Starting phenix.real_space_refine on Tue Jan 14 05:50:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ero_19928/01_2025/9ero_19928.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ero_19928/01_2025/9ero_19928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ero_19928/01_2025/9ero_19928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ero_19928/01_2025/9ero_19928.map" model { file = "/net/cci-nas-00/data/ceres_data/9ero_19928/01_2025/9ero_19928.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ero_19928/01_2025/9ero_19928.cif" } resolution = 2.9 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= 0.001 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 3625 2.51 5 N 1070 2.21 5 O 1070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 5775 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 581 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Conformer: "B" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} bond proxies already assigned to first conformer: 574 Chain: "B" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Restraints were copied for chains: C, E, G, I, D, F, H, J Time building chain proxies: 3.63, per 1000 atoms: 0.63 Number of scatterers: 5775 At special positions: 0 Unit cell: (121.952, 131.84, 45.32, 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 1070 8.00 N 1070 7.00 C 3625 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: 1.21 Conformation dependent library (CDL) restraints added in 1.0 seconds 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1330 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 47.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'G' and resid 306 through 310 removed outlier: 6.299A pdb=" N GLN E 307 " --> pdb=" O ILE G 308 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N TYR G 310 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL E 309 " --> pdb=" O TYR G 310 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN A 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N TYR E 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL A 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 313 through 314 removed outlier: 6.725A pdb=" N VAL E 313 " --> pdb=" O ASP G 314 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 317 through 318 removed outlier: 6.345A pdb=" N LYS E 317 " --> pdb=" O VAL G 318 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LYS A 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 321 through 330 removed outlier: 6.453A pdb=" N LYS E 321 " --> pdb=" O CYS G 322 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N SER G 324 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N GLY E 323 " --> pdb=" O SER G 324 " (cutoff:3.500A) removed outlier: 10.047A pdb=" N GLY G 326 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N LEU E 325 " --> pdb=" O GLY G 326 " (cutoff:3.500A) removed outlier: 9.392A pdb=" N ILE G 328 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASN E 327 " --> pdb=" O ILE G 328 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N HIS G 330 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N HIS E 329 " --> pdb=" O HIS G 330 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LYS A 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N SER E 324 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N GLY A 323 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 10.047A pdb=" N GLY E 326 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N LEU A 325 " --> pdb=" O GLY E 326 " (cutoff:3.500A) removed outlier: 9.392A pdb=" N ILE E 328 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASN A 327 " --> pdb=" O ILE E 328 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N HIS E 330 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N HIS A 329 " --> pdb=" O HIS E 330 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER A 324 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU C 325 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLY A 326 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN C 327 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER C 324 " --> pdb=" O GLY I 323 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU I 325 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLY C 326 " --> pdb=" O LEU I 325 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN I 327 " --> pdb=" O GLY C 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 337 through 346 removed outlier: 6.826A pdb=" N LEU E 344 " --> pdb=" O LYS G 343 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASP G 345 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N PHE E 346 " --> pdb=" O ASP G 345 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU A 344 " --> pdb=" O LYS E 343 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASP E 345 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N PHE A 346 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N LYS C 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL A 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N GLU C 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N SER A 341 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU C 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LYS A 343 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 9.995A pdb=" N PHE C 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL C 337 " --> pdb=" O GLU I 338 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N LYS I 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL C 339 " --> pdb=" O LYS I 340 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N GLU I 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N SER C 341 " --> pdb=" O GLU I 342 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU I 344 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LYS C 343 " --> pdb=" O LEU I 344 " (cutoff:3.500A) removed outlier: 9.995A pdb=" N PHE I 346 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N ASP C 345 " --> pdb=" O PHE I 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 350 through 351 removed outlier: 6.299A pdb=" N VAL A 350 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL C 350 " --> pdb=" O GLN I 351 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 354 through 357 removed outlier: 6.020A pdb=" N ILE A 354 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU C 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER A 356 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ILE C 354 " --> pdb=" O GLY I 355 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU I 357 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER C 356 " --> pdb=" O LEU I 357 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 360 through 362 removed outlier: 6.421A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR C 361 " --> pdb=" O HIS I 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 371 through 378 removed outlier: 6.568A pdb=" N GLU A 372 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N LYS C 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N HIS A 374 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N THR C 377 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU A 376 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU C 372 " --> pdb=" O THR I 373 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N LYS I 375 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N HIS C 374 " --> pdb=" O LYS I 375 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N THR I 377 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU C 376 " --> pdb=" O THR I 377 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 306 through 310 removed outlier: 6.392A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLN D 307 " --> pdb=" O ILE J 308 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N TYR J 310 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL D 309 " --> pdb=" O TYR J 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 313 through 314 removed outlier: 6.784A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL D 313 " --> pdb=" O ASP J 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 317 through 325 removed outlier: 6.858A pdb=" N VAL H 318 " --> pdb=" O LYS F 317 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR F 319 " --> pdb=" O VAL H 318 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N SER H 320 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS F 321 " --> pdb=" O SER H 320 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N CYS H 322 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLY F 323 " --> pdb=" O CYS H 322 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL F 318 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR B 319 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N SER F 320 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS B 321 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N CYS F 322 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLY B 323 " --> pdb=" O CYS F 322 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N VAL B 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 10.692A pdb=" N LYS D 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 9.227A pdb=" N SER B 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 10.212A pdb=" N GLY D 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N CYS B 322 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU D 325 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N SER B 324 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N VAL D 318 " --> pdb=" O THR J 319 " (cutoff:3.500A) removed outlier: 10.692A pdb=" N LYS J 321 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 9.228A pdb=" N SER D 320 " --> pdb=" O LYS J 321 " (cutoff:3.500A) removed outlier: 10.212A pdb=" N GLY J 323 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N CYS D 322 " --> pdb=" O GLY J 323 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU J 325 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N SER D 324 " --> pdb=" O LEU J 325 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 337 through 342 removed outlier: 6.516A pdb=" N VAL F 337 " --> pdb=" O GLU H 338 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N LYS H 340 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL F 339 " --> pdb=" O LYS H 340 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N GLU H 342 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N SER F 341 " --> pdb=" O GLU H 342 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL B 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N LYS F 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL B 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N GLU F 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N SER B 341 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 345 through 346 removed outlier: 6.405A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ASP D 345 " --> pdb=" O PHE J 346 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 350 through 351 removed outlier: 6.368A pdb=" N VAL F 350 " --> pdb=" O GLN H 351 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL B 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 354 through 357 removed outlier: 6.014A pdb=" N ILE F 354 " --> pdb=" O GLY H 355 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU H 357 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER F 356 " --> pdb=" O LEU H 357 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE B 354 " --> pdb=" O GLY F 355 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU F 357 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER B 356 " --> pdb=" O LEU F 357 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 360 through 362 removed outlier: 6.451A pdb=" N THR F 361 " --> pdb=" O HIS H 362 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR B 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 369 through 378 removed outlier: 6.373A pdb=" N LYS F 370 " --> pdb=" O ILE H 371 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N THR H 373 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLU F 372 " --> pdb=" O THR H 373 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N LYS H 375 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N HIS F 374 " --> pdb=" O LYS H 375 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N THR H 377 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU F 376 " --> pdb=" O THR H 377 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYS B 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N THR F 373 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLU B 372 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N LYS F 375 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N HIS B 374 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N THR F 377 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU B 376 " --> pdb=" O THR F 377 " (cutoff:3.500A) 116 hydrogen bonds defined for protein. 346 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: 1.36 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1382 1.33 - 1.45: 1330 1.45 - 1.57: 3153 1.57 - 1.70: 0 1.70 - 1.82: 10 Bond restraints: 5875 Sorted by residual: bond pdb=" CG HIS I 330 " pdb=" CD2 HIS I 330 " ideal model delta sigma weight residual 1.354 1.296 0.058 1.10e-02 8.26e+03 2.75e+01 bond pdb=" CG HIS A 330 " pdb=" CD2 HIS A 330 " ideal model delta sigma weight residual 1.354 1.297 0.057 1.10e-02 8.26e+03 2.72e+01 bond pdb=" CG HIS C 330 " pdb=" CD2 HIS C 330 " ideal model delta sigma weight residual 1.354 1.297 0.057 1.10e-02 8.26e+03 2.72e+01 bond pdb=" CG HIS G 330 " pdb=" CD2 HIS G 330 " ideal model delta sigma weight residual 1.354 1.297 0.057 1.10e-02 8.26e+03 2.70e+01 bond pdb=" CG HIS E 330 " pdb=" CD2 HIS E 330 " ideal model delta sigma weight residual 1.354 1.297 0.057 1.10e-02 8.26e+03 2.68e+01 ... (remaining 5870 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 5766 1.65 - 3.31: 1613 3.31 - 4.96: 387 4.96 - 6.62: 89 6.62 - 8.27: 15 Bond angle restraints: 7870 Sorted by residual: angle pdb=" CA HIS H 330 " pdb=" CB HIS H 330 " pdb=" CG HIS H 330 " ideal model delta sigma weight residual 113.80 120.13 -6.33 1.00e+00 1.00e+00 4.00e+01 angle pdb=" CA HIS B 330 " pdb=" CB HIS B 330 " pdb=" CG HIS B 330 " ideal model delta sigma weight residual 113.80 120.12 -6.32 1.00e+00 1.00e+00 4.00e+01 angle pdb=" CA HIS F 330 " pdb=" CB HIS F 330 " pdb=" CG HIS F 330 " ideal model delta sigma weight residual 113.80 120.12 -6.32 1.00e+00 1.00e+00 3.99e+01 angle pdb=" CA HIS J 330 " pdb=" CB HIS J 330 " pdb=" CG HIS J 330 " ideal model delta sigma weight residual 113.80 120.11 -6.31 1.00e+00 1.00e+00 3.99e+01 angle pdb=" CA HIS D 330 " pdb=" CB HIS D 330 " pdb=" CG HIS D 330 " ideal model delta sigma weight residual 113.80 120.09 -6.29 1.00e+00 1.00e+00 3.96e+01 ... (remaining 7865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.60: 2835 10.60 - 21.20: 540 21.20 - 31.80: 155 31.80 - 42.40: 25 42.40 - 53.00: 35 Dihedral angle restraints: 3590 sinusoidal: 1500 harmonic: 2090 Sorted by residual: dihedral pdb=" CA PRO D 332 " pdb=" C PRO D 332 " pdb=" N GLY D 333 " pdb=" CA GLY D 333 " ideal model delta harmonic sigma weight residual -180.00 -140.16 -39.84 0 5.00e+00 4.00e-02 6.35e+01 dihedral pdb=" CA PRO J 332 " pdb=" C PRO J 332 " pdb=" N GLY J 333 " pdb=" CA GLY J 333 " ideal model delta harmonic sigma weight residual -180.00 -140.17 -39.83 0 5.00e+00 4.00e-02 6.34e+01 dihedral pdb=" CA PRO B 332 " pdb=" C PRO B 332 " pdb=" N GLY B 333 " pdb=" CA GLY B 333 " ideal model delta harmonic sigma weight residual -180.00 -140.18 -39.82 0 5.00e+00 4.00e-02 6.34e+01 ... (remaining 3587 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.054: 342 0.054 - 0.107: 343 0.107 - 0.159: 139 0.159 - 0.212: 41 0.212 - 0.264: 20 Chirality restraints: 885 Sorted by residual: chirality pdb=" CB ILE C 328 " pdb=" CA ILE C 328 " pdb=" CG1 ILE C 328 " pdb=" CG2 ILE C 328 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CB ILE A 328 " pdb=" CA ILE A 328 " pdb=" CG1 ILE A 328 " pdb=" CG2 ILE A 328 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CB ILE E 328 " pdb=" CA ILE E 328 " pdb=" CG1 ILE E 328 " pdb=" CG2 ILE E 328 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 882 not shown) Planarity restraints: 1000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 362 " -0.027 2.00e-02 2.50e+03 2.16e-02 7.00e+00 pdb=" CG HIS C 362 " 0.041 2.00e-02 2.50e+03 pdb=" ND1 HIS C 362 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS C 362 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS C 362 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS C 362 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 362 " -0.026 2.00e-02 2.50e+03 2.15e-02 6.93e+00 pdb=" CG HIS A 362 " 0.041 2.00e-02 2.50e+03 pdb=" ND1 HIS A 362 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS A 362 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS A 362 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS A 362 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS G 362 " -0.026 2.00e-02 2.50e+03 2.15e-02 6.93e+00 pdb=" CG HIS G 362 " 0.041 2.00e-02 2.50e+03 pdb=" ND1 HIS G 362 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS G 362 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS G 362 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS G 362 " -0.019 2.00e-02 2.50e+03 ... (remaining 997 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 2165 2.92 - 3.42: 5189 3.42 - 3.91: 9284 3.91 - 4.41: 9861 4.41 - 4.90: 20275 Nonbonded interactions: 46774 Sorted by model distance: nonbonded pdb=" OD1 ASP I 314 " pdb=" OG SER I 316 " model vdw 2.427 3.040 nonbonded pdb=" OD1 ASP G 314 " pdb=" OG SER G 316 " model vdw 2.427 3.040 nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.427 3.040 nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.427 3.040 nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.428 3.040 ... (remaining 46769 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 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: 2.690 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.100 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 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 : 0.010 0.069 5875 Z= 0.643 Angle : 1.675 8.271 7870 Z= 1.070 Chirality : 0.091 0.264 885 Planarity : 0.011 0.046 1000 Dihedral : 13.222 53.002 2260 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 5.26 % Allowed : 6.02 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.39 % 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: -4.12 (0.17), residues: 735 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.13), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.007 HIS C 374 PHE 0.026 0.006 PHE G 346 TYR 0.021 0.007 TYR H 310 ARG 0.009 0.002 ARG J 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: B 317 LYS cc_start: 0.7966 (pttt) cc_final: 0.7500 (ptpt) REVERT: B 338 GLU cc_start: 0.8554 (tt0) cc_final: 0.8222 (tm-30) REVERT: B 340 LYS cc_start: 0.8127 (mttt) cc_final: 0.7402 (tppp) REVERT: D 338 GLU cc_start: 0.8491 (tt0) cc_final: 0.8059 (tm-30) REVERT: D 340 LYS cc_start: 0.8215 (mttt) cc_final: 0.7386 (tppp) REVERT: F 317 LYS cc_start: 0.8005 (pttt) cc_final: 0.7742 (ptmm) REVERT: F 338 GLU cc_start: 0.8522 (tt0) cc_final: 0.8209 (tm-30) REVERT: F 340 LYS cc_start: 0.8083 (mttt) cc_final: 0.7378 (tppp) REVERT: G 340 LYS cc_start: 0.8769 (mttt) cc_final: 0.8470 (mmtp) REVERT: G 378 PHE cc_start: 0.7443 (t80) cc_final: 0.7233 (t80) REVERT: H 329 HIS cc_start: 0.7875 (OUTLIER) cc_final: 0.7649 (t-90) REVERT: H 338 GLU cc_start: 0.8643 (tt0) cc_final: 0.8401 (tm-30) REVERT: H 349 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.5542 (mmm160) REVERT: I 349 ARG cc_start: 0.8401 (mtt180) cc_final: 0.7063 (mmp-170) REVERT: J 317 LYS cc_start: 0.8516 (pttt) cc_final: 0.8248 (ptmt) REVERT: J 338 GLU cc_start: 0.8659 (tt0) cc_final: 0.8449 (tm-30) REVERT: J 340 LYS cc_start: 0.8468 (mttt) cc_final: 0.7789 (tppp) REVERT: J 349 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7491 (ptp-170) REVERT: J 375 LYS cc_start: 0.8597 (tttt) cc_final: 0.8293 (tttm) outliers start: 35 outliers final: 8 residues processed: 157 average time/residue: 1.4440 time to fit residues: 234.8403 Evaluate side-chains 110 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain H residue 329 HIS Chi-restraints excluded: chain H residue 349 ARG Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain J residue 325 LEU Chi-restraints excluded: chain J residue 349 ARG Chi-restraints excluded: chain J residue 350 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 54 optimal weight: 0.4980 chunk 21 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** J 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.137143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.106916 restraints weight = 20776.290| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 4.12 r_work: 0.3837 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3821 r_free = 0.3821 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3821 r_free = 0.3821 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5875 Z= 0.246 Angle : 0.692 7.460 7870 Z= 0.343 Chirality : 0.051 0.136 885 Planarity : 0.003 0.024 1000 Dihedral : 7.798 56.160 803 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 3.76 % Allowed : 15.34 % Favored : 80.90 % 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: -2.51 (0.24), residues: 735 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.18), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS I 330 PHE 0.013 0.002 PHE A 378 TYR 0.017 0.003 TYR F 310 ARG 0.001 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.716 Fit side-chains REVERT: B 379 ARG cc_start: 0.6876 (mmt90) cc_final: 0.6600 (mmt90) REVERT: C 340 LYS cc_start: 0.8240 (mttt) cc_final: 0.7817 (mttp) REVERT: G 340 LYS cc_start: 0.8642 (mttt) cc_final: 0.8249 (mtpp) REVERT: G 342 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8338 (mp0) REVERT: H 317 LYS cc_start: 0.8167 (pttt) cc_final: 0.7713 (ptmt) REVERT: H 340 LYS cc_start: 0.7601 (mttt) cc_final: 0.7400 (mttp) REVERT: I 349 ARG cc_start: 0.7827 (mtt180) cc_final: 0.6156 (mmm160) outliers start: 25 outliers final: 7 residues processed: 95 average time/residue: 1.1684 time to fit residues: 116.4360 Evaluate side-chains 65 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 350 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 56 optimal weight: 0.3980 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.164465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.132831 restraints weight = 18145.115| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 4.14 r_work: 0.3889 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3873 r_free = 0.3873 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3873 r_free = 0.3873 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5875 Z= 0.248 Angle : 0.669 7.458 7870 Z= 0.328 Chirality : 0.050 0.134 885 Planarity : 0.003 0.022 1000 Dihedral : 5.894 36.848 785 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 3.61 % Allowed : 17.74 % Favored : 78.65 % 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: -2.00 (0.25), residues: 735 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.19), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS I 330 PHE 0.014 0.002 PHE A 378 TYR 0.018 0.004 TYR F 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.668 Fit side-chains REVERT: B 379 ARG cc_start: 0.6634 (mmt90) cc_final: 0.6382 (mmt90) REVERT: C 347 LYS cc_start: 0.8164 (mmtp) cc_final: 0.7886 (mmtp) REVERT: D 348 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.7505 (t0) REVERT: E 340 LYS cc_start: 0.7817 (mttt) cc_final: 0.7304 (mtpp) REVERT: F 349 ARG cc_start: 0.6166 (ptp-170) cc_final: 0.5936 (ptp-170) REVERT: G 318 VAL cc_start: 0.7927 (OUTLIER) cc_final: 0.7659 (m) REVERT: G 340 LYS cc_start: 0.8565 (mttt) cc_final: 0.8025 (mtpp) REVERT: G 342 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8203 (mp0) REVERT: H 349 ARG cc_start: 0.6832 (ptp-170) cc_final: 0.6490 (ptp-170) REVERT: I 349 ARG cc_start: 0.7524 (mtt180) cc_final: 0.5798 (mmm160) REVERT: J 338 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8387 (tm-30) outliers start: 24 outliers final: 9 residues processed: 80 average time/residue: 1.2805 time to fit residues: 107.2949 Evaluate side-chains 70 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain H residue 348 ASP Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain J residue 350 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 2 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.165729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.133730 restraints weight = 21358.363| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 4.44 r_work: 0.3894 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3878 r_free = 0.3878 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3878 r_free = 0.3878 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5875 Z= 0.210 Angle : 0.641 8.104 7870 Z= 0.309 Chirality : 0.049 0.130 885 Planarity : 0.003 0.019 1000 Dihedral : 5.523 34.263 785 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 3.31 % Allowed : 18.20 % Favored : 78.50 % 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: -1.79 (0.26), residues: 735 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.19), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 330 PHE 0.015 0.001 PHE A 378 TYR 0.016 0.003 TYR F 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: B 379 ARG cc_start: 0.6687 (mmt90) cc_final: 0.6395 (mmt90) REVERT: C 347 LYS cc_start: 0.8127 (mmtp) cc_final: 0.7800 (mmtp) REVERT: D 317 LYS cc_start: 0.7829 (ptmt) cc_final: 0.7135 (ptpt) REVERT: E 340 LYS cc_start: 0.7847 (mttt) cc_final: 0.7281 (mtpp) REVERT: G 318 VAL cc_start: 0.7983 (OUTLIER) cc_final: 0.7710 (m) REVERT: G 342 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8260 (mp0) REVERT: H 317 LYS cc_start: 0.8149 (pttt) cc_final: 0.7714 (ptmt) REVERT: H 338 GLU cc_start: 0.7816 (tt0) cc_final: 0.7440 (tm-30) REVERT: H 369 LYS cc_start: 0.8114 (mttp) cc_final: 0.7399 (mtpt) REVERT: I 349 ARG cc_start: 0.7542 (mtt180) cc_final: 0.5760 (mmm160) REVERT: J 338 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8326 (tm-30) REVERT: J 348 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7741 (t0) outliers start: 22 outliers final: 10 residues processed: 88 average time/residue: 1.4103 time to fit residues: 129.7561 Evaluate side-chains 71 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 311 LYS Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain H residue 348 ASP Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain I residue 311 LYS Chi-restraints excluded: chain J residue 320 SER Chi-restraints excluded: chain J residue 348 ASP Chi-restraints excluded: chain J residue 350 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 44 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.160316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.129337 restraints weight = 15843.088| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 3.90 r_work: 0.3871 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3841 r_free = 0.3841 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3841 r_free = 0.3841 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5875 Z= 0.320 Angle : 0.693 8.214 7870 Z= 0.342 Chirality : 0.050 0.128 885 Planarity : 0.003 0.018 1000 Dihedral : 6.005 41.491 785 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 4.06 % Allowed : 17.59 % Favored : 78.35 % 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: -1.79 (0.26), residues: 735 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 362 PHE 0.018 0.002 PHE A 378 TYR 0.022 0.005 TYR F 310 ARG 0.002 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 0.670 Fit side-chains REVERT: B 348 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.7822 (t0) REVERT: C 342 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7691 (mp0) REVERT: D 348 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.7463 (t0) REVERT: E 340 LYS cc_start: 0.7875 (mttt) cc_final: 0.7359 (mtpp) REVERT: E 342 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7599 (mp0) REVERT: E 378 PHE cc_start: 0.7280 (t80) cc_final: 0.6605 (t80) REVERT: G 318 VAL cc_start: 0.8020 (OUTLIER) cc_final: 0.7747 (m) REVERT: G 340 LYS cc_start: 0.8586 (mttt) cc_final: 0.8194 (mtpm) REVERT: G 342 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8190 (mp0) REVERT: G 378 PHE cc_start: 0.7349 (t80) cc_final: 0.6930 (t80) REVERT: H 338 GLU cc_start: 0.7806 (tt0) cc_final: 0.7392 (tm-30) REVERT: I 342 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7598 (mp0) REVERT: I 349 ARG cc_start: 0.7536 (mtt180) cc_final: 0.5779 (mmm160) REVERT: J 338 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8319 (tm-30) REVERT: J 348 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7737 (t0) outliers start: 27 outliers final: 12 residues processed: 92 average time/residue: 1.2820 time to fit residues: 123.3110 Evaluate side-chains 84 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 311 LYS Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain H residue 348 ASP Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain I residue 311 LYS Chi-restraints excluded: chain J residue 348 ASP Chi-restraints excluded: chain J residue 350 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 46 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 0.3980 chunk 10 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 overall best weight: 5.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.128915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.096933 restraints weight = 21174.348| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 4.44 r_work: 0.3792 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3771 r_free = 0.3771 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3771 r_free = 0.3771 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 5875 Z= 0.490 Angle : 0.792 8.007 7870 Z= 0.403 Chirality : 0.053 0.129 885 Planarity : 0.004 0.018 1000 Dihedral : 6.584 46.460 785 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.66 % Allowed : 18.20 % Favored : 77.14 % 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: -1.96 (0.25), residues: 735 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.19), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS D 362 PHE 0.015 0.002 PHE I 378 TYR 0.030 0.007 TYR F 310 ARG 0.003 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 71 time to evaluate : 0.708 Fit side-chains REVERT: B 348 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.7835 (t0) REVERT: C 342 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7768 (mp0) REVERT: D 348 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.7309 (t0) REVERT: E 340 LYS cc_start: 0.7921 (mttt) cc_final: 0.7408 (mtpp) REVERT: E 342 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7657 (mp0) REVERT: E 378 PHE cc_start: 0.7314 (t80) cc_final: 0.6632 (t80) REVERT: G 340 LYS cc_start: 0.8609 (mttt) cc_final: 0.8224 (mtpm) REVERT: G 342 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8175 (mp0) REVERT: G 378 PHE cc_start: 0.7448 (t80) cc_final: 0.6942 (t80) REVERT: H 338 GLU cc_start: 0.7839 (tt0) cc_final: 0.7427 (tm-30) REVERT: I 342 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7672 (mp0) REVERT: I 349 ARG cc_start: 0.7564 (mtt180) cc_final: 0.5887 (mmm160) REVERT: J 338 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8460 (tm-30) REVERT: J 348 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7783 (t0) outliers start: 31 outliers final: 13 residues processed: 96 average time/residue: 1.2220 time to fit residues: 123.0950 Evaluate side-chains 91 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain H residue 348 ASP Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain I residue 311 LYS Chi-restraints excluded: chain J residue 338 GLU Chi-restraints excluded: chain J residue 348 ASP Chi-restraints excluded: chain J residue 350 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 0.2980 chunk 10 optimal weight: 9.9990 chunk 16 optimal weight: 0.0980 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.165535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.133809 restraints weight = 21783.221| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 4.47 r_work: 0.3906 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3867 r_free = 0.3867 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3867 r_free = 0.3867 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 5875 Z= 0.180 Angle : 0.640 8.911 7870 Z= 0.307 Chirality : 0.049 0.123 885 Planarity : 0.002 0.015 1000 Dihedral : 5.404 32.973 785 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 2.71 % Allowed : 20.60 % Favored : 76.69 % 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: -1.73 (0.26), residues: 735 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 330 PHE 0.016 0.001 PHE C 378 TYR 0.014 0.003 TYR F 310 ARG 0.002 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.548 Fit side-chains REVERT: C 342 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7709 (mp0) REVERT: E 342 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7548 (mp0) REVERT: E 378 PHE cc_start: 0.7123 (t80) cc_final: 0.6468 (t80) REVERT: F 338 GLU cc_start: 0.7905 (tt0) cc_final: 0.7437 (tm-30) REVERT: G 342 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8121 (mp0) REVERT: G 347 LYS cc_start: 0.8564 (mmtp) cc_final: 0.7003 (pptt) REVERT: G 378 PHE cc_start: 0.7264 (t80) cc_final: 0.6787 (t80) REVERT: H 338 GLU cc_start: 0.7759 (tt0) cc_final: 0.7392 (tm-30) REVERT: I 342 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7592 (mp0) REVERT: I 349 ARG cc_start: 0.7530 (mtt180) cc_final: 0.5747 (mmm160) REVERT: J 338 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8395 (tm-30) REVERT: J 348 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7746 (t0) outliers start: 18 outliers final: 9 residues processed: 86 average time/residue: 1.2071 time to fit residues: 108.6437 Evaluate side-chains 81 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain H residue 348 ASP Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain J residue 338 GLU Chi-restraints excluded: chain J residue 348 ASP Chi-restraints excluded: chain J residue 350 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 51 optimal weight: 0.0670 chunk 60 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 overall best weight: 4.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.130786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.098382 restraints weight = 23324.604| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 4.64 r_work: 0.3819 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3776 r_free = 0.3776 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3776 r_free = 0.3776 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5875 Z= 0.372 Angle : 0.734 8.682 7870 Z= 0.365 Chirality : 0.051 0.130 885 Planarity : 0.003 0.019 1000 Dihedral : 6.140 42.332 785 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.01 % Allowed : 20.30 % Favored : 76.69 % 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: -1.81 (0.26), residues: 735 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS D 362 PHE 0.012 0.001 PHE I 378 TYR 0.024 0.005 TYR F 310 ARG 0.002 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.721 Fit side-chains REVERT: C 342 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7785 (mp0) REVERT: D 348 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.7437 (t0) REVERT: E 340 LYS cc_start: 0.7886 (mttt) cc_final: 0.7379 (mtpp) REVERT: E 342 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7648 (mp0) REVERT: E 378 PHE cc_start: 0.7306 (t80) cc_final: 0.6650 (t80) REVERT: F 338 GLU cc_start: 0.7938 (tt0) cc_final: 0.7429 (tm-30) REVERT: G 340 LYS cc_start: 0.8599 (mttt) cc_final: 0.8227 (mtpm) REVERT: G 342 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8187 (mp0) REVERT: G 347 LYS cc_start: 0.8563 (mmtp) cc_final: 0.7041 (pptt) REVERT: G 378 PHE cc_start: 0.7402 (t80) cc_final: 0.6911 (t80) REVERT: H 338 GLU cc_start: 0.7801 (tt0) cc_final: 0.7350 (tm-30) REVERT: H 349 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6707 (ptp-170) REVERT: I 342 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7676 (mp0) REVERT: I 349 ARG cc_start: 0.7579 (mtt180) cc_final: 0.5862 (mmm160) REVERT: J 338 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8394 (tm-30) REVERT: J 348 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7725 (t0) outliers start: 20 outliers final: 10 residues processed: 87 average time/residue: 1.2794 time to fit residues: 116.4255 Evaluate side-chains 84 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain H residue 348 ASP Chi-restraints excluded: chain H residue 349 ARG Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain I residue 311 LYS Chi-restraints excluded: chain J residue 338 GLU Chi-restraints excluded: chain J residue 348 ASP Chi-restraints excluded: chain J residue 350 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 20 optimal weight: 3.9990 chunk 49 optimal weight: 0.2980 chunk 60 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 16 optimal weight: 0.2980 chunk 55 optimal weight: 0.2980 chunk 51 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.166248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.135157 restraints weight = 17389.124| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 4.07 r_work: 0.3933 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3914 r_free = 0.3914 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3914 r_free = 0.3914 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5875 Z= 0.168 Angle : 0.647 9.157 7870 Z= 0.306 Chirality : 0.049 0.122 885 Planarity : 0.002 0.016 1000 Dihedral : 5.223 30.095 785 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 2.86 % Allowed : 20.45 % Favored : 76.69 % 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: -1.65 (0.26), residues: 735 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 330 PHE 0.006 0.001 PHE I 378 TYR 0.012 0.002 TYR F 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.678 Fit side-chains REVERT: C 342 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7722 (mp0) REVERT: D 348 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.7465 (t0) REVERT: E 342 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7533 (mp0) REVERT: E 378 PHE cc_start: 0.7071 (t80) cc_final: 0.6408 (t80) REVERT: F 338 GLU cc_start: 0.7861 (tt0) cc_final: 0.7404 (tm-30) REVERT: G 342 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8123 (mp0) REVERT: G 378 PHE cc_start: 0.7213 (t80) cc_final: 0.6740 (t80) REVERT: H 338 GLU cc_start: 0.7764 (tt0) cc_final: 0.7366 (tm-30) REVERT: H 349 ARG cc_start: 0.6832 (OUTLIER) cc_final: 0.6542 (ptp-170) REVERT: I 342 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7615 (mp0) REVERT: I 349 ARG cc_start: 0.7578 (mtt180) cc_final: 0.5742 (mmm160) REVERT: J 338 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8475 (tm-30) REVERT: J 348 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7715 (t0) outliers start: 19 outliers final: 10 residues processed: 82 average time/residue: 1.1958 time to fit residues: 102.9393 Evaluate side-chains 79 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain H residue 325 LEU Chi-restraints excluded: chain H residue 348 ASP Chi-restraints excluded: chain H residue 349 ARG Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain I residue 311 LYS Chi-restraints excluded: chain J residue 348 ASP Chi-restraints excluded: chain J residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 19 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.160653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.128745 restraints weight = 22678.582| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 4.49 r_work: 0.3831 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3814 r_free = 0.3814 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3814 r_free = 0.3814 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5875 Z= 0.307 Angle : 0.712 9.060 7870 Z= 0.349 Chirality : 0.050 0.123 885 Planarity : 0.003 0.018 1000 Dihedral : 5.741 37.015 785 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.86 % Allowed : 20.60 % Favored : 76.54 % 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: -1.69 (0.26), residues: 735 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 362 PHE 0.007 0.001 PHE I 378 TYR 0.022 0.005 TYR F 310 ARG 0.002 0.000 ARG J 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.679 Fit side-chains REVERT: B 348 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.7743 (t0) REVERT: C 342 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7668 (mp0) REVERT: D 348 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.7440 (t0) REVERT: E 340 LYS cc_start: 0.7818 (mttt) cc_final: 0.7306 (mtpp) REVERT: E 342 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7569 (mp0) REVERT: E 378 PHE cc_start: 0.7195 (t80) cc_final: 0.6550 (t80) REVERT: F 338 GLU cc_start: 0.7917 (tt0) cc_final: 0.7422 (tm-30) REVERT: G 342 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8139 (mp0) REVERT: G 378 PHE cc_start: 0.7320 (t80) cc_final: 0.6819 (t80) REVERT: H 338 GLU cc_start: 0.7774 (tt0) cc_final: 0.7338 (tm-30) REVERT: H 349 ARG cc_start: 0.6861 (OUTLIER) cc_final: 0.6649 (ptp-170) REVERT: I 342 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7573 (mp0) REVERT: I 349 ARG cc_start: 0.7496 (mtt180) cc_final: 0.5762 (mmm160) REVERT: J 338 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8469 (tm-30) REVERT: J 348 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7686 (t0) outliers start: 19 outliers final: 10 residues processed: 79 average time/residue: 1.2652 time to fit residues: 105.5063 Evaluate side-chains 82 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 311 LYS Chi-restraints excluded: chain H residue 348 ASP Chi-restraints excluded: chain H residue 349 ARG Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain I residue 311 LYS Chi-restraints excluded: chain J residue 338 GLU Chi-restraints excluded: chain J residue 348 ASP Chi-restraints excluded: chain J residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 24 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 67 optimal weight: 0.2980 chunk 18 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 48 optimal weight: 0.0670 overall best weight: 1.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.165964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.134926 restraints weight = 16877.725| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 4.02 r_work: 0.3933 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3910 r_free = 0.3910 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3910 r_free = 0.3910 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5875 Z= 0.174 Angle : 0.658 9.305 7870 Z= 0.312 Chirality : 0.049 0.124 885 Planarity : 0.002 0.019 1000 Dihedral : 5.274 30.523 785 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 2.26 % Allowed : 21.35 % Favored : 76.39 % 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: -1.63 (0.27), residues: 735 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 330 PHE 0.005 0.001 PHE F 378 TYR 0.015 0.003 TYR H 310 ARG 0.002 0.000 ARG J 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5833.46 seconds wall clock time: 104 minutes 14.37 seconds (6254.37 seconds total)