Starting phenix.real_space_refine on Thu Jul 24 09:40:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nrv_12551/07_2025/7nrv_12551.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nrv_12551/07_2025/7nrv_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7nrv_12551/07_2025/7nrv_12551.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nrv_12551/07_2025/7nrv_12551.map" model { file = "/net/cci-nas-00/data/ceres_data/7nrv_12551/07_2025/7nrv_12551.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nrv_12551/07_2025/7nrv_12551.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.11, per 1000 atoms: 0.70 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: 1.34 Conformation dependent library (CDL) restraints added in 903.7 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: 0.81 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: 1.28 Time building geometry restraints manager: 1.60 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: 0.01 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: 1.140 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.450 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.720 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (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 HIS 0.003 0.001 HIS C 329 PHE 0.014 0.005 PHE E 346 TYR 0.008 0.003 TYR A 310 ARG 0.001 0.000 ARG E 379 Details of bonding type rmsd hydrogen bonds : bond 0.10997 ( 107) hydrogen bonds : angle 8.19003 ( 321) covalent geometry : bond 0.00705 ( 5960) covalent geometry : angle 1.14862 ( 7970) *********************** 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 : 0.805 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: 1.0996 time to fit residues: 107.6141 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 : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN B 368 ASN C 368 ASN D 368 ASN G 368 ASN I 368 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.148969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.115301 restraints weight = 6612.501| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.56 r_work: 0.3883 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3765 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 5960 Z= 0.260 Angle : 0.731 11.888 7970 Z= 0.352 Chirality : 0.052 0.155 890 Planarity : 0.004 0.034 1020 Dihedral : 5.941 17.753 790 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.90 % Allowed : 9.55 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.26), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 330 PHE 0.007 0.002 PHE G 346 TYR 0.018 0.004 TYR D 310 ARG 0.002 0.000 ARG G 379 Details of bonding type rmsd hydrogen bonds : bond 0.02575 ( 107) hydrogen bonds : angle 5.28332 ( 321) covalent geometry : bond 0.00586 ( 5960) covalent geometry : angle 0.73129 ( 7970) *********************** 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 86 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.712 Fit side-chains REVERT: A 315 LEU cc_start: 0.7819 (tt) cc_final: 0.7300 (mp) REVERT: A 321 LYS cc_start: 0.7830 (mttt) cc_final: 0.6889 (ttpp) REVERT: F 331 LYS cc_start: 0.8931 (ttmm) cc_final: 0.8529 (mtpt) REVERT: B 316 SER cc_start: 0.8789 (p) cc_final: 0.8569 (p) REVERT: B 321 LYS cc_start: 0.8270 (mttt) cc_final: 0.7198 (tttm) REVERT: B 361 THR cc_start: 0.9225 (m) cc_final: 0.8991 (m) REVERT: B 368 ASN cc_start: 0.8982 (m110) cc_final: 0.8651 (m-40) REVERT: B 369 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8150 (mttm) REVERT: C 315 LEU cc_start: 0.8298 (mp) cc_final: 0.7839 (tt) REVERT: C 331 LYS cc_start: 0.9237 (ttmt) cc_final: 0.8646 (mtpt) REVERT: C 342 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7616 (mm-30) REVERT: D 358 ASP cc_start: 0.8593 (m-30) cc_final: 0.8390 (m-30) REVERT: E 315 LEU cc_start: 0.7668 (mp) cc_final: 0.7184 (tt) REVERT: E 331 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8330 (mtpt) REVERT: H 331 LYS cc_start: 0.9056 (ttmm) cc_final: 0.8761 (mtmt) REVERT: I 315 LEU cc_start: 0.8388 (mp) cc_final: 0.7916 (tt) REVERT: J 331 LYS cc_start: 0.8952 (ttmt) cc_final: 0.8542 (ttmm) REVERT: J 349 ARG cc_start: 0.7332 (mtm180) cc_final: 0.6225 (mmm160) outliers start: 6 outliers final: 2 residues processed: 82 average time/residue: 1.1443 time to fit residues: 98.7792 Evaluate side-chains 74 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain I residue 320 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 30 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 17 optimal weight: 0.0980 chunk 66 optimal weight: 5.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN D 368 ASN E 336 GLN G 368 ASN I 336 GLN I 368 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.149919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.116255 restraints weight = 6611.704| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 2.55 r_work: 0.3900 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3780 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 5960 Z= 0.217 Angle : 0.667 12.083 7970 Z= 0.321 Chirality : 0.050 0.123 890 Planarity : 0.003 0.025 1020 Dihedral : 5.614 16.963 790 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.19 % Allowed : 12.69 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.26), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 330 PHE 0.006 0.002 PHE H 378 TYR 0.013 0.003 TYR B 310 ARG 0.001 0.000 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.02094 ( 107) hydrogen bonds : angle 4.70826 ( 321) covalent geometry : bond 0.00481 ( 5960) covalent geometry : angle 0.66658 ( 7970) *********************** 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 83 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.691 Fit side-chains REVERT: A 315 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7301 (mp) REVERT: A 321 LYS cc_start: 0.7953 (mttt) cc_final: 0.7067 (ttpp) REVERT: F 331 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8575 (mtpt) REVERT: B 321 LYS cc_start: 0.8300 (mttt) cc_final: 0.7207 (tttm) REVERT: B 361 THR cc_start: 0.9223 (m) cc_final: 0.9001 (m) REVERT: B 369 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8135 (mttm) REVERT: C 331 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8567 (mtpt) REVERT: C 342 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7709 (mm-30) REVERT: E 315 LEU cc_start: 0.7678 (mp) cc_final: 0.7185 (tt) REVERT: E 331 LYS cc_start: 0.8877 (ttmt) cc_final: 0.8402 (mtpt) REVERT: G 311 LYS cc_start: 0.8359 (tmtt) cc_final: 0.7804 (ttpt) REVERT: H 315 LEU cc_start: 0.8376 (tt) cc_final: 0.7741 (mp) REVERT: H 331 LYS cc_start: 0.8873 (ttmm) cc_final: 0.8668 (mtmt) REVERT: H 336 GLN cc_start: 0.9056 (tp40) cc_final: 0.8845 (tp40) REVERT: J 331 LYS cc_start: 0.8885 (ttmt) cc_final: 0.8556 (ttmm) REVERT: J 349 ARG cc_start: 0.7341 (mtm180) cc_final: 0.6228 (mmm160) outliers start: 8 outliers final: 4 residues processed: 76 average time/residue: 1.0829 time to fit residues: 87.0250 Evaluate side-chains 80 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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 369 LYS Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 358 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 66 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.4467 r_free = 0.4467 target = 0.150688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.116975 restraints weight = 6732.892| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 2.58 r_work: 0.3909 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3789 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5960 Z= 0.185 Angle : 0.622 8.339 7970 Z= 0.301 Chirality : 0.049 0.129 890 Planarity : 0.003 0.022 1020 Dihedral : 5.386 15.514 790 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.49 % Allowed : 14.03 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.26), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.005 0.002 PHE J 346 TYR 0.011 0.003 TYR D 310 ARG 0.001 0.000 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.01803 ( 107) hydrogen bonds : angle 4.50851 ( 321) covalent geometry : bond 0.00407 ( 5960) covalent geometry : angle 0.62159 ( 7970) *********************** 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 93 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.703 Fit side-chains REVERT: A 315 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7282 (mp) REVERT: A 321 LYS cc_start: 0.7980 (mttt) cc_final: 0.7065 (ttpp) REVERT: A 342 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7517 (mm-30) REVERT: F 331 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8560 (mtpt) REVERT: B 315 LEU cc_start: 0.8250 (tt) cc_final: 0.7729 (mp) REVERT: B 321 LYS cc_start: 0.8306 (mttt) cc_final: 0.7201 (tttp) REVERT: B 342 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.6621 (mp0) REVERT: B 361 THR cc_start: 0.9196 (m) cc_final: 0.8986 (m) REVERT: B 369 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8128 (mttm) REVERT: C 331 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8507 (mtpt) REVERT: C 342 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7712 (mm-30) REVERT: E 315 LEU cc_start: 0.7689 (mp) cc_final: 0.7194 (tt) REVERT: E 321 LYS cc_start: 0.7919 (mttt) cc_final: 0.7506 (mttm) REVERT: E 331 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8241 (mtpt) REVERT: E 349 ARG cc_start: 0.7442 (mtm180) cc_final: 0.6443 (mmm160) REVERT: G 311 LYS cc_start: 0.8395 (tmtt) cc_final: 0.7800 (ttpt) REVERT: H 315 LEU cc_start: 0.8492 (tt) cc_final: 0.7866 (mp) REVERT: H 331 LYS cc_start: 0.8879 (ttmm) cc_final: 0.8675 (mtmt) REVERT: H 336 GLN cc_start: 0.9105 (tp40) cc_final: 0.8898 (tp40) REVERT: J 331 LYS cc_start: 0.8874 (ttmt) cc_final: 0.8524 (ttmm) REVERT: J 349 ARG cc_start: 0.7416 (mtm180) cc_final: 0.6279 (mmm160) outliers start: 10 outliers final: 3 residues processed: 86 average time/residue: 1.1207 time to fit residues: 101.6987 Evaluate side-chains 89 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.656 ------------------------------------------------------------------------------- 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 331 LYS Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain I residue 320 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 34 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 = 0.4458 r_free = 0.4458 target = 0.153411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.119324 restraints weight = 6543.019| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 2.55 r_work: 0.3888 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3767 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2175 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= 0.195 Angle : 0.622 8.231 7970 Z= 0.303 Chirality : 0.049 0.128 890 Planarity : 0.003 0.020 1020 Dihedral : 5.337 15.770 790 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.24 % Allowed : 14.33 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (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 HIS 0.002 0.001 HIS B 330 PHE 0.006 0.002 PHE E 378 TYR 0.012 0.003 TYR D 310 ARG 0.001 0.000 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.01772 ( 107) hydrogen bonds : angle 4.43825 ( 321) covalent geometry : bond 0.00431 ( 5960) covalent geometry : angle 0.62237 ( 7970) *********************** 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 90 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.705 Fit side-chains REVERT: A 315 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7343 (mp) REVERT: A 321 LYS cc_start: 0.8105 (mttt) cc_final: 0.7224 (tttp) REVERT: F 331 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8643 (mtpt) REVERT: B 315 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7782 (mp) REVERT: B 321 LYS cc_start: 0.8371 (mttt) cc_final: 0.7348 (tttm) REVERT: B 342 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.6694 (mp0) REVERT: B 369 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8199 (mttm) REVERT: C 331 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8603 (mtpt) REVERT: C 342 GLU cc_start: 0.8416 (mm-30) cc_final: 0.7794 (mm-30) REVERT: D 356 SER cc_start: 0.9302 (p) cc_final: 0.8973 (t) REVERT: E 315 LEU cc_start: 0.7732 (mp) cc_final: 0.7251 (tt) REVERT: E 321 LYS cc_start: 0.8014 (mttt) cc_final: 0.7642 (mttm) REVERT: E 331 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8395 (mtpt) REVERT: E 349 ARG cc_start: 0.7505 (mtm180) cc_final: 0.6550 (mmm160) REVERT: H 315 LEU cc_start: 0.8516 (tt) cc_final: 0.7932 (mp) REVERT: H 331 LYS cc_start: 0.9002 (ttmm) cc_final: 0.8792 (mtmt) REVERT: H 336 GLN cc_start: 0.9206 (tp40) cc_final: 0.8963 (tp40) REVERT: J 331 LYS cc_start: 0.8978 (ttmt) cc_final: 0.8662 (ttmm) REVERT: J 349 ARG cc_start: 0.7448 (mtm180) cc_final: 0.6469 (mmm160) outliers start: 15 outliers final: 3 residues processed: 82 average time/residue: 1.0902 time to fit residues: 94.2899 Evaluate side-chains 86 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 331 LYS Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain I residue 320 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 25 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 ASN ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.147147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.113010 restraints weight = 6704.692| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.53 r_work: 0.3791 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3669 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.057 5960 Z= 0.436 Angle : 0.809 9.218 7970 Z= 0.410 Chirality : 0.054 0.160 890 Planarity : 0.004 0.025 1020 Dihedral : 5.950 19.113 790 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.99 % Allowed : 15.52 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.25), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 330 PHE 0.012 0.003 PHE H 378 TYR 0.025 0.006 TYR B 310 ARG 0.002 0.000 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.02288 ( 107) hydrogen bonds : angle 4.65817 ( 321) covalent geometry : bond 0.00988 ( 5960) covalent geometry : angle 0.80889 ( 7970) *********************** 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 104 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.713 Fit side-chains REVERT: A 315 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7319 (mp) REVERT: A 321 LYS cc_start: 0.7948 (mttt) cc_final: 0.7055 (tttp) REVERT: F 327 ASN cc_start: 0.8611 (t0) cc_final: 0.8384 (m-40) REVERT: F 331 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8623 (mtpt) REVERT: F 353 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8705 (tttp) REVERT: B 315 LEU cc_start: 0.8311 (tt) cc_final: 0.7795 (mp) REVERT: B 342 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.6707 (mp0) REVERT: B 369 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8300 (mttm) REVERT: C 331 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8621 (mtpt) REVERT: C 342 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8198 (mm-30) REVERT: C 349 ARG cc_start: 0.8117 (mtm180) cc_final: 0.6536 (mmm160) REVERT: D 321 LYS cc_start: 0.7870 (mttt) cc_final: 0.7490 (mttm) REVERT: D 342 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7876 (mm-30) REVERT: E 321 LYS cc_start: 0.8271 (mttt) cc_final: 0.7875 (mttm) REVERT: E 331 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8356 (mtpt) REVERT: E 349 ARG cc_start: 0.7887 (mtm180) cc_final: 0.6600 (mmm160) REVERT: G 311 LYS cc_start: 0.8513 (tmtt) cc_final: 0.7925 (ttpt) REVERT: H 315 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7798 (mp) REVERT: J 311 LYS cc_start: 0.8396 (tttm) cc_final: 0.8072 (tmmm) REVERT: J 331 LYS cc_start: 0.9076 (ttmt) cc_final: 0.8800 (ttmm) REVERT: J 349 ARG cc_start: 0.7630 (mtm180) cc_final: 0.6337 (mmm160) outliers start: 20 outliers final: 7 residues processed: 95 average time/residue: 0.9984 time to fit residues: 100.2508 Evaluate side-chains 99 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 F residue 353 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 D residue 342 GLU Chi-restraints excluded: chain E residue 331 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 ASN I 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.155113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.120922 restraints weight = 6539.831| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 2.58 r_work: 0.3914 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3793 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 5960 Z= 0.147 Angle : 0.608 8.243 7970 Z= 0.295 Chirality : 0.050 0.134 890 Planarity : 0.002 0.020 1020 Dihedral : 5.296 15.368 790 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.94 % Allowed : 17.31 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.26), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS J 330 PHE 0.004 0.001 PHE J 346 TYR 0.009 0.002 TYR D 310 ARG 0.000 0.000 ARG J 349 Details of bonding type rmsd hydrogen bonds : bond 0.01507 ( 107) hydrogen bonds : angle 4.27060 ( 321) covalent geometry : bond 0.00322 ( 5960) covalent geometry : angle 0.60766 ( 7970) *********************** 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 87 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.710 Fit side-chains REVERT: A 315 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7460 (mp) REVERT: A 321 LYS cc_start: 0.8115 (mttt) cc_final: 0.7203 (tttp) REVERT: F 331 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8655 (mtpt) REVERT: B 342 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.6702 (mp0) REVERT: B 369 LYS cc_start: 0.8802 (mtmt) cc_final: 0.8177 (mttm) REVERT: C 331 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8599 (mtpt) REVERT: C 342 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7837 (mm-30) REVERT: E 315 LEU cc_start: 0.7979 (mp) cc_final: 0.7462 (tt) REVERT: E 321 LYS cc_start: 0.8211 (mttt) cc_final: 0.7813 (mttm) REVERT: E 331 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8582 (mttm) REVERT: E 349 ARG cc_start: 0.7678 (mtm180) cc_final: 0.6622 (mmm160) REVERT: G 311 LYS cc_start: 0.8451 (tmtt) cc_final: 0.7891 (ttpt) REVERT: H 315 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7916 (mp) REVERT: H 336 GLN cc_start: 0.9214 (tp40) cc_final: 0.8979 (tp40) REVERT: J 331 LYS cc_start: 0.8996 (ttmt) cc_final: 0.8689 (ttmm) REVERT: J 349 ARG cc_start: 0.7500 (mtm180) cc_final: 0.6374 (mmm160) outliers start: 13 outliers final: 3 residues processed: 78 average time/residue: 1.1123 time to fit residues: 91.5262 Evaluate side-chains 80 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 C residue 331 LYS Chi-restraints excluded: chain E residue 331 LYS 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 J residue 325 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 26 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 8 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.142562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.108542 restraints weight = 6805.445| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.56 r_work: 0.3796 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.065 5960 Z= 0.498 Angle : 0.856 9.267 7970 Z= 0.438 Chirality : 0.056 0.157 890 Planarity : 0.004 0.022 1020 Dihedral : 6.039 19.320 790 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 2.69 % Allowed : 17.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.24), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 330 PHE 0.012 0.003 PHE J 378 TYR 0.029 0.007 TYR B 310 ARG 0.003 0.001 ARG H 349 Details of bonding type rmsd hydrogen bonds : bond 0.02407 ( 107) hydrogen bonds : angle 4.67734 ( 321) covalent geometry : bond 0.01130 ( 5960) covalent geometry : angle 0.85565 ( 7970) *********************** 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 107 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.978 Fit side-chains REVERT: A 315 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7367 (mp) REVERT: A 321 LYS cc_start: 0.7858 (mttt) cc_final: 0.6918 (tttp) REVERT: F 327 ASN cc_start: 0.8524 (t0) cc_final: 0.8303 (m-40) REVERT: F 331 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8507 (mtpt) REVERT: B 342 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.6668 (mp0) REVERT: B 369 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8184 (mttm) REVERT: C 331 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8484 (mtpt) REVERT: C 349 ARG cc_start: 0.8137 (mtm180) cc_final: 0.6511 (mmm160) REVERT: C 369 LYS cc_start: 0.8766 (mtpt) cc_final: 0.8065 (mttt) REVERT: D 321 LYS cc_start: 0.7875 (mttt) cc_final: 0.7499 (mttm) REVERT: D 342 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7769 (mm-30) REVERT: E 311 LYS cc_start: 0.8224 (tttm) cc_final: 0.7972 (tmtp) REVERT: E 321 LYS cc_start: 0.8060 (mttt) cc_final: 0.7641 (mttm) REVERT: E 331 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8192 (mtpt) REVERT: E 349 ARG cc_start: 0.7878 (mtm180) cc_final: 0.6450 (mmm160) REVERT: G 311 LYS cc_start: 0.8504 (tmtt) cc_final: 0.7918 (ttpt) REVERT: G 321 LYS cc_start: 0.8286 (mttt) cc_final: 0.7002 (ttpp) REVERT: G 328 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8819 (mp) REVERT: H 311 LYS cc_start: 0.8289 (tttm) cc_final: 0.7827 (tmtp) REVERT: H 315 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7714 (mp) REVERT: I 311 LYS cc_start: 0.8371 (tmtt) cc_final: 0.7759 (ttpt) REVERT: J 311 LYS cc_start: 0.8423 (tttm) cc_final: 0.7986 (tmmm) REVERT: J 331 LYS cc_start: 0.8979 (ttmt) cc_final: 0.8666 (ttmm) REVERT: J 349 ARG cc_start: 0.7716 (mtm180) cc_final: 0.6296 (mmm160) outliers start: 18 outliers final: 5 residues processed: 98 average time/residue: 1.2653 time to fit residues: 130.5773 Evaluate side-chains 100 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 2.221 ------------------------------------------------------------------------------- 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 D residue 342 GLU Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain G residue 328 ILE 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 57 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 GLN ** 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 = 0.4539 r_free = 0.4539 target = 0.161402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.128675 restraints weight = 6555.769| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 2.70 r_work: 0.4010 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3888 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5960 Z= 0.096 Angle : 0.578 7.789 7970 Z= 0.277 Chirality : 0.049 0.122 890 Planarity : 0.002 0.020 1020 Dihedral : 5.127 16.162 790 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.19 % Allowed : 19.70 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.26), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 330 PHE 0.003 0.001 PHE H 346 TYR 0.005 0.001 TYR I 310 ARG 0.001 0.000 ARG I 349 Details of bonding type rmsd hydrogen bonds : bond 0.01260 ( 107) hydrogen bonds : angle 4.13296 ( 321) covalent geometry : bond 0.00208 ( 5960) covalent geometry : angle 0.57765 ( 7970) *********************** 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 94 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.720 Fit side-chains REVERT: A 315 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7282 (mp) REVERT: A 321 LYS cc_start: 0.7910 (mttt) cc_final: 0.6942 (tttp) REVERT: F 331 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8334 (mtpt) REVERT: B 369 LYS cc_start: 0.8730 (mtmt) cc_final: 0.8060 (mttm) REVERT: C 331 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8280 (mtpt) REVERT: C 342 GLU cc_start: 0.8533 (tp30) cc_final: 0.7846 (mm-30) REVERT: C 349 ARG cc_start: 0.7903 (mtm180) cc_final: 0.6357 (mmm160) REVERT: C 359 ASN cc_start: 0.8642 (m-40) cc_final: 0.8433 (m110) REVERT: E 315 LEU cc_start: 0.7935 (mp) cc_final: 0.7416 (tt) REVERT: E 321 LYS cc_start: 0.7922 (mttt) cc_final: 0.7517 (mttm) REVERT: E 331 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.7884 (mtpt) REVERT: E 349 ARG cc_start: 0.7537 (mtm180) cc_final: 0.6440 (mmm160) REVERT: G 311 LYS cc_start: 0.8320 (tmtt) cc_final: 0.7724 (ttpt) REVERT: H 311 LYS cc_start: 0.8192 (tttm) cc_final: 0.7786 (tmtp) REVERT: H 315 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7883 (mp) REVERT: H 336 GLN cc_start: 0.9070 (tp40) cc_final: 0.8746 (tp40) REVERT: J 331 LYS cc_start: 0.8779 (ttmt) cc_final: 0.8421 (ttmm) REVERT: J 349 ARG cc_start: 0.7378 (mtm180) cc_final: 0.6324 (mmm160) outliers start: 8 outliers final: 0 residues processed: 90 average time/residue: 1.1660 time to fit residues: 110.3065 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 : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain H residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 32 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 44 optimal weight: 0.0980 chunk 41 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 359 ASN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 GLN ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.150182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.115912 restraints weight = 6621.097| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 2.62 r_work: 0.3897 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3778 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 5960 Z= 0.208 Angle : 0.655 8.295 7970 Z= 0.316 Chirality : 0.050 0.131 890 Planarity : 0.003 0.020 1020 Dihedral : 5.271 15.355 790 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.34 % Allowed : 20.30 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.26), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 330 PHE 0.005 0.001 PHE F 378 TYR 0.012 0.003 TYR D 310 ARG 0.001 0.000 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.01619 ( 107) hydrogen bonds : angle 4.14834 ( 321) covalent geometry : bond 0.00466 ( 5960) covalent geometry : angle 0.65546 ( 7970) ********************** 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 92 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.732 Fit side-chains REVERT: A 315 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7247 (mp) REVERT: A 321 LYS cc_start: 0.7996 (mttt) cc_final: 0.7046 (tttp) REVERT: F 321 LYS cc_start: 0.7902 (mttt) cc_final: 0.7411 (mttp) REVERT: F 331 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8519 (mtpt) REVERT: B 315 LEU cc_start: 0.8308 (tt) cc_final: 0.7691 (mp) REVERT: B 369 LYS cc_start: 0.8766 (mtmt) cc_final: 0.8110 (mttm) REVERT: C 331 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8445 (mtpt) REVERT: C 342 GLU cc_start: 0.8550 (tp30) cc_final: 0.7829 (mm-30) REVERT: C 349 ARG cc_start: 0.8043 (mtm180) cc_final: 0.6509 (mmm160) REVERT: C 361 THR cc_start: 0.9111 (m) cc_final: 0.8878 (m) REVERT: D 321 LYS cc_start: 0.7704 (mttt) cc_final: 0.7298 (mttm) REVERT: D 356 SER cc_start: 0.9224 (p) cc_final: 0.8930 (t) REVERT: E 315 LEU cc_start: 0.7915 (mp) cc_final: 0.7399 (tt) REVERT: E 321 LYS cc_start: 0.8027 (mttt) cc_final: 0.7601 (mttp) REVERT: E 331 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8334 (mttm) REVERT: E 349 ARG cc_start: 0.7749 (mtm180) cc_final: 0.6551 (mmm160) REVERT: G 311 LYS cc_start: 0.8358 (tmtt) cc_final: 0.7751 (ttpt) REVERT: H 315 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7839 (mp) REVERT: H 336 GLN cc_start: 0.9145 (tp40) cc_final: 0.8899 (tp40) REVERT: J 331 LYS cc_start: 0.8905 (ttmt) cc_final: 0.8556 (ttmm) REVERT: J 349 ARG cc_start: 0.7649 (mtm180) cc_final: 0.6461 (mmm160) outliers start: 9 outliers final: 0 residues processed: 85 average time/residue: 1.1739 time to fit residues: 104.8996 Evaluate side-chains 86 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain H residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 61 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4447 r_free = 0.4447 target = 0.149211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.114733 restraints weight = 6719.253| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 2.62 r_work: 0.3879 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3758 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 5960 Z= 0.239 Angle : 0.689 8.332 7970 Z= 0.335 Chirality : 0.050 0.134 890 Planarity : 0.003 0.020 1020 Dihedral : 5.398 16.298 790 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.90 % Allowed : 20.60 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.26), residues: 750 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 329 PHE 0.006 0.001 PHE H 378 TYR 0.014 0.003 TYR D 310 ARG 0.001 0.000 ARG D 349 Details of bonding type rmsd hydrogen bonds : bond 0.01688 ( 107) hydrogen bonds : angle 4.18683 ( 321) covalent geometry : bond 0.00535 ( 5960) covalent geometry : angle 0.68892 ( 7970) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4229.33 seconds wall clock time: 74 minutes 32.70 seconds (4472.70 seconds total)