Starting phenix.real_space_refine on Wed Sep 17 06:05:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ero_19928/09_2025/9ero_19928.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ero_19928/09_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_19928/09_2025/9ero_19928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ero_19928/09_2025/9ero_19928.map" model { file = "/net/cci-nas-00/data/ceres_data/9ero_19928/09_2025/9ero_19928.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ero_19928/09_2025/9ero_19928.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.07, per 1000 atoms: 0.19 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: 0.42 Conformation dependent library (CDL) restraints added in 316.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.17 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: 0.68 Time building geometry restraints manager: 0.54 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: 0.01 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: 6.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.960 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 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:9.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.310 ------------------------------------------------------------------------------- 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= 0.659 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.002 ARG J 349 TYR 0.021 0.007 TYR H 310 PHE 0.026 0.006 PHE G 346 HIS 0.015 0.007 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00956 ( 5875) covalent geometry : angle 1.67480 ( 7870) hydrogen bonds : bond 0.17847 ( 116) hydrogen bonds : angle 6.79493 ( 346) *********************** 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 : 0.239 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: 0.8206 (tm-30) REVERT: B 340 LYS cc_start: 0.8127 (mttt) cc_final: 0.7397 (tppp) REVERT: D 338 GLU cc_start: 0.8491 (tt0) cc_final: 0.8060 (tm-30) REVERT: D 340 LYS cc_start: 0.8215 (mttt) cc_final: 0.7391 (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: 0.8206 (tm-30) REVERT: F 340 LYS cc_start: 0.8083 (mttt) cc_final: 0.7377 (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: 0.7041 time to fit residues: 114.4416 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 : 0.334 ------------------------------------------------------------------------------- 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 49 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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** J 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.144280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.114272 restraints weight = 15531.907| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 3.77 r_work: 0.3919 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3918 r_free = 0.3918 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3918 r_free = 0.3918 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5875 Z= 0.112 Angle : 0.644 7.617 7870 Z= 0.315 Chirality : 0.050 0.140 885 Planarity : 0.003 0.021 1000 Dihedral : 7.433 58.399 803 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 4.06 % Allowed : 14.74 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.49 (0.24), residues: 735 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.18), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 379 TYR 0.011 0.002 TYR F 310 PHE 0.011 0.001 PHE A 378 HIS 0.006 0.001 HIS I 330 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 5875) covalent geometry : angle 0.64440 ( 7870) hydrogen bonds : bond 0.02139 ( 116) hydrogen bonds : angle 4.73473 ( 346) *********************** 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 100 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.219 Fit side-chains REVERT: G 340 LYS cc_start: 0.8607 (mttt) cc_final: 0.8222 (mtpp) REVERT: G 341 SER cc_start: 0.9054 (m) cc_final: 0.8773 (m) REVERT: G 342 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8313 (mp0) REVERT: H 317 LYS cc_start: 0.8122 (pttt) cc_final: 0.7687 (ptmt) REVERT: H 340 LYS cc_start: 0.7544 (mttt) cc_final: 0.6735 (tmtp) REVERT: I 349 ARG cc_start: 0.7836 (mtt180) cc_final: 0.6112 (mmm160) outliers start: 27 outliers final: 7 residues processed: 98 average time/residue: 0.5153 time to fit residues: 53.0428 Evaluate side-chains 66 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 29 optimal weight: 20.0000 chunk 6 optimal weight: 0.0030 chunk 66 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 56 optimal weight: 0.2980 chunk 2 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 overall best weight: 2.2596 ------------------------------------------------------------------------------- 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 = 0.4580 r_free = 0.4580 target = 0.285810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.245933 restraints weight = 16884.114| |-----------------------------------------------------------------------------| r_work (start): 0.4400 rms_B_bonded: 2.09 r_work: 0.4226 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.4106 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3904 r_free = 0.3904 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3904 r_free = 0.3904 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2600 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= 0.149 Angle : 0.651 7.345 7870 Z= 0.320 Chirality : 0.049 0.136 885 Planarity : 0.003 0.025 1000 Dihedral : 5.770 35.216 785 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 3.61 % Allowed : 17.44 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.99 (0.26), residues: 735 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 349 TYR 0.019 0.004 TYR F 310 PHE 0.014 0.001 PHE A 378 HIS 0.005 0.001 HIS I 330 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 5875) covalent geometry : angle 0.65142 ( 7870) hydrogen bonds : bond 0.02240 ( 116) hydrogen bonds : angle 4.52164 ( 346) *********************** 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 90 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.252 Fit side-chains REVERT: D 348 ASP cc_start: 0.8785 (OUTLIER) cc_final: 0.8056 (t0) REVERT: E 340 LYS cc_start: 0.8120 (mttt) cc_final: 0.7743 (mtpp) REVERT: G 340 LYS cc_start: 0.8570 (mttt) cc_final: 0.8268 (mtpp) REVERT: G 342 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8463 (mp0) REVERT: H 349 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6995 (ptp-170) REVERT: I 349 ARG cc_start: 0.7957 (mtt180) cc_final: 0.6293 (mmm160) outliers start: 24 outliers final: 7 residues processed: 83 average time/residue: 0.5790 time to fit residues: 50.3595 Evaluate side-chains 69 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL 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 348 ASP Chi-restraints excluded: chain H residue 349 ARG 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 51 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.4514 r_free = 0.4514 target = 0.157428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.126186 restraints weight = 18404.686| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 4.09 r_work: 0.3817 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3792 r_free = 0.3792 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 = 0.3792 r_free = 0.3792 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 5875 Z= 0.271 Angle : 0.758 7.683 7870 Z= 0.382 Chirality : 0.052 0.130 885 Planarity : 0.004 0.033 1000 Dihedral : 6.517 46.680 785 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.25), residues: 735 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.19), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 349 TYR 0.028 0.006 TYR F 310 PHE 0.018 0.002 PHE A 378 HIS 0.006 0.002 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00607 ( 5875) covalent geometry : angle 0.75771 ( 7870) hydrogen bonds : bond 0.02821 ( 116) hydrogen bonds : angle 4.66796 ( 346) *********************** 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 97 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.422 Fit side-chains REVERT: B 348 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.7888 (t0) REVERT: B 379 ARG cc_start: 0.6685 (mmt90) cc_final: 0.6440 (mmt90) REVERT: D 348 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7299 (t0) REVERT: E 340 LYS cc_start: 0.7850 (mttt) cc_final: 0.7348 (mtpp) REVERT: E 342 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7545 (mp0) REVERT: E 378 PHE cc_start: 0.7292 (t80) cc_final: 0.6628 (t80) REVERT: F 343 LYS cc_start: 0.7258 (OUTLIER) cc_final: 0.6862 (ttpp) REVERT: G 340 LYS cc_start: 0.8581 (mttt) cc_final: 0.8205 (mtpm) REVERT: G 342 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8231 (mp0) REVERT: G 378 PHE cc_start: 0.7355 (t80) cc_final: 0.6867 (t80) REVERT: H 338 GLU cc_start: 0.7894 (tt0) cc_final: 0.7426 (tm-30) REVERT: H 349 ARG cc_start: 0.6900 (OUTLIER) cc_final: 0.6493 (ptp-170) REVERT: I 342 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7625 (mp0) REVERT: I 349 ARG cc_start: 0.7502 (mtt180) cc_final: 0.5831 (mmm160) REVERT: J 348 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.7828 (t0) outliers start: 22 outliers final: 10 residues processed: 89 average time/residue: 0.5569 time to fit residues: 51.9930 Evaluate side-chains 81 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 350 VAL 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 F residue 343 LYS Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 358 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 48 optimal weight: 0.0970 chunk 24 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 overall best weight: 3.5784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.159224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.128288 restraints weight = 16881.489| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 3.96 r_work: 0.3858 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3827 r_free = 0.3827 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3827 r_free = 0.3827 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2849 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= 0.216 Angle : 0.716 8.126 7870 Z= 0.356 Chirality : 0.050 0.129 885 Planarity : 0.003 0.029 1000 Dihedral : 6.225 44.334 785 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 3.76 % Allowed : 18.05 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.25), residues: 735 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.19), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 349 TYR 0.022 0.005 TYR F 310 PHE 0.014 0.001 PHE I 378 HIS 0.005 0.001 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 5875) covalent geometry : angle 0.71577 ( 7870) hydrogen bonds : bond 0.02422 ( 116) hydrogen bonds : angle 4.54290 ( 346) *********************** 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 97 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.200 Fit side-chains REVERT: A 331 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7921 (mtpp) REVERT: B 348 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.7826 (t0) REVERT: B 379 ARG cc_start: 0.6790 (mmt90) cc_final: 0.6553 (mmt90) REVERT: C 342 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7736 (mp0) REVERT: D 348 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.7293 (t0) REVERT: E 340 LYS cc_start: 0.7913 (mttt) cc_final: 0.7378 (mtpp) REVERT: E 342 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7600 (mp0) REVERT: E 378 PHE cc_start: 0.7320 (t80) cc_final: 0.6640 (t80) REVERT: F 343 LYS cc_start: 0.7313 (OUTLIER) cc_final: 0.6898 (ttpp) REVERT: G 340 LYS cc_start: 0.8566 (mttt) cc_final: 0.8183 (mtpm) REVERT: G 342 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8208 (mp0) REVERT: G 378 PHE cc_start: 0.7438 (t80) cc_final: 0.6886 (t80) REVERT: H 338 GLU cc_start: 0.7761 (tt0) cc_final: 0.7378 (tm-30) REVERT: H 349 ARG cc_start: 0.6937 (OUTLIER) cc_final: 0.6534 (ptp-170) REVERT: I 342 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7613 (mp0) REVERT: I 349 ARG cc_start: 0.7574 (mtt180) cc_final: 0.5836 (mmm160) REVERT: J 348 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.7809 (t0) outliers start: 25 outliers final: 11 residues processed: 89 average time/residue: 0.6100 time to fit residues: 56.6121 Evaluate side-chains 83 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 350 VAL 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 343 LYS 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 I residue 345 ASP Chi-restraints excluded: chain J residue 348 ASP Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain J residue 358 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 8 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 0.1980 chunk 6 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 55 optimal weight: 0.0040 chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 overall best weight: 1.1796 ------------------------------------------------------------------------------- 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 = 0.4600 r_free = 0.4600 target = 0.287277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.248640 restraints weight = 18650.877| |-----------------------------------------------------------------------------| r_work (start): 0.4442 rms_B_bonded: 2.48 r_work: 0.4230 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.4106 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3911 r_free = 0.3911 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3911 r_free = 0.3911 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 5875 Z= 0.099 Angle : 0.621 8.905 7870 Z= 0.294 Chirality : 0.048 0.124 885 Planarity : 0.002 0.026 1000 Dihedral : 5.170 31.541 785 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 3.76 % Allowed : 19.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.26), residues: 735 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 349 TYR 0.011 0.002 TYR H 310 PHE 0.010 0.001 PHE I 378 HIS 0.003 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 5875) covalent geometry : angle 0.62086 ( 7870) hydrogen bonds : bond 0.01501 ( 116) hydrogen bonds : angle 4.25735 ( 346) *********************** 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 93 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 68 time to evaluate : 0.189 Fit side-chains REVERT: B 348 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.8229 (t0) REVERT: C 342 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8191 (mp0) REVERT: D 348 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.7837 (t0) REVERT: E 342 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8038 (mp0) REVERT: E 347 LYS cc_start: 0.8655 (mmtp) cc_final: 0.8423 (mmtp) REVERT: E 378 PHE cc_start: 0.7480 (t80) cc_final: 0.6853 (t80) REVERT: G 342 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8408 (mp0) REVERT: G 378 PHE cc_start: 0.7482 (t80) cc_final: 0.7009 (t80) REVERT: H 349 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6947 (ptp-170) REVERT: I 342 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8058 (mp0) REVERT: I 349 ARG cc_start: 0.7995 (mtt180) cc_final: 0.6268 (mmm160) outliers start: 25 outliers final: 10 residues processed: 85 average time/residue: 0.5995 time to fit residues: 53.0983 Evaluate side-chains 77 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 D residue 343 LYS Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 311 LYS Chi-restraints excluded: chain H residue 349 ARG Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain I residue 345 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 5 optimal weight: 9.9990 chunk 57 optimal weight: 0.2980 chunk 44 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 13 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 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** ** 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 = 0.4564 r_free = 0.4564 target = 0.162873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.130935 restraints weight = 21622.435| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 4.42 r_work: 0.3863 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3847 r_free = 0.3847 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 = 0.3847 r_free = 0.3847 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3074 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= 0.152 Angle : 0.663 8.750 7870 Z= 0.320 Chirality : 0.049 0.126 885 Planarity : 0.003 0.034 1000 Dihedral : 5.526 34.303 785 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.91 % Allowed : 19.85 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.26), residues: 735 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 349 TYR 0.018 0.004 TYR F 310 PHE 0.012 0.001 PHE I 378 HIS 0.004 0.001 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 5875) covalent geometry : angle 0.66302 ( 7870) hydrogen bonds : bond 0.01969 ( 116) hydrogen bonds : angle 4.32235 ( 346) *********************** 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 94 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 0.234 Fit side-chains REVERT: B 348 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.7763 (t0) REVERT: C 342 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7667 (mp0) REVERT: D 348 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7371 (t0) REVERT: E 340 LYS cc_start: 0.7836 (mttt) cc_final: 0.7326 (mtpp) REVERT: E 342 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7549 (mp0) REVERT: E 378 PHE cc_start: 0.7150 (t80) cc_final: 0.6502 (t80) REVERT: F 338 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7707 (tm-30) REVERT: G 342 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8131 (mp0) REVERT: G 378 PHE cc_start: 0.7235 (t80) cc_final: 0.6688 (t80) REVERT: H 338 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7877 (tm-30) REVERT: H 349 ARG cc_start: 0.6922 (OUTLIER) cc_final: 0.6515 (ptp-170) REVERT: I 342 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7553 (mp0) REVERT: I 349 ARG cc_start: 0.7551 (mtt180) cc_final: 0.5738 (mmm160) outliers start: 26 outliers final: 15 residues processed: 89 average time/residue: 0.5773 time to fit residues: 53.7245 Evaluate side-chains 85 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 320 SER 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 F residue 348 ASP 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 I residue 345 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 21 optimal weight: 8.9990 chunk 46 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 54 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- 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** G 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.130585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.098295 restraints weight = 22336.752| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 4.55 r_work: 0.3821 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3795 r_free = 0.3795 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3795 r_free = 0.3795 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 5875 Z= 0.253 Angle : 0.752 8.632 7870 Z= 0.376 Chirality : 0.051 0.133 885 Planarity : 0.004 0.035 1000 Dihedral : 6.217 43.622 785 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.31 % Allowed : 20.60 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.26), residues: 735 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 379 TYR 0.026 0.006 TYR F 310 PHE 0.013 0.001 PHE I 378 HIS 0.006 0.002 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00565 ( 5875) covalent geometry : angle 0.75224 ( 7870) hydrogen bonds : bond 0.02616 ( 116) hydrogen bonds : angle 4.47301 ( 346) *********************** 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 91 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.217 Fit side-chains REVERT: B 348 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.7818 (t0) REVERT: C 342 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7741 (mp0) REVERT: D 348 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.7403 (t0) REVERT: E 340 LYS cc_start: 0.7922 (mttt) cc_final: 0.7419 (mtpp) REVERT: E 342 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7648 (mp0) REVERT: E 378 PHE cc_start: 0.7325 (t80) cc_final: 0.6689 (t80) REVERT: G 342 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8172 (mp0) REVERT: G 378 PHE cc_start: 0.7476 (t80) cc_final: 0.6882 (t80) REVERT: H 338 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7807 (tm-30) REVERT: H 349 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6702 (ptp-170) REVERT: I 342 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7680 (mp0) REVERT: I 349 ARG cc_start: 0.7598 (mtt180) cc_final: 0.5904 (mmm160) outliers start: 22 outliers final: 12 residues processed: 85 average time/residue: 0.5539 time to fit residues: 49.3611 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 : 0.248 ------------------------------------------------------------------------------- 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 E residue 311 LYS Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 311 LYS 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 350 VAL Chi-restraints excluded: chain J residue 358 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 67 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.160362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.128973 restraints weight = 18767.731| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 4.15 r_work: 0.3862 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3837 r_free = 0.3837 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3837 r_free = 0.3837 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5875 Z= 0.193 Angle : 0.714 8.981 7870 Z= 0.350 Chirality : 0.050 0.130 885 Planarity : 0.003 0.035 1000 Dihedral : 5.940 41.683 785 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.16 % Allowed : 20.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG F 349 TYR 0.021 0.005 TYR F 310 PHE 0.010 0.001 PHE I 378 HIS 0.005 0.001 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 5875) covalent geometry : angle 0.71449 ( 7870) hydrogen bonds : bond 0.02241 ( 116) hydrogen bonds : angle 4.39888 ( 346) *********************** 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 89 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.237 Fit side-chains REVERT: B 348 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.7800 (t0) REVERT: C 342 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7717 (mp0) REVERT: D 348 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7471 (t0) REVERT: E 342 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7567 (mp0) REVERT: E 378 PHE cc_start: 0.7221 (t80) cc_final: 0.6599 (t80) REVERT: G 342 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8112 (mp0) REVERT: G 378 PHE cc_start: 0.7408 (t80) cc_final: 0.6820 (t80) REVERT: H 338 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7747 (tm-30) REVERT: H 349 ARG cc_start: 0.6876 (OUTLIER) cc_final: 0.6489 (ptp-170) REVERT: I 342 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7632 (mp0) REVERT: I 349 ARG cc_start: 0.7576 (mtt180) cc_final: 0.5873 (mmm160) outliers start: 21 outliers final: 13 residues processed: 84 average time/residue: 0.5314 time to fit residues: 46.7114 Evaluate side-chains 83 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 320 SER 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 F residue 350 VAL Chi-restraints excluded: chain G residue 311 LYS Chi-restraints excluded: chain H residue 338 GLU 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 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 58 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 44 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 42 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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** 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 = 0.163031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.131475 restraints weight = 19730.872| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 4.26 r_work: 0.3872 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3861 r_free = 0.3861 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 = 0.3861 r_free = 0.3861 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5875 Z= 0.150 Angle : 0.689 9.187 7870 Z= 0.332 Chirality : 0.049 0.123 885 Planarity : 0.003 0.038 1000 Dihedral : 5.654 37.463 785 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 3.16 % Allowed : 20.60 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.26), residues: 735 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 349 TYR 0.018 0.004 TYR F 310 PHE 0.007 0.001 PHE I 378 HIS 0.004 0.001 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 5875) covalent geometry : angle 0.68913 ( 7870) hydrogen bonds : bond 0.01965 ( 116) hydrogen bonds : angle 4.33418 ( 346) ********************** 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 87 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.245 Fit side-chains REVERT: B 348 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.7750 (t0) REVERT: C 342 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7696 (mp0) REVERT: D 348 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7293 (t0) REVERT: E 342 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7511 (mp0) REVERT: E 378 PHE cc_start: 0.7153 (t80) cc_final: 0.6537 (t80) REVERT: F 311 LYS cc_start: 0.7728 (mttt) cc_final: 0.6763 (tttt) REVERT: G 342 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8078 (mp0) REVERT: G 378 PHE cc_start: 0.7236 (t80) cc_final: 0.6693 (t80) REVERT: H 338 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7747 (tm-30) REVERT: H 349 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6514 (ptp-170) REVERT: I 342 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7603 (mp0) REVERT: I 349 ARG cc_start: 0.7497 (mtt180) cc_final: 0.5708 (mmm160) REVERT: J 348 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7755 (t0) outliers start: 21 outliers final: 12 residues processed: 81 average time/residue: 0.5548 time to fit residues: 47.1662 Evaluate side-chains 83 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 320 SER 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 F residue 350 VAL Chi-restraints excluded: chain G residue 311 LYS Chi-restraints excluded: chain H residue 338 GLU 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 69 optimal weight: 0.7980 chunk 59 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 44 optimal weight: 0.4980 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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** ** 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 = 0.4594 r_free = 0.4594 target = 0.165851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.134268 restraints weight = 19537.301| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 4.26 r_work: 0.3914 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3899 r_free = 0.3899 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3899 r_free = 0.3899 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5875 Z= 0.118 Angle : 0.671 9.275 7870 Z= 0.317 Chirality : 0.049 0.121 885 Planarity : 0.003 0.041 1000 Dihedral : 5.285 30.789 785 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.01 % Allowed : 21.05 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG B 379 TYR 0.016 0.003 TYR B 310 PHE 0.006 0.001 PHE I 378 HIS 0.003 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 5875) covalent geometry : angle 0.67106 ( 7870) hydrogen bonds : bond 0.01700 ( 116) hydrogen bonds : angle 4.25620 ( 346) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2814.00 seconds wall clock time: 48 minutes 52.61 seconds (2932.61 seconds total)