Starting phenix.real_space_refine on Thu Nov 14 09:50:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9czi_46417/11_2024/9czi_46417_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9czi_46417/11_2024/9czi_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9czi_46417/11_2024/9czi_46417.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9czi_46417/11_2024/9czi_46417.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9czi_46417/11_2024/9czi_46417_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9czi_46417/11_2024/9czi_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-5513/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: 2.46, per 1000 atoms: 0.44 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: 1.33 Conformation dependent library (CDL) restraints added in 689.5 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: 0.81 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: 1.33 Time building geometry restraints manager: 1.57 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.120 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.570 ------------------------------------------------------------------------------- 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 : 0.631 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: 1.4457 time to fit residues: 389.8966 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 : 0.717 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 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 : 0.689 Fit side-chains REVERT: A 321 LYS cc_start: 0.8280 (tttt) cc_final: 0.7546 (tmtt) REVERT: A 343 LYS cc_start: 0.8296 (tttt) cc_final: 0.7785 (mmtt) REVERT: A 360 ILE cc_start: 0.8952 (mt) cc_final: 0.8684 (mp) REVERT: B 321 LYS cc_start: 0.8239 (tttt) cc_final: 0.7404 (tmtt) REVERT: B 325 LEU cc_start: 0.8806 (tp) cc_final: 0.8574 (tp) REVERT: B 342 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.6856 (mp0) REVERT: B 343 LYS cc_start: 0.8437 (tttt) cc_final: 0.7844 (mmtt) REVERT: B 360 ILE cc_start: 0.9022 (mt) cc_final: 0.8713 (mp) REVERT: B 369 LYS cc_start: 0.8533 (mttt) cc_final: 0.7839 (mttp) REVERT: C 321 LYS cc_start: 0.7970 (tttt) cc_final: 0.7452 (mttm) REVERT: C 338 GLU cc_start: 0.9012 (tt0) cc_final: 0.8589 (tt0) REVERT: C 343 LYS cc_start: 0.8016 (tttt) cc_final: 0.7321 (mmtt) REVERT: C 360 ILE cc_start: 0.9085 (mt) cc_final: 0.8857 (mp) REVERT: D 321 LYS cc_start: 0.7942 (tttt) cc_final: 0.7314 (tttm) REVERT: D 342 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7863 (mt-10) REVERT: D 343 LYS cc_start: 0.7948 (tttt) cc_final: 0.7339 (mmtt) REVERT: D 356 SER cc_start: 0.9215 (p) cc_final: 0.8385 (m) REVERT: D 360 ILE cc_start: 0.9254 (mt) cc_final: 0.9000 (mp) REVERT: D 370 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8744 (tttp) REVERT: E 321 LYS cc_start: 0.7842 (tttt) cc_final: 0.7128 (ttpt) REVERT: E 360 ILE cc_start: 0.9103 (mt) cc_final: 0.8854 (mp) REVERT: E 369 LYS cc_start: 0.8428 (mttt) cc_final: 0.7720 (mttp) REVERT: E 370 LYS cc_start: 0.8998 (tttm) cc_final: 0.8761 (tttm) REVERT: F 321 LYS cc_start: 0.8086 (tttt) cc_final: 0.7447 (mttp) REVERT: F 342 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7936 (mm-30) REVERT: F 343 LYS cc_start: 0.7993 (tttt) cc_final: 0.7141 (mmtt) REVERT: F 360 ILE cc_start: 0.9047 (mt) cc_final: 0.8790 (mp) REVERT: F 369 LYS cc_start: 0.8838 (mppt) cc_final: 0.8038 (mttp) REVERT: G 321 LYS cc_start: 0.7992 (tttt) cc_final: 0.7358 (mttp) REVERT: G 342 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7281 (mm-30) REVERT: G 343 LYS cc_start: 0.7942 (tttt) cc_final: 0.7370 (mmtt) REVERT: G 360 ILE cc_start: 0.9001 (mt) cc_final: 0.8770 (mp) REVERT: G 375 LYS cc_start: 0.8111 (tttt) cc_final: 0.7768 (ttpt) REVERT: H 321 LYS cc_start: 0.7969 (tttt) cc_final: 0.7328 (mttp) REVERT: H 358 ASP cc_start: 0.8755 (m-30) cc_final: 0.8337 (m-30) REVERT: H 360 ILE cc_start: 0.9156 (mt) cc_final: 0.8913 (mp) REVERT: H 369 LYS cc_start: 0.8632 (mttt) cc_final: 0.8361 (mttp) REVERT: I 316 SER cc_start: 0.8839 (p) cc_final: 0.8620 (p) REVERT: I 321 LYS cc_start: 0.7781 (tttt) cc_final: 0.7349 (mttm) REVERT: I 331 LYS cc_start: 0.8978 (mtpt) cc_final: 0.8653 (mtmt) REVERT: I 343 LYS cc_start: 0.7600 (tttt) cc_final: 0.7063 (mptp) REVERT: I 345 ASP cc_start: 0.7584 (t0) cc_final: 0.7086 (t0) REVERT: I 349 ARG cc_start: 0.7638 (mtm180) cc_final: 0.7256 (mtm180) REVERT: I 360 ILE cc_start: 0.9152 (mt) cc_final: 0.8893 (mp) REVERT: I 369 LYS cc_start: 0.8667 (mttt) cc_final: 0.7916 (mttp) REVERT: I 370 LYS cc_start: 0.8765 (tttm) cc_final: 0.8343 (tmtm) REVERT: J 321 LYS cc_start: 0.7979 (tttt) cc_final: 0.7582 (mttp) REVERT: J 343 LYS cc_start: 0.7807 (tttt) cc_final: 0.7353 (mmtt) REVERT: J 360 ILE cc_start: 0.9162 (mt) cc_final: 0.8846 (mp) REVERT: J 370 LYS cc_start: 0.8895 (tttm) cc_final: 0.8366 (tptt) outliers start: 16 outliers final: 2 residues processed: 223 average time/residue: 1.3166 time to fit residues: 304.5300 Evaluate side-chains 216 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 210 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 35 optimal weight: 9.9990 chunk 19 optimal weight: 0.7980 chunk 52 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 overall best weight: 4.3586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 5660 Z= 0.455 Angle : 0.722 6.547 7580 Z= 0.370 Chirality : 0.050 0.136 860 Planarity : 0.004 0.038 960 Dihedral : 5.492 19.036 740 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 4.06 % Allowed : 13.44 % Favored : 82.50 % 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: -1.83 (0.29), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS I 330 PHE 0.011 0.002 PHE A 378 TYR 0.013 0.003 TYR D 310 ARG 0.002 0.000 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 267 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 241 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8164 (tttt) cc_final: 0.7451 (tmtt) REVERT: A 343 LYS cc_start: 0.8303 (tttt) cc_final: 0.7797 (mmtt) REVERT: A 360 ILE cc_start: 0.9051 (mt) cc_final: 0.8809 (mp) REVERT: B 321 LYS cc_start: 0.8197 (tttt) cc_final: 0.7267 (ttpt) REVERT: B 342 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.6862 (mp0) REVERT: B 343 LYS cc_start: 0.8424 (tttt) cc_final: 0.7904 (mmtt) REVERT: B 347 LYS cc_start: 0.7126 (mttp) cc_final: 0.5918 (mtmt) REVERT: B 360 ILE cc_start: 0.9055 (mt) cc_final: 0.8741 (mp) REVERT: B 369 LYS cc_start: 0.8551 (mttt) cc_final: 0.7903 (mttp) REVERT: C 321 LYS cc_start: 0.7824 (tttt) cc_final: 0.7314 (mttp) REVERT: C 327 ASN cc_start: 0.8160 (m-40) cc_final: 0.7724 (t0) REVERT: C 343 LYS cc_start: 0.8036 (tttt) cc_final: 0.7290 (mmtt) REVERT: C 349 ARG cc_start: 0.7764 (mtm180) cc_final: 0.7343 (mtp-110) REVERT: D 321 LYS cc_start: 0.7835 (tttt) cc_final: 0.7084 (ttpt) REVERT: D 327 ASN cc_start: 0.8292 (m-40) cc_final: 0.7752 (t0) REVERT: D 342 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7351 (mm-30) REVERT: D 343 LYS cc_start: 0.8025 (tttt) cc_final: 0.7379 (mmtt) REVERT: D 349 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7141 (mtm180) REVERT: D 356 SER cc_start: 0.9160 (p) cc_final: 0.8439 (m) REVERT: D 360 ILE cc_start: 0.9227 (mt) cc_final: 0.9024 (mp) REVERT: D 370 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8894 (tttp) REVERT: E 311 LYS cc_start: 0.8249 (mttt) cc_final: 0.7290 (pttt) REVERT: E 321 LYS cc_start: 0.7765 (tttt) cc_final: 0.7104 (ttpt) REVERT: E 342 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7739 (mt-10) REVERT: E 343 LYS cc_start: 0.8033 (tttt) cc_final: 0.7165 (mmtt) REVERT: E 356 SER cc_start: 0.9108 (p) cc_final: 0.8309 (m) REVERT: E 360 ILE cc_start: 0.9135 (mt) cc_final: 0.8873 (mp) REVERT: E 369 LYS cc_start: 0.8594 (mttt) cc_final: 0.7682 (mttp) REVERT: E 370 LYS cc_start: 0.9036 (tttm) cc_final: 0.8824 (tttm) REVERT: F 321 LYS cc_start: 0.8109 (tttt) cc_final: 0.7162 (tmtt) REVERT: F 343 LYS cc_start: 0.8151 (tttt) cc_final: 0.7177 (mmtt) REVERT: F 360 ILE cc_start: 0.9057 (mt) cc_final: 0.8810 (mp) REVERT: F 369 LYS cc_start: 0.8844 (mtpt) cc_final: 0.8072 (mttp) REVERT: G 321 LYS cc_start: 0.7963 (tttt) cc_final: 0.7334 (mttp) REVERT: G 343 LYS cc_start: 0.7899 (tttt) cc_final: 0.7312 (mmtt) REVERT: G 360 ILE cc_start: 0.9027 (mt) cc_final: 0.8762 (mp) REVERT: G 370 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8917 (tttp) REVERT: H 321 LYS cc_start: 0.7776 (tttt) cc_final: 0.7177 (mttp) REVERT: H 342 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7974 (mm-30) REVERT: H 358 ASP cc_start: 0.8677 (m-30) cc_final: 0.8363 (m-30) REVERT: H 360 ILE cc_start: 0.9141 (mt) cc_final: 0.8882 (mp) REVERT: H 369 LYS cc_start: 0.8790 (mttt) cc_final: 0.8571 (mttp) REVERT: I 321 LYS cc_start: 0.7823 (tttt) cc_final: 0.7346 (mttm) REVERT: I 331 LYS cc_start: 0.9013 (mtpt) cc_final: 0.8779 (mtmt) REVERT: I 343 LYS cc_start: 0.7860 (tttt) cc_final: 0.7195 (mptp) REVERT: I 345 ASP cc_start: 0.7445 (t0) cc_final: 0.6867 (t0) REVERT: I 349 ARG cc_start: 0.7942 (mtm180) cc_final: 0.7452 (mtm180) REVERT: I 360 ILE cc_start: 0.9198 (mt) cc_final: 0.8968 (mp) REVERT: I 369 LYS cc_start: 0.8709 (mttt) cc_final: 0.7915 (mttp) REVERT: J 317 LYS cc_start: 0.8264 (tttt) cc_final: 0.7853 (ttmm) REVERT: J 321 LYS cc_start: 0.8046 (tttt) cc_final: 0.7606 (mttp) REVERT: J 325 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8535 (tt) REVERT: J 343 LYS cc_start: 0.7959 (tttt) cc_final: 0.7432 (mmtt) REVERT: J 358 ASP cc_start: 0.8632 (m-30) cc_final: 0.8292 (m-30) outliers start: 26 outliers final: 8 residues processed: 247 average time/residue: 1.3039 time to fit residues: 334.0721 Evaluate side-chains 249 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 233 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 LEU 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 D residue 370 LYS 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 370 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 47 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5660 Z= 0.161 Angle : 0.558 6.230 7580 Z= 0.289 Chirality : 0.049 0.121 860 Planarity : 0.003 0.034 960 Dihedral : 4.893 15.610 740 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.59 % Allowed : 17.50 % Favored : 78.91 % 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: -1.86 (0.29), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 374 PHE 0.004 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 239 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 216 time to evaluate : 0.638 Fit side-chains REVERT: A 321 LYS cc_start: 0.8232 (tttt) cc_final: 0.7473 (tmtt) REVERT: A 342 GLU cc_start: 0.8109 (mt-10) cc_final: 0.6516 (pm20) REVERT: A 343 LYS cc_start: 0.8188 (tttt) cc_final: 0.7711 (mmtt) REVERT: A 347 LYS cc_start: 0.7083 (mttp) cc_final: 0.5958 (mtmt) REVERT: A 360 ILE cc_start: 0.8982 (mt) cc_final: 0.8693 (mp) REVERT: B 321 LYS cc_start: 0.8280 (tttt) cc_final: 0.7446 (tmtt) REVERT: B 342 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.6706 (mp0) REVERT: B 343 LYS cc_start: 0.8483 (tttt) cc_final: 0.7845 (mmtt) REVERT: B 347 LYS cc_start: 0.6997 (mttp) cc_final: 0.5759 (mtmt) REVERT: B 360 ILE cc_start: 0.9030 (mt) cc_final: 0.8752 (mp) REVERT: B 369 LYS cc_start: 0.8525 (mttt) cc_final: 0.7802 (mttp) REVERT: C 321 LYS cc_start: 0.7874 (tttt) cc_final: 0.7361 (mttm) REVERT: C 327 ASN cc_start: 0.7887 (m-40) cc_final: 0.7483 (t0) REVERT: C 338 GLU cc_start: 0.9076 (tt0) cc_final: 0.8705 (tt0) REVERT: C 342 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8295 (mm-30) REVERT: C 343 LYS cc_start: 0.8124 (tttt) cc_final: 0.7269 (mmtt) REVERT: C 349 ARG cc_start: 0.7753 (mtm180) cc_final: 0.7296 (mtp-110) REVERT: C 356 SER cc_start: 0.9142 (p) cc_final: 0.8316 (m) REVERT: D 321 LYS cc_start: 0.7898 (tttt) cc_final: 0.7283 (tttm) REVERT: D 327 ASN cc_start: 0.8040 (m-40) cc_final: 0.7544 (t0) REVERT: D 342 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7407 (mm-30) REVERT: D 343 LYS cc_start: 0.8022 (tttt) cc_final: 0.7276 (mmtt) REVERT: D 349 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7231 (mtm180) REVERT: D 356 SER cc_start: 0.9165 (p) cc_final: 0.8432 (m) REVERT: D 360 ILE cc_start: 0.9247 (mt) cc_final: 0.9004 (mp) REVERT: D 370 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8809 (tttm) REVERT: E 321 LYS cc_start: 0.7744 (tttt) cc_final: 0.7087 (ttpt) REVERT: E 342 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7954 (mm-30) REVERT: E 360 ILE cc_start: 0.9119 (mt) cc_final: 0.8855 (mp) REVERT: E 369 LYS cc_start: 0.8615 (mttt) cc_final: 0.7824 (mttp) REVERT: F 321 LYS cc_start: 0.8071 (tttt) cc_final: 0.7401 (mttp) REVERT: F 343 LYS cc_start: 0.8029 (tttt) cc_final: 0.7031 (mmtt) REVERT: F 360 ILE cc_start: 0.9063 (mt) cc_final: 0.8819 (mp) REVERT: F 369 LYS cc_start: 0.8856 (mtpt) cc_final: 0.8097 (mttp) REVERT: G 321 LYS cc_start: 0.7988 (tttt) cc_final: 0.7387 (mttp) REVERT: G 342 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8287 (mm-30) REVERT: G 343 LYS cc_start: 0.7876 (tttt) cc_final: 0.7398 (mmtt) REVERT: G 358 ASP cc_start: 0.8599 (m-30) cc_final: 0.8291 (m-30) REVERT: G 360 ILE cc_start: 0.9051 (mt) cc_final: 0.8816 (mp) REVERT: H 321 LYS cc_start: 0.7778 (tttt) cc_final: 0.7267 (mttp) REVERT: H 342 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7524 (mm-30) REVERT: H 358 ASP cc_start: 0.8661 (m-30) cc_final: 0.8270 (m-30) REVERT: H 360 ILE cc_start: 0.9138 (mt) cc_final: 0.8906 (mp) REVERT: H 369 LYS cc_start: 0.8743 (mttt) cc_final: 0.8491 (mttt) REVERT: I 321 LYS cc_start: 0.7816 (tttt) cc_final: 0.7381 (mttp) REVERT: I 331 LYS cc_start: 0.9007 (mtpt) cc_final: 0.8792 (mtmt) REVERT: I 343 LYS cc_start: 0.7745 (tttt) cc_final: 0.7120 (mptp) REVERT: I 345 ASP cc_start: 0.7404 (t0) cc_final: 0.6802 (t0) REVERT: I 349 ARG cc_start: 0.7901 (mtm180) cc_final: 0.7462 (mtm180) REVERT: I 358 ASP cc_start: 0.8477 (m-30) cc_final: 0.8258 (m-30) REVERT: I 360 ILE cc_start: 0.9164 (mt) cc_final: 0.8922 (mp) REVERT: I 369 LYS cc_start: 0.8719 (mttt) cc_final: 0.7915 (mttp) REVERT: I 370 LYS cc_start: 0.8997 (ttpp) cc_final: 0.8628 (tmtm) REVERT: J 317 LYS cc_start: 0.8194 (tttt) cc_final: 0.7770 (ttmm) REVERT: J 321 LYS cc_start: 0.8006 (tttt) cc_final: 0.7626 (mttp) REVERT: J 343 LYS cc_start: 0.7948 (tttt) cc_final: 0.7438 (mmtt) REVERT: J 345 ASP cc_start: 0.7230 (t0) cc_final: 0.6632 (t0) REVERT: J 356 SER cc_start: 0.9030 (p) cc_final: 0.8669 (p) REVERT: J 357 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8548 (tp) REVERT: J 358 ASP cc_start: 0.8452 (m-30) cc_final: 0.7839 (m-30) outliers start: 23 outliers final: 5 residues processed: 222 average time/residue: 1.3241 time to fit residues: 304.7667 Evaluate side-chains 223 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 211 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 LEU 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 349 ARG Chi-restraints excluded: chain D residue 370 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 342 GLU Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain J residue 357 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 327 ASN F 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.052 5660 Z= 0.623 Angle : 0.780 7.763 7580 Z= 0.394 Chirality : 0.051 0.124 860 Planarity : 0.005 0.049 960 Dihedral : 5.615 20.312 740 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 5.47 % Allowed : 16.56 % 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: -2.11 (0.28), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 374 PHE 0.007 0.002 PHE G 378 TYR 0.011 0.002 TYR C 310 ARG 0.002 0.001 ARG J 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 263 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 228 time to evaluate : 0.717 Fit side-chains REVERT: A 321 LYS cc_start: 0.8119 (tttt) cc_final: 0.7467 (tmtt) REVERT: A 342 GLU cc_start: 0.8476 (mt-10) cc_final: 0.6819 (pm20) REVERT: A 343 LYS cc_start: 0.8250 (tttt) cc_final: 0.7673 (mmtt) REVERT: A 347 LYS cc_start: 0.7204 (mttp) cc_final: 0.6489 (mtpt) REVERT: A 360 ILE cc_start: 0.9077 (mt) cc_final: 0.8821 (mp) REVERT: B 317 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7513 (ttpp) REVERT: B 321 LYS cc_start: 0.8229 (tttt) cc_final: 0.7604 (mttp) REVERT: B 342 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.6665 (mp0) REVERT: B 343 LYS cc_start: 0.8400 (tttt) cc_final: 0.7930 (mmtt) REVERT: B 347 LYS cc_start: 0.7061 (mttp) cc_final: 0.5700 (mtmt) REVERT: B 360 ILE cc_start: 0.9082 (mt) cc_final: 0.8773 (mp) REVERT: B 369 LYS cc_start: 0.8641 (mttt) cc_final: 0.7923 (mttp) REVERT: C 321 LYS cc_start: 0.7885 (tttt) cc_final: 0.7352 (mttp) REVERT: C 327 ASN cc_start: 0.8163 (m-40) cc_final: 0.7756 (t0) REVERT: C 343 LYS cc_start: 0.8138 (tttt) cc_final: 0.7230 (mmtt) REVERT: C 349 ARG cc_start: 0.7860 (mtm180) cc_final: 0.7584 (mtm180) REVERT: D 321 LYS cc_start: 0.7724 (tttt) cc_final: 0.7088 (ttpt) REVERT: D 327 ASN cc_start: 0.8326 (m-40) cc_final: 0.7824 (t0) REVERT: D 342 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7296 (mm-30) REVERT: D 343 LYS cc_start: 0.8051 (tttt) cc_final: 0.7384 (mmtt) REVERT: D 349 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7232 (mtm180) REVERT: D 356 SER cc_start: 0.9175 (p) cc_final: 0.8434 (m) REVERT: D 360 ILE cc_start: 0.9139 (mt) cc_final: 0.8936 (mp) REVERT: D 370 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8808 (tttp) REVERT: E 311 LYS cc_start: 0.8226 (mttt) cc_final: 0.7293 (pttt) REVERT: E 321 LYS cc_start: 0.7829 (tttt) cc_final: 0.7113 (ttpt) REVERT: E 342 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7693 (mt-10) REVERT: E 343 LYS cc_start: 0.8066 (tttt) cc_final: 0.7236 (mmtt) REVERT: E 347 LYS cc_start: 0.6810 (mttp) cc_final: 0.6278 (mmtp) REVERT: E 356 SER cc_start: 0.9141 (p) cc_final: 0.8286 (m) REVERT: E 360 ILE cc_start: 0.9109 (mt) cc_final: 0.8837 (mp) REVERT: E 369 LYS cc_start: 0.8723 (mttt) cc_final: 0.7845 (mttp) REVERT: F 321 LYS cc_start: 0.8091 (tttt) cc_final: 0.7220 (tmtt) REVERT: F 343 LYS cc_start: 0.8062 (tttt) cc_final: 0.7075 (mmtt) REVERT: F 369 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8099 (mttp) REVERT: G 321 LYS cc_start: 0.7879 (tttt) cc_final: 0.7282 (mttp) REVERT: G 342 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.7477 (mm-30) REVERT: G 343 LYS cc_start: 0.7853 (tttt) cc_final: 0.7291 (mmtt) REVERT: G 360 ILE cc_start: 0.9053 (mt) cc_final: 0.8774 (mp) REVERT: H 321 LYS cc_start: 0.7838 (tttt) cc_final: 0.7213 (mttp) REVERT: H 342 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7739 (mm-30) REVERT: H 358 ASP cc_start: 0.8664 (m-30) cc_final: 0.8401 (m-30) REVERT: H 360 ILE cc_start: 0.9148 (mt) cc_final: 0.8900 (mp) REVERT: H 369 LYS cc_start: 0.8785 (mttt) cc_final: 0.8572 (mttp) REVERT: I 321 LYS cc_start: 0.7901 (tttt) cc_final: 0.7405 (mttm) REVERT: I 331 LYS cc_start: 0.9004 (mtpt) cc_final: 0.8795 (mtmt) REVERT: I 342 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.6922 (mt-10) REVERT: I 343 LYS cc_start: 0.7890 (tttt) cc_final: 0.7140 (mptp) REVERT: I 345 ASP cc_start: 0.7447 (t0) cc_final: 0.6796 (t0) REVERT: I 349 ARG cc_start: 0.8046 (mtm180) cc_final: 0.7709 (mtm180) REVERT: I 360 ILE cc_start: 0.9268 (mt) cc_final: 0.8963 (mp) REVERT: I 369 LYS cc_start: 0.8778 (mttt) cc_final: 0.8016 (mttp) REVERT: J 317 LYS cc_start: 0.8200 (tttt) cc_final: 0.7787 (ttmm) REVERT: J 321 LYS cc_start: 0.8017 (tttt) cc_final: 0.7580 (mttp) REVERT: J 343 LYS cc_start: 0.7992 (tttt) cc_final: 0.7365 (mmtt) REVERT: J 357 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8791 (tp) REVERT: J 358 ASP cc_start: 0.8646 (m-30) cc_final: 0.8281 (m-30) outliers start: 35 outliers final: 10 residues processed: 240 average time/residue: 1.3275 time to fit residues: 330.1919 Evaluate side-chains 247 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 226 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 LEU 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 D residue 342 GLU Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 370 LYS 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 369 LYS 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 I residue 370 LYS Chi-restraints excluded: chain J residue 325 LEU Chi-restraints excluded: chain J residue 357 LEU 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 16 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5660 Z= 0.181 Angle : 0.563 5.812 7580 Z= 0.293 Chirality : 0.049 0.123 860 Planarity : 0.003 0.042 960 Dihedral : 4.984 15.647 740 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.97 % Allowed : 19.22 % Favored : 77.81 % 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: -2.01 (0.29), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 374 PHE 0.005 0.001 PHE G 378 TYR 0.009 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 228 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 209 time to evaluate : 0.719 Fit side-chains REVERT: A 321 LYS cc_start: 0.8255 (tttt) cc_final: 0.7503 (tmtt) REVERT: A 342 GLU cc_start: 0.8143 (mt-10) cc_final: 0.6537 (pm20) REVERT: A 343 LYS cc_start: 0.8187 (tttt) cc_final: 0.7634 (mmtt) REVERT: A 347 LYS cc_start: 0.7099 (mttp) cc_final: 0.6481 (mtpt) REVERT: A 360 ILE cc_start: 0.9018 (mt) cc_final: 0.8725 (mp) REVERT: A 369 LYS cc_start: 0.8676 (mttt) cc_final: 0.8440 (mttt) REVERT: B 321 LYS cc_start: 0.8259 (tttt) cc_final: 0.7396 (ttpt) REVERT: B 342 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.6613 (mp0) REVERT: B 343 LYS cc_start: 0.8468 (tttt) cc_final: 0.7837 (mmtt) REVERT: B 347 LYS cc_start: 0.7182 (mttp) cc_final: 0.5685 (mtmt) REVERT: B 360 ILE cc_start: 0.9045 (mt) cc_final: 0.8748 (mp) REVERT: B 369 LYS cc_start: 0.8601 (mttt) cc_final: 0.7866 (mttp) REVERT: C 321 LYS cc_start: 0.7890 (tttt) cc_final: 0.7360 (mttp) REVERT: C 327 ASN cc_start: 0.7872 (m-40) cc_final: 0.7486 (t0) REVERT: C 338 GLU cc_start: 0.9094 (tt0) cc_final: 0.8706 (tt0) REVERT: C 342 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8251 (mm-30) REVERT: C 343 LYS cc_start: 0.8113 (tttt) cc_final: 0.7256 (mmtt) REVERT: C 349 ARG cc_start: 0.7830 (mtm180) cc_final: 0.7449 (mtm180) REVERT: C 356 SER cc_start: 0.9144 (p) cc_final: 0.8340 (m) REVERT: D 311 LYS cc_start: 0.8541 (pttp) cc_final: 0.7391 (tttt) REVERT: D 321 LYS cc_start: 0.7905 (tttt) cc_final: 0.7269 (tttm) REVERT: D 327 ASN cc_start: 0.8099 (m-40) cc_final: 0.7567 (t0) REVERT: D 342 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7412 (mm-30) REVERT: D 343 LYS cc_start: 0.8022 (tttt) cc_final: 0.7265 (mmtt) REVERT: D 356 SER cc_start: 0.9170 (p) cc_final: 0.8473 (m) REVERT: D 370 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8818 (tttp) REVERT: E 321 LYS cc_start: 0.7738 (tttt) cc_final: 0.7083 (ttpt) REVERT: E 342 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7985 (mm-30) REVERT: E 360 ILE cc_start: 0.9112 (mt) cc_final: 0.8820 (mp) REVERT: E 369 LYS cc_start: 0.8721 (mttt) cc_final: 0.7912 (mttp) REVERT: F 321 LYS cc_start: 0.8048 (tttt) cc_final: 0.7383 (mttp) REVERT: F 343 LYS cc_start: 0.8050 (tttt) cc_final: 0.7049 (mmtt) REVERT: F 360 ILE cc_start: 0.9163 (mt) cc_final: 0.8957 (mp) REVERT: G 321 LYS cc_start: 0.7949 (tttt) cc_final: 0.7335 (mttp) REVERT: G 342 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8357 (mm-30) REVERT: G 343 LYS cc_start: 0.7866 (tttt) cc_final: 0.7379 (mmtt) REVERT: G 360 ILE cc_start: 0.9058 (mt) cc_final: 0.8809 (mp) REVERT: H 321 LYS cc_start: 0.7864 (tttt) cc_final: 0.7284 (mttp) REVERT: H 342 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7478 (mm-30) REVERT: H 358 ASP cc_start: 0.8657 (m-30) cc_final: 0.8269 (m-30) REVERT: H 369 LYS cc_start: 0.8744 (mttt) cc_final: 0.8499 (mttt) REVERT: I 321 LYS cc_start: 0.7819 (tttt) cc_final: 0.7325 (mttp) REVERT: I 343 LYS cc_start: 0.7837 (tttt) cc_final: 0.7134 (mptp) REVERT: I 345 ASP cc_start: 0.7406 (t0) cc_final: 0.6775 (t0) REVERT: I 349 ARG cc_start: 0.7955 (mtm180) cc_final: 0.7519 (mtm180) REVERT: I 360 ILE cc_start: 0.9205 (mt) cc_final: 0.8955 (mp) REVERT: I 369 LYS cc_start: 0.8754 (mttt) cc_final: 0.7964 (mttp) REVERT: J 317 LYS cc_start: 0.8218 (tttt) cc_final: 0.7827 (ttmm) REVERT: J 321 LYS cc_start: 0.7981 (tttt) cc_final: 0.7621 (mttp) REVERT: J 343 LYS cc_start: 0.7942 (tttt) cc_final: 0.7354 (mmtt) REVERT: J 345 ASP cc_start: 0.7252 (t0) cc_final: 0.6641 (t0) REVERT: J 356 SER cc_start: 0.9024 (p) cc_final: 0.8665 (p) REVERT: J 357 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8563 (tp) REVERT: J 358 ASP cc_start: 0.8420 (m-30) cc_final: 0.7758 (m-30) REVERT: J 360 ILE cc_start: 0.9169 (mt) cc_final: 0.8909 (mp) outliers start: 19 outliers final: 5 residues processed: 217 average time/residue: 1.4103 time to fit residues: 317.2485 Evaluate side-chains 216 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 204 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 LEU 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 370 LYS 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 J residue 357 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 42 optimal weight: 0.3980 chunk 41 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 5660 Z= 0.478 Angle : 0.698 7.007 7580 Z= 0.355 Chirality : 0.049 0.123 860 Planarity : 0.004 0.050 960 Dihedral : 5.421 18.556 740 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 3.91 % Allowed : 18.44 % Favored : 77.66 % 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: -2.18 (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 0.004 0.001 HIS D 374 PHE 0.005 0.001 PHE A 346 TYR 0.011 0.002 TYR C 310 ARG 0.002 0.000 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 246 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 221 time to evaluate : 0.724 Fit side-chains REVERT: A 321 LYS cc_start: 0.8123 (tttt) cc_final: 0.7465 (ttpt) REVERT: A 342 GLU cc_start: 0.8394 (mt-10) cc_final: 0.6804 (pm20) REVERT: A 343 LYS cc_start: 0.8258 (tttt) cc_final: 0.7699 (mmtt) REVERT: A 347 LYS cc_start: 0.7270 (mttp) cc_final: 0.6498 (mtpt) REVERT: A 360 ILE cc_start: 0.9088 (mt) cc_final: 0.8807 (mp) REVERT: A 369 LYS cc_start: 0.8757 (mttt) cc_final: 0.8509 (mttt) REVERT: B 321 LYS cc_start: 0.8213 (tttt) cc_final: 0.7304 (ttpt) REVERT: B 342 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.6684 (mp0) REVERT: B 343 LYS cc_start: 0.8395 (tttt) cc_final: 0.7880 (mmtt) REVERT: B 347 LYS cc_start: 0.7159 (mttp) cc_final: 0.5756 (mtmt) REVERT: B 360 ILE cc_start: 0.9083 (mt) cc_final: 0.8758 (mp) REVERT: B 369 LYS cc_start: 0.8650 (mttt) cc_final: 0.7910 (mttp) REVERT: C 321 LYS cc_start: 0.7907 (tttt) cc_final: 0.7355 (mttm) REVERT: C 327 ASN cc_start: 0.8062 (m-40) cc_final: 0.7744 (t0) REVERT: C 338 GLU cc_start: 0.9086 (tt0) cc_final: 0.8885 (tt0) REVERT: C 343 LYS cc_start: 0.8130 (tttt) cc_final: 0.7271 (mmtt) REVERT: C 349 ARG cc_start: 0.7815 (mtm180) cc_final: 0.7367 (mtm180) REVERT: D 321 LYS cc_start: 0.7875 (tttt) cc_final: 0.7192 (ttpt) REVERT: D 327 ASN cc_start: 0.8273 (m-40) cc_final: 0.7781 (t0) REVERT: D 342 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7305 (mm-30) REVERT: D 343 LYS cc_start: 0.7995 (tttt) cc_final: 0.7269 (mmtt) REVERT: D 349 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7229 (mtm180) REVERT: D 356 SER cc_start: 0.9161 (p) cc_final: 0.8481 (m) REVERT: D 370 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8869 (tttp) REVERT: E 311 LYS cc_start: 0.8174 (mttt) cc_final: 0.7221 (pttt) REVERT: E 321 LYS cc_start: 0.7811 (tttt) cc_final: 0.7108 (ttpt) REVERT: E 342 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7852 (mm-30) REVERT: E 343 LYS cc_start: 0.8123 (tttt) cc_final: 0.7223 (mmtt) REVERT: E 347 LYS cc_start: 0.6790 (mttp) cc_final: 0.6222 (mmtp) REVERT: E 356 SER cc_start: 0.9146 (p) cc_final: 0.8289 (m) REVERT: E 360 ILE cc_start: 0.9129 (mt) cc_final: 0.8840 (mp) REVERT: E 369 LYS cc_start: 0.8761 (mttt) cc_final: 0.7895 (mttp) REVERT: F 321 LYS cc_start: 0.8089 (tttt) cc_final: 0.7213 (tmtt) REVERT: F 343 LYS cc_start: 0.8091 (tttt) cc_final: 0.7095 (mmtt) REVERT: F 356 SER cc_start: 0.9124 (p) cc_final: 0.8524 (m) REVERT: G 321 LYS cc_start: 0.7982 (tttt) cc_final: 0.7368 (mttp) REVERT: G 342 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7549 (mm-30) REVERT: G 343 LYS cc_start: 0.7883 (tttt) cc_final: 0.7268 (mmtt) REVERT: G 360 ILE cc_start: 0.9071 (mt) cc_final: 0.8844 (mp) REVERT: H 321 LYS cc_start: 0.7995 (tttt) cc_final: 0.7328 (mttp) REVERT: H 342 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7695 (mm-30) REVERT: H 358 ASP cc_start: 0.8627 (m-30) cc_final: 0.8361 (m-30) REVERT: H 369 LYS cc_start: 0.8795 (mttt) cc_final: 0.7374 (mptt) REVERT: I 321 LYS cc_start: 0.7831 (tttt) cc_final: 0.7320 (mttm) REVERT: I 342 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7036 (mt-10) REVERT: I 343 LYS cc_start: 0.7903 (tttt) cc_final: 0.7144 (mptp) REVERT: I 345 ASP cc_start: 0.7479 (t0) cc_final: 0.6866 (t0) REVERT: I 349 ARG cc_start: 0.7992 (mtm180) cc_final: 0.7594 (mtm180) REVERT: I 360 ILE cc_start: 0.9272 (mt) cc_final: 0.8972 (mp) REVERT: I 369 LYS cc_start: 0.8759 (mttt) cc_final: 0.7998 (mttp) REVERT: J 317 LYS cc_start: 0.8218 (tttt) cc_final: 0.7809 (ttmm) REVERT: J 321 LYS cc_start: 0.8008 (tttt) cc_final: 0.7571 (mttp) REVERT: J 343 LYS cc_start: 0.7961 (tttt) cc_final: 0.7340 (mmtt) REVERT: J 358 ASP cc_start: 0.8590 (m-30) cc_final: 0.8151 (m-30) outliers start: 25 outliers final: 9 residues processed: 231 average time/residue: 1.4253 time to fit residues: 341.0777 Evaluate side-chains 239 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 223 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 LEU 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 D residue 370 LYS 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 H residue 370 LYS Chi-restraints excluded: chain I residue 370 LYS Chi-restraints excluded: chain J residue 357 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5660 Z= 0.263 Angle : 0.605 5.616 7580 Z= 0.312 Chirality : 0.049 0.120 860 Planarity : 0.004 0.048 960 Dihedral : 5.179 16.665 740 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.44 % Allowed : 18.75 % Favored : 77.81 % 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: -2.16 (0.28), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 374 PHE 0.004 0.001 PHE A 346 TYR 0.009 0.002 TYR C 310 ARG 0.001 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 235 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 213 time to evaluate : 0.683 Fit side-chains REVERT: A 321 LYS cc_start: 0.8189 (tttt) cc_final: 0.7497 (tmtt) REVERT: A 342 GLU cc_start: 0.8308 (mt-10) cc_final: 0.6580 (pm20) REVERT: A 343 LYS cc_start: 0.8281 (tttt) cc_final: 0.7689 (mmtt) REVERT: A 347 LYS cc_start: 0.7059 (mttp) cc_final: 0.6393 (mtpt) REVERT: A 360 ILE cc_start: 0.9056 (mt) cc_final: 0.8765 (mp) REVERT: A 369 LYS cc_start: 0.8736 (mttt) cc_final: 0.8482 (mttt) REVERT: B 321 LYS cc_start: 0.8285 (tttt) cc_final: 0.7414 (ttpt) REVERT: B 342 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.6638 (mp0) REVERT: B 343 LYS cc_start: 0.8442 (tttt) cc_final: 0.7864 (mmtt) REVERT: B 347 LYS cc_start: 0.7153 (mttp) cc_final: 0.5696 (mtmt) REVERT: B 360 ILE cc_start: 0.9067 (mt) cc_final: 0.8756 (mp) REVERT: B 369 LYS cc_start: 0.8639 (mttt) cc_final: 0.7908 (mttp) REVERT: C 321 LYS cc_start: 0.7893 (tttt) cc_final: 0.7349 (mttp) REVERT: C 327 ASN cc_start: 0.7985 (m-40) cc_final: 0.7564 (t0) REVERT: C 343 LYS cc_start: 0.8142 (tttt) cc_final: 0.7268 (mmtt) REVERT: C 349 ARG cc_start: 0.7759 (mtm180) cc_final: 0.7441 (mtm180) REVERT: C 351 GLN cc_start: 0.8082 (tt0) cc_final: 0.7798 (tt0) REVERT: D 321 LYS cc_start: 0.7840 (tttt) cc_final: 0.7304 (tttm) REVERT: D 327 ASN cc_start: 0.8175 (m-40) cc_final: 0.7683 (t0) REVERT: D 342 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7384 (mm-30) REVERT: D 343 LYS cc_start: 0.8062 (tttt) cc_final: 0.7249 (mmtt) REVERT: D 349 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7267 (mtm180) REVERT: D 356 SER cc_start: 0.9166 (p) cc_final: 0.8505 (m) REVERT: D 370 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8831 (tttp) REVERT: E 321 LYS cc_start: 0.7790 (tttt) cc_final: 0.7094 (ttpt) REVERT: E 342 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8019 (mm-30) REVERT: E 356 SER cc_start: 0.8986 (p) cc_final: 0.8263 (m) REVERT: E 360 ILE cc_start: 0.9127 (mt) cc_final: 0.8835 (mp) REVERT: E 369 LYS cc_start: 0.8748 (mttt) cc_final: 0.7921 (mttp) REVERT: F 321 LYS cc_start: 0.8075 (tttt) cc_final: 0.7412 (mttp) REVERT: F 343 LYS cc_start: 0.8051 (tttt) cc_final: 0.7086 (mmtt) REVERT: F 356 SER cc_start: 0.9020 (p) cc_final: 0.8500 (m) REVERT: G 321 LYS cc_start: 0.7980 (tttt) cc_final: 0.7370 (mttp) REVERT: G 342 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7633 (mm-30) REVERT: G 343 LYS cc_start: 0.7870 (tttt) cc_final: 0.7383 (mmtt) REVERT: G 360 ILE cc_start: 0.9055 (mt) cc_final: 0.8810 (mp) REVERT: H 321 LYS cc_start: 0.7909 (tttt) cc_final: 0.7262 (mttp) REVERT: H 342 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7493 (mm-30) REVERT: H 358 ASP cc_start: 0.8614 (m-30) cc_final: 0.8331 (m-30) REVERT: H 369 LYS cc_start: 0.8761 (mttt) cc_final: 0.7345 (mptt) REVERT: I 321 LYS cc_start: 0.7825 (tttt) cc_final: 0.7324 (mttm) REVERT: I 343 LYS cc_start: 0.7987 (tttt) cc_final: 0.7268 (mptp) REVERT: I 345 ASP cc_start: 0.7418 (t0) cc_final: 0.6805 (t0) REVERT: I 349 ARG cc_start: 0.7971 (mtm180) cc_final: 0.7533 (mtm180) REVERT: I 360 ILE cc_start: 0.9253 (mt) cc_final: 0.8993 (mp) REVERT: I 369 LYS cc_start: 0.8757 (mttt) cc_final: 0.7970 (mttp) REVERT: J 317 LYS cc_start: 0.8244 (tttt) cc_final: 0.7844 (ttmm) REVERT: J 321 LYS cc_start: 0.7979 (tttt) cc_final: 0.7557 (mttp) REVERT: J 343 LYS cc_start: 0.7983 (tttt) cc_final: 0.7385 (mmtt) REVERT: J 345 ASP cc_start: 0.7332 (t0) cc_final: 0.6708 (t0) REVERT: J 356 SER cc_start: 0.9053 (p) cc_final: 0.8676 (p) REVERT: J 358 ASP cc_start: 0.8507 (m-30) cc_final: 0.7835 (m-30) outliers start: 22 outliers final: 9 residues processed: 218 average time/residue: 1.3680 time to fit residues: 308.8202 Evaluate side-chains 226 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 210 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 LEU 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 D residue 357 LEU Chi-restraints excluded: chain D residue 370 LYS 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 H residue 370 LYS Chi-restraints excluded: chain I residue 317 LYS Chi-restraints excluded: chain J residue 357 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 59 optimal weight: 0.0670 chunk 62 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 31 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 overall best weight: 2.7524 ------------------------------------------------------------------------------- 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 G 327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5660 Z= 0.299 Angle : 0.618 5.855 7580 Z= 0.316 Chirality : 0.049 0.119 860 Planarity : 0.004 0.049 960 Dihedral : 5.184 16.615 740 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.59 % Allowed : 19.38 % Favored : 77.03 % 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: -2.17 (0.28), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 362 PHE 0.008 0.001 PHE G 378 TYR 0.010 0.002 TYR C 310 ARG 0.001 0.000 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 233 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 210 time to evaluate : 0.725 Fit side-chains REVERT: A 321 LYS cc_start: 0.8216 (tttt) cc_final: 0.7516 (ttpt) REVERT: A 342 GLU cc_start: 0.8217 (mt-10) cc_final: 0.6575 (pm20) REVERT: A 343 LYS cc_start: 0.8280 (tttt) cc_final: 0.7740 (mmtt) REVERT: A 347 LYS cc_start: 0.7038 (mttp) cc_final: 0.6379 (mtpt) REVERT: A 360 ILE cc_start: 0.9063 (mt) cc_final: 0.8777 (mp) REVERT: A 369 LYS cc_start: 0.8706 (mttt) cc_final: 0.8457 (mttt) REVERT: B 321 LYS cc_start: 0.8299 (tttt) cc_final: 0.7424 (ttpt) REVERT: B 342 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.6625 (mp0) REVERT: B 343 LYS cc_start: 0.8440 (tttt) cc_final: 0.7864 (mmtt) REVERT: B 347 LYS cc_start: 0.7177 (mttp) cc_final: 0.5739 (mtmt) REVERT: B 360 ILE cc_start: 0.9068 (mt) cc_final: 0.8732 (mp) REVERT: B 369 LYS cc_start: 0.8637 (mttt) cc_final: 0.7905 (mttp) REVERT: C 321 LYS cc_start: 0.7904 (tttt) cc_final: 0.7343 (mttp) REVERT: C 327 ASN cc_start: 0.8001 (m-40) cc_final: 0.7562 (t0) REVERT: C 342 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8257 (mm-30) REVERT: C 343 LYS cc_start: 0.8149 (tttt) cc_final: 0.7273 (mmtt) REVERT: C 349 ARG cc_start: 0.7754 (mtm180) cc_final: 0.7443 (mtm180) REVERT: D 321 LYS cc_start: 0.7875 (tttt) cc_final: 0.7336 (tttm) REVERT: D 327 ASN cc_start: 0.8201 (m-40) cc_final: 0.7645 (t0) REVERT: D 342 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7281 (mm-30) REVERT: D 343 LYS cc_start: 0.8076 (tttt) cc_final: 0.7245 (mmtt) REVERT: D 349 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7294 (mtm180) REVERT: D 356 SER cc_start: 0.9123 (p) cc_final: 0.8457 (m) REVERT: D 370 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8777 (tttp) REVERT: E 321 LYS cc_start: 0.7794 (tttt) cc_final: 0.7116 (ttpt) REVERT: E 342 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8019 (mm-30) REVERT: E 356 SER cc_start: 0.9133 (p) cc_final: 0.8278 (m) REVERT: E 360 ILE cc_start: 0.9117 (mt) cc_final: 0.8819 (mp) REVERT: E 369 LYS cc_start: 0.8753 (mttt) cc_final: 0.7923 (mttp) REVERT: F 321 LYS cc_start: 0.8079 (tttt) cc_final: 0.7410 (mttp) REVERT: F 343 LYS cc_start: 0.8064 (tttt) cc_final: 0.7104 (mmtt) REVERT: F 356 SER cc_start: 0.9005 (p) cc_final: 0.8514 (m) REVERT: F 369 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8115 (mttp) REVERT: G 321 LYS cc_start: 0.7981 (tttt) cc_final: 0.7374 (mttp) REVERT: G 342 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7449 (mm-30) REVERT: G 343 LYS cc_start: 0.7883 (tttt) cc_final: 0.7396 (mmtt) REVERT: G 360 ILE cc_start: 0.9074 (mt) cc_final: 0.8839 (mp) REVERT: H 321 LYS cc_start: 0.7908 (tttt) cc_final: 0.7311 (mttp) REVERT: H 342 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7437 (mm-30) REVERT: H 358 ASP cc_start: 0.8614 (m-30) cc_final: 0.8341 (m-30) REVERT: H 369 LYS cc_start: 0.8745 (mttt) cc_final: 0.7355 (mptt) REVERT: I 321 LYS cc_start: 0.7831 (tttt) cc_final: 0.7323 (mttm) REVERT: I 342 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.6598 (mt-10) REVERT: I 343 LYS cc_start: 0.7988 (tttt) cc_final: 0.7267 (mptp) REVERT: I 345 ASP cc_start: 0.7428 (t0) cc_final: 0.6817 (t0) REVERT: I 349 ARG cc_start: 0.7975 (mtm180) cc_final: 0.7565 (mtm180) REVERT: I 360 ILE cc_start: 0.9228 (mt) cc_final: 0.8978 (mp) REVERT: I 369 LYS cc_start: 0.8757 (mttt) cc_final: 0.7971 (mttp) REVERT: J 317 LYS cc_start: 0.8255 (tttt) cc_final: 0.7860 (ttmm) REVERT: J 321 LYS cc_start: 0.7981 (tttt) cc_final: 0.7568 (mttp) REVERT: J 343 LYS cc_start: 0.7986 (tttt) cc_final: 0.7386 (mmtt) REVERT: J 358 ASP cc_start: 0.8555 (m-30) cc_final: 0.8166 (m-30) outliers start: 23 outliers final: 8 residues processed: 217 average time/residue: 1.3763 time to fit residues: 309.1391 Evaluate side-chains 228 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 211 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 D residue 357 LEU Chi-restraints excluded: chain D residue 370 LYS 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 369 LYS 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 370 LYS Chi-restraints excluded: chain I residue 317 LYS Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain J residue 357 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 59 optimal weight: 0.3980 chunk 17 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- 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 G 327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3402 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= 0.290 Angle : 0.606 5.482 7580 Z= 0.313 Chirality : 0.049 0.120 860 Planarity : 0.004 0.049 960 Dihedral : 5.195 16.600 740 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.97 % Allowed : 19.22 % Favored : 77.81 % 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: -2.19 (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 0.003 0.001 HIS B 362 PHE 0.008 0.001 PHE G 378 TYR 0.009 0.002 TYR C 310 ARG 0.001 0.000 ARG I 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 229 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 210 time to evaluate : 0.621 Fit side-chains REVERT: A 321 LYS cc_start: 0.8241 (tttt) cc_final: 0.7550 (ttpt) REVERT: A 342 GLU cc_start: 0.8212 (mt-10) cc_final: 0.6543 (pm20) REVERT: A 343 LYS cc_start: 0.8299 (tttt) cc_final: 0.7735 (mmtt) REVERT: A 347 LYS cc_start: 0.7031 (mttp) cc_final: 0.6379 (mtpt) REVERT: A 360 ILE cc_start: 0.9061 (mt) cc_final: 0.8773 (mp) REVERT: A 369 LYS cc_start: 0.8706 (mttt) cc_final: 0.8457 (mttt) REVERT: B 321 LYS cc_start: 0.8298 (tttt) cc_final: 0.7425 (ttpt) REVERT: B 342 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.6619 (mp0) REVERT: B 343 LYS cc_start: 0.8438 (tttt) cc_final: 0.7851 (mmtt) REVERT: B 347 LYS cc_start: 0.7155 (mttp) cc_final: 0.5692 (mtmt) REVERT: B 360 ILE cc_start: 0.9067 (mt) cc_final: 0.8731 (mp) REVERT: B 369 LYS cc_start: 0.8638 (mttt) cc_final: 0.7906 (mttp) REVERT: C 321 LYS cc_start: 0.7901 (tttt) cc_final: 0.7352 (mttp) REVERT: C 327 ASN cc_start: 0.7999 (m-40) cc_final: 0.7570 (t0) REVERT: C 342 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8171 (mm-30) REVERT: C 343 LYS cc_start: 0.8142 (tttt) cc_final: 0.7286 (mmtt) REVERT: C 349 ARG cc_start: 0.7736 (mtm180) cc_final: 0.7425 (mtm180) REVERT: D 311 LYS cc_start: 0.8556 (pttp) cc_final: 0.7384 (tttt) REVERT: D 321 LYS cc_start: 0.7865 (tttt) cc_final: 0.7334 (tttm) REVERT: D 327 ASN cc_start: 0.8207 (m-40) cc_final: 0.7659 (t0) REVERT: D 342 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7253 (mm-30) REVERT: D 343 LYS cc_start: 0.8072 (tttt) cc_final: 0.7240 (mmtt) REVERT: D 349 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7265 (mtm180) REVERT: D 356 SER cc_start: 0.9153 (p) cc_final: 0.8515 (m) REVERT: D 370 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8789 (tttp) REVERT: E 321 LYS cc_start: 0.7789 (tttt) cc_final: 0.7091 (ttpt) REVERT: E 342 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8025 (mm-30) REVERT: E 356 SER cc_start: 0.9119 (p) cc_final: 0.8274 (m) REVERT: E 360 ILE cc_start: 0.9116 (mt) cc_final: 0.8823 (mp) REVERT: E 369 LYS cc_start: 0.8755 (mttt) cc_final: 0.7925 (mttp) REVERT: F 321 LYS cc_start: 0.8077 (tttt) cc_final: 0.7410 (mttp) REVERT: F 343 LYS cc_start: 0.8054 (tttt) cc_final: 0.7097 (mmtt) REVERT: F 356 SER cc_start: 0.8996 (p) cc_final: 0.8513 (m) REVERT: F 369 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8115 (mttp) REVERT: G 321 LYS cc_start: 0.7982 (tttt) cc_final: 0.7377 (mttp) REVERT: G 342 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7466 (mm-30) REVERT: G 343 LYS cc_start: 0.7877 (tttt) cc_final: 0.7393 (mmtt) REVERT: G 360 ILE cc_start: 0.9073 (mt) cc_final: 0.8841 (mp) REVERT: H 321 LYS cc_start: 0.7919 (tttt) cc_final: 0.7319 (mttp) REVERT: H 342 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7454 (mm-30) REVERT: H 349 ARG cc_start: 0.7695 (mtm-85) cc_final: 0.6938 (mtm180) REVERT: H 358 ASP cc_start: 0.8621 (m-30) cc_final: 0.8348 (m-30) REVERT: H 369 LYS cc_start: 0.8745 (mttt) cc_final: 0.7354 (mptt) REVERT: I 321 LYS cc_start: 0.7826 (tttt) cc_final: 0.7320 (mttm) REVERT: I 342 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.6497 (mt-10) REVERT: I 343 LYS cc_start: 0.8010 (tttt) cc_final: 0.7272 (mptp) REVERT: I 345 ASP cc_start: 0.7426 (t0) cc_final: 0.6813 (t0) REVERT: I 349 ARG cc_start: 0.7965 (mtm180) cc_final: 0.7552 (mtm180) REVERT: I 360 ILE cc_start: 0.9227 (mt) cc_final: 0.8977 (mp) REVERT: I 369 LYS cc_start: 0.8759 (mttt) cc_final: 0.7972 (mttp) REVERT: J 317 LYS cc_start: 0.8262 (tttt) cc_final: 0.7864 (ttmm) REVERT: J 321 LYS cc_start: 0.7982 (tttt) cc_final: 0.7567 (mttp) REVERT: J 343 LYS cc_start: 0.7972 (tttt) cc_final: 0.7379 (mmtt) REVERT: J 345 ASP cc_start: 0.7353 (t0) cc_final: 0.6726 (t0) REVERT: J 358 ASP cc_start: 0.8526 (m-30) cc_final: 0.8178 (m-30) outliers start: 19 outliers final: 9 residues processed: 216 average time/residue: 1.3781 time to fit residues: 308.2392 Evaluate side-chains 227 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 D residue 357 LEU Chi-restraints excluded: chain D residue 370 LYS 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 369 LYS 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 370 LYS Chi-restraints excluded: chain I residue 317 LYS Chi-restraints excluded: chain I residue 342 GLU Chi-restraints excluded: chain I residue 370 LYS Chi-restraints excluded: chain J residue 357 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 G 327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.152626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.122615 restraints weight = 5539.635| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.76 r_work: 0.3395 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 5660 Z= 0.395 Angle : 0.666 6.682 7580 Z= 0.339 Chirality : 0.049 0.129 860 Planarity : 0.004 0.052 960 Dihedral : 5.370 17.748 740 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 2.97 % Allowed : 19.69 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.24 (0.28), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 362 PHE 0.010 0.001 PHE G 378 TYR 0.010 0.002 TYR C 310 ARG 0.002 0.000 ARG I 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4323.65 seconds wall clock time: 77 minutes 27.99 seconds (4647.99 seconds total)