Starting phenix.real_space_refine on Mon Apr 6 11:58:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10ij_75195/04_2026/10ij_75195.cif Found real_map, /net/cci-nas-00/data/ceres_data/10ij_75195/04_2026/10ij_75195.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10ij_75195/04_2026/10ij_75195.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10ij_75195/04_2026/10ij_75195.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10ij_75195/04_2026/10ij_75195.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10ij_75195/04_2026/10ij_75195.map" } resolution = 3.1 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: 5 Type Number sf(0) Gaussians S 22 5.16 5 C 5577 2.51 5 N 1661 2.21 5 O 1661 1.98 5 H 9427 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18348 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1668 Classifications: {'peptide': 107} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 102} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K Time building chain proxies: 1.86, per 1000 atoms: 0.10 Number of scatterers: 18348 At special positions: 0 Unit cell: (132.606, 80.064, 71.724, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 O 1661 8.00 N 1661 7.00 C 5577 6.00 H 9427 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 525.5 milliseconds 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2046 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 276 through 277 Processing sheet with id=AA2, first strand: chain 'A' and resid 286 through 287 removed outlier: 6.907A pdb=" N ASN A 286 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASN B 286 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN C 286 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN D 286 " --> pdb=" O VAL E 287 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN E 286 " --> pdb=" O VAL F 287 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASN F 286 " --> pdb=" O VAL G 287 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASN G 286 " --> pdb=" O VAL H 287 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASN H 286 " --> pdb=" O VAL I 287 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASN I 286 " --> pdb=" O VAL J 287 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN J 286 " --> pdb=" O VAL K 287 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.453A pdb=" N GLN A 307 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N TYR B 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL A 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLN B 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N TYR C 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL B 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLN C 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N TYR D 310 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL C 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLN D 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N TYR E 310 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL D 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLN E 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N TYR F 310 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL E 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN F 307 " --> pdb=" O ILE G 308 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N TYR G 310 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL F 309 " --> pdb=" O TYR G 310 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN G 307 " --> pdb=" O ILE H 308 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N TYR H 310 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL G 309 " --> pdb=" O TYR H 310 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLN H 307 " --> pdb=" O ILE I 308 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N TYR I 310 " --> pdb=" O GLN H 307 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL H 309 " --> pdb=" O TYR I 310 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLN I 307 " --> pdb=" O ILE J 308 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N TYR J 310 " --> pdb=" O GLN I 307 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL I 309 " --> pdb=" O TYR J 310 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLN J 307 " --> pdb=" O ILE K 308 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N TYR K 310 " --> pdb=" O GLN J 307 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL J 309 " --> pdb=" O TYR K 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 319 removed outlier: 6.354A pdb=" N VAL A 318 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL B 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL C 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL D 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL E 318 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL F 318 " --> pdb=" O THR G 319 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL G 318 " --> pdb=" O THR H 319 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL H 318 " --> pdb=" O THR I 319 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL I 318 " --> pdb=" O THR J 319 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL J 318 " --> pdb=" O THR K 319 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 335 through 346 removed outlier: 3.585A pdb=" N GLU B 342 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LYS A 343 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU B 344 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASP A 345 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N PHE B 346 " --> pdb=" O ASP A 345 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLY B 335 " --> pdb=" O GLN C 336 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N GLU C 338 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL B 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LYS C 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL B 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N GLU C 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N SER B 341 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU C 344 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 9.251A pdb=" N LYS B 343 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N PHE C 346 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N ASP B 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLY C 335 " --> pdb=" O GLN D 336 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N GLU D 338 " --> pdb=" O GLY C 335 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL C 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LYS D 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL C 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N GLU D 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N SER C 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU D 344 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N LYS C 343 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 10.540A pdb=" N PHE D 346 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N ASP C 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLY D 335 " --> pdb=" O GLN E 336 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N GLU E 338 " --> pdb=" O GLY D 335 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL D 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N LYS E 340 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL D 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N GLU E 342 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 9.328A pdb=" N SER D 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU E 344 " --> pdb=" O SER D 341 " (cutoff:3.500A) removed outlier: 9.273A pdb=" N LYS D 343 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 10.559A pdb=" N PHE E 346 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N ASP D 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLY E 335 " --> pdb=" O GLN F 336 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N GLU F 338 " --> pdb=" O GLY E 335 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL E 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LYS F 340 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL E 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N GLU F 342 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N SER E 341 " --> pdb=" O GLU F 342 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU F 344 " --> pdb=" O SER E 341 " (cutoff:3.500A) removed outlier: 9.251A pdb=" N LYS E 343 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N PHE F 346 " --> pdb=" O LYS E 343 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N ASP E 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLY F 335 " --> pdb=" O GLN G 336 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N GLU G 338 " --> pdb=" O GLY F 335 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL F 337 " --> pdb=" O GLU G 338 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N LYS G 340 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL F 339 " --> pdb=" O LYS G 340 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N GLU G 342 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N SER F 341 " --> pdb=" O GLU G 342 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU G 344 " --> pdb=" O SER F 341 " (cutoff:3.500A) removed outlier: 9.245A pdb=" N LYS F 343 " --> pdb=" O LEU G 344 " (cutoff:3.500A) removed outlier: 10.520A pdb=" N PHE G 346 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N ASP F 345 " --> pdb=" O PHE G 346 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLY G 335 " --> pdb=" O GLN H 336 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLU H 338 " --> pdb=" O GLY G 335 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL G 337 " --> pdb=" O GLU H 338 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LYS H 340 " --> pdb=" O VAL G 337 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL G 339 " --> pdb=" O LYS H 340 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N GLU H 342 " --> pdb=" O VAL G 339 " (cutoff:3.500A) removed outlier: 9.363A pdb=" N SER G 341 " --> pdb=" O GLU H 342 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU H 344 " --> pdb=" O SER G 341 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N LYS G 343 " --> pdb=" O LEU H 344 " (cutoff:3.500A) removed outlier: 10.541A pdb=" N PHE H 346 " --> pdb=" O LYS G 343 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N ASP G 345 " --> pdb=" O PHE H 346 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLY H 335 " --> pdb=" O GLN I 336 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N GLU I 338 " --> pdb=" O GLY H 335 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL H 337 " --> pdb=" O GLU I 338 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N LYS I 340 " --> pdb=" O VAL H 337 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL H 339 " --> pdb=" O LYS I 340 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N GLU I 342 " --> pdb=" O VAL H 339 " (cutoff:3.500A) removed outlier: 9.348A pdb=" N SER H 341 " --> pdb=" O GLU I 342 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU I 344 " --> pdb=" O SER H 341 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N LYS H 343 " --> pdb=" O LEU I 344 " (cutoff:3.500A) removed outlier: 10.541A pdb=" N PHE I 346 " --> pdb=" O LYS H 343 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N ASP H 345 " --> pdb=" O PHE I 346 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLY I 335 " --> pdb=" O GLN J 336 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N GLU J 338 " --> pdb=" O GLY I 335 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL I 337 " --> pdb=" O GLU J 338 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N LYS J 340 " --> pdb=" O VAL I 337 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL I 339 " --> pdb=" O LYS J 340 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N GLU J 342 " --> pdb=" O VAL I 339 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N SER I 341 " --> pdb=" O GLU J 342 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU J 344 " --> pdb=" O SER I 341 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N LYS I 343 " --> pdb=" O LEU J 344 " (cutoff:3.500A) removed outlier: 10.538A pdb=" N PHE J 346 " --> pdb=" O LYS I 343 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N ASP I 345 " --> pdb=" O PHE J 346 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLY J 335 " --> pdb=" O GLN K 336 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLU K 338 " --> pdb=" O GLY J 335 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL J 337 " --> pdb=" O GLU K 338 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N LYS K 340 " --> pdb=" O VAL J 337 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL J 339 " --> pdb=" O LYS K 340 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N GLU K 342 " --> pdb=" O VAL J 339 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N SER J 341 " --> pdb=" O GLU K 342 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LEU K 344 " --> pdb=" O SER J 341 " (cutoff:3.500A) removed outlier: 9.257A pdb=" N LYS J 343 " --> pdb=" O LEU K 344 " (cutoff:3.500A) removed outlier: 10.540A pdb=" N PHE K 346 " --> pdb=" O LYS J 343 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N ASP J 345 " --> pdb=" O PHE K 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 357 through 358 removed outlier: 6.678A pdb=" N LEU A 357 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU B 357 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU C 357 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU D 357 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU E 357 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU F 357 " --> pdb=" O ASP G 358 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU G 357 " --> pdb=" O ASP H 358 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU H 357 " --> pdb=" O ASP I 358 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU I 357 " --> pdb=" O ASP J 358 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU J 357 " --> pdb=" O ASP K 358 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.679A pdb=" N THR A 361 " --> pdb=" O HIS B 362 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR B 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR C 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR D 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR E 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR F 361 " --> pdb=" O HIS G 362 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR G 361 " --> pdb=" O HIS H 362 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR H 361 " --> pdb=" O HIS I 362 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR I 361 " --> pdb=" O HIS J 362 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR J 361 " --> pdb=" O HIS K 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 371 through 376 removed outlier: 6.045A pdb=" N ILE A 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N HIS B 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR A 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N LEU B 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LYS A 375 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE B 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N HIS C 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR B 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N LEU C 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LYS B 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE C 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N HIS D 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR C 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N LEU D 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LYS C 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE D 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N HIS E 374 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR D 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N LEU E 376 " --> pdb=" O THR D 373 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LYS D 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE E 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N HIS F 374 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR E 373 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N LEU F 376 " --> pdb=" O THR E 373 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LYS E 375 " --> pdb=" O LEU F 376 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE F 371 " --> pdb=" O GLU G 372 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N HIS G 374 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR F 373 " --> pdb=" O HIS G 374 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N LEU G 376 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LYS F 375 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ILE G 371 " --> pdb=" O GLU H 372 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N HIS H 374 " --> pdb=" O ILE G 371 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR G 373 " --> pdb=" O HIS H 374 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N LEU H 376 " --> pdb=" O THR G 373 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LYS G 375 " --> pdb=" O LEU H 376 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ILE H 371 " --> pdb=" O GLU I 372 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N HIS I 374 " --> pdb=" O ILE H 371 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR H 373 " --> pdb=" O HIS I 374 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N LEU I 376 " --> pdb=" O THR H 373 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LYS H 375 " --> pdb=" O LEU I 376 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE I 371 " --> pdb=" O GLU J 372 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N HIS J 374 " --> pdb=" O ILE I 371 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR I 373 " --> pdb=" O HIS J 374 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N LEU J 376 " --> pdb=" O THR I 373 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LYS I 375 " --> pdb=" O LEU J 376 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE J 371 " --> pdb=" O GLU K 372 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N HIS K 374 " --> pdb=" O ILE J 371 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR J 373 " --> pdb=" O HIS K 374 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N LEU K 376 " --> pdb=" O THR J 373 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LYS J 375 " --> pdb=" O LEU K 376 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 16 hydrogen bonds defined for protein. 48 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: 4.17 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9405 1.03 - 1.22: 32 1.22 - 1.42: 3433 1.42 - 1.61: 5577 1.61 - 1.81: 22 Bond restraints: 18469 Sorted by residual: bond pdb=" CB CYS F 322 " pdb=" SG CYS F 322 " ideal model delta sigma weight residual 1.808 1.744 0.064 3.30e-02 9.18e+02 3.75e+00 bond pdb=" CB CYS I 322 " pdb=" SG CYS I 322 " ideal model delta sigma weight residual 1.808 1.744 0.064 3.30e-02 9.18e+02 3.72e+00 bond pdb=" CB CYS J 322 " pdb=" SG CYS J 322 " ideal model delta sigma weight residual 1.808 1.745 0.063 3.30e-02 9.18e+02 3.68e+00 bond pdb=" CB CYS E 322 " pdb=" SG CYS E 322 " ideal model delta sigma weight residual 1.808 1.745 0.063 3.30e-02 9.18e+02 3.65e+00 bond pdb=" CB CYS C 322 " pdb=" SG CYS C 322 " ideal model delta sigma weight residual 1.808 1.745 0.063 3.30e-02 9.18e+02 3.64e+00 ... (remaining 18464 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 33572 2.70 - 5.39: 165 5.39 - 8.09: 0 8.09 - 10.79: 11 10.79 - 13.48: 11 Bond angle restraints: 33759 Sorted by residual: angle pdb=" CA CYS I 322 " pdb=" CB CYS I 322 " pdb=" SG CYS I 322 " ideal model delta sigma weight residual 114.40 100.92 13.48 2.30e+00 1.89e-01 3.44e+01 angle pdb=" CA CYS A 322 " pdb=" CB CYS A 322 " pdb=" SG CYS A 322 " ideal model delta sigma weight residual 114.40 100.94 13.46 2.30e+00 1.89e-01 3.43e+01 angle pdb=" CA CYS E 322 " pdb=" CB CYS E 322 " pdb=" SG CYS E 322 " ideal model delta sigma weight residual 114.40 100.94 13.46 2.30e+00 1.89e-01 3.43e+01 angle pdb=" CA CYS H 322 " pdb=" CB CYS H 322 " pdb=" SG CYS H 322 " ideal model delta sigma weight residual 114.40 100.95 13.45 2.30e+00 1.89e-01 3.42e+01 angle pdb=" CA CYS D 322 " pdb=" CB CYS D 322 " pdb=" SG CYS D 322 " ideal model delta sigma weight residual 114.40 100.96 13.44 2.30e+00 1.89e-01 3.42e+01 ... (remaining 33754 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.55: 6929 14.55 - 29.10: 859 29.10 - 43.65: 374 43.65 - 58.20: 198 58.20 - 72.75: 77 Dihedral angle restraints: 8437 sinusoidal: 4895 harmonic: 3542 Sorted by residual: dihedral pdb=" CA LYS E 321 " pdb=" C LYS E 321 " pdb=" N CYS E 322 " pdb=" CA CYS E 322 " ideal model delta harmonic sigma weight residual -180.00 -157.10 -22.90 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA LYS D 321 " pdb=" C LYS D 321 " pdb=" N CYS D 322 " pdb=" CA CYS D 322 " ideal model delta harmonic sigma weight residual 180.00 -157.11 -22.89 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA LYS B 321 " pdb=" C LYS B 321 " pdb=" N CYS B 322 " pdb=" CA CYS B 322 " ideal model delta harmonic sigma weight residual 180.00 -157.12 -22.88 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 8434 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 729 0.028 - 0.057: 399 0.057 - 0.085: 74 0.085 - 0.114: 128 0.114 - 0.142: 34 Chirality restraints: 1364 Sorted by residual: chirality pdb=" CA ILE I 277 " pdb=" N ILE I 277 " pdb=" C ILE I 277 " pdb=" CB ILE I 277 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA ILE B 277 " pdb=" N ILE B 277 " pdb=" C ILE B 277 " pdb=" CB ILE B 277 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ILE K 277 " pdb=" N ILE K 277 " pdb=" C ILE K 277 " pdb=" CB ILE K 277 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 1361 not shown) Planarity restraints: 2673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS I 281 " -0.006 2.00e-02 2.50e+03 1.24e-02 1.54e+00 pdb=" C LYS I 281 " 0.021 2.00e-02 2.50e+03 pdb=" O LYS I 281 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU I 282 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 281 " -0.006 2.00e-02 2.50e+03 1.24e-02 1.54e+00 pdb=" C LYS C 281 " 0.021 2.00e-02 2.50e+03 pdb=" O LYS C 281 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU C 282 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 281 " -0.006 2.00e-02 2.50e+03 1.23e-02 1.51e+00 pdb=" C LYS A 281 " 0.021 2.00e-02 2.50e+03 pdb=" O LYS A 281 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU A 282 " -0.007 2.00e-02 2.50e+03 ... (remaining 2670 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 2584 2.24 - 2.83: 43511 2.83 - 3.42: 46544 3.42 - 4.01: 69919 4.01 - 4.60: 104520 Nonbonded interactions: 267078 Sorted by model distance: nonbonded pdb=" HD1 PHE A 378 " pdb=" H ARG B 379 " model vdw 1.651 2.100 nonbonded pdb=" HD1 PHE F 378 " pdb=" H ARG G 379 " model vdw 1.651 2.100 nonbonded pdb=" HD1 PHE G 378 " pdb=" H ARG H 379 " model vdw 1.685 2.100 nonbonded pdb=" HD1 PHE I 378 " pdb=" H ARG J 379 " model vdw 1.726 2.100 nonbonded pdb=" HD1 PHE B 378 " pdb=" H ARG C 379 " model vdw 1.734 2.100 ... (remaining 267073 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 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: 0.100 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.460 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 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 : 0.004 0.064 9042 Z= 0.186 Angle : 0.810 13.485 12089 Z= 0.419 Chirality : 0.048 0.142 1364 Planarity : 0.004 0.024 1551 Dihedral : 15.827 59.932 3520 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 4.30 % Allowed : 17.20 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.01 (0.17), residues: 1155 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.13), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 349 TYR 0.003 0.001 TYR F 310 PHE 0.011 0.003 PHE I 378 HIS 0.003 0.001 HIS I 362 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 9042) covalent geometry : angle 0.80953 (12089) hydrogen bonds : bond 0.24092 ( 16) hydrogen bonds : angle 7.15609 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 165 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 349 ARG cc_start: 0.7450 (mtp-110) cc_final: 0.6747 (mtt180) REVERT: C 358 ASP cc_start: 0.7690 (m-30) cc_final: 0.7448 (m-30) REVERT: C 363 VAL cc_start: 0.7258 (OUTLIER) cc_final: 0.6632 (p) REVERT: E 340 LYS cc_start: 0.7983 (mttt) cc_final: 0.7600 (mttp) REVERT: F 317 LYS cc_start: 0.7548 (mmtm) cc_final: 0.7024 (tptt) REVERT: F 321 LYS cc_start: 0.5673 (pttp) cc_final: 0.5381 (mptt) REVERT: G 338 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7981 (mt-10) REVERT: G 345 ASP cc_start: 0.7709 (m-30) cc_final: 0.7500 (m-30) REVERT: H 338 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8071 (mt-10) REVERT: H 340 LYS cc_start: 0.7863 (mttt) cc_final: 0.7610 (mttm) REVERT: H 376 LEU cc_start: 0.5045 (mm) cc_final: 0.4819 (tp) REVERT: I 295 ASP cc_start: 0.6285 (p0) cc_final: 0.6034 (p0) REVERT: I 317 LYS cc_start: 0.8093 (mmtm) cc_final: 0.7708 (mmtt) REVERT: J 295 ASP cc_start: 0.5830 (p0) cc_final: 0.5443 (p0) REVERT: K 317 LYS cc_start: 0.7633 (mmtm) cc_final: 0.7345 (mmmt) REVERT: K 340 LYS cc_start: 0.8452 (mttt) cc_final: 0.8193 (mttm) outliers start: 44 outliers final: 28 residues processed: 196 average time/residue: 0.3019 time to fit residues: 75.8661 Evaluate side-chains 154 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain H residue 363 VAL Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 363 VAL Chi-restraints excluded: chain I residue 379 ARG Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 379 ARG Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 379 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 ASN D 296 ASN E 276 GLN E 296 ASN F 296 ASN F 329 HIS G 296 ASN G 327 ASN H 296 ASN I 296 ASN J 296 ASN K 296 ASN ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.160604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.126674 restraints weight = 30714.231| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.43 r_work: 0.3884 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3766 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 9042 Z= 0.201 Angle : 0.761 13.924 12089 Z= 0.381 Chirality : 0.051 0.158 1364 Planarity : 0.004 0.037 1551 Dihedral : 8.747 59.394 1265 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 5.77 % Allowed : 17.20 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.13 (0.17), residues: 1155 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.13), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 379 TYR 0.007 0.001 TYR B 310 PHE 0.014 0.003 PHE D 378 HIS 0.007 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 9042) covalent geometry : angle 0.76104 (12089) hydrogen bonds : bond 0.08926 ( 16) hydrogen bonds : angle 4.75159 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 134 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.6795 (mptt) REVERT: B 280 LYS cc_start: 0.6606 (OUTLIER) cc_final: 0.5990 (mptt) REVERT: B 349 ARG cc_start: 0.7669 (mtp-110) cc_final: 0.6917 (mtt180) REVERT: C 363 VAL cc_start: 0.7422 (OUTLIER) cc_final: 0.6796 (p) REVERT: D 322 CYS cc_start: 0.5774 (OUTLIER) cc_final: 0.5297 (p) REVERT: D 347 LYS cc_start: 0.8477 (mmmm) cc_final: 0.8201 (mtpt) REVERT: E 280 LYS cc_start: 0.6018 (OUTLIER) cc_final: 0.5733 (mptt) REVERT: E 295 ASP cc_start: 0.6947 (p0) cc_final: 0.6665 (p0) REVERT: E 340 LYS cc_start: 0.8029 (mttt) cc_final: 0.7725 (mttp) REVERT: F 280 LYS cc_start: 0.5957 (OUTLIER) cc_final: 0.5331 (mptt) REVERT: F 317 LYS cc_start: 0.7580 (mmtm) cc_final: 0.7096 (tptt) REVERT: F 321 LYS cc_start: 0.5903 (pttp) cc_final: 0.5435 (mptt) REVERT: G 314 ASP cc_start: 0.7852 (t70) cc_final: 0.7479 (t70) REVERT: G 338 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7829 (mt-10) REVERT: G 340 LYS cc_start: 0.7718 (mttt) cc_final: 0.7503 (mttm) REVERT: G 363 VAL cc_start: 0.7836 (OUTLIER) cc_final: 0.7232 (p) REVERT: H 280 LYS cc_start: 0.6543 (OUTLIER) cc_final: 0.6240 (mptt) REVERT: H 295 ASP cc_start: 0.6721 (p0) cc_final: 0.6341 (p0) REVERT: H 338 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7937 (mt-10) REVERT: H 340 LYS cc_start: 0.7949 (mttt) cc_final: 0.7674 (mttm) REVERT: H 376 LEU cc_start: 0.5177 (mm) cc_final: 0.4971 (tp) REVERT: I 294 LYS cc_start: 0.7990 (tptp) cc_final: 0.7422 (tptt) REVERT: I 295 ASP cc_start: 0.6507 (p0) cc_final: 0.5097 (p0) REVERT: I 317 LYS cc_start: 0.8144 (mmtm) cc_final: 0.7703 (mmtt) REVERT: I 338 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7865 (mt-10) REVERT: J 295 ASP cc_start: 0.6169 (p0) cc_final: 0.5306 (m-30) REVERT: J 322 CYS cc_start: 0.5539 (OUTLIER) cc_final: 0.5060 (p) REVERT: J 340 LYS cc_start: 0.8426 (mttt) cc_final: 0.8158 (mttp) REVERT: K 274 LYS cc_start: 0.6075 (mtpt) cc_final: 0.5696 (pttm) REVERT: K 280 LYS cc_start: 0.6931 (OUTLIER) cc_final: 0.6671 (mmmm) REVERT: K 317 LYS cc_start: 0.7589 (mmtm) cc_final: 0.7214 (mmmt) REVERT: K 321 LYS cc_start: 0.6002 (pttt) cc_final: 0.5464 (tppt) REVERT: K 322 CYS cc_start: 0.6112 (OUTLIER) cc_final: 0.5722 (p) REVERT: K 340 LYS cc_start: 0.8478 (mttt) cc_final: 0.8278 (mttm) outliers start: 59 outliers final: 35 residues processed: 185 average time/residue: 0.3003 time to fit residues: 71.9520 Evaluate side-chains 167 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 119 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 322 CYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 327 ASN Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 280 LYS Chi-restraints excluded: chain H residue 325 LEU Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain H residue 363 VAL Chi-restraints excluded: chain H residue 379 ARG Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 363 VAL Chi-restraints excluded: chain I residue 379 ARG Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 322 CYS Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 379 ARG Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 280 LYS Chi-restraints excluded: chain K residue 322 CYS Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 379 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 41 optimal weight: 2.9990 chunk 104 optimal weight: 0.0670 chunk 76 optimal weight: 2.9990 chunk 98 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 ASN D 296 ASN ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 276 GLN E 296 ASN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 362 HIS F 296 ASN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 296 ASN ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 327 ASN H 296 ASN ** H 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 329 HIS I 296 ASN ** I 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN ** J 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.159199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.124794 restraints weight = 30932.909| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.46 r_work: 0.3862 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3745 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 9042 Z= 0.171 Angle : 0.718 13.391 12089 Z= 0.363 Chirality : 0.050 0.158 1364 Planarity : 0.004 0.044 1551 Dihedral : 8.657 57.968 1265 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer: Outliers : 5.18 % Allowed : 17.40 % Favored : 77.42 % 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 are not related in a simple way. whole: -4.20 (0.17), residues: 1155 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.13), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 349 TYR 0.006 0.001 TYR B 310 PHE 0.012 0.003 PHE D 378 HIS 0.008 0.001 HIS G 362 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 9042) covalent geometry : angle 0.71840 (12089) hydrogen bonds : bond 0.06944 ( 16) hydrogen bonds : angle 5.25258 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 119 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.6790 (mptt) REVERT: A 379 ARG cc_start: 0.1666 (OUTLIER) cc_final: 0.0870 (tpt-90) REVERT: B 280 LYS cc_start: 0.6769 (OUTLIER) cc_final: 0.6104 (mptt) REVERT: B 349 ARG cc_start: 0.7682 (mtp-110) cc_final: 0.6938 (mtt180) REVERT: C 295 ASP cc_start: 0.6583 (p0) cc_final: 0.6301 (p0) REVERT: C 363 VAL cc_start: 0.7465 (OUTLIER) cc_final: 0.6859 (p) REVERT: D 322 CYS cc_start: 0.5787 (OUTLIER) cc_final: 0.5360 (p) REVERT: D 347 LYS cc_start: 0.8530 (mmmm) cc_final: 0.8245 (mtpt) REVERT: E 280 LYS cc_start: 0.6139 (OUTLIER) cc_final: 0.5846 (mptt) REVERT: E 295 ASP cc_start: 0.7015 (p0) cc_final: 0.6744 (p0) REVERT: E 340 LYS cc_start: 0.8051 (mttt) cc_final: 0.7749 (mttp) REVERT: E 362 HIS cc_start: 0.6895 (OUTLIER) cc_final: 0.6645 (t-170) REVERT: F 280 LYS cc_start: 0.6054 (OUTLIER) cc_final: 0.5353 (mptt) REVERT: F 317 LYS cc_start: 0.7627 (mmtm) cc_final: 0.7132 (tptt) REVERT: F 321 LYS cc_start: 0.5830 (pttp) cc_final: 0.5426 (mptt) REVERT: G 321 LYS cc_start: 0.5784 (pttp) cc_final: 0.5315 (mmtt) REVERT: G 363 VAL cc_start: 0.7874 (OUTLIER) cc_final: 0.7304 (p) REVERT: H 280 LYS cc_start: 0.6683 (OUTLIER) cc_final: 0.6115 (mptt) REVERT: H 340 LYS cc_start: 0.7953 (mttt) cc_final: 0.7708 (mttm) REVERT: H 376 LEU cc_start: 0.5115 (mm) cc_final: 0.4904 (tp) REVERT: I 294 LYS cc_start: 0.8008 (tptp) cc_final: 0.7447 (tptt) REVERT: I 295 ASP cc_start: 0.6666 (p0) cc_final: 0.5532 (p0) REVERT: I 317 LYS cc_start: 0.8146 (mmtm) cc_final: 0.7679 (mmtt) REVERT: J 295 ASP cc_start: 0.6364 (p0) cc_final: 0.5001 (m-30) REVERT: J 340 LYS cc_start: 0.8440 (mttt) cc_final: 0.8159 (mttp) REVERT: K 274 LYS cc_start: 0.6172 (mtpt) cc_final: 0.5775 (pttm) REVERT: K 280 LYS cc_start: 0.6991 (OUTLIER) cc_final: 0.6672 (mmmm) REVERT: K 282 LEU cc_start: 0.7475 (mp) cc_final: 0.7239 (mp) REVERT: K 295 ASP cc_start: 0.6656 (p0) cc_final: 0.5999 (m-30) REVERT: K 321 LYS cc_start: 0.6064 (pttt) cc_final: 0.5555 (tppt) REVERT: K 322 CYS cc_start: 0.6069 (OUTLIER) cc_final: 0.5652 (p) REVERT: K 340 LYS cc_start: 0.8496 (mttt) cc_final: 0.8279 (mttm) outliers start: 53 outliers final: 35 residues processed: 162 average time/residue: 0.2769 time to fit residues: 58.0177 Evaluate side-chains 163 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 116 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 322 CYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 362 HIS Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 327 ASN Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 280 LYS Chi-restraints excluded: chain H residue 328 ILE Chi-restraints excluded: chain H residue 363 VAL Chi-restraints excluded: chain H residue 379 ARG Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 328 ILE Chi-restraints excluded: chain I residue 363 VAL Chi-restraints excluded: chain I residue 379 ARG Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 279 ASN Chi-restraints excluded: chain J residue 322 CYS Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 379 ARG Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 280 LYS Chi-restraints excluded: chain K residue 322 CYS Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 379 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 362 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 = 0.4398 r_free = 0.4398 target = 0.154816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.119943 restraints weight = 31074.519| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.46 r_work: 0.3813 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 9042 Z= 0.243 Angle : 0.757 13.438 12089 Z= 0.390 Chirality : 0.052 0.159 1364 Planarity : 0.005 0.051 1551 Dihedral : 8.563 54.485 1259 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.29 % Favored : 87.71 % Rotamer: Outliers : 4.99 % Allowed : 18.18 % Favored : 76.83 % 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 are not related in a simple way. whole: -4.43 (0.17), residues: 1155 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.13), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.009 0.002 TYR B 310 PHE 0.014 0.003 PHE E 378 HIS 0.016 0.002 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00590 ( 9042) covalent geometry : angle 0.75693 (12089) hydrogen bonds : bond 0.06300 ( 16) hydrogen bonds : angle 6.23263 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 116 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.6936 (mptt) REVERT: A 379 ARG cc_start: 0.1614 (OUTLIER) cc_final: 0.0938 (tpt-90) REVERT: C 295 ASP cc_start: 0.6691 (p0) cc_final: 0.6468 (p0) REVERT: C 363 VAL cc_start: 0.7646 (OUTLIER) cc_final: 0.7060 (p) REVERT: C 379 ARG cc_start: 0.0798 (OUTLIER) cc_final: 0.0332 (tpt-90) REVERT: D 282 LEU cc_start: 0.7403 (mp) cc_final: 0.7202 (mp) REVERT: D 295 ASP cc_start: 0.7044 (p0) cc_final: 0.6682 (p0) REVERT: D 322 CYS cc_start: 0.5815 (OUTLIER) cc_final: 0.5508 (p) REVERT: D 347 LYS cc_start: 0.8574 (mmmm) cc_final: 0.8269 (mtpt) REVERT: E 295 ASP cc_start: 0.7116 (p0) cc_final: 0.6786 (p0) REVERT: E 314 ASP cc_start: 0.7540 (t70) cc_final: 0.7265 (t0) REVERT: E 340 LYS cc_start: 0.8204 (mttt) cc_final: 0.7808 (mttp) REVERT: E 363 VAL cc_start: 0.7578 (OUTLIER) cc_final: 0.6854 (p) REVERT: F 280 LYS cc_start: 0.6212 (OUTLIER) cc_final: 0.5465 (mptt) REVERT: F 295 ASP cc_start: 0.7463 (p0) cc_final: 0.6853 (p0) REVERT: F 317 LYS cc_start: 0.7593 (mmtm) cc_final: 0.7093 (tptt) REVERT: F 321 LYS cc_start: 0.5900 (pttp) cc_final: 0.5698 (mptt) REVERT: F 363 VAL cc_start: 0.7869 (OUTLIER) cc_final: 0.7146 (p) REVERT: G 314 ASP cc_start: 0.7993 (t70) cc_final: 0.7739 (t70) REVERT: G 338 GLU cc_start: 0.8200 (tt0) cc_final: 0.7916 (tt0) REVERT: G 340 LYS cc_start: 0.7898 (mttt) cc_final: 0.7445 (tttp) REVERT: G 363 VAL cc_start: 0.8001 (OUTLIER) cc_final: 0.7375 (p) REVERT: H 280 LYS cc_start: 0.6800 (OUTLIER) cc_final: 0.6197 (mptt) REVERT: H 340 LYS cc_start: 0.7949 (mttt) cc_final: 0.7657 (mttm) REVERT: H 376 LEU cc_start: 0.5225 (mm) cc_final: 0.5008 (tp) REVERT: I 295 ASP cc_start: 0.6833 (p0) cc_final: 0.5543 (p0) REVERT: I 317 LYS cc_start: 0.8154 (mmtm) cc_final: 0.7635 (mmtt) REVERT: J 295 ASP cc_start: 0.6528 (p0) cc_final: 0.5044 (m-30) REVERT: J 340 LYS cc_start: 0.8416 (mttt) cc_final: 0.8069 (mttm) REVERT: K 274 LYS cc_start: 0.6310 (mtpt) cc_final: 0.5798 (pttp) REVERT: K 280 LYS cc_start: 0.7081 (OUTLIER) cc_final: 0.6793 (mmtp) REVERT: K 282 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7238 (mp) REVERT: K 322 CYS cc_start: 0.6098 (OUTLIER) cc_final: 0.5424 (p) REVERT: K 340 LYS cc_start: 0.8484 (mttt) cc_final: 0.8262 (mttm) outliers start: 51 outliers final: 32 residues processed: 161 average time/residue: 0.2755 time to fit residues: 58.6431 Evaluate side-chains 149 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 104 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain C residue 322 CYS Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 322 CYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 280 LYS Chi-restraints excluded: chain H residue 328 ILE Chi-restraints excluded: chain H residue 379 ARG Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 328 ILE Chi-restraints excluded: chain I residue 363 VAL Chi-restraints excluded: chain I residue 379 ARG Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 279 ASN Chi-restraints excluded: chain J residue 322 CYS Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 379 ARG Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 280 LYS Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain K residue 322 CYS Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 368 ASN Chi-restraints excluded: chain K residue 379 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 105 optimal weight: 0.4980 chunk 82 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.152681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.117040 restraints weight = 31301.890| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.47 r_work: 0.3834 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3720 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9042 Z= 0.168 Angle : 0.676 10.237 12089 Z= 0.347 Chirality : 0.051 0.158 1364 Planarity : 0.004 0.046 1551 Dihedral : 8.137 54.215 1254 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 5.57 % Allowed : 18.48 % Favored : 75.95 % 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 are not related in a simple way. whole: -4.46 (0.18), residues: 1155 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.13), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 349 TYR 0.006 0.001 TYR B 310 PHE 0.012 0.003 PHE C 378 HIS 0.011 0.001 HIS G 362 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 9042) covalent geometry : angle 0.67555 (12089) hydrogen bonds : bond 0.05955 ( 16) hydrogen bonds : angle 6.19676 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 113 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.6992 (mptt) REVERT: A 379 ARG cc_start: 0.1552 (OUTLIER) cc_final: 0.0960 (tpt-90) REVERT: B 280 LYS cc_start: 0.6828 (OUTLIER) cc_final: 0.6245 (mptt) REVERT: C 295 ASP cc_start: 0.6748 (p0) cc_final: 0.6511 (p0) REVERT: C 363 VAL cc_start: 0.7626 (OUTLIER) cc_final: 0.6798 (p) REVERT: C 379 ARG cc_start: 0.0814 (OUTLIER) cc_final: 0.0334 (tpt-90) REVERT: D 295 ASP cc_start: 0.7178 (p0) cc_final: 0.6786 (p0) REVERT: D 347 LYS cc_start: 0.8528 (mmmm) cc_final: 0.8226 (mtpt) REVERT: D 363 VAL cc_start: 0.7773 (OUTLIER) cc_final: 0.7119 (p) REVERT: E 285 SER cc_start: 0.7908 (OUTLIER) cc_final: 0.7586 (t) REVERT: E 295 ASP cc_start: 0.7137 (p0) cc_final: 0.6902 (p0) REVERT: E 314 ASP cc_start: 0.7503 (t70) cc_final: 0.7280 (t0) REVERT: F 295 ASP cc_start: 0.7443 (p0) cc_final: 0.6845 (p0) REVERT: F 317 LYS cc_start: 0.7548 (mmtm) cc_final: 0.6981 (tptt) REVERT: F 321 LYS cc_start: 0.6002 (pttp) cc_final: 0.5594 (mptt) REVERT: F 363 VAL cc_start: 0.7843 (OUTLIER) cc_final: 0.7191 (p) REVERT: G 314 ASP cc_start: 0.8020 (t70) cc_final: 0.7782 (t70) REVERT: G 321 LYS cc_start: 0.6046 (pttp) cc_final: 0.5485 (mmtt) REVERT: G 338 GLU cc_start: 0.8232 (tt0) cc_final: 0.7983 (tt0) REVERT: G 340 LYS cc_start: 0.7980 (mttt) cc_final: 0.7509 (tttp) REVERT: G 363 VAL cc_start: 0.7959 (OUTLIER) cc_final: 0.7331 (p) REVERT: H 280 LYS cc_start: 0.6735 (OUTLIER) cc_final: 0.6178 (mptt) REVERT: H 340 LYS cc_start: 0.7938 (mttt) cc_final: 0.7637 (mttm) REVERT: H 376 LEU cc_start: 0.5202 (mm) cc_final: 0.4969 (tp) REVERT: I 295 ASP cc_start: 0.6905 (p0) cc_final: 0.6614 (p0) REVERT: J 340 LYS cc_start: 0.8444 (mttt) cc_final: 0.8097 (mttm) REVERT: K 274 LYS cc_start: 0.6377 (mtpt) cc_final: 0.5846 (pttp) REVERT: K 282 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7368 (mp) REVERT: K 321 LYS cc_start: 0.5988 (pttt) cc_final: 0.5319 (tppt) REVERT: K 340 LYS cc_start: 0.8472 (mttt) cc_final: 0.8238 (mttm) outliers start: 57 outliers final: 30 residues processed: 160 average time/residue: 0.2404 time to fit residues: 51.7924 Evaluate side-chains 149 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 108 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 285 SER Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 280 LYS Chi-restraints excluded: chain H residue 328 ILE Chi-restraints excluded: chain H residue 379 ARG Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 363 VAL Chi-restraints excluded: chain I residue 379 ARG Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 322 CYS Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 379 ARG Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain K residue 328 ILE Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 379 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 102 optimal weight: 0.0970 chunk 57 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 299 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 = 0.4419 r_free = 0.4419 target = 0.153421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.117623 restraints weight = 31112.547| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 2.49 r_work: 0.3841 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9042 Z= 0.140 Angle : 0.637 8.787 12089 Z= 0.327 Chirality : 0.050 0.157 1364 Planarity : 0.004 0.043 1551 Dihedral : 7.972 54.365 1253 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 4.50 % Allowed : 19.45 % Favored : 76.05 % 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 are not related in a simple way. whole: -4.36 (0.18), residues: 1155 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.14), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 349 TYR 0.004 0.001 TYR B 310 PHE 0.013 0.003 PHE F 378 HIS 0.009 0.001 HIS G 362 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9042) covalent geometry : angle 0.63731 (12089) hydrogen bonds : bond 0.05627 ( 16) hydrogen bonds : angle 6.22037 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 118 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.6969 (mptt) REVERT: A 379 ARG cc_start: 0.1504 (OUTLIER) cc_final: 0.0948 (tpt-90) REVERT: B 280 LYS cc_start: 0.6833 (OUTLIER) cc_final: 0.6253 (mptt) REVERT: C 295 ASP cc_start: 0.6733 (p0) cc_final: 0.6440 (p0) REVERT: C 349 ARG cc_start: 0.7874 (mtp-110) cc_final: 0.7665 (mtp180) REVERT: C 363 VAL cc_start: 0.7692 (OUTLIER) cc_final: 0.6901 (p) REVERT: C 379 ARG cc_start: 0.0879 (OUTLIER) cc_final: 0.0417 (tpt-90) REVERT: D 363 VAL cc_start: 0.7728 (OUTLIER) cc_final: 0.6923 (p) REVERT: E 285 SER cc_start: 0.7894 (OUTLIER) cc_final: 0.7615 (t) REVERT: E 363 VAL cc_start: 0.7612 (OUTLIER) cc_final: 0.6780 (p) REVERT: F 295 ASP cc_start: 0.7458 (p0) cc_final: 0.6892 (p0) REVERT: F 317 LYS cc_start: 0.7511 (mmtm) cc_final: 0.6982 (tptt) REVERT: F 363 VAL cc_start: 0.7903 (OUTLIER) cc_final: 0.7084 (p) REVERT: G 325 LEU cc_start: 0.8228 (tp) cc_final: 0.7965 (pp) REVERT: G 338 GLU cc_start: 0.8246 (tt0) cc_final: 0.7994 (tt0) REVERT: G 340 LYS cc_start: 0.8008 (mttt) cc_final: 0.7543 (tttp) REVERT: G 363 VAL cc_start: 0.7975 (OUTLIER) cc_final: 0.7384 (p) REVERT: H 280 LYS cc_start: 0.6720 (OUTLIER) cc_final: 0.6153 (mptt) REVERT: H 340 LYS cc_start: 0.7925 (mttt) cc_final: 0.7623 (mttm) REVERT: H 376 LEU cc_start: 0.5341 (mm) cc_final: 0.5120 (tp) REVERT: I 294 LYS cc_start: 0.7950 (tptp) cc_final: 0.7426 (tptt) REVERT: I 295 ASP cc_start: 0.6982 (p0) cc_final: 0.6686 (p0) REVERT: K 274 LYS cc_start: 0.6461 (mtpt) cc_final: 0.5922 (pttp) REVERT: K 282 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7362 (mp) REVERT: K 340 LYS cc_start: 0.8465 (mttt) cc_final: 0.8188 (mttm) outliers start: 46 outliers final: 29 residues processed: 157 average time/residue: 0.2656 time to fit residues: 55.4466 Evaluate side-chains 151 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 110 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 285 SER Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 280 LYS Chi-restraints excluded: chain H residue 328 ILE Chi-restraints excluded: chain H residue 379 ARG Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 328 ILE Chi-restraints excluded: chain I residue 363 VAL Chi-restraints excluded: chain I residue 379 ARG Chi-restraints excluded: chain J residue 322 CYS Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 379 ARG Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain K residue 328 ILE Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 379 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 36 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 HIS ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 374 HIS ** I 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 362 HIS ** J 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.152655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.116668 restraints weight = 31397.399| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.47 r_work: 0.3840 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9042 Z= 0.165 Angle : 0.655 10.336 12089 Z= 0.335 Chirality : 0.050 0.198 1364 Planarity : 0.004 0.045 1551 Dihedral : 7.976 54.947 1252 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.95 % Favored : 88.05 % Rotamer: Outliers : 4.59 % Allowed : 20.63 % Favored : 74.78 % 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 are not related in a simple way. whole: -4.41 (0.18), residues: 1155 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.14), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 349 TYR 0.006 0.001 TYR B 310 PHE 0.013 0.003 PHE D 378 HIS 0.012 0.001 HIS I 362 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 9042) covalent geometry : angle 0.65550 (12089) hydrogen bonds : bond 0.05660 ( 16) hydrogen bonds : angle 6.45187 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 113 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.6975 (mptt) REVERT: B 379 ARG cc_start: 0.0951 (OUTLIER) cc_final: 0.0218 (tpm-80) REVERT: C 295 ASP cc_start: 0.6753 (p0) cc_final: 0.6450 (p0) REVERT: C 349 ARG cc_start: 0.7896 (mtp-110) cc_final: 0.7689 (mtp180) REVERT: C 363 VAL cc_start: 0.7763 (OUTLIER) cc_final: 0.7003 (p) REVERT: C 379 ARG cc_start: 0.1033 (OUTLIER) cc_final: 0.0622 (tpt-90) REVERT: D 363 VAL cc_start: 0.7709 (OUTLIER) cc_final: 0.6903 (p) REVERT: E 285 SER cc_start: 0.7929 (OUTLIER) cc_final: 0.7666 (t) REVERT: E 363 VAL cc_start: 0.7696 (OUTLIER) cc_final: 0.6895 (p) REVERT: F 295 ASP cc_start: 0.7455 (p0) cc_final: 0.6846 (p0) REVERT: F 317 LYS cc_start: 0.7508 (mmtm) cc_final: 0.7002 (tptt) REVERT: F 321 LYS cc_start: 0.6857 (mmtt) cc_final: 0.5995 (mptt) REVERT: F 363 VAL cc_start: 0.7927 (OUTLIER) cc_final: 0.7143 (p) REVERT: G 321 LYS cc_start: 0.6252 (pttp) cc_final: 0.5454 (mmtt) REVERT: G 338 GLU cc_start: 0.8241 (tt0) cc_final: 0.8024 (tt0) REVERT: G 340 LYS cc_start: 0.8035 (mttt) cc_final: 0.7531 (tttp) REVERT: G 363 VAL cc_start: 0.8011 (OUTLIER) cc_final: 0.7443 (p) REVERT: H 280 LYS cc_start: 0.6748 (OUTLIER) cc_final: 0.6197 (mptt) REVERT: H 340 LYS cc_start: 0.7958 (mttt) cc_final: 0.7639 (mttm) REVERT: H 376 LEU cc_start: 0.5393 (mm) cc_final: 0.5181 (tp) REVERT: I 294 LYS cc_start: 0.7972 (tptp) cc_final: 0.7462 (tptt) REVERT: I 295 ASP cc_start: 0.7015 (p0) cc_final: 0.6697 (p0) REVERT: K 274 LYS cc_start: 0.6525 (mtpt) cc_final: 0.5921 (pttp) REVERT: K 321 LYS cc_start: 0.5653 (pttt) cc_final: 0.4915 (mttp) REVERT: K 340 LYS cc_start: 0.8436 (mttt) cc_final: 0.8153 (mttm) outliers start: 47 outliers final: 29 residues processed: 152 average time/residue: 0.2645 time to fit residues: 53.8572 Evaluate side-chains 150 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 111 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 285 SER Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 280 LYS Chi-restraints excluded: chain H residue 285 SER Chi-restraints excluded: chain H residue 328 ILE Chi-restraints excluded: chain H residue 379 ARG Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 328 ILE Chi-restraints excluded: chain I residue 362 HIS Chi-restraints excluded: chain I residue 363 VAL Chi-restraints excluded: chain I residue 379 ARG Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 379 ARG Chi-restraints excluded: chain K residue 328 ILE Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 379 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 8 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 HIS ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.151255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.115072 restraints weight = 31279.437| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 2.45 r_work: 0.3818 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3704 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9042 Z= 0.212 Angle : 0.687 12.548 12089 Z= 0.354 Chirality : 0.051 0.155 1364 Planarity : 0.005 0.047 1551 Dihedral : 7.938 55.625 1248 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 4.30 % Allowed : 21.90 % Favored : 73.80 % 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 are not related in a simple way. whole: -4.46 (0.18), residues: 1155 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.14), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.008 0.001 TYR B 310 PHE 0.014 0.003 PHE D 378 HIS 0.014 0.001 HIS I 362 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 9042) covalent geometry : angle 0.68701 (12089) hydrogen bonds : bond 0.05726 ( 16) hydrogen bonds : angle 6.74430 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 117 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.6985 (mptt) REVERT: B 280 LYS cc_start: 0.6819 (OUTLIER) cc_final: 0.6239 (mptt) REVERT: B 379 ARG cc_start: 0.1096 (OUTLIER) cc_final: 0.0288 (tpm-80) REVERT: C 295 ASP cc_start: 0.6788 (p0) cc_final: 0.6485 (p0) REVERT: C 347 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8397 (mtpt) REVERT: C 349 ARG cc_start: 0.7922 (mtp-110) cc_final: 0.7705 (mtp180) REVERT: C 363 VAL cc_start: 0.7860 (OUTLIER) cc_final: 0.7114 (p) REVERT: C 379 ARG cc_start: 0.1130 (OUTLIER) cc_final: 0.0723 (tpt-90) REVERT: D 347 LYS cc_start: 0.8548 (mmmm) cc_final: 0.8281 (mtpt) REVERT: D 363 VAL cc_start: 0.7731 (OUTLIER) cc_final: 0.7088 (p) REVERT: F 295 ASP cc_start: 0.7504 (p0) cc_final: 0.6908 (p0) REVERT: F 317 LYS cc_start: 0.7516 (mmtm) cc_final: 0.7016 (tptt) REVERT: F 321 LYS cc_start: 0.6894 (mmtt) cc_final: 0.6084 (mptt) REVERT: F 363 VAL cc_start: 0.7959 (OUTLIER) cc_final: 0.7276 (p) REVERT: G 321 LYS cc_start: 0.6311 (pttp) cc_final: 0.5526 (mmtt) REVERT: G 338 GLU cc_start: 0.8221 (tt0) cc_final: 0.8019 (tt0) REVERT: G 340 LYS cc_start: 0.8051 (mttt) cc_final: 0.7545 (tttp) REVERT: G 363 VAL cc_start: 0.8001 (OUTLIER) cc_final: 0.7433 (p) REVERT: H 280 LYS cc_start: 0.6769 (OUTLIER) cc_final: 0.6241 (mptt) REVERT: H 340 LYS cc_start: 0.7968 (mttt) cc_final: 0.7635 (mttm) REVERT: H 376 LEU cc_start: 0.5450 (mm) cc_final: 0.5239 (tp) REVERT: H 379 ARG cc_start: 0.1117 (OUTLIER) cc_final: 0.0909 (tpt-90) REVERT: I 294 LYS cc_start: 0.7998 (tptp) cc_final: 0.7499 (tptt) REVERT: I 295 ASP cc_start: 0.7020 (p0) cc_final: 0.6783 (p0) REVERT: J 277 ILE cc_start: 0.7536 (mm) cc_final: 0.7294 (mt) REVERT: K 274 LYS cc_start: 0.6634 (mtpt) cc_final: 0.5972 (pttp) REVERT: K 321 LYS cc_start: 0.5587 (pttt) cc_final: 0.4704 (mttp) REVERT: K 322 CYS cc_start: 0.5628 (OUTLIER) cc_final: 0.5079 (m) REVERT: K 340 LYS cc_start: 0.8431 (mttt) cc_final: 0.8140 (mttm) outliers start: 44 outliers final: 30 residues processed: 155 average time/residue: 0.2693 time to fit residues: 55.5179 Evaluate side-chains 153 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 111 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 327 ASN Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 280 LYS Chi-restraints excluded: chain H residue 285 SER Chi-restraints excluded: chain H residue 328 ILE Chi-restraints excluded: chain H residue 379 ARG Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 328 ILE Chi-restraints excluded: chain I residue 362 HIS Chi-restraints excluded: chain I residue 363 VAL Chi-restraints excluded: chain I residue 379 ARG Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 379 ARG Chi-restraints excluded: chain K residue 322 CYS Chi-restraints excluded: chain K residue 328 ILE Chi-restraints excluded: chain K residue 379 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 85 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS E 362 HIS ** F 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 362 HIS ** J 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.150932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.114344 restraints weight = 31094.023| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.48 r_work: 0.3805 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9042 Z= 0.205 Angle : 0.688 12.406 12089 Z= 0.352 Chirality : 0.051 0.156 1364 Planarity : 0.005 0.047 1551 Dihedral : 7.939 56.029 1247 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.73 % Favored : 87.27 % Rotamer: Outliers : 4.01 % Allowed : 22.48 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.45 (0.18), residues: 1155 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.14), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.007 0.001 TYR B 310 PHE 0.014 0.003 PHE D 378 HIS 0.011 0.001 HIS I 362 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 9042) covalent geometry : angle 0.68799 (12089) hydrogen bonds : bond 0.05750 ( 16) hydrogen bonds : angle 6.82478 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 111 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.6995 (mptt) REVERT: B 280 LYS cc_start: 0.6863 (OUTLIER) cc_final: 0.6250 (mptt) REVERT: B 379 ARG cc_start: 0.1151 (OUTLIER) cc_final: 0.0566 (tpt-90) REVERT: C 280 LYS cc_start: 0.6914 (OUTLIER) cc_final: 0.6702 (mttm) REVERT: C 295 ASP cc_start: 0.6703 (p0) cc_final: 0.6399 (p0) REVERT: C 347 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8395 (mtpt) REVERT: C 349 ARG cc_start: 0.7918 (mtp-110) cc_final: 0.7698 (mtp180) REVERT: C 363 VAL cc_start: 0.7881 (OUTLIER) cc_final: 0.7139 (p) REVERT: C 379 ARG cc_start: 0.1204 (OUTLIER) cc_final: 0.0735 (tpt-90) REVERT: D 347 LYS cc_start: 0.8545 (mmmm) cc_final: 0.8281 (mtpt) REVERT: D 363 VAL cc_start: 0.7853 (OUTLIER) cc_final: 0.7268 (p) REVERT: F 295 ASP cc_start: 0.7511 (p0) cc_final: 0.6901 (p0) REVERT: F 321 LYS cc_start: 0.6829 (mmtt) cc_final: 0.6038 (mptt) REVERT: F 363 VAL cc_start: 0.7952 (OUTLIER) cc_final: 0.7277 (p) REVERT: G 321 LYS cc_start: 0.6371 (pttp) cc_final: 0.5661 (mmtt) REVERT: G 338 GLU cc_start: 0.8209 (tt0) cc_final: 0.7992 (tt0) REVERT: G 340 LYS cc_start: 0.8058 (mttt) cc_final: 0.7525 (tttp) REVERT: G 363 VAL cc_start: 0.7972 (OUTLIER) cc_final: 0.7419 (p) REVERT: H 280 LYS cc_start: 0.6768 (OUTLIER) cc_final: 0.6419 (mmtt) REVERT: H 340 LYS cc_start: 0.7978 (mttt) cc_final: 0.7636 (mttm) REVERT: H 376 LEU cc_start: 0.5458 (mm) cc_final: 0.5254 (tp) REVERT: H 379 ARG cc_start: 0.0952 (OUTLIER) cc_final: 0.0750 (tpt-90) REVERT: I 294 LYS cc_start: 0.8014 (tptp) cc_final: 0.7518 (tptt) REVERT: I 295 ASP cc_start: 0.7098 (p0) cc_final: 0.6851 (p0) REVERT: K 274 LYS cc_start: 0.6733 (mtpt) cc_final: 0.6001 (pttp) REVERT: K 321 LYS cc_start: 0.5472 (pttt) cc_final: 0.4673 (mttp) REVERT: K 322 CYS cc_start: 0.5716 (OUTLIER) cc_final: 0.5195 (m) REVERT: K 340 LYS cc_start: 0.8443 (mttt) cc_final: 0.8146 (mttm) outliers start: 41 outliers final: 28 residues processed: 146 average time/residue: 0.2681 time to fit residues: 51.8557 Evaluate side-chains 151 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 110 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 327 ASN Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 280 LYS Chi-restraints excluded: chain H residue 285 SER Chi-restraints excluded: chain H residue 328 ILE Chi-restraints excluded: chain H residue 379 ARG Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 328 ILE Chi-restraints excluded: chain I residue 362 HIS Chi-restraints excluded: chain I residue 363 VAL Chi-restraints excluded: chain I residue 379 ARG Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 379 ARG Chi-restraints excluded: chain K residue 322 CYS Chi-restraints excluded: chain K residue 328 ILE Chi-restraints excluded: chain K residue 379 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 95 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 HIS ** F 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 HIS ** G 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 362 HIS ** H 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 362 HIS ** I 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 362 HIS ** J 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.152670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.117058 restraints weight = 30772.245| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.44 r_work: 0.3859 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3740 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9042 Z= 0.251 Angle : 0.729 12.785 12089 Z= 0.374 Chirality : 0.052 0.157 1364 Planarity : 0.005 0.048 1551 Dihedral : 8.127 56.592 1247 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.46 % Favored : 85.54 % Rotamer: Outliers : 4.20 % Allowed : 22.58 % Favored : 73.22 % 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 are not related in a simple way. whole: -4.51 (0.18), residues: 1155 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.14), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.009 0.002 TYR B 310 PHE 0.016 0.003 PHE D 378 HIS 0.015 0.001 HIS I 362 Details of bonding type rmsd covalent geometry : bond 0.00587 ( 9042) covalent geometry : angle 0.72874 (12089) hydrogen bonds : bond 0.05944 ( 16) hydrogen bonds : angle 6.85178 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 115 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7017 (mptt) REVERT: B 280 LYS cc_start: 0.6895 (OUTLIER) cc_final: 0.6326 (mptt) REVERT: B 379 ARG cc_start: 0.1224 (OUTLIER) cc_final: 0.0672 (tpt-90) REVERT: C 280 LYS cc_start: 0.7026 (OUTLIER) cc_final: 0.6774 (mttm) REVERT: C 295 ASP cc_start: 0.6681 (p0) cc_final: 0.6384 (p0) REVERT: C 347 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8419 (mtpt) REVERT: C 363 VAL cc_start: 0.7870 (OUTLIER) cc_final: 0.7391 (p) REVERT: C 379 ARG cc_start: 0.1151 (OUTLIER) cc_final: 0.0712 (tpt-90) REVERT: D 347 LYS cc_start: 0.8588 (mmmm) cc_final: 0.8317 (mtpt) REVERT: F 295 ASP cc_start: 0.7557 (p0) cc_final: 0.7087 (p0) REVERT: F 321 LYS cc_start: 0.6812 (mmtt) cc_final: 0.6515 (mmtt) REVERT: F 363 VAL cc_start: 0.7974 (OUTLIER) cc_final: 0.7341 (p) REVERT: G 321 LYS cc_start: 0.6249 (pttp) cc_final: 0.5792 (mmtt) REVERT: G 338 GLU cc_start: 0.8215 (tt0) cc_final: 0.8014 (tt0) REVERT: G 340 LYS cc_start: 0.8073 (mttt) cc_final: 0.7599 (mtpp) REVERT: G 363 VAL cc_start: 0.8102 (OUTLIER) cc_final: 0.7598 (p) REVERT: H 280 LYS cc_start: 0.6856 (OUTLIER) cc_final: 0.6518 (mmtt) REVERT: H 340 LYS cc_start: 0.8034 (mttt) cc_final: 0.7707 (mttm) REVERT: H 376 LEU cc_start: 0.5510 (mm) cc_final: 0.5296 (tp) REVERT: I 294 LYS cc_start: 0.8054 (tptp) cc_final: 0.7637 (tptt) REVERT: I 295 ASP cc_start: 0.7208 (p0) cc_final: 0.6999 (p0) REVERT: J 277 ILE cc_start: 0.7653 (mm) cc_final: 0.7368 (mt) REVERT: K 274 LYS cc_start: 0.6695 (mtpt) cc_final: 0.5941 (pttp) REVERT: K 321 LYS cc_start: 0.5424 (pttt) cc_final: 0.4613 (mttp) REVERT: K 322 CYS cc_start: 0.5710 (OUTLIER) cc_final: 0.5187 (m) REVERT: K 340 LYS cc_start: 0.8415 (mttt) cc_final: 0.8129 (mttm) REVERT: K 363 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.7939 (p) outliers start: 43 outliers final: 29 residues processed: 152 average time/residue: 0.2607 time to fit residues: 52.5147 Evaluate side-chains 152 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 111 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 327 ASN Chi-restraints excluded: chain G residue 363 VAL Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain H residue 280 LYS Chi-restraints excluded: chain H residue 285 SER Chi-restraints excluded: chain H residue 328 ILE Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 328 ILE Chi-restraints excluded: chain I residue 362 HIS Chi-restraints excluded: chain I residue 363 VAL Chi-restraints excluded: chain I residue 379 ARG Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 379 ARG Chi-restraints excluded: chain K residue 322 CYS Chi-restraints excluded: chain K residue 328 ILE Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 379 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 42 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 53 optimal weight: 0.0980 chunk 26 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 362 HIS ** J 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.153662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.116229 restraints weight = 30984.456| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.52 r_work: 0.3858 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3740 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9042 Z= 0.118 Angle : 0.653 12.536 12089 Z= 0.328 Chirality : 0.051 0.156 1364 Planarity : 0.004 0.044 1551 Dihedral : 7.710 55.578 1247 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % Rotamer: Outliers : 3.81 % Allowed : 22.58 % Favored : 73.61 % 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 are not related in a simple way. whole: -4.38 (0.18), residues: 1155 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.14), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 349 TYR 0.004 0.001 TYR B 310 PHE 0.013 0.002 PHE F 378 HIS 0.010 0.001 HIS I 362 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9042) covalent geometry : angle 0.65327 (12089) hydrogen bonds : bond 0.05477 ( 16) hydrogen bonds : angle 6.61893 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4957.58 seconds wall clock time: 85 minutes 36.24 seconds (5136.24 seconds total)