_12551/03_2026/7nrv_12551.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nrv_12551/03_2026/7nrv_12551.map" } resolution = 3.0 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= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 3670 2.51 5 N 1080 2.21 5 O 1110 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5870 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "F" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "B" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "C" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "D" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "E" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "G" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "H" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "I" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "J" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Time building chain proxies: 1.40, per 1000 atoms: 0.24 Number of scatterers: 5870 At special positions: 0 Unit cell: (155.25, 71.3, 44.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 1110 8.00 N 1080 7.00 C 3670 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: 0.33 Conformation dependent library (CDL) restraints added in 304.7 milliseconds 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1340 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 39.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.211A pdb=" N VAL B 306 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL D 309 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE B 308 " --> pdb=" O VAL D 309 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL A 306 " --> pdb=" O GLN I 307 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL I 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE A 308 " --> pdb=" O VAL I 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.913A pdb=" N VAL A 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL G 313 " --> pdb=" O ASP I 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 321 removed outlier: 6.183A pdb=" N VAL B 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N LYS D 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N SER B 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 326 removed outlier: 6.433A pdb=" N LEU A 325 " --> pdb=" O GLY I 326 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 329 through 330 removed outlier: 6.448A pdb=" N HIS A 329 " --> pdb=" O HIS D 330 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N HIS G 329 " --> pdb=" O HIS I 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 337 through 340 removed outlier: 6.302A pdb=" N GLU A 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLU G 338 " --> pdb=" O VAL I 339 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 343 through 356 removed outlier: 6.468A pdb=" N LEU B 344 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LYS D 347 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N PHE B 346 " --> pdb=" O LYS D 347 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ARG D 349 " --> pdb=" O PHE B 346 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ASP B 348 " --> pdb=" O ARG D 349 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N GLN D 351 " --> pdb=" O ASP B 348 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL B 350 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N LYS D 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N SER B 352 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N GLY D 355 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ILE B 354 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP D 348 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG A 349 " --> pdb=" O ASP D 348 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY A 355 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER D 356 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU A 344 " --> pdb=" O ASP I 345 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LYS I 347 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N PHE A 346 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ARG I 349 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ASP A 348 " --> pdb=" O ARG I 349 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N GLN I 351 " --> pdb=" O ASP A 348 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL A 350 " --> pdb=" O GLN I 351 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LYS I 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N SER A 352 " --> pdb=" O LYS I 353 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N GLY I 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ILE A 354 " --> pdb=" O GLY I 355 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASP I 348 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ARG G 349 " --> pdb=" O ASP I 348 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLY G 355 " --> pdb=" O ILE I 354 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N SER I 356 " --> pdb=" O GLY G 355 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 359 through 362 removed outlier: 6.438A pdb=" N ILE A 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASN A 359 " --> pdb=" O ILE I 360 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N HIS I 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N THR A 361 " --> pdb=" O HIS I 362 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE G 360 " --> pdb=" O THR I 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 374 through 378 removed outlier: 6.491A pdb=" N LYS A 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N PHE D 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N THR A 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS G 375 " --> pdb=" O LEU I 376 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N PHE I 378 " --> pdb=" O LYS G 375 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N THR G 377 " --> pdb=" O PHE I 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.684A pdb=" N GLN F 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N TYR E 310 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL F 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N VAL F 306 " --> pdb=" O GLN J 307 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N VAL J 309 " --> pdb=" O VAL F 306 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE F 308 " --> pdb=" O VAL J 309 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLN H 307 " --> pdb=" O ILE J 308 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N TYR J 310 " --> pdb=" O GLN H 307 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL H 309 " --> pdb=" O TYR J 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.723A pdb=" N VAL F 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL H 313 " --> pdb=" O ASP J 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 317 through 319 removed outlier: 6.228A pdb=" N VAL C 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL F 318 " --> pdb=" O THR J 319 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.690A pdb=" N ILE C 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE F 328 " --> pdb=" O HIS J 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 337 through 340 removed outlier: 6.430A pdb=" N VAL C 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N LYS E 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL C 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU F 338 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL F 337 " --> pdb=" O GLU J 338 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N LYS J 340 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL F 339 " --> pdb=" O LYS J 340 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 343 through 351 removed outlier: 6.275A pdb=" N LEU C 344 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LYS E 347 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N PHE C 346 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ARG E 349 " --> pdb=" O PHE C 346 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ASP C 348 " --> pdb=" O ARG E 349 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N GLN E 351 " --> pdb=" O ASP C 348 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL C 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASP E 348 " --> pdb=" O LYS F 347 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ARG F 349 " --> pdb=" O ASP E 348 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU F 344 " --> pdb=" O ASP J 345 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LYS J 347 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N PHE F 346 " --> pdb=" O LYS J 347 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ARG J 349 " --> pdb=" O PHE F 346 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ASP F 348 " --> pdb=" O ARG J 349 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N GLN J 351 " --> pdb=" O ASP F 348 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL F 350 " --> pdb=" O GLN J 351 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ASP J 348 " --> pdb=" O LYS H 347 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ARG H 349 " --> pdb=" O ASP J 348 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 355 through 356 removed outlier: 6.695A pdb=" N GLY C 355 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLY F 355 " --> pdb=" O SER J 356 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 359 through 362 removed outlier: 6.559A pdb=" N ASN C 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N HIS E 362 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N THR C 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 374 through 378 removed outlier: 6.488A pdb=" N LYS F 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N PHE E 378 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N THR F 377 " --> pdb=" O PHE E 378 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS H 375 " --> pdb=" O LEU J 376 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N PHE J 378 " --> pdb=" O LYS H 375 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N THR H 377 " --> pdb=" O PHE J 378 " (cutoff:3.500A) 107 hydrogen bonds defined for protein. 321 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.04 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 990 1.31 - 1.43: 1380 1.43 - 1.56: 3580 1.56 - 1.68: 0 1.68 - 1.80: 10 Bond restraints: 5960 Sorted by residual: bond pdb=" CG GLN E 336 " pdb=" CD GLN E 336 " ideal model delta sigma weight residual 1.516 1.436 0.080 2.50e-02 1.60e+03 1.03e+01 bond pdb=" CG GLN H 336 " pdb=" CD GLN H 336 " ideal model delta sigma weight residual 1.516 1.436 0.080 2.50e-02 1.60e+03 1.03e+01 bond pdb=" CG GLN J 336 " pdb=" CD GLN J 336 " ideal model delta sigma weight residual 1.516 1.436 0.080 2.50e-02 1.60e+03 1.02e+01 bond pdb=" CG GLN C 336 " pdb=" CD GLN C 336 " ideal model delta sigma weight residual 1.516 1.436 0.080 2.50e-02 1.60e+03 1.02e+01 bond pdb=" CG GLN F 336 " pdb=" CD GLN F 336 " ideal model delta sigma weight residual 1.516 1.436 0.080 2.50e-02 1.60e+03 1.01e+01 ... (remaining 5955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 7723 2.54 - 5.07: 177 5.07 - 7.61: 35 7.61 - 10.14: 25 10.14 - 12.68: 10 Bond angle restraints: 7970 Sorted by residual: angle pdb=" CB GLN J 336 " pdb=" CG GLN J 336 " pdb=" CD GLN J 336 " ideal model delta sigma weight residual 112.60 122.72 -10.12 1.70e+00 3.46e-01 3.54e+01 angle pdb=" CB GLN C 336 " pdb=" CG GLN C 336 " pdb=" CD GLN C 336 " ideal model delta sigma weight residual 112.60 122.71 -10.11 1.70e+00 3.46e-01 3.54e+01 angle pdb=" CB GLN H 336 " pdb=" CG GLN H 336 " pdb=" CD GLN H 336 " ideal model delta sigma weight residual 112.60 122.69 -10.09 1.70e+00 3.46e-01 3.52e+01 angle pdb=" CB GLN F 336 " pdb=" CG GLN F 336 " pdb=" CD GLN F 336 " ideal model delta sigma weight residual 112.60 122.68 -10.08 1.70e+00 3.46e-01 3.52e+01 angle pdb=" CB GLN E 336 " pdb=" CG GLN E 336 " pdb=" CD GLN E 336 " ideal model delta sigma weight residual 112.60 122.67 -10.07 1.70e+00 3.46e-01 3.51e+01 ... (remaining 7965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.82: 3146 13.82 - 27.63: 384 27.63 - 41.45: 65 41.45 - 55.27: 30 55.27 - 69.09: 5 Dihedral angle restraints: 3630 sinusoidal: 1520 harmonic: 2110 Sorted by residual: dihedral pdb=" CD ARG A 379 " pdb=" NE ARG A 379 " pdb=" CZ ARG A 379 " pdb=" NH1 ARG A 379 " ideal model delta sinusoidal sigma weight residual 0.00 -45.09 45.09 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CD ARG B 379 " pdb=" NE ARG B 379 " pdb=" CZ ARG B 379 " pdb=" NH1 ARG B 379 " ideal model delta sinusoidal sigma weight residual 0.00 -45.06 45.06 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CD ARG I 379 " pdb=" NE ARG I 379 " pdb=" CZ ARG I 379 " pdb=" NH1 ARG I 379 " ideal model delta sinusoidal sigma weight residual 0.00 -45.06 45.06 1 1.00e+01 1.00e-02 2.82e+01 ... (remaining 3627 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.111: 816 0.111 - 0.221: 64 0.221 - 0.332: 5 0.332 - 0.442: 0 0.442 - 0.552: 5 Chirality restraints: 890 Sorted by residual: chirality pdb=" CG LEU B 344 " pdb=" CB LEU B 344 " pdb=" CD1 LEU B 344 " pdb=" CD2 LEU B 344 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.62e+00 chirality pdb=" CG LEU A 344 " pdb=" CB LEU A 344 " pdb=" CD1 LEU A 344 " pdb=" CD2 LEU A 344 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.53e+00 chirality pdb=" CG LEU I 344 " pdb=" CB LEU I 344 " pdb=" CD1 LEU I 344 " pdb=" CD2 LEU I 344 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.53e+00 ... (remaining 887 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 379 " 0.776 9.50e-02 1.11e+02 3.48e-01 7.35e+01 pdb=" NE ARG A 379 " -0.046 2.00e-02 2.50e+03 pdb=" CZ ARG A 379 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 379 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 379 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 379 " 0.776 9.50e-02 1.11e+02 3.48e-01 7.35e+01 pdb=" NE ARG B 379 " -0.046 2.00e-02 2.50e+03 pdb=" CZ ARG B 379 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 379 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 379 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 379 " 0.776 9.50e-02 1.11e+02 3.48e-01 7.35e+01 pdb=" NE ARG I 379 " -0.046 2.00e-02 2.50e+03 pdb=" CZ ARG I 379 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG I 379 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG I 379 " 0.023 2.00e-02 2.50e+03 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 2024 2.89 - 3.39: 4719 3.39 - 3.89: 10111 3.89 - 4.40: 10378 4.40 - 4.90: 22082 Nonbonded interactions: 49314 Sorted by model distance: nonbonded pdb=" NZ LYS I 370 " pdb=" OE2 GLU I 372 " model vdw 2.385 3.120 nonbonded pdb=" NZ LYS A 370 " pdb=" OE2 GLU A 372 " model vdw 2.385 3.120 nonbonded pdb=" NZ LYS B 370 " pdb=" OE2 GLU B 372 " model vdw 2.385 3.120 nonbonded pdb=" NZ LYS D 370 " pdb=" OE2 GLU D 372 " model vdw 2.385 3.120 nonbonded pdb=" NZ LYS G 370 " pdb=" OE2 GLU G 372 " model vdw 2.386 3.120 ... (remaining 49309 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.210 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 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 : 0.007 0.080 5960 Z= 0.308 Angle : 1.149 12.675 7970 Z= 0.557 Chirality : 0.074 0.552 890 Planarity : 0.025 0.348 1020 Dihedral : 12.811 69.085 2290 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 are not related in a simple way. whole: -3.05 (0.26), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 379 TYR 0.008 0.003 TYR A 310 PHE 0.014 0.005 PHE E 346 HIS 0.003 0.001 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00705 ( 5960) covalent geometry : angle 1.14862 ( 7970) hydrogen bonds : bond 0.10997 ( 107) hydrogen bonds : angle 8.19003 ( 321) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.225 Fit side-chains REVERT: F 315 LEU cc_start: 0.8087 (mp) cc_final: 0.7787 (tt) REVERT: B 321 LYS cc_start: 0.7958 (mttt) cc_final: 0.7742 (tttm) REVERT: B 356 SER cc_start: 0.9066 (p) cc_final: 0.8684 (p) REVERT: C 315 LEU cc_start: 0.8344 (mp) cc_final: 0.8071 (tt) REVERT: D 315 LEU cc_start: 0.7912 (mp) cc_final: 0.7684 (tt) REVERT: G 315 LEU cc_start: 0.8060 (mp) cc_final: 0.7769 (tt) REVERT: I 315 LEU cc_start: 0.8116 (mp) cc_final: 0.7895 (tt) REVERT: J 353 LYS cc_start: 0.8839 (tttt) cc_final: 0.8584 (tttp) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.5556 time to fit residues: 54.0825 Evaluate side-chains 77 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 368 ASN B 368 ASN C 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.151110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.117055 restraints weight = 6675.246| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 2.60 r_work: 0.3908 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3787 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5960 Z= 0.196 Angle : 0.685 11.906 7970 Z= 0.326 Chirality : 0.051 0.148 890 Planarity : 0.004 0.033 1020 Dihedral : 5.758 17.358 790 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.75 % Allowed : 8.96 % Favored : 90.30 % 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 are not related in a simple way. whole: -2.87 (0.26), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 379 TYR 0.015 0.003 TYR D 310 PHE 0.007 0.002 PHE J 346 HIS 0.003 0.001 HIS G 330 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 5960) covalent geometry : angle 0.68486 ( 7970) hydrogen bonds : bond 0.02426 ( 107) hydrogen bonds : angle 5.26866 ( 321) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.233 Fit side-chains REVERT: A 321 LYS cc_start: 0.7863 (mttt) cc_final: 0.6970 (ttpp) REVERT: A 358 ASP cc_start: 0.8556 (m-30) cc_final: 0.8337 (m-30) REVERT: F 331 LYS cc_start: 0.8866 (ttmm) cc_final: 0.8465 (mtpt) REVERT: B 321 LYS cc_start: 0.8259 (mttt) cc_final: 0.7229 (tttp) REVERT: B 361 THR cc_start: 0.9236 (m) cc_final: 0.9006 (m) REVERT: B 368 ASN cc_start: 0.8904 (m110) cc_final: 0.8600 (m-40) REVERT: B 369 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8132 (mttm) REVERT: C 315 LEU cc_start: 0.8248 (mp) cc_final: 0.7792 (tt) REVERT: C 331 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8642 (mtpt) REVERT: C 342 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7611 (mm-30) REVERT: D 315 LEU cc_start: 0.7898 (mp) cc_final: 0.7390 (tt) REVERT: E 315 LEU cc_start: 0.7642 (mp) cc_final: 0.7178 (tt) REVERT: E 331 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8335 (mtpt) REVERT: G 315 LEU cc_start: 0.8384 (mp) cc_final: 0.7836 (tt) REVERT: G 336 GLN cc_start: 0.8970 (tp40) cc_final: 0.8763 (tp40) REVERT: H 331 LYS cc_start: 0.8976 (ttmm) cc_final: 0.8664 (mtmt) REVERT: H 359 ASN cc_start: 0.8981 (m-40) cc_final: 0.8781 (m-40) REVERT: I 315 LEU cc_start: 0.8317 (mp) cc_final: 0.7928 (tt) REVERT: J 331 LYS cc_start: 0.8892 (ttmt) cc_final: 0.8482 (ttmm) REVERT: J 353 LYS cc_start: 0.8717 (tttt) cc_final: 0.8485 (tttm) outliers start: 5 outliers final: 1 residues processed: 78 average time/residue: 0.5681 time to fit residues: 46.3786 Evaluate side-chains 77 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain G residue 357 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 23 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.151881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.118154 restraints weight = 6561.037| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 2.58 r_work: 0.3922 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3801 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 5960 Z= 0.170 Angle : 0.632 12.213 7970 Z= 0.300 Chirality : 0.049 0.118 890 Planarity : 0.003 0.023 1020 Dihedral : 5.400 14.955 790 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.04 % Allowed : 12.09 % Favored : 86.87 % 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 are not related in a simple way. whole: -2.85 (0.26), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.011 0.003 TYR B 310 PHE 0.005 0.002 PHE I 346 HIS 0.002 0.001 HIS I 330 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 5960) covalent geometry : angle 0.63157 ( 7970) hydrogen bonds : bond 0.01942 ( 107) hydrogen bonds : angle 4.62963 ( 321) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.232 Fit side-chains REVERT: A 315 LEU cc_start: 0.7786 (tt) cc_final: 0.7260 (mp) REVERT: A 321 LYS cc_start: 0.7953 (mttt) cc_final: 0.7053 (ttpp) REVERT: F 331 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8508 (mtpt) REVERT: F 353 LYS cc_start: 0.8788 (ttpt) cc_final: 0.8578 (ttpp) REVERT: B 321 LYS cc_start: 0.8276 (mttt) cc_final: 0.7180 (tttm) REVERT: B 361 THR cc_start: 0.9216 (m) cc_final: 0.8988 (m) REVERT: B 369 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8117 (mttm) REVERT: C 331 LYS cc_start: 0.9170 (ttmt) cc_final: 0.8561 (mtpt) REVERT: C 342 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7701 (mm-30) REVERT: E 315 LEU cc_start: 0.7671 (mp) cc_final: 0.7183 (tt) REVERT: G 311 LYS cc_start: 0.8323 (tmtt) cc_final: 0.7755 (ttpt) REVERT: H 331 LYS cc_start: 0.8977 (ttmm) cc_final: 0.8710 (mtmt) REVERT: H 336 GLN cc_start: 0.9073 (tp40) cc_final: 0.8830 (tp40) REVERT: J 331 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8440 (mtmt) REVERT: J 349 ARG cc_start: 0.7374 (mtm180) cc_final: 0.6237 (mmm160) REVERT: J 353 LYS cc_start: 0.8737 (tttt) cc_final: 0.8493 (tttm) outliers start: 7 outliers final: 4 residues processed: 82 average time/residue: 0.5750 time to fit residues: 49.3686 Evaluate side-chains 83 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain J residue 331 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 12 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 368 ASN I 336 GLN I 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.152396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.118766 restraints weight = 6649.798| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 2.55 r_work: 0.3864 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 5960 Z= 0.227 Angle : 0.666 12.669 7970 Z= 0.321 Chirality : 0.050 0.128 890 Planarity : 0.003 0.022 1020 Dihedral : 5.475 16.120 790 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.49 % Allowed : 13.73 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.26), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 349 TYR 0.014 0.003 TYR B 310 PHE 0.006 0.002 PHE E 378 HIS 0.003 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00504 ( 5960) covalent geometry : angle 0.66635 ( 7970) hydrogen bonds : bond 0.01939 ( 107) hydrogen bonds : angle 4.48549 ( 321) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.233 Fit side-chains REVERT: A 315 LEU cc_start: 0.7806 (tt) cc_final: 0.7282 (mp) REVERT: A 321 LYS cc_start: 0.8108 (mttt) cc_final: 0.7238 (ttpp) REVERT: F 331 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8653 (mtpt) REVERT: B 315 LEU cc_start: 0.8355 (tt) cc_final: 0.7852 (mp) REVERT: B 321 LYS cc_start: 0.8371 (mttt) cc_final: 0.7300 (tttm) REVERT: B 369 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8141 (mttm) REVERT: C 331 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8643 (mtpt) REVERT: C 342 GLU cc_start: 0.8431 (mm-30) cc_final: 0.7800 (mm-30) REVERT: E 315 LEU cc_start: 0.7753 (mp) cc_final: 0.7259 (tt) REVERT: E 331 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8397 (mtpt) REVERT: E 349 ARG cc_start: 0.7446 (mtm180) cc_final: 0.6508 (mmm160) REVERT: G 311 LYS cc_start: 0.8357 (tmtt) cc_final: 0.7824 (ttpt) REVERT: H 315 LEU cc_start: 0.8360 (tt) cc_final: 0.7722 (mp) REVERT: H 331 LYS cc_start: 0.9002 (ttmm) cc_final: 0.8772 (mtmt) REVERT: H 336 GLN cc_start: 0.9174 (tp40) cc_final: 0.8892 (tp40) REVERT: J 331 LYS cc_start: 0.8978 (ttmt) cc_final: 0.8674 (ttmm) REVERT: J 349 ARG cc_start: 0.7518 (mtm180) cc_final: 0.6371 (mmm160) REVERT: J 353 LYS cc_start: 0.8813 (tttt) cc_final: 0.8529 (tttt) outliers start: 10 outliers final: 4 residues processed: 83 average time/residue: 0.5623 time to fit residues: 48.9395 Evaluate side-chains 87 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain J residue 357 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 10 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 62 optimal weight: 0.6980 chunk 11 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 368 ASN B 368 ASN G 368 ASN I 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.150727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.116415 restraints weight = 6752.768| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.59 r_work: 0.3844 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3722 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 5960 Z= 0.265 Angle : 0.680 9.296 7970 Z= 0.335 Chirality : 0.050 0.140 890 Planarity : 0.003 0.021 1020 Dihedral : 5.567 16.766 790 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.94 % Allowed : 14.33 % Favored : 83.73 % 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 are not related in a simple way. whole: -2.80 (0.26), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 349 TYR 0.016 0.004 TYR B 310 PHE 0.008 0.002 PHE E 378 HIS 0.003 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00592 ( 5960) covalent geometry : angle 0.67958 ( 7970) hydrogen bonds : bond 0.01927 ( 107) hydrogen bonds : angle 4.46754 ( 321) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.205 Fit side-chains REVERT: A 315 LEU cc_start: 0.7694 (tt) cc_final: 0.7225 (mp) REVERT: A 321 LYS cc_start: 0.8092 (mttt) cc_final: 0.7202 (ttpp) REVERT: F 331 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8631 (mtpt) REVERT: B 315 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7815 (mp) REVERT: B 321 LYS cc_start: 0.8337 (mttt) cc_final: 0.7251 (tttm) REVERT: B 342 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.6619 (mp0) REVERT: B 369 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8229 (mttm) REVERT: C 331 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8663 (mtpt) REVERT: C 342 GLU cc_start: 0.8455 (mm-30) cc_final: 0.7831 (mm-30) REVERT: E 315 LEU cc_start: 0.7871 (mp) cc_final: 0.7406 (tt) REVERT: E 321 LYS cc_start: 0.8082 (mttt) cc_final: 0.7669 (mttp) REVERT: E 331 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8335 (mtpt) REVERT: E 349 ARG cc_start: 0.7450 (mtm180) cc_final: 0.6481 (mmm160) REVERT: G 311 LYS cc_start: 0.8420 (tmtt) cc_final: 0.7857 (ttpt) REVERT: H 315 LEU cc_start: 0.8348 (tt) cc_final: 0.7798 (mp) REVERT: H 331 LYS cc_start: 0.9036 (ttmm) cc_final: 0.8797 (mtmt) REVERT: H 336 GLN cc_start: 0.9188 (tp40) cc_final: 0.8925 (tp40) REVERT: I 342 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7659 (mm-30) REVERT: J 331 LYS cc_start: 0.8989 (ttmt) cc_final: 0.8688 (ttmm) REVERT: J 349 ARG cc_start: 0.7411 (mtm180) cc_final: 0.6406 (mmm160) REVERT: J 353 LYS cc_start: 0.8736 (tttt) cc_final: 0.8443 (tttt) outliers start: 13 outliers final: 4 residues processed: 85 average time/residue: 0.5436 time to fit residues: 48.3365 Evaluate side-chains 91 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain J residue 357 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 50 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 368 ASN B 368 ASN J 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.151423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.117432 restraints weight = 6662.025| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.57 r_work: 0.3855 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3732 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 5960 Z= 0.235 Angle : 0.650 8.229 7970 Z= 0.319 Chirality : 0.050 0.141 890 Planarity : 0.003 0.020 1020 Dihedral : 5.472 16.491 790 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.69 % Allowed : 15.07 % Favored : 82.24 % 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 are not related in a simple way. whole: -2.75 (0.26), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 349 TYR 0.014 0.003 TYR D 310 PHE 0.006 0.002 PHE J 378 HIS 0.002 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00522 ( 5960) covalent geometry : angle 0.65039 ( 7970) hydrogen bonds : bond 0.01814 ( 107) hydrogen bonds : angle 4.43436 ( 321) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.235 Fit side-chains REVERT: A 315 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7236 (mp) REVERT: A 321 LYS cc_start: 0.8097 (mttt) cc_final: 0.7198 (tttp) REVERT: F 331 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8639 (mtpt) REVERT: B 315 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7871 (mp) REVERT: B 321 LYS cc_start: 0.8350 (mttt) cc_final: 0.7254 (tttp) REVERT: B 342 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.6693 (mp0) REVERT: B 369 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8194 (mttm) REVERT: C 331 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8645 (mtpt) REVERT: C 342 GLU cc_start: 0.8430 (mm-30) cc_final: 0.7820 (mm-30) REVERT: D 356 SER cc_start: 0.9272 (p) cc_final: 0.8942 (t) REVERT: E 315 LEU cc_start: 0.7925 (mp) cc_final: 0.7468 (tt) REVERT: E 321 LYS cc_start: 0.8170 (mttt) cc_final: 0.7775 (mttp) REVERT: E 331 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8331 (mtpt) REVERT: E 349 ARG cc_start: 0.7487 (mtm180) cc_final: 0.6464 (mmm160) REVERT: G 311 LYS cc_start: 0.8402 (tmtt) cc_final: 0.7805 (ttpt) REVERT: H 315 LEU cc_start: 0.8397 (tt) cc_final: 0.7880 (mp) REVERT: H 336 GLN cc_start: 0.9180 (tp40) cc_final: 0.8937 (tp40) REVERT: J 331 LYS cc_start: 0.8981 (ttmt) cc_final: 0.8672 (ttmm) REVERT: J 349 ARG cc_start: 0.7419 (mtm180) cc_final: 0.6346 (mmm160) REVERT: J 353 LYS cc_start: 0.8733 (tttt) cc_final: 0.8441 (tttt) outliers start: 18 outliers final: 5 residues processed: 88 average time/residue: 0.5449 time to fit residues: 50.3046 Evaluate side-chains 90 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 331 LYS Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain J residue 357 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 20 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.4463 r_free = 0.4463 target = 0.153365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.119221 restraints weight = 6647.178| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 2.58 r_work: 0.3887 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3765 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5960 Z= 0.196 Angle : 0.628 8.130 7970 Z= 0.306 Chirality : 0.050 0.135 890 Planarity : 0.003 0.020 1020 Dihedral : 5.328 15.973 790 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.54 % Allowed : 15.52 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.26), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.011 0.003 TYR D 310 PHE 0.005 0.001 PHE J 378 HIS 0.002 0.001 HIS J 329 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 5960) covalent geometry : angle 0.62839 ( 7970) hydrogen bonds : bond 0.01674 ( 107) hydrogen bonds : angle 4.36816 ( 321) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.222 Fit side-chains REVERT: A 315 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7270 (mp) REVERT: A 321 LYS cc_start: 0.8140 (mttt) cc_final: 0.7229 (tttp) REVERT: F 331 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8655 (mtpt) REVERT: B 321 LYS cc_start: 0.8352 (mttt) cc_final: 0.7283 (tttp) REVERT: B 342 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.6682 (mp0) REVERT: B 357 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8979 (tt) REVERT: B 369 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8193 (mttm) REVERT: C 331 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8637 (mtpt) REVERT: C 342 GLU cc_start: 0.8430 (mm-30) cc_final: 0.7818 (mm-30) REVERT: E 315 LEU cc_start: 0.7791 (mp) cc_final: 0.7315 (tt) REVERT: E 321 LYS cc_start: 0.8172 (mttt) cc_final: 0.7779 (mttp) REVERT: E 331 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8395 (mtpt) REVERT: E 349 ARG cc_start: 0.7537 (mtm180) cc_final: 0.6523 (mmm160) REVERT: G 311 LYS cc_start: 0.8409 (tmtt) cc_final: 0.7823 (ttpt) REVERT: H 315 LEU cc_start: 0.8389 (tt) cc_final: 0.7899 (mp) REVERT: H 336 GLN cc_start: 0.9183 (tp40) cc_final: 0.8941 (tp40) REVERT: J 331 LYS cc_start: 0.8984 (ttmt) cc_final: 0.8674 (ttmm) REVERT: J 349 ARG cc_start: 0.7465 (mtm180) cc_final: 0.6384 (mmm160) REVERT: J 353 LYS cc_start: 0.8750 (tttt) cc_final: 0.8444 (tttt) outliers start: 17 outliers final: 5 residues processed: 86 average time/residue: 0.4954 time to fit residues: 44.6767 Evaluate side-chains 87 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 331 LYS Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain J residue 357 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 21 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.148109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.113971 restraints weight = 6690.895| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.53 r_work: 0.3802 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3683 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.053 5960 Z= 0.404 Angle : 0.786 9.069 7970 Z= 0.397 Chirality : 0.053 0.150 890 Planarity : 0.003 0.020 1020 Dihedral : 5.794 18.620 790 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.69 % Allowed : 15.97 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.25), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 349 TYR 0.023 0.006 TYR B 310 PHE 0.010 0.002 PHE J 378 HIS 0.004 0.001 HIS I 330 Details of bonding type rmsd covalent geometry : bond 0.00913 ( 5960) covalent geometry : angle 0.78634 ( 7970) hydrogen bonds : bond 0.02182 ( 107) hydrogen bonds : angle 4.57249 ( 321) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.244 Fit side-chains REVERT: A 315 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7442 (mp) REVERT: A 321 LYS cc_start: 0.7998 (mttt) cc_final: 0.7153 (tttp) REVERT: F 327 ASN cc_start: 0.8563 (t0) cc_final: 0.8346 (m-40) REVERT: F 331 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8604 (mtpt) REVERT: B 342 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: B 369 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8273 (mttm) REVERT: C 331 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8598 (mtpt) REVERT: C 349 ARG cc_start: 0.8123 (mtm180) cc_final: 0.6530 (mmm160) REVERT: D 321 LYS cc_start: 0.7862 (mttt) cc_final: 0.7477 (mttp) REVERT: E 321 LYS cc_start: 0.8146 (mttt) cc_final: 0.7744 (mttm) REVERT: E 331 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8321 (mtpt) REVERT: E 349 ARG cc_start: 0.7873 (mtm180) cc_final: 0.6579 (mmm160) REVERT: G 311 LYS cc_start: 0.8534 (tmtt) cc_final: 0.7952 (ttpt) REVERT: G 328 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.8930 (mt) REVERT: H 315 LEU cc_start: 0.8221 (tt) cc_final: 0.7776 (mp) REVERT: H 340 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8025 (ttmm) REVERT: J 311 LYS cc_start: 0.8385 (tttm) cc_final: 0.8047 (tmmm) REVERT: J 331 LYS cc_start: 0.9026 (ttmt) cc_final: 0.8738 (ttmm) REVERT: J 349 ARG cc_start: 0.7603 (mtm180) cc_final: 0.6377 (mmm160) REVERT: J 353 LYS cc_start: 0.8890 (tttt) cc_final: 0.8606 (tttt) outliers start: 18 outliers final: 7 residues processed: 93 average time/residue: 0.5177 time to fit residues: 50.6174 Evaluate side-chains 97 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 331 LYS Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain H residue 340 LYS Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain J residue 357 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 42 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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 = 0.4469 r_free = 0.4469 target = 0.150190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.116206 restraints weight = 6728.188| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 2.60 r_work: 0.3906 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3784 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 5960 Z= 0.187 Angle : 0.642 8.136 7970 Z= 0.312 Chirality : 0.050 0.133 890 Planarity : 0.002 0.020 1020 Dihedral : 5.366 15.384 790 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.24 % Allowed : 17.61 % Favored : 80.15 % 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 are not related in a simple way. whole: -2.65 (0.25), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.011 0.002 TYR D 310 PHE 0.005 0.001 PHE J 378 HIS 0.002 0.001 HIS J 329 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 5960) covalent geometry : angle 0.64191 ( 7970) hydrogen bonds : bond 0.01626 ( 107) hydrogen bonds : angle 4.29013 ( 321) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.180 Fit side-chains REVERT: A 315 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7372 (mp) REVERT: A 321 LYS cc_start: 0.7981 (mttt) cc_final: 0.7010 (tttp) REVERT: F 331 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8528 (mtpt) REVERT: B 342 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.6576 (mp0) REVERT: B 369 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8108 (mttm) REVERT: C 331 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8524 (mtpt) REVERT: C 342 GLU cc_start: 0.8593 (tp30) cc_final: 0.7918 (mm-30) REVERT: C 349 ARG cc_start: 0.8011 (mtm180) cc_final: 0.6482 (mmm160) REVERT: D 321 LYS cc_start: 0.7697 (mttt) cc_final: 0.6768 (tttp) REVERT: E 315 LEU cc_start: 0.8064 (mp) cc_final: 0.7565 (tt) REVERT: E 321 LYS cc_start: 0.8010 (mttt) cc_final: 0.7595 (mttm) REVERT: E 331 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8188 (mtpt) REVERT: E 349 ARG cc_start: 0.7713 (mtm180) cc_final: 0.6521 (mmm160) REVERT: G 311 LYS cc_start: 0.8357 (tmtt) cc_final: 0.7748 (ttpt) REVERT: H 315 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7887 (mp) REVERT: H 336 GLN cc_start: 0.9101 (tp40) cc_final: 0.8898 (tp40) REVERT: J 331 LYS cc_start: 0.8895 (ttmt) cc_final: 0.8556 (ttmm) REVERT: J 349 ARG cc_start: 0.7451 (mtm180) cc_final: 0.6258 (mmm160) REVERT: J 353 LYS cc_start: 0.8676 (tttt) cc_final: 0.8362 (tttt) outliers start: 15 outliers final: 7 residues processed: 82 average time/residue: 0.5496 time to fit residues: 47.1876 Evaluate side-chains 89 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 331 LYS Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain H residue 315 LEU Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain J residue 325 LEU Chi-restraints excluded: chain J residue 357 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 45 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 = 0.4463 r_free = 0.4463 target = 0.149800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.115501 restraints weight = 6695.593| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 2.62 r_work: 0.3898 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3777 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 5960 Z= 0.206 Angle : 0.653 9.572 7970 Z= 0.315 Chirality : 0.050 0.127 890 Planarity : 0.003 0.020 1020 Dihedral : 5.330 15.782 790 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.09 % Allowed : 18.21 % Favored : 79.70 % 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 are not related in a simple way. whole: -2.61 (0.26), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 349 TYR 0.012 0.003 TYR D 310 PHE 0.005 0.001 PHE E 378 HIS 0.002 0.001 HIS J 329 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 5960) covalent geometry : angle 0.65253 ( 7970) hydrogen bonds : bond 0.01673 ( 107) hydrogen bonds : angle 4.29773 ( 321) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.273 Fit side-chains REVERT: A 315 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7368 (mp) REVERT: A 321 LYS cc_start: 0.7975 (mttt) cc_final: 0.7001 (tttp) REVERT: F 331 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8538 (mtpt) REVERT: B 342 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.6573 (mp0) REVERT: B 369 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8134 (mttm) REVERT: C 331 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8511 (mtpt) REVERT: C 342 GLU cc_start: 0.8620 (tp30) cc_final: 0.7921 (mm-30) REVERT: C 349 ARG cc_start: 0.8024 (mtm180) cc_final: 0.6496 (mmm160) REVERT: D 321 LYS cc_start: 0.7670 (mttt) cc_final: 0.6767 (tttp) REVERT: E 315 LEU cc_start: 0.7931 (mp) cc_final: 0.7424 (tt) REVERT: E 321 LYS cc_start: 0.8001 (mttt) cc_final: 0.7588 (mttm) REVERT: E 331 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8181 (mtpt) REVERT: E 349 ARG cc_start: 0.7735 (mtm180) cc_final: 0.6517 (mmm160) REVERT: G 311 LYS cc_start: 0.8359 (tmtt) cc_final: 0.7748 (ttpt) REVERT: H 315 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7794 (mp) REVERT: H 340 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7781 (ttmm) REVERT: J 331 LYS cc_start: 0.8886 (ttmt) cc_final: 0.8540 (ttmm) REVERT: J 349 ARG cc_start: 0.7480 (mtm180) cc_final: 0.6304 (mmm160) REVERT: J 353 LYS cc_start: 0.8687 (tttt) cc_final: 0.8381 (tttt) outliers start: 14 outliers final: 6 residues processed: 83 average time/residue: 0.5696 time to fit residues: 49.4770 Evaluate side-chains 89 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain G residue 320 SER Chi-restraints excluded: chain G residue 331 LYS Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain H residue 315 LEU Chi-restraints excluded: chain H residue 340 LYS Chi-restraints excluded: chain I residue 320 SER Chi-restraints excluded: chain J residue 325 LEU Chi-restraints excluded: chain J residue 357 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 8 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.148454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.113961 restraints weight = 6674.809| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 2.60 r_work: 0.3870 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 5960 Z= 0.259 Angle : 0.693 10.290 7970 Z= 0.338 Chirality : 0.051 0.128 890 Planarity : 0.003 0.020 1020 Dihedral : 5.440 16.052 790 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.39 % Allowed : 18.21 % Favored : 79.40 % 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 are not related in a simple way. whole: -2.62 (0.25), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 349 TYR 0.015 0.004 TYR D 310 PHE 0.007 0.002 PHE J 378 HIS 0.003 0.001 HIS J 329 Details of bonding type rmsd covalent geometry : bond 0.00579 ( 5960) covalent geometry : angle 0.69285 ( 7970) hydrogen bonds : bond 0.01793 ( 107) hydrogen bonds : angle 4.36599 ( 321) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1962.81 seconds wall clock time: 34 minutes 31.80 seconds (2071.80 seconds total)