Starting phenix.real_space_refine on Thu Mar 6 08:28:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9czi_46417/03_2025/9czi_46417_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9czi_46417/03_2025/9czi_46417.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/9czi_46417/03_2025/9czi_46417.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9czi_46417/03_2025/9czi_46417.map" model { file = "/net/cci-nas-00/data/ceres_data/9czi_46417/03_2025/9czi_46417_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9czi_46417/03_2025/9czi_46417_neut.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= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 3510 2.51 5 N 1010 2.21 5 O 1040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5570 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 2.31, per 1000 atoms: 0.41 Number of scatterers: 5570 At special positions: 0 Unit cell: (77.996, 144.398, 44.268, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 1040 8.00 N 1010 7.00 C 3510 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 648.5 milliseconds 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1280 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 61.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 307 through 310 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 330 removed outlier: 6.970A pdb=" N VAL C 318 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR A 319 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER C 320 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS A 321 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N CYS C 322 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY A 323 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE C 328 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N HIS A 329 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N HIS C 330 " --> pdb=" O HIS A 329 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL E 318 " --> pdb=" O LYS C 317 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR C 319 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER E 320 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS C 321 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N CYS E 322 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLY C 323 " --> pdb=" O CYS E 322 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE E 328 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N HIS C 329 " --> pdb=" O ILE E 328 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N HIS E 330 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL G 318 " --> pdb=" O LYS E 317 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR E 319 " --> pdb=" O VAL G 318 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER G 320 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS E 321 " --> pdb=" O SER G 320 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N CYS G 322 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLY E 323 " --> pdb=" O CYS G 322 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE G 328 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N HIS E 329 " --> pdb=" O ILE G 328 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N HIS G 330 " --> pdb=" O HIS E 329 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL I 318 " --> pdb=" O LYS G 317 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR G 319 " --> pdb=" O VAL I 318 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER I 320 " --> pdb=" O THR G 319 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS G 321 " --> pdb=" O SER I 320 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N CYS I 322 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY G 323 " --> pdb=" O CYS I 322 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE I 328 " --> pdb=" O ASN G 327 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N HIS G 329 " --> pdb=" O ILE I 328 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N HIS I 330 " --> pdb=" O HIS G 329 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 340 removed outlier: 6.503A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LYS C 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL A 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL C 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LYS E 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL C 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL E 337 " --> pdb=" O GLU G 338 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LYS G 340 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL E 339 " --> pdb=" O LYS G 340 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL G 337 " --> pdb=" O GLU I 338 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LYS I 340 " --> pdb=" O VAL G 337 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL G 339 " --> pdb=" O LYS I 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 356 removed outlier: 6.431A pdb=" N LEU A 344 " --> pdb=" O ASP C 345 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LYS C 347 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N PHE A 346 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ARG C 349 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASP A 348 " --> pdb=" O ARG C 349 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N GLN C 351 " --> pdb=" O ASP A 348 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL A 350 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LYS C 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER A 352 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLY C 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ILE A 354 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU C 344 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LYS E 347 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N PHE C 346 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARG E 349 " --> pdb=" O PHE C 346 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ASP C 348 " --> pdb=" O ARG E 349 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N GLN E 351 " --> pdb=" O ASP C 348 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL C 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LYS E 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER C 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLY E 355 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ILE C 354 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU E 344 " --> pdb=" O ASP G 345 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LYS G 347 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N PHE E 346 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ARG G 349 " --> pdb=" O PHE E 346 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ASP E 348 " --> pdb=" O ARG G 349 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N GLN G 351 " --> pdb=" O ASP E 348 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL E 350 " --> pdb=" O GLN G 351 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LYS G 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER E 352 " --> pdb=" O LYS G 353 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N GLY G 355 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ILE E 354 " --> pdb=" O GLY G 355 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU G 344 " --> pdb=" O ASP I 345 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LYS I 347 " --> pdb=" O LEU G 344 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N PHE G 346 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ARG I 349 " --> pdb=" O PHE G 346 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ASP G 348 " --> pdb=" O ARG I 349 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N GLN I 351 " --> pdb=" O ASP G 348 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL G 350 " --> pdb=" O GLN I 351 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LYS I 353 " --> pdb=" O VAL G 350 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER G 352 " --> pdb=" O LYS I 353 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N GLY I 355 " --> pdb=" O SER G 352 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ILE G 354 " --> pdb=" O GLY I 355 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 359 through 362 removed outlier: 6.510A pdb=" N ASN A 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N HIS C 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASN C 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N HIS E 362 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR C 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASN E 359 " --> pdb=" O ILE G 360 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N HIS G 362 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR E 361 " --> pdb=" O HIS G 362 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASN G 359 " --> pdb=" O ILE I 360 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N HIS I 362 " --> pdb=" O ASN G 359 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR G 361 " --> pdb=" O HIS I 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 369 through 377 Processing sheet with id=AA8, first strand: chain 'B' and resid 307 through 310 Processing sheet with id=AA9, first strand: chain 'B' and resid 313 through 314 Processing sheet with id=AB1, first strand: chain 'B' and resid 317 through 330 removed outlier: 6.970A pdb=" N VAL D 318 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR B 319 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER D 320 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS B 321 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N CYS D 322 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY B 323 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE D 328 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N HIS B 329 " --> pdb=" O ILE D 328 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N HIS D 330 " --> pdb=" O HIS B 329 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL F 318 " --> pdb=" O LYS D 317 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR D 319 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER F 320 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS D 321 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N CYS F 322 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY D 323 " --> pdb=" O CYS F 322 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE F 328 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N HIS D 329 " --> pdb=" O ILE F 328 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N HIS F 330 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL H 318 " --> pdb=" O LYS F 317 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR F 319 " --> pdb=" O VAL H 318 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER H 320 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS F 321 " --> pdb=" O SER H 320 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N CYS H 322 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLY F 323 " --> pdb=" O CYS H 322 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE H 328 " --> pdb=" O ASN F 327 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N HIS F 329 " --> pdb=" O ILE H 328 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N HIS H 330 " --> pdb=" O HIS F 329 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL J 318 " --> pdb=" O LYS H 317 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR H 319 " --> pdb=" O VAL J 318 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER J 320 " --> pdb=" O THR H 319 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS H 321 " --> pdb=" O SER J 320 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N CYS J 322 " --> pdb=" O LYS H 321 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLY H 323 " --> pdb=" O CYS J 322 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE J 328 " --> pdb=" O ASN H 327 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N HIS H 329 " --> pdb=" O ILE J 328 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N HIS J 330 " --> pdb=" O HIS H 329 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 336 through 340 removed outlier: 6.504A pdb=" N VAL B 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LYS D 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL B 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL D 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N LYS F 340 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL D 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL F 337 " --> pdb=" O GLU H 338 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LYS H 340 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL F 339 " --> pdb=" O LYS H 340 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL H 337 " --> pdb=" O GLU J 338 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LYS J 340 " --> pdb=" O VAL H 337 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL H 339 " --> pdb=" O LYS J 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 343 through 356 removed outlier: 6.431A pdb=" N LEU B 344 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LYS D 347 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N PHE B 346 " --> pdb=" O LYS D 347 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARG D 349 " --> pdb=" O PHE B 346 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASP B 348 " --> pdb=" O ARG D 349 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N GLN D 351 " --> pdb=" O ASP B 348 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL B 350 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LYS D 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER B 352 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLY D 355 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ILE B 354 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU D 344 " --> pdb=" O ASP F 345 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LYS F 347 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N PHE D 346 " --> pdb=" O LYS F 347 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ARG F 349 " --> pdb=" O PHE D 346 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASP D 348 " --> pdb=" O ARG F 349 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N GLN F 351 " --> pdb=" O ASP D 348 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL D 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LYS F 353 " --> pdb=" O VAL D 350 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER D 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N GLY F 355 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ILE D 354 " --> pdb=" O GLY F 355 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU F 344 " --> pdb=" O ASP H 345 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LYS H 347 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N PHE F 346 " --> pdb=" O LYS H 347 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARG H 349 " --> pdb=" O PHE F 346 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASP F 348 " --> pdb=" O ARG H 349 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N GLN H 351 " --> pdb=" O ASP F 348 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL F 350 " --> pdb=" O GLN H 351 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LYS H 353 " --> pdb=" O VAL F 350 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER F 352 " --> pdb=" O LYS H 353 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLY H 355 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ILE F 354 " --> pdb=" O GLY H 355 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU H 344 " --> pdb=" O ASP J 345 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LYS J 347 " --> pdb=" O LEU H 344 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N PHE H 346 " --> pdb=" O LYS J 347 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARG J 349 " --> pdb=" O PHE H 346 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ASP H 348 " --> pdb=" O ARG J 349 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N GLN J 351 " --> pdb=" O ASP H 348 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL H 350 " --> pdb=" O GLN J 351 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LYS J 353 " --> pdb=" O VAL H 350 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER H 352 " --> pdb=" O LYS J 353 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N GLY J 355 " --> pdb=" O SER H 352 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ILE H 354 " --> pdb=" O GLY J 355 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 359 through 362 removed outlier: 6.509A pdb=" N ASN B 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N HIS D 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASN D 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N HIS F 362 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR D 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASN F 359 " --> pdb=" O ILE H 360 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N HIS H 362 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR F 361 " --> pdb=" O HIS H 362 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASN H 359 " --> pdb=" O ILE J 360 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N HIS J 362 " --> pdb=" O ASN H 359 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR H 361 " --> pdb=" O HIS J 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 369 through 377 128 hydrogen bonds defined for protein. 384 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: 1.43 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1512 1.32 - 1.45: 1072 1.45 - 1.58: 3006 1.58 - 1.70: 60 1.70 - 1.83: 10 Bond restraints: 5660 Sorted by residual: bond pdb=" CB HIS D 374 " pdb=" CG HIS D 374 " ideal model delta sigma weight residual 1.497 1.434 0.063 1.40e-02 5.10e+03 2.03e+01 bond pdb=" CB HIS J 374 " pdb=" CG HIS J 374 " ideal model delta sigma weight residual 1.497 1.434 0.063 1.40e-02 5.10e+03 2.01e+01 bond pdb=" CB HIS F 374 " pdb=" CG HIS F 374 " ideal model delta sigma weight residual 1.497 1.435 0.062 1.40e-02 5.10e+03 1.99e+01 bond pdb=" CB HIS G 374 " pdb=" CG HIS G 374 " ideal model delta sigma weight residual 1.497 1.435 0.062 1.40e-02 5.10e+03 1.99e+01 bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.435 0.062 1.40e-02 5.10e+03 1.98e+01 ... (remaining 5655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 5391 1.61 - 3.21: 1419 3.21 - 4.81: 511 4.81 - 6.42: 169 6.42 - 8.02: 90 Bond angle restraints: 7580 Sorted by residual: angle pdb=" C LYS H 331 " pdb=" N PRO H 332 " pdb=" CA PRO H 332 " ideal model delta sigma weight residual 119.83 125.80 -5.97 1.08e+00 8.57e-01 3.05e+01 angle pdb=" C LYS B 331 " pdb=" N PRO B 332 " pdb=" CA PRO B 332 " ideal model delta sigma weight residual 119.83 125.78 -5.95 1.08e+00 8.57e-01 3.04e+01 angle pdb=" C LYS G 331 " pdb=" N PRO G 332 " pdb=" CA PRO G 332 " ideal model delta sigma weight residual 119.83 125.77 -5.94 1.08e+00 8.57e-01 3.02e+01 angle pdb=" C LYS E 331 " pdb=" N PRO E 332 " pdb=" CA PRO E 332 " ideal model delta sigma weight residual 119.83 125.76 -5.93 1.08e+00 8.57e-01 3.02e+01 angle pdb=" C LYS I 331 " pdb=" N PRO I 332 " pdb=" CA PRO I 332 " ideal model delta sigma weight residual 119.83 125.76 -5.93 1.08e+00 8.57e-01 3.01e+01 ... (remaining 7575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.54: 3280 12.54 - 25.09: 110 25.09 - 37.63: 30 37.63 - 50.17: 0 50.17 - 62.71: 20 Dihedral angle restraints: 3440 sinusoidal: 1430 harmonic: 2010 Sorted by residual: dihedral pdb=" C GLN H 336 " pdb=" N GLN H 336 " pdb=" CA GLN H 336 " pdb=" CB GLN H 336 " ideal model delta harmonic sigma weight residual -122.60 -113.50 -9.10 0 2.50e+00 1.60e-01 1.33e+01 dihedral pdb=" C GLN F 336 " pdb=" N GLN F 336 " pdb=" CA GLN F 336 " pdb=" CB GLN F 336 " ideal model delta harmonic sigma weight residual -122.60 -113.50 -9.10 0 2.50e+00 1.60e-01 1.32e+01 dihedral pdb=" C GLN J 336 " pdb=" N GLN J 336 " pdb=" CA GLN J 336 " pdb=" CB GLN J 336 " ideal model delta harmonic sigma weight residual -122.60 -113.50 -9.10 0 2.50e+00 1.60e-01 1.32e+01 ... (remaining 3437 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.085: 588 0.085 - 0.169: 192 0.169 - 0.252: 70 0.252 - 0.336: 0 0.336 - 0.419: 10 Chirality restraints: 860 Sorted by residual: chirality pdb=" CB VAL J 306 " pdb=" CA VAL J 306 " pdb=" CG1 VAL J 306 " pdb=" CG2 VAL J 306 " both_signs ideal model delta sigma weight residual False -2.63 -3.05 0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CB VAL E 306 " pdb=" CA VAL E 306 " pdb=" CG1 VAL E 306 " pdb=" CG2 VAL E 306 " both_signs ideal model delta sigma weight residual False -2.63 -3.04 0.42 2.00e-01 2.50e+01 4.32e+00 chirality pdb=" CB VAL A 306 " pdb=" CA VAL A 306 " pdb=" CG1 VAL A 306 " pdb=" CG2 VAL A 306 " both_signs ideal model delta sigma weight residual False -2.63 -3.04 0.42 2.00e-01 2.50e+01 4.32e+00 ... (remaining 857 not shown) Planarity restraints: 960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO I 332 " -0.015 2.00e-02 2.50e+03 2.91e-02 8.50e+00 pdb=" C PRO I 332 " 0.050 2.00e-02 2.50e+03 pdb=" O PRO I 332 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY I 333 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 332 " -0.015 2.00e-02 2.50e+03 2.90e-02 8.40e+00 pdb=" C PRO E 332 " 0.050 2.00e-02 2.50e+03 pdb=" O PRO E 332 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY E 333 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO G 332 " -0.015 2.00e-02 2.50e+03 2.90e-02 8.38e+00 pdb=" C PRO G 332 " 0.050 2.00e-02 2.50e+03 pdb=" O PRO G 332 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY G 333 " -0.017 2.00e-02 2.50e+03 ... (remaining 957 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 2342 2.93 - 3.42: 4551 3.42 - 3.91: 9620 3.91 - 4.41: 10462 4.41 - 4.90: 20321 Nonbonded interactions: 47296 Sorted by model distance: nonbonded pdb=" NZ LYS C 331 " pdb=" OE1 GLU D 338 " model vdw 2.435 3.120 nonbonded pdb=" NZ LYS B 331 " pdb=" OE1 GLU C 338 " model vdw 2.435 3.120 nonbonded pdb=" NZ LYS D 331 " pdb=" OE1 GLU E 338 " model vdw 2.435 3.120 nonbonded pdb=" NZ LYS I 331 " pdb=" OE1 GLU J 338 " model vdw 2.435 3.120 nonbonded pdb=" NZ LYS E 331 " pdb=" OE1 GLU F 338 " model vdw 2.435 3.120 ... (remaining 47291 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 15.800 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 29.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 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 : 0.021 0.128 5660 Z= 1.402 Angle : 1.918 8.024 7580 Z= 1.231 Chirality : 0.101 0.419 860 Planarity : 0.009 0.029 960 Dihedral : 9.104 62.709 2160 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % 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: -1.72 (0.27), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS C 362 PHE 0.018 0.006 PHE I 346 TYR 0.016 0.007 TYR J 310 ARG 0.002 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.739 Fit side-chains REVERT: A 321 LYS cc_start: 0.8157 (tttt) cc_final: 0.7477 (tmtt) REVERT: A 342 GLU cc_start: 0.8292 (mt-10) cc_final: 0.6861 (pm20) REVERT: A 343 LYS cc_start: 0.8179 (tttt) cc_final: 0.7588 (mmtt) REVERT: A 349 ARG cc_start: 0.7701 (mtm180) cc_final: 0.7427 (mtm180) REVERT: A 356 SER cc_start: 0.8777 (p) cc_final: 0.8535 (p) REVERT: A 360 ILE cc_start: 0.8927 (mt) cc_final: 0.8716 (mp) REVERT: A 369 LYS cc_start: 0.8744 (mttt) cc_final: 0.8194 (mttm) REVERT: A 370 LYS cc_start: 0.9112 (tttm) cc_final: 0.8840 (tttm) REVERT: B 316 SER cc_start: 0.8649 (p) cc_final: 0.8440 (p) REVERT: B 321 LYS cc_start: 0.8208 (tttt) cc_final: 0.7453 (tmtt) REVERT: B 343 LYS cc_start: 0.8415 (tttt) cc_final: 0.7874 (mmtt) REVERT: B 360 ILE cc_start: 0.9020 (mt) cc_final: 0.8709 (mp) REVERT: B 369 LYS cc_start: 0.8685 (mttt) cc_final: 0.7884 (mttp) REVERT: B 370 LYS cc_start: 0.9044 (tttm) cc_final: 0.8791 (tttm) REVERT: C 321 LYS cc_start: 0.7936 (tttt) cc_final: 0.7413 (mttp) REVERT: C 343 LYS cc_start: 0.8057 (tttt) cc_final: 0.7592 (mmtp) REVERT: C 360 ILE cc_start: 0.9001 (mt) cc_final: 0.8744 (mp) REVERT: D 321 LYS cc_start: 0.7958 (tttt) cc_final: 0.7371 (tttm) REVERT: D 360 ILE cc_start: 0.9092 (mt) cc_final: 0.8819 (mp) REVERT: E 311 LYS cc_start: 0.8219 (mttt) cc_final: 0.7575 (pttt) REVERT: E 321 LYS cc_start: 0.7769 (tttt) cc_final: 0.7099 (tttt) REVERT: E 360 ILE cc_start: 0.9057 (mt) cc_final: 0.8742 (mp) REVERT: E 369 LYS cc_start: 0.8586 (mttt) cc_final: 0.7852 (mttp) REVERT: E 370 LYS cc_start: 0.8949 (tttm) cc_final: 0.8684 (tttm) REVERT: F 311 LYS cc_start: 0.8191 (mttt) cc_final: 0.7510 (pttt) REVERT: F 321 LYS cc_start: 0.7992 (tttt) cc_final: 0.7288 (mttp) REVERT: F 342 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7921 (mm-30) REVERT: F 343 LYS cc_start: 0.7885 (tttt) cc_final: 0.7257 (mmtt) REVERT: F 360 ILE cc_start: 0.9045 (mt) cc_final: 0.8685 (mp) REVERT: G 311 LYS cc_start: 0.8366 (mttt) cc_final: 0.7947 (tttt) REVERT: G 321 LYS cc_start: 0.7939 (tttt) cc_final: 0.7291 (mttp) REVERT: G 343 LYS cc_start: 0.7768 (tttt) cc_final: 0.7342 (mmtt) REVERT: G 358 ASP cc_start: 0.8478 (m-30) cc_final: 0.8250 (m-30) REVERT: G 360 ILE cc_start: 0.8955 (mt) cc_final: 0.8705 (mp) REVERT: G 369 LYS cc_start: 0.8743 (mttt) cc_final: 0.8540 (mttt) REVERT: G 375 LYS cc_start: 0.8287 (tttt) cc_final: 0.7985 (ttpt) REVERT: H 311 LYS cc_start: 0.8061 (mttt) cc_final: 0.7544 (tttt) REVERT: H 321 LYS cc_start: 0.7949 (tttt) cc_final: 0.7323 (mttp) REVERT: H 343 LYS cc_start: 0.7771 (tttt) cc_final: 0.7304 (mptt) REVERT: H 358 ASP cc_start: 0.8501 (m-30) cc_final: 0.8242 (m-30) REVERT: H 360 ILE cc_start: 0.9173 (mt) cc_final: 0.8905 (mp) REVERT: H 369 LYS cc_start: 0.8658 (mttt) cc_final: 0.8415 (mttp) REVERT: I 311 LYS cc_start: 0.8282 (mttt) cc_final: 0.7674 (tttt) REVERT: I 316 SER cc_start: 0.8847 (p) cc_final: 0.8530 (p) REVERT: I 321 LYS cc_start: 0.7752 (tttt) cc_final: 0.7334 (mttm) REVERT: I 331 LYS cc_start: 0.8864 (mtpt) cc_final: 0.8578 (mtmt) REVERT: I 338 GLU cc_start: 0.8724 (tt0) cc_final: 0.8471 (tt0) REVERT: I 343 LYS cc_start: 0.7700 (tttt) cc_final: 0.7190 (mptp) REVERT: I 349 ARG cc_start: 0.7568 (mtm180) cc_final: 0.7293 (mtm180) REVERT: I 358 ASP cc_start: 0.8449 (m-30) cc_final: 0.8182 (m-30) REVERT: I 360 ILE cc_start: 0.9106 (mt) cc_final: 0.8820 (mp) REVERT: I 369 LYS cc_start: 0.8671 (mttt) cc_final: 0.7944 (mttp) REVERT: I 370 LYS cc_start: 0.9060 (tttm) cc_final: 0.8598 (tttm) REVERT: J 311 LYS cc_start: 0.8317 (mttt) cc_final: 0.7634 (tttt) REVERT: J 321 LYS cc_start: 0.7930 (tttt) cc_final: 0.7565 (mttm) REVERT: J 358 ASP cc_start: 0.8422 (m-30) cc_final: 0.8067 (m-30) REVERT: J 360 ILE cc_start: 0.9110 (mt) cc_final: 0.8780 (mp) REVERT: J 369 LYS cc_start: 0.8751 (mttt) cc_final: 0.8494 (mppt) REVERT: J 370 LYS cc_start: 0.8884 (tttm) cc_final: 0.8646 (tttm) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 1.3809 time to fit residues: 372.7206 Evaluate side-chains 211 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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: 4.9990 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 18 optimal weight: 0.4980 chunk 35 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 ASN E 327 ASN E 336 GLN ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 336 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.156695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.126828 restraints weight = 5415.191| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.75 r_work: 0.3452 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 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 : 0.003 0.020 5660 Z= 0.186 Angle : 0.592 5.150 7580 Z= 0.318 Chirality : 0.050 0.150 860 Planarity : 0.003 0.021 960 Dihedral : 4.990 16.563 740 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.50 % Allowed : 12.03 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.29), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 374 PHE 0.004 0.001 PHE H 346 TYR 0.011 0.002 TYR D 310 ARG 0.001 0.000 ARG I 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 219 time to evaluate : 0.711 Fit side-chains REVERT: A 321 LYS cc_start: 0.8322 (tttt) cc_final: 0.8112 (tmtt) REVERT: A 343 LYS cc_start: 0.8415 (tttt) cc_final: 0.8203 (mmtt) REVERT: A 360 ILE cc_start: 0.9222 (mt) cc_final: 0.8977 (mp) REVERT: B 321 LYS cc_start: 0.8304 (tttt) cc_final: 0.7947 (tmtt) REVERT: B 342 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.7400 (mp0) REVERT: B 343 LYS cc_start: 0.8542 (tttt) cc_final: 0.8214 (mmtt) REVERT: B 360 ILE cc_start: 0.9265 (mt) cc_final: 0.8977 (mp) REVERT: B 369 LYS cc_start: 0.8881 (mttt) cc_final: 0.8322 (mttp) REVERT: C 338 GLU cc_start: 0.9143 (tt0) cc_final: 0.8815 (tt0) REVERT: C 343 LYS cc_start: 0.8258 (tttt) cc_final: 0.7911 (mmtt) REVERT: D 321 LYS cc_start: 0.8269 (tttt) cc_final: 0.7973 (tttm) REVERT: D 342 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8225 (mt-10) REVERT: D 343 LYS cc_start: 0.8236 (tttt) cc_final: 0.7880 (mmtt) REVERT: D 356 SER cc_start: 0.9356 (p) cc_final: 0.8653 (m) REVERT: D 370 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.9037 (tttp) REVERT: E 321 LYS cc_start: 0.8227 (tttt) cc_final: 0.7920 (ttpt) REVERT: E 369 LYS cc_start: 0.8849 (mttt) cc_final: 0.8307 (mttp) REVERT: F 343 LYS cc_start: 0.8251 (tttt) cc_final: 0.7620 (mmtt) REVERT: F 369 LYS cc_start: 0.9187 (mppt) cc_final: 0.8526 (mttp) REVERT: G 342 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7491 (mm-30) REVERT: G 343 LYS cc_start: 0.8085 (tttt) cc_final: 0.7727 (mmtt) REVERT: G 375 LYS cc_start: 0.8318 (tttt) cc_final: 0.8010 (ttpt) REVERT: H 358 ASP cc_start: 0.9122 (m-30) cc_final: 0.8849 (m-30) REVERT: H 369 LYS cc_start: 0.8993 (mttt) cc_final: 0.8790 (mttp) REVERT: I 331 LYS cc_start: 0.9316 (mtpt) cc_final: 0.9089 (mtmt) REVERT: I 343 LYS cc_start: 0.7676 (tttt) cc_final: 0.7475 (mptp) REVERT: I 345 ASP cc_start: 0.8188 (t0) cc_final: 0.7832 (t0) REVERT: I 349 ARG cc_start: 0.8072 (mtm180) cc_final: 0.7737 (mtm180) REVERT: I 360 ILE cc_start: 0.9445 (mt) cc_final: 0.9228 (mp) REVERT: I 369 LYS cc_start: 0.8997 (mttt) cc_final: 0.8400 (mttp) REVERT: I 370 LYS cc_start: 0.8994 (tttm) cc_final: 0.8693 (tmtm) REVERT: J 360 ILE cc_start: 0.9502 (mt) cc_final: 0.9216 (mp) REVERT: J 370 LYS cc_start: 0.9127 (tttm) cc_final: 0.8685 (tptt) outliers start: 16 outliers final: 2 residues processed: 223 average time/residue: 1.2559 time to fit residues: 290.6548 Evaluate side-chains 211 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 205 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain G residue 342 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 41 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN D 336 GLN E 327 ASN F 327 ASN H 336 GLN I 351 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.150120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.120236 restraints weight = 5531.148| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.74 r_work: 0.3364 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.064 5660 Z= 0.735 Angle : 0.867 8.374 7580 Z= 0.440 Chirality : 0.053 0.136 860 Planarity : 0.005 0.041 960 Dihedral : 5.889 21.626 740 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 5.31 % Allowed : 14.06 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.29), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS I 330 PHE 0.013 0.002 PHE A 378 TYR 0.014 0.003 TYR D 310 ARG 0.003 0.001 ARG I 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 234 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8383 (tttt) cc_final: 0.8104 (tmtt) REVERT: B 321 LYS cc_start: 0.8405 (tttt) cc_final: 0.8192 (mttp) REVERT: B 342 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: B 343 LYS cc_start: 0.8559 (tttt) cc_final: 0.8297 (mmtt) REVERT: B 347 LYS cc_start: 0.7662 (mttp) cc_final: 0.6652 (mtmt) REVERT: B 360 ILE cc_start: 0.9397 (mt) cc_final: 0.9126 (mp) REVERT: B 369 LYS cc_start: 0.9017 (mttt) cc_final: 0.8342 (mttp) REVERT: C 327 ASN cc_start: 0.8708 (m-40) cc_final: 0.8409 (t0) REVERT: C 338 GLU cc_start: 0.9193 (tt0) cc_final: 0.8890 (tt0) REVERT: C 343 LYS cc_start: 0.8420 (tttt) cc_final: 0.7971 (mmtt) REVERT: C 349 ARG cc_start: 0.8408 (mtm180) cc_final: 0.8082 (mtp-110) REVERT: D 327 ASN cc_start: 0.8626 (m-40) cc_final: 0.8360 (t0) REVERT: D 338 GLU cc_start: 0.9064 (tt0) cc_final: 0.8857 (tt0) REVERT: D 342 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7867 (mm-30) REVERT: D 343 LYS cc_start: 0.8341 (tttt) cc_final: 0.7922 (mmtt) REVERT: D 349 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7874 (mtm180) REVERT: E 311 LYS cc_start: 0.8413 (mttt) cc_final: 0.7619 (pttt) REVERT: E 321 LYS cc_start: 0.8282 (tttt) cc_final: 0.7921 (ttpt) REVERT: E 342 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8200 (mt-10) REVERT: E 343 LYS cc_start: 0.8374 (tttt) cc_final: 0.7759 (mmtt) REVERT: E 347 LYS cc_start: 0.7529 (mttp) cc_final: 0.7110 (mmtp) REVERT: E 369 LYS cc_start: 0.9122 (mttt) cc_final: 0.8446 (mttp) REVERT: F 311 LYS cc_start: 0.8375 (mttt) cc_final: 0.7728 (pttt) REVERT: F 343 LYS cc_start: 0.8403 (tttt) cc_final: 0.7737 (mmtt) REVERT: F 358 ASP cc_start: 0.9119 (m-30) cc_final: 0.8883 (m-30) REVERT: F 369 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8552 (mttp) REVERT: G 343 LYS cc_start: 0.8160 (tttt) cc_final: 0.7756 (mmtt) REVERT: H 342 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8105 (mm-30) REVERT: H 358 ASP cc_start: 0.9062 (m-30) cc_final: 0.8782 (m-30) REVERT: I 343 LYS cc_start: 0.8178 (tttt) cc_final: 0.7755 (mptp) REVERT: I 345 ASP cc_start: 0.8057 (t0) cc_final: 0.7628 (t0) REVERT: I 349 ARG cc_start: 0.8412 (mtm180) cc_final: 0.8062 (mtm180) REVERT: I 353 LYS cc_start: 0.9127 (ttpt) cc_final: 0.8925 (ttpp) REVERT: I 356 SER cc_start: 0.9329 (p) cc_final: 0.9086 (p) REVERT: I 360 ILE cc_start: 0.9541 (mt) cc_final: 0.9291 (mp) REVERT: I 369 LYS cc_start: 0.9088 (mttt) cc_final: 0.8441 (mttp) REVERT: J 317 LYS cc_start: 0.8597 (tttt) cc_final: 0.8364 (ttmm) REVERT: J 325 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8949 (tt) outliers start: 34 outliers final: 11 residues processed: 243 average time/residue: 1.3196 time to fit residues: 332.3635 Evaluate side-chains 245 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 227 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 369 LYS Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain H residue 361 THR Chi-restraints excluded: chain I residue 317 LYS Chi-restraints excluded: chain J residue 325 LEU 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 24 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 35 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 327 ASN F 327 ASN I 327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.157407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.127572 restraints weight = 5597.300| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.77 r_work: 0.3467 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5660 Z= 0.182 Angle : 0.577 6.317 7580 Z= 0.300 Chirality : 0.049 0.137 860 Planarity : 0.003 0.036 960 Dihedral : 5.046 16.833 740 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.59 % Allowed : 18.44 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.29), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 374 PHE 0.005 0.001 PHE A 346 TYR 0.008 0.001 TYR C 310 ARG 0.001 0.000 ARG I 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 210 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8462 (tttt) cc_final: 0.8105 (tmtt) REVERT: A 342 GLU cc_start: 0.8577 (mt-10) cc_final: 0.7512 (pm20) REVERT: B 342 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.7291 (mp0) REVERT: B 343 LYS cc_start: 0.8542 (tttt) cc_final: 0.8218 (mmtt) REVERT: B 347 LYS cc_start: 0.7688 (mttp) cc_final: 0.6559 (mtmt) REVERT: B 360 ILE cc_start: 0.9326 (mt) cc_final: 0.9078 (mp) REVERT: B 369 LYS cc_start: 0.8980 (mttt) cc_final: 0.8414 (mttp) REVERT: C 327 ASN cc_start: 0.8189 (m-40) cc_final: 0.7949 (t0) REVERT: C 338 GLU cc_start: 0.9153 (tt0) cc_final: 0.8822 (tt0) REVERT: C 343 LYS cc_start: 0.8383 (tttt) cc_final: 0.7917 (mmtt) REVERT: C 349 ARG cc_start: 0.8369 (mtm180) cc_final: 0.8024 (mtp-110) REVERT: C 356 SER cc_start: 0.9357 (p) cc_final: 0.8732 (m) REVERT: D 321 LYS cc_start: 0.8786 (mttm) cc_final: 0.8051 (tmmt) REVERT: D 327 ASN cc_start: 0.8371 (m-40) cc_final: 0.8147 (t0) REVERT: D 342 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7885 (mm-30) REVERT: D 343 LYS cc_start: 0.8310 (tttt) cc_final: 0.7796 (mmtt) REVERT: D 356 SER cc_start: 0.9378 (p) cc_final: 0.8814 (m) REVERT: E 317 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8004 (tttt) REVERT: E 321 LYS cc_start: 0.8164 (tttt) cc_final: 0.7878 (ttpt) REVERT: E 342 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8205 (mm-30) REVERT: E 343 LYS cc_start: 0.8309 (tttt) cc_final: 0.7709 (mmtt) REVERT: E 369 LYS cc_start: 0.9090 (mttt) cc_final: 0.8528 (mttp) REVERT: F 343 LYS cc_start: 0.8311 (tttt) cc_final: 0.7564 (mmtt) REVERT: F 369 LYS cc_start: 0.9157 (mtpt) cc_final: 0.8552 (mttp) REVERT: G 321 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8502 (mttp) REVERT: G 342 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8316 (mm-30) REVERT: G 343 LYS cc_start: 0.8099 (tttt) cc_final: 0.7768 (mmtt) REVERT: H 342 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7703 (mm-30) REVERT: H 358 ASP cc_start: 0.9005 (m-30) cc_final: 0.8744 (m-30) REVERT: I 343 LYS cc_start: 0.7928 (tttt) cc_final: 0.7543 (mptp) REVERT: I 345 ASP cc_start: 0.8033 (t0) cc_final: 0.7599 (t0) REVERT: I 349 ARG cc_start: 0.8253 (mtm180) cc_final: 0.7996 (mtm180) REVERT: I 360 ILE cc_start: 0.9446 (mt) cc_final: 0.9204 (mp) REVERT: I 369 LYS cc_start: 0.9037 (mttt) cc_final: 0.8393 (mttp) REVERT: J 345 ASP cc_start: 0.7888 (t0) cc_final: 0.7417 (t0) outliers start: 23 outliers final: 3 residues processed: 217 average time/residue: 1.3491 time to fit residues: 303.1555 Evaluate side-chains 216 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 206 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain E residue 317 LYS Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain H residue 342 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 5 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 11 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 327 ASN F 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.151889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.121931 restraints weight = 5589.571| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.76 r_work: 0.3392 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 5660 Z= 0.426 Angle : 0.684 6.817 7580 Z= 0.348 Chirality : 0.049 0.134 860 Planarity : 0.004 0.044 960 Dihedral : 5.399 18.708 740 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 5.31 % Allowed : 18.44 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.29), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 329 PHE 0.006 0.001 PHE G 378 TYR 0.010 0.002 TYR C 310 ARG 0.002 0.000 ARG I 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 221 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8356 (tttt) cc_final: 0.8071 (ttpt) REVERT: A 342 GLU cc_start: 0.8615 (mt-10) cc_final: 0.7491 (pm20) REVERT: A 369 LYS cc_start: 0.9144 (mttt) cc_final: 0.8834 (mttt) REVERT: B 342 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: B 343 LYS cc_start: 0.8498 (tttt) cc_final: 0.8213 (mmtt) REVERT: B 347 LYS cc_start: 0.7701 (mttp) cc_final: 0.6519 (mtmt) REVERT: B 360 ILE cc_start: 0.9344 (mt) cc_final: 0.9091 (mp) REVERT: B 369 LYS cc_start: 0.9021 (mttt) cc_final: 0.8448 (mttp) REVERT: C 327 ASN cc_start: 0.8370 (m-40) cc_final: 0.8073 (t0) REVERT: C 343 LYS cc_start: 0.8403 (tttt) cc_final: 0.8024 (mmtt) REVERT: C 349 ARG cc_start: 0.8462 (mtm180) cc_final: 0.8180 (mtm180) REVERT: D 321 LYS cc_start: 0.8756 (mttm) cc_final: 0.7985 (tmmt) REVERT: D 327 ASN cc_start: 0.8510 (m-40) cc_final: 0.8257 (t0) REVERT: D 342 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7783 (mm-30) REVERT: D 343 LYS cc_start: 0.8309 (tttt) cc_final: 0.7860 (mmtt) REVERT: D 349 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7814 (mtm180) REVERT: D 356 SER cc_start: 0.9378 (p) cc_final: 0.8781 (m) REVERT: E 311 LYS cc_start: 0.8306 (mttt) cc_final: 0.7560 (pttt) REVERT: E 321 LYS cc_start: 0.8216 (tttt) cc_final: 0.7883 (ttpt) REVERT: E 342 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8305 (mm-30) REVERT: E 343 LYS cc_start: 0.8357 (tttt) cc_final: 0.7760 (mmtt) REVERT: E 356 SER cc_start: 0.9352 (p) cc_final: 0.8725 (m) REVERT: E 369 LYS cc_start: 0.9156 (mttt) cc_final: 0.8505 (mttp) REVERT: F 343 LYS cc_start: 0.8407 (tttt) cc_final: 0.7646 (mmtt) REVERT: G 342 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.7947 (mm-30) REVERT: G 343 LYS cc_start: 0.8088 (tttt) cc_final: 0.7712 (mmtt) REVERT: H 342 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7953 (mm-30) REVERT: H 358 ASP cc_start: 0.9057 (m-30) cc_final: 0.8791 (m-30) REVERT: I 342 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7332 (mt-10) REVERT: I 343 LYS cc_start: 0.8174 (tttt) cc_final: 0.7684 (mptp) REVERT: I 345 ASP cc_start: 0.8058 (t0) cc_final: 0.7613 (t0) REVERT: I 349 ARG cc_start: 0.8378 (mtm180) cc_final: 0.8052 (mtm180) REVERT: I 356 SER cc_start: 0.9329 (p) cc_final: 0.9105 (p) REVERT: I 369 LYS cc_start: 0.9108 (mttt) cc_final: 0.8464 (mttp) REVERT: J 345 ASP cc_start: 0.7852 (t0) cc_final: 0.7394 (t0) outliers start: 34 outliers final: 9 residues processed: 232 average time/residue: 1.3477 time to fit residues: 323.7003 Evaluate side-chains 237 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 221 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain H residue 361 THR Chi-restraints excluded: chain H residue 370 LYS Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain J residue 321 LYS Chi-restraints excluded: chain J residue 373 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 21 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS E 327 ASN F 327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.154010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.124012 restraints weight = 5516.840| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.75 r_work: 0.3421 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5660 Z= 0.283 Angle : 0.622 6.642 7580 Z= 0.319 Chirality : 0.049 0.124 860 Planarity : 0.004 0.045 960 Dihedral : 5.219 17.028 740 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 4.69 % Allowed : 18.91 % Favored : 76.41 % 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: -2.08 (0.28), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 374 PHE 0.006 0.001 PHE G 378 TYR 0.010 0.002 TYR C 310 ARG 0.001 0.000 ARG I 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 210 time to evaluate : 0.721 Fit side-chains REVERT: A 321 LYS cc_start: 0.8421 (tttt) cc_final: 0.8117 (tmtt) REVERT: A 342 GLU cc_start: 0.8602 (mt-10) cc_final: 0.7557 (pm20) REVERT: A 347 LYS cc_start: 0.7739 (mttp) cc_final: 0.7242 (mtpt) REVERT: A 369 LYS cc_start: 0.9138 (mttt) cc_final: 0.8829 (mttt) REVERT: B 321 LYS cc_start: 0.8785 (mttp) cc_final: 0.7862 (ttpt) REVERT: B 342 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: B 343 LYS cc_start: 0.8560 (tttt) cc_final: 0.8228 (mmtt) REVERT: B 347 LYS cc_start: 0.7638 (mttp) cc_final: 0.6451 (mtmt) REVERT: B 360 ILE cc_start: 0.9351 (mt) cc_final: 0.9080 (mp) REVERT: B 369 LYS cc_start: 0.9021 (mttt) cc_final: 0.8448 (mttp) REVERT: C 327 ASN cc_start: 0.8281 (m-40) cc_final: 0.7993 (t0) REVERT: C 343 LYS cc_start: 0.8392 (tttt) cc_final: 0.7917 (mmtt) REVERT: C 349 ARG cc_start: 0.8387 (mtm180) cc_final: 0.8100 (mtm180) REVERT: C 351 GLN cc_start: 0.8601 (tt0) cc_final: 0.8338 (tt0) REVERT: D 321 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.7918 (tmmt) REVERT: D 327 ASN cc_start: 0.8449 (m-40) cc_final: 0.8185 (t0) REVERT: D 342 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7745 (mm-30) REVERT: D 343 LYS cc_start: 0.8327 (tttt) cc_final: 0.7786 (mmtt) REVERT: D 349 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7824 (mtm180) REVERT: D 356 SER cc_start: 0.9369 (p) cc_final: 0.8799 (m) REVERT: E 321 LYS cc_start: 0.8180 (tttt) cc_final: 0.7874 (ttpt) REVERT: E 342 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8364 (mm-30) REVERT: E 356 SER cc_start: 0.9320 (p) cc_final: 0.8729 (m) REVERT: E 369 LYS cc_start: 0.9121 (mttt) cc_final: 0.8524 (mttp) REVERT: F 343 LYS cc_start: 0.8314 (tttt) cc_final: 0.7606 (mmtt) REVERT: G 321 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8586 (mttp) REVERT: G 342 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.7898 (mm-30) REVERT: G 343 LYS cc_start: 0.8105 (tttt) cc_final: 0.7819 (mmtt) REVERT: H 342 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7769 (mm-30) REVERT: I 343 LYS cc_start: 0.8220 (tttt) cc_final: 0.7778 (mptp) REVERT: I 345 ASP cc_start: 0.8061 (t0) cc_final: 0.7633 (t0) REVERT: I 349 ARG cc_start: 0.8319 (mtm180) cc_final: 0.8008 (mtm180) REVERT: I 369 LYS cc_start: 0.9073 (mttt) cc_final: 0.8421 (mttp) REVERT: J 345 ASP cc_start: 0.7885 (t0) cc_final: 0.7438 (t0) outliers start: 30 outliers final: 9 residues processed: 218 average time/residue: 1.4995 time to fit residues: 338.5788 Evaluate side-chains 224 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 207 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain H residue 370 LYS Chi-restraints excluded: chain I residue 357 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 0 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 14 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 327 ASN F 327 ASN ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.150080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.120147 restraints weight = 5618.138| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.75 r_work: 0.3361 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.049 5660 Z= 0.581 Angle : 0.764 9.197 7580 Z= 0.385 Chirality : 0.051 0.125 860 Planarity : 0.005 0.053 960 Dihedral : 5.626 19.218 740 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 5.31 % Allowed : 19.38 % Favored : 75.31 % 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: -2.22 (0.28), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 362 PHE 0.007 0.001 PHE G 378 TYR 0.010 0.002 TYR B 310 ARG 0.002 0.001 ARG I 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 211 time to evaluate : 0.705 Fit side-chains REVERT: A 321 LYS cc_start: 0.8378 (tttt) cc_final: 0.8089 (ttpt) REVERT: A 342 GLU cc_start: 0.8681 (mt-10) cc_final: 0.7620 (pm20) REVERT: A 347 LYS cc_start: 0.7874 (mttp) cc_final: 0.7328 (mtpt) REVERT: A 369 LYS cc_start: 0.9177 (mttt) cc_final: 0.8931 (mttt) REVERT: B 317 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.7731 (ttpp) REVERT: B 321 LYS cc_start: 0.8811 (mttp) cc_final: 0.7919 (tttt) REVERT: B 342 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: B 343 LYS cc_start: 0.8512 (tttt) cc_final: 0.8254 (mmtt) REVERT: B 347 LYS cc_start: 0.7751 (mttp) cc_final: 0.6563 (mtmt) REVERT: B 360 ILE cc_start: 0.9393 (mt) cc_final: 0.9116 (mp) REVERT: B 369 LYS cc_start: 0.9053 (mttt) cc_final: 0.8430 (mttp) REVERT: C 327 ASN cc_start: 0.8453 (m-40) cc_final: 0.8188 (t0) REVERT: C 343 LYS cc_start: 0.8413 (tttt) cc_final: 0.8008 (mmtt) REVERT: C 349 ARG cc_start: 0.8452 (mtm180) cc_final: 0.8095 (mtm180) REVERT: D 321 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.7887 (tmmt) REVERT: D 327 ASN cc_start: 0.8583 (m-40) cc_final: 0.8303 (t0) REVERT: D 342 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7799 (mm-30) REVERT: D 343 LYS cc_start: 0.8301 (tttt) cc_final: 0.7838 (mmtt) REVERT: D 349 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7842 (mtm180) REVERT: D 356 SER cc_start: 0.9371 (p) cc_final: 0.8776 (m) REVERT: E 311 LYS cc_start: 0.8227 (mttt) cc_final: 0.7482 (pttt) REVERT: E 321 LYS cc_start: 0.8274 (tttt) cc_final: 0.7911 (ttpt) REVERT: E 342 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8333 (mm-30) REVERT: E 343 LYS cc_start: 0.8360 (tttt) cc_final: 0.7675 (mmtt) REVERT: E 347 LYS cc_start: 0.7570 (mttp) cc_final: 0.7083 (mmtp) REVERT: E 356 SER cc_start: 0.9350 (p) cc_final: 0.8718 (m) REVERT: E 369 LYS cc_start: 0.9166 (mttt) cc_final: 0.8549 (mttp) REVERT: F 343 LYS cc_start: 0.8318 (tttt) cc_final: 0.7632 (mmtt) REVERT: G 321 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8532 (mttp) REVERT: G 342 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.7968 (mm-30) REVERT: G 343 LYS cc_start: 0.8163 (tttt) cc_final: 0.7727 (mmtt) REVERT: H 342 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7924 (mm-30) REVERT: I 343 LYS cc_start: 0.8204 (tttt) cc_final: 0.7732 (mptp) REVERT: I 345 ASP cc_start: 0.8074 (t0) cc_final: 0.7630 (t0) REVERT: I 349 ARG cc_start: 0.8430 (mtm180) cc_final: 0.8136 (mtm180) REVERT: I 356 SER cc_start: 0.9323 (p) cc_final: 0.9117 (p) REVERT: I 369 LYS cc_start: 0.9108 (mttt) cc_final: 0.8432 (mttp) REVERT: J 345 ASP cc_start: 0.7894 (t0) cc_final: 0.7444 (t0) outliers start: 34 outliers final: 10 residues processed: 224 average time/residue: 1.4048 time to fit residues: 325.7826 Evaluate side-chains 232 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 213 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain H residue 361 THR Chi-restraints excluded: chain I residue 370 LYS Chi-restraints excluded: chain J residue 321 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 52 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 374 HIS E 327 ASN F 327 ASN ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 327 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.156096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.126318 restraints weight = 5585.439| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.77 r_work: 0.3461 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5660 Z= 0.182 Angle : 0.573 5.850 7580 Z= 0.296 Chirality : 0.049 0.119 860 Planarity : 0.004 0.046 960 Dihedral : 5.068 14.982 740 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.59 % Allowed : 20.94 % Favored : 75.47 % 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: -2.13 (0.29), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 374 PHE 0.006 0.001 PHE G 378 TYR 0.009 0.002 TYR D 310 ARG 0.000 0.000 ARG I 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 0.722 Fit side-chains REVERT: A 321 LYS cc_start: 0.8427 (tttt) cc_final: 0.8137 (tmtt) REVERT: A 342 GLU cc_start: 0.8524 (mt-10) cc_final: 0.7429 (pm20) REVERT: A 347 LYS cc_start: 0.7804 (mttp) cc_final: 0.7273 (mtpt) REVERT: A 369 LYS cc_start: 0.9162 (mttt) cc_final: 0.8849 (mttt) REVERT: B 321 LYS cc_start: 0.8805 (mttp) cc_final: 0.7945 (tmmt) REVERT: B 342 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: B 343 LYS cc_start: 0.8544 (tttt) cc_final: 0.8208 (mmtt) REVERT: B 347 LYS cc_start: 0.7716 (mttp) cc_final: 0.6523 (mtmt) REVERT: B 360 ILE cc_start: 0.9331 (mt) cc_final: 0.9059 (mp) REVERT: B 369 LYS cc_start: 0.9017 (mttt) cc_final: 0.8444 (mttp) REVERT: C 343 LYS cc_start: 0.8367 (tttt) cc_final: 0.7949 (mmtt) REVERT: C 349 ARG cc_start: 0.8339 (mtm180) cc_final: 0.8103 (mtm180) REVERT: C 356 SER cc_start: 0.9352 (p) cc_final: 0.8760 (m) REVERT: D 311 LYS cc_start: 0.8578 (pttp) cc_final: 0.7588 (tttt) REVERT: D 321 LYS cc_start: 0.8780 (mttm) cc_final: 0.7954 (tmmt) REVERT: D 327 ASN cc_start: 0.8316 (m-40) cc_final: 0.8115 (t0) REVERT: D 342 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7723 (mm-30) REVERT: D 343 LYS cc_start: 0.8311 (tttt) cc_final: 0.7747 (mmtt) REVERT: D 349 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7860 (mtm180) REVERT: D 356 SER cc_start: 0.9356 (p) cc_final: 0.8825 (m) REVERT: E 321 LYS cc_start: 0.8159 (tttt) cc_final: 0.7875 (ttpt) REVERT: E 342 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8275 (mm-30) REVERT: E 343 LYS cc_start: 0.8214 (tttt) cc_final: 0.7786 (mptt) REVERT: E 356 SER cc_start: 0.9243 (p) cc_final: 0.8799 (m) REVERT: E 369 LYS cc_start: 0.9125 (mttt) cc_final: 0.8521 (mttp) REVERT: F 343 LYS cc_start: 0.8256 (tttt) cc_final: 0.7569 (mmtt) REVERT: G 342 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7822 (mm-30) REVERT: G 343 LYS cc_start: 0.8048 (tttt) cc_final: 0.7786 (mmtt) REVERT: G 349 ARG cc_start: 0.8110 (mtm180) cc_final: 0.7765 (ttp-170) REVERT: H 342 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7749 (mm-30) REVERT: I 343 LYS cc_start: 0.8075 (tttt) cc_final: 0.7655 (mptp) REVERT: I 345 ASP cc_start: 0.7998 (t0) cc_final: 0.7550 (t0) REVERT: I 349 ARG cc_start: 0.8318 (mtm180) cc_final: 0.7993 (mtm180) REVERT: I 369 LYS cc_start: 0.9115 (mttt) cc_final: 0.8461 (mttp) REVERT: J 345 ASP cc_start: 0.7933 (t0) cc_final: 0.7504 (t0) REVERT: J 360 ILE cc_start: 0.9475 (mt) cc_final: 0.9270 (mp) outliers start: 23 outliers final: 7 residues processed: 209 average time/residue: 1.3545 time to fit residues: 293.2167 Evaluate side-chains 212 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 199 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain I residue 317 LYS Chi-restraints excluded: chain I residue 357 LEU Chi-restraints excluded: chain J residue 321 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 66 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 327 ASN E 327 ASN F 327 ASN ** F 374 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 = 0.3898 r_free = 0.3898 target = 0.150439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.120363 restraints weight = 5612.242| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.75 r_work: 0.3330 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 5660 Z= 0.543 Angle : 0.747 8.828 7580 Z= 0.375 Chirality : 0.051 0.161 860 Planarity : 0.005 0.053 960 Dihedral : 5.584 18.501 740 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 3.59 % Allowed : 21.56 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.28), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 362 PHE 0.009 0.001 PHE G 378 TYR 0.011 0.002 TYR D 310 ARG 0.003 0.001 ARG I 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 212 time to evaluate : 0.697 Fit side-chains REVERT: A 321 LYS cc_start: 0.8366 (tttt) cc_final: 0.8072 (ttpt) REVERT: A 342 GLU cc_start: 0.8688 (mt-10) cc_final: 0.7643 (pm20) REVERT: A 347 LYS cc_start: 0.7849 (mttp) cc_final: 0.7311 (mtpt) REVERT: A 369 LYS cc_start: 0.9173 (mttt) cc_final: 0.8923 (mttt) REVERT: B 321 LYS cc_start: 0.8845 (mttp) cc_final: 0.7987 (tmmt) REVERT: B 342 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.7287 (mp0) REVERT: B 343 LYS cc_start: 0.8502 (tttt) cc_final: 0.8256 (mmtt) REVERT: B 347 LYS cc_start: 0.7787 (mttp) cc_final: 0.6589 (mtmt) REVERT: B 360 ILE cc_start: 0.9394 (mt) cc_final: 0.9120 (mp) REVERT: B 369 LYS cc_start: 0.9070 (mttt) cc_final: 0.8430 (mttp) REVERT: C 317 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8458 (ttpt) REVERT: C 343 LYS cc_start: 0.8406 (tttt) cc_final: 0.7969 (mmtt) REVERT: C 349 ARG cc_start: 0.8429 (mtm180) cc_final: 0.8070 (mtm180) REVERT: D 321 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.7979 (tmmt) REVERT: D 327 ASN cc_start: 0.8580 (m-40) cc_final: 0.8320 (t0) REVERT: D 342 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7843 (mm-30) REVERT: D 343 LYS cc_start: 0.8342 (tttt) cc_final: 0.7875 (mmtt) REVERT: D 349 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7821 (mtm180) REVERT: D 356 SER cc_start: 0.9361 (p) cc_final: 0.8752 (m) REVERT: E 311 LYS cc_start: 0.8204 (mttt) cc_final: 0.7494 (pttt) REVERT: E 321 LYS cc_start: 0.8272 (tttt) cc_final: 0.7917 (ttpt) REVERT: E 342 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8323 (mm-30) REVERT: E 343 LYS cc_start: 0.8312 (tttt) cc_final: 0.7748 (mmtt) REVERT: E 347 LYS cc_start: 0.7552 (mttp) cc_final: 0.7048 (mmtp) REVERT: E 356 SER cc_start: 0.9342 (p) cc_final: 0.8712 (m) REVERT: E 369 LYS cc_start: 0.9167 (mttt) cc_final: 0.8579 (mttp) REVERT: F 343 LYS cc_start: 0.8377 (tttt) cc_final: 0.7677 (mmtt) REVERT: G 342 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8014 (mm-30) REVERT: G 343 LYS cc_start: 0.8157 (tttt) cc_final: 0.7755 (mmtt) REVERT: G 349 ARG cc_start: 0.8218 (mtm180) cc_final: 0.7858 (ttp-170) REVERT: H 342 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7891 (mm-30) REVERT: H 358 ASP cc_start: 0.9023 (m-30) cc_final: 0.8805 (m-30) REVERT: I 342 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7388 (mt-10) REVERT: I 343 LYS cc_start: 0.8223 (tttt) cc_final: 0.7750 (mptp) REVERT: I 345 ASP cc_start: 0.8096 (t0) cc_final: 0.7683 (t0) REVERT: I 356 SER cc_start: 0.9314 (p) cc_final: 0.9089 (p) REVERT: I 369 LYS cc_start: 0.9159 (mttt) cc_final: 0.8499 (mttp) REVERT: J 345 ASP cc_start: 0.7932 (t0) cc_final: 0.7493 (t0) outliers start: 23 outliers final: 7 residues processed: 219 average time/residue: 1.4424 time to fit residues: 326.5961 Evaluate side-chains 228 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 213 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain I residue 370 LYS Chi-restraints excluded: chain J residue 321 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 41 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 327 ASN E 327 ASN F 327 ASN F 374 HIS I 327 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.158172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.128293 restraints weight = 5586.518| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.77 r_work: 0.3499 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 5660 Z= 0.147 Angle : 0.549 6.598 7580 Z= 0.285 Chirality : 0.048 0.118 860 Planarity : 0.004 0.044 960 Dihedral : 5.003 14.609 740 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.41 % Allowed : 23.75 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.29), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS G 374 PHE 0.007 0.001 PHE G 378 TYR 0.008 0.001 TYR D 310 ARG 0.001 0.000 ARG H 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 195 time to evaluate : 0.723 Fit side-chains REVERT: A 321 LYS cc_start: 0.8414 (tttt) cc_final: 0.8140 (tmtt) REVERT: A 342 GLU cc_start: 0.8535 (mt-10) cc_final: 0.7394 (pm20) REVERT: A 347 LYS cc_start: 0.7750 (mttp) cc_final: 0.7236 (mtpt) REVERT: A 369 LYS cc_start: 0.9133 (mttt) cc_final: 0.8817 (mttt) REVERT: B 321 LYS cc_start: 0.8823 (mttp) cc_final: 0.7963 (tmmt) REVERT: B 342 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: B 343 LYS cc_start: 0.8511 (tttt) cc_final: 0.8166 (mmtt) REVERT: B 347 LYS cc_start: 0.7739 (mttp) cc_final: 0.6508 (mtmt) REVERT: B 360 ILE cc_start: 0.9299 (mt) cc_final: 0.9038 (mp) REVERT: B 369 LYS cc_start: 0.9008 (mttt) cc_final: 0.8433 (mttp) REVERT: C 343 LYS cc_start: 0.8309 (tttt) cc_final: 0.7948 (mmtt) REVERT: C 349 ARG cc_start: 0.8296 (mtm180) cc_final: 0.8067 (mtm180) REVERT: C 356 SER cc_start: 0.9335 (p) cc_final: 0.8764 (m) REVERT: D 311 LYS cc_start: 0.8507 (pttp) cc_final: 0.7618 (tttt) REVERT: D 321 LYS cc_start: 0.8776 (mttm) cc_final: 0.7941 (tmmt) REVERT: D 342 GLU cc_start: 0.8477 (mt-10) cc_final: 0.7833 (mm-30) REVERT: D 343 LYS cc_start: 0.8233 (tttt) cc_final: 0.7694 (mmtt) REVERT: D 356 SER cc_start: 0.9325 (p) cc_final: 0.8810 (m) REVERT: E 321 LYS cc_start: 0.8197 (tttt) cc_final: 0.7896 (ttpt) REVERT: E 342 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8187 (mm-30) REVERT: E 343 LYS cc_start: 0.8163 (tttt) cc_final: 0.7705 (mptt) REVERT: E 369 LYS cc_start: 0.9097 (mttt) cc_final: 0.8521 (mttp) REVERT: F 343 LYS cc_start: 0.8200 (tttt) cc_final: 0.7566 (mmtt) REVERT: G 342 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7768 (mm-30) REVERT: G 343 LYS cc_start: 0.7990 (tttt) cc_final: 0.7725 (mmtt) REVERT: G 349 ARG cc_start: 0.8054 (mtm180) cc_final: 0.7728 (ttp-170) REVERT: G 358 ASP cc_start: 0.9062 (m-30) cc_final: 0.8756 (m-30) REVERT: H 342 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7673 (mm-30) REVERT: H 349 ARG cc_start: 0.8139 (mtm-85) cc_final: 0.7512 (mtm180) REVERT: H 358 ASP cc_start: 0.8948 (m-30) cc_final: 0.8632 (m-30) REVERT: I 343 LYS cc_start: 0.8017 (tttt) cc_final: 0.7605 (mptp) REVERT: I 345 ASP cc_start: 0.8011 (t0) cc_final: 0.7672 (t0) REVERT: I 369 LYS cc_start: 0.9090 (mttt) cc_final: 0.8429 (mttp) REVERT: J 317 LYS cc_start: 0.8503 (ttpt) cc_final: 0.8160 (ttmm) REVERT: J 345 ASP cc_start: 0.7939 (t0) cc_final: 0.7502 (t0) REVERT: J 360 ILE cc_start: 0.9462 (mt) cc_final: 0.9229 (mp) outliers start: 9 outliers final: 2 residues processed: 201 average time/residue: 1.4066 time to fit residues: 292.6769 Evaluate side-chains 201 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 195 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 370 LYS Chi-restraints excluded: chain G residue 342 GLU Chi-restraints excluded: chain H residue 342 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 69 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 2 optimal weight: 0.6980 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 327 ASN D 327 ASN E 327 ASN F 327 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.151823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.121533 restraints weight = 5632.532| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.76 r_work: 0.3393 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 5660 Z= 0.429 Angle : 0.698 7.049 7580 Z= 0.349 Chirality : 0.050 0.148 860 Planarity : 0.004 0.052 960 Dihedral : 5.453 17.422 740 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 2.50 % Allowed : 22.66 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.28), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 362 PHE 0.009 0.001 PHE G 378 TYR 0.011 0.002 TYR D 310 ARG 0.001 0.000 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5973.04 seconds wall clock time: 103 minutes 2.38 seconds (6182.38 seconds total)