Starting phenix.real_space_refine on Fri Feb 6 10:20:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vdv_64992/02_2026/9vdv_64992.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vdv_64992/02_2026/9vdv_64992.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vdv_64992/02_2026/9vdv_64992.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vdv_64992/02_2026/9vdv_64992.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vdv_64992/02_2026/9vdv_64992.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vdv_64992/02_2026/9vdv_64992.map" } resolution = 2.7 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= 0.062 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 15522 2.51 5 N 4020 2.21 5 O 4584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24258 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4043 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 476} Chain breaks: 1 Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 4.19, per 1000 atoms: 0.17 Number of scatterers: 24258 At special positions: 0 Unit cell: (137.75, 131.1, 103.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 4584 8.00 N 4020 7.00 C 15522 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 1.0 seconds 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5664 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 12 sheets defined 63.2% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 5 through 16 removed outlier: 3.777A pdb=" N LEU A 15 " --> pdb=" O TYR A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 50 Processing helix chain 'A' and resid 81 through 95 removed outlier: 3.908A pdb=" N LYS A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 127 through 139 Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 161 through 168 Processing helix chain 'A' and resid 168 through 176 Processing helix chain 'A' and resid 186 through 199 removed outlier: 3.872A pdb=" N LYS A 199 " --> pdb=" O GLN A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 231 removed outlier: 4.081A pdb=" N ALA A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 266 removed outlier: 3.503A pdb=" N LEU A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.525A pdb=" N SER A 290 " --> pdb=" O ASP A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 311 through 329 Processing helix chain 'A' and resid 333 through 343 Processing helix chain 'A' and resid 344 through 346 No H-bonds generated for 'chain 'A' and resid 344 through 346' Processing helix chain 'A' and resid 349 through 365 removed outlier: 4.627A pdb=" N GLN A 353 " --> pdb=" O TYR A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 Proline residue: A 370 - end of helix Processing helix chain 'A' and resid 371 through 376 removed outlier: 4.051A pdb=" N LEU A 375 " --> pdb=" O TYR A 371 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 371 through 376' Processing helix chain 'A' and resid 385 through 402 Processing helix chain 'A' and resid 403 through 417 Processing helix chain 'A' and resid 422 through 433 removed outlier: 3.725A pdb=" N LYS A 428 " --> pdb=" O ASP A 424 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY A 433 " --> pdb=" O ILE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 445 removed outlier: 3.665A pdb=" N ASP A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 462 removed outlier: 3.858A pdb=" N ASP A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 470 Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 490 through 498 Processing helix chain 'B' and resid 6 through 16 removed outlier: 3.777A pdb=" N LEU B 15 " --> pdb=" O TYR B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 50 Processing helix chain 'B' and resid 81 through 95 removed outlier: 3.907A pdb=" N LYS B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 127 through 139 Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' Processing helix chain 'B' and resid 161 through 168 Processing helix chain 'B' and resid 168 through 176 Processing helix chain 'B' and resid 186 through 199 removed outlier: 3.871A pdb=" N LYS B 199 " --> pdb=" O GLN B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 231 removed outlier: 4.081A pdb=" N ALA B 223 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 266 removed outlier: 3.502A pdb=" N LEU B 256 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 295 removed outlier: 3.524A pdb=" N SER B 290 " --> pdb=" O ASP B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 309 Processing helix chain 'B' and resid 311 through 329 Processing helix chain 'B' and resid 333 through 343 Processing helix chain 'B' and resid 344 through 346 No H-bonds generated for 'chain 'B' and resid 344 through 346' Processing helix chain 'B' and resid 349 through 365 removed outlier: 4.627A pdb=" N GLN B 353 " --> pdb=" O TYR B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 Proline residue: B 370 - end of helix Processing helix chain 'B' and resid 371 through 376 removed outlier: 4.051A pdb=" N LEU B 375 " --> pdb=" O TYR B 371 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 371 through 376' Processing helix chain 'B' and resid 385 through 402 Processing helix chain 'B' and resid 403 through 417 Processing helix chain 'B' and resid 422 through 433 removed outlier: 3.724A pdb=" N LYS B 428 " --> pdb=" O ASP B 424 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY B 433 " --> pdb=" O ILE B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 445 removed outlier: 3.666A pdb=" N ASP B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 462 removed outlier: 3.859A pdb=" N ASP B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 470 Processing helix chain 'B' and resid 470 through 480 Processing helix chain 'B' and resid 490 through 498 Processing helix chain 'C' and resid 6 through 16 removed outlier: 3.778A pdb=" N LEU C 15 " --> pdb=" O TYR C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 50 Processing helix chain 'C' and resid 81 through 95 removed outlier: 3.908A pdb=" N LYS C 87 " --> pdb=" O LYS C 83 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 100 Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 127 through 139 Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 161 through 168 Processing helix chain 'C' and resid 168 through 176 Processing helix chain 'C' and resid 186 through 199 removed outlier: 3.872A pdb=" N LYS C 199 " --> pdb=" O GLN C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 231 removed outlier: 4.083A pdb=" N ALA C 223 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 266 removed outlier: 3.502A pdb=" N LEU C 256 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 295 removed outlier: 3.524A pdb=" N SER C 290 " --> pdb=" O ASP C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 309 Processing helix chain 'C' and resid 311 through 329 Processing helix chain 'C' and resid 333 through 343 Processing helix chain 'C' and resid 344 through 346 No H-bonds generated for 'chain 'C' and resid 344 through 346' Processing helix chain 'C' and resid 349 through 365 removed outlier: 4.627A pdb=" N GLN C 353 " --> pdb=" O TYR C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 370 Proline residue: C 370 - end of helix Processing helix chain 'C' and resid 371 through 376 removed outlier: 4.051A pdb=" N LEU C 375 " --> pdb=" O TYR C 371 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE C 376 " --> pdb=" O LEU C 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 371 through 376' Processing helix chain 'C' and resid 385 through 402 Processing helix chain 'C' and resid 403 through 417 Processing helix chain 'C' and resid 422 through 433 removed outlier: 3.724A pdb=" N LYS C 428 " --> pdb=" O ASP C 424 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY C 433 " --> pdb=" O ILE C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 445 removed outlier: 3.665A pdb=" N ASP C 445 " --> pdb=" O LEU C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 462 removed outlier: 3.858A pdb=" N ASP C 462 " --> pdb=" O ILE C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 470 Processing helix chain 'C' and resid 470 through 480 Processing helix chain 'C' and resid 490 through 498 Processing helix chain 'D' and resid 6 through 16 removed outlier: 3.778A pdb=" N LEU D 15 " --> pdb=" O TYR D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 50 Processing helix chain 'D' and resid 81 through 95 removed outlier: 3.907A pdb=" N LYS D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU D 88 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 101 through 103 No H-bonds generated for 'chain 'D' and resid 101 through 103' Processing helix chain 'D' and resid 127 through 139 Processing helix chain 'D' and resid 158 through 160 No H-bonds generated for 'chain 'D' and resid 158 through 160' Processing helix chain 'D' and resid 161 through 168 Processing helix chain 'D' and resid 168 through 176 Processing helix chain 'D' and resid 186 through 199 removed outlier: 3.871A pdb=" N LYS D 199 " --> pdb=" O GLN D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 4.082A pdb=" N ALA D 223 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL D 224 " --> pdb=" O ILE D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 266 removed outlier: 3.502A pdb=" N LEU D 256 " --> pdb=" O ALA D 252 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 295 removed outlier: 3.525A pdb=" N SER D 290 " --> pdb=" O ASP D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 309 Processing helix chain 'D' and resid 311 through 329 Processing helix chain 'D' and resid 333 through 343 Processing helix chain 'D' and resid 344 through 346 No H-bonds generated for 'chain 'D' and resid 344 through 346' Processing helix chain 'D' and resid 349 through 365 removed outlier: 4.627A pdb=" N GLN D 353 " --> pdb=" O TYR D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 370 Proline residue: D 370 - end of helix Processing helix chain 'D' and resid 371 through 376 removed outlier: 4.051A pdb=" N LEU D 375 " --> pdb=" O TYR D 371 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE D 376 " --> pdb=" O LEU D 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 371 through 376' Processing helix chain 'D' and resid 385 through 402 Processing helix chain 'D' and resid 403 through 417 Processing helix chain 'D' and resid 422 through 433 removed outlier: 3.724A pdb=" N LYS D 428 " --> pdb=" O ASP D 424 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY D 433 " --> pdb=" O ILE D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 445 removed outlier: 3.665A pdb=" N ASP D 445 " --> pdb=" O LEU D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 462 removed outlier: 3.858A pdb=" N ASP D 462 " --> pdb=" O ILE D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 470 Processing helix chain 'D' and resid 470 through 480 Processing helix chain 'D' and resid 490 through 498 Processing helix chain 'E' and resid 6 through 16 removed outlier: 3.778A pdb=" N LEU E 15 " --> pdb=" O TYR E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 50 Processing helix chain 'E' and resid 81 through 95 removed outlier: 3.908A pdb=" N LYS E 87 " --> pdb=" O LYS E 83 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU E 88 " --> pdb=" O ALA E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 100 Processing helix chain 'E' and resid 101 through 103 No H-bonds generated for 'chain 'E' and resid 101 through 103' Processing helix chain 'E' and resid 127 through 139 Processing helix chain 'E' and resid 158 through 160 No H-bonds generated for 'chain 'E' and resid 158 through 160' Processing helix chain 'E' and resid 161 through 168 Processing helix chain 'E' and resid 168 through 176 Processing helix chain 'E' and resid 186 through 199 removed outlier: 3.872A pdb=" N LYS E 199 " --> pdb=" O GLN E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 231 removed outlier: 4.082A pdb=" N ALA E 223 " --> pdb=" O ILE E 219 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL E 224 " --> pdb=" O ILE E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 266 removed outlier: 3.502A pdb=" N LEU E 256 " --> pdb=" O ALA E 252 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR E 266 " --> pdb=" O GLU E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 295 removed outlier: 3.525A pdb=" N SER E 290 " --> pdb=" O ASP E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 309 Processing helix chain 'E' and resid 311 through 329 Processing helix chain 'E' and resid 333 through 343 Processing helix chain 'E' and resid 344 through 346 No H-bonds generated for 'chain 'E' and resid 344 through 346' Processing helix chain 'E' and resid 349 through 365 removed outlier: 4.627A pdb=" N GLN E 353 " --> pdb=" O TYR E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 370 Proline residue: E 370 - end of helix Processing helix chain 'E' and resid 371 through 376 removed outlier: 4.050A pdb=" N LEU E 375 " --> pdb=" O TYR E 371 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE E 376 " --> pdb=" O LEU E 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 371 through 376' Processing helix chain 'E' and resid 385 through 402 Processing helix chain 'E' and resid 403 through 417 Processing helix chain 'E' and resid 422 through 433 removed outlier: 3.724A pdb=" N LYS E 428 " --> pdb=" O ASP E 424 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY E 433 " --> pdb=" O ILE E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 445 removed outlier: 3.665A pdb=" N ASP E 445 " --> pdb=" O LEU E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 462 removed outlier: 3.858A pdb=" N ASP E 462 " --> pdb=" O ILE E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 470 Processing helix chain 'E' and resid 470 through 480 Processing helix chain 'E' and resid 490 through 498 Processing helix chain 'F' and resid 6 through 16 removed outlier: 3.778A pdb=" N LEU F 15 " --> pdb=" O TYR F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 50 Processing helix chain 'F' and resid 81 through 95 removed outlier: 3.909A pdb=" N LYS F 87 " --> pdb=" O LYS F 83 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU F 88 " --> pdb=" O ALA F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 100 Processing helix chain 'F' and resid 101 through 103 No H-bonds generated for 'chain 'F' and resid 101 through 103' Processing helix chain 'F' and resid 127 through 139 Processing helix chain 'F' and resid 158 through 160 No H-bonds generated for 'chain 'F' and resid 158 through 160' Processing helix chain 'F' and resid 161 through 168 Processing helix chain 'F' and resid 168 through 176 Processing helix chain 'F' and resid 186 through 199 removed outlier: 3.872A pdb=" N LYS F 199 " --> pdb=" O GLN F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 231 removed outlier: 4.082A pdb=" N ALA F 223 " --> pdb=" O ILE F 219 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL F 224 " --> pdb=" O ILE F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 266 removed outlier: 3.502A pdb=" N LEU F 256 " --> pdb=" O ALA F 252 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR F 266 " --> pdb=" O GLU F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 295 removed outlier: 3.525A pdb=" N SER F 290 " --> pdb=" O ASP F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 309 Processing helix chain 'F' and resid 311 through 329 Processing helix chain 'F' and resid 333 through 343 Processing helix chain 'F' and resid 344 through 346 No H-bonds generated for 'chain 'F' and resid 344 through 346' Processing helix chain 'F' and resid 349 through 365 removed outlier: 4.627A pdb=" N GLN F 353 " --> pdb=" O TYR F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 370 Proline residue: F 370 - end of helix Processing helix chain 'F' and resid 371 through 376 removed outlier: 4.051A pdb=" N LEU F 375 " --> pdb=" O TYR F 371 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE F 376 " --> pdb=" O LEU F 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 371 through 376' Processing helix chain 'F' and resid 385 through 402 Processing helix chain 'F' and resid 403 through 417 Processing helix chain 'F' and resid 422 through 433 removed outlier: 3.725A pdb=" N LYS F 428 " --> pdb=" O ASP F 424 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY F 433 " --> pdb=" O ILE F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 445 removed outlier: 3.665A pdb=" N ASP F 445 " --> pdb=" O LEU F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 462 removed outlier: 3.859A pdb=" N ASP F 462 " --> pdb=" O ILE F 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 470 Processing helix chain 'F' and resid 470 through 480 Processing helix chain 'F' and resid 490 through 498 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 234 through 238 removed outlier: 4.586A pdb=" N LEU A 234 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 11.268A pdb=" N LYS A 145 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 9.551A pdb=" N THR A 275 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N ASN A 147 " --> pdb=" O HIS A 273 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N HIS A 273 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP A 149 " --> pdb=" O ASN A 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 62 through 68 Processing sheet with id=AA4, first strand: chain 'B' and resid 234 through 238 removed outlier: 4.587A pdb=" N LEU B 234 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 11.267A pdb=" N LYS B 145 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 9.551A pdb=" N THR B 275 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N ASN B 147 " --> pdb=" O HIS B 273 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N HIS B 273 " --> pdb=" O ASN B 147 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP B 149 " --> pdb=" O ASN B 271 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 62 through 68 Processing sheet with id=AA6, first strand: chain 'C' and resid 234 through 238 removed outlier: 4.587A pdb=" N LEU C 234 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 11.269A pdb=" N LYS C 145 " --> pdb=" O THR C 275 " (cutoff:3.500A) removed outlier: 9.550A pdb=" N THR C 275 " --> pdb=" O LYS C 145 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N ASN C 147 " --> pdb=" O HIS C 273 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N HIS C 273 " --> pdb=" O ASN C 147 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP C 149 " --> pdb=" O ASN C 271 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 62 through 68 Processing sheet with id=AA8, first strand: chain 'D' and resid 234 through 238 removed outlier: 4.587A pdb=" N LEU D 234 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 11.267A pdb=" N LYS D 145 " --> pdb=" O THR D 275 " (cutoff:3.500A) removed outlier: 9.551A pdb=" N THR D 275 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N ASN D 147 " --> pdb=" O HIS D 273 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N HIS D 273 " --> pdb=" O ASN D 147 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP D 149 " --> pdb=" O ASN D 271 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 62 through 68 Processing sheet with id=AB1, first strand: chain 'E' and resid 234 through 238 removed outlier: 4.587A pdb=" N LEU E 234 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 11.268A pdb=" N LYS E 145 " --> pdb=" O THR E 275 " (cutoff:3.500A) removed outlier: 9.551A pdb=" N THR E 275 " --> pdb=" O LYS E 145 " (cutoff:3.500A) removed outlier: 10.078A pdb=" N ASN E 147 " --> pdb=" O HIS E 273 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N HIS E 273 " --> pdb=" O ASN E 147 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASP E 149 " --> pdb=" O ASN E 271 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 62 through 68 Processing sheet with id=AB3, first strand: chain 'F' and resid 234 through 238 removed outlier: 4.587A pdb=" N LEU F 234 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 11.269A pdb=" N LYS F 145 " --> pdb=" O THR F 275 " (cutoff:3.500A) removed outlier: 9.551A pdb=" N THR F 275 " --> pdb=" O LYS F 145 " (cutoff:3.500A) removed outlier: 10.078A pdb=" N ASN F 147 " --> pdb=" O HIS F 273 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N HIS F 273 " --> pdb=" O ASN F 147 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP F 149 " --> pdb=" O ASN F 271 " (cutoff:3.500A) 1231 hydrogen bonds defined for protein. 3639 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: 4.53 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5703 1.33 - 1.45: 5531 1.45 - 1.58: 13414 1.58 - 1.70: 6 1.70 - 1.82: 186 Bond restraints: 24840 Sorted by residual: bond pdb=" CG PRO E 74 " pdb=" CD PRO E 74 " ideal model delta sigma weight residual 1.503 1.269 0.234 3.40e-02 8.65e+02 4.75e+01 bond pdb=" CG PRO F 74 " pdb=" CD PRO F 74 " ideal model delta sigma weight residual 1.503 1.269 0.234 3.40e-02 8.65e+02 4.75e+01 bond pdb=" CG PRO D 74 " pdb=" CD PRO D 74 " ideal model delta sigma weight residual 1.503 1.269 0.234 3.40e-02 8.65e+02 4.74e+01 bond pdb=" CG PRO C 74 " pdb=" CD PRO C 74 " ideal model delta sigma weight residual 1.503 1.269 0.234 3.40e-02 8.65e+02 4.74e+01 bond pdb=" CG PRO A 74 " pdb=" CD PRO A 74 " ideal model delta sigma weight residual 1.503 1.269 0.234 3.40e-02 8.65e+02 4.73e+01 ... (remaining 24835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 32998 3.05 - 6.10: 512 6.10 - 9.15: 90 9.15 - 12.20: 18 12.20 - 15.25: 6 Bond angle restraints: 33624 Sorted by residual: angle pdb=" N PRO E 74 " pdb=" CD PRO E 74 " pdb=" CG PRO E 74 " ideal model delta sigma weight residual 103.20 87.95 15.25 1.50e+00 4.44e-01 1.03e+02 angle pdb=" N PRO F 74 " pdb=" CD PRO F 74 " pdb=" CG PRO F 74 " ideal model delta sigma weight residual 103.20 87.97 15.23 1.50e+00 4.44e-01 1.03e+02 angle pdb=" N PRO C 74 " pdb=" CD PRO C 74 " pdb=" CG PRO C 74 " ideal model delta sigma weight residual 103.20 87.97 15.23 1.50e+00 4.44e-01 1.03e+02 angle pdb=" N PRO A 74 " pdb=" CD PRO A 74 " pdb=" CG PRO A 74 " ideal model delta sigma weight residual 103.20 87.97 15.23 1.50e+00 4.44e-01 1.03e+02 angle pdb=" N PRO D 74 " pdb=" CD PRO D 74 " pdb=" CG PRO D 74 " ideal model delta sigma weight residual 103.20 87.98 15.22 1.50e+00 4.44e-01 1.03e+02 ... (remaining 33619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 12397 17.81 - 35.62: 1704 35.62 - 53.44: 605 53.44 - 71.25: 96 71.25 - 89.06: 48 Dihedral angle restraints: 14850 sinusoidal: 6048 harmonic: 8802 Sorted by residual: dihedral pdb=" CA THR B 350 " pdb=" C THR B 350 " pdb=" N ILE B 351 " pdb=" CA ILE B 351 " ideal model delta harmonic sigma weight residual 180.00 -155.81 -24.19 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA THR F 350 " pdb=" C THR F 350 " pdb=" N ILE F 351 " pdb=" CA ILE F 351 " ideal model delta harmonic sigma weight residual -180.00 -155.85 -24.15 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA THR C 350 " pdb=" C THR C 350 " pdb=" N ILE C 351 " pdb=" CA ILE C 351 " ideal model delta harmonic sigma weight residual -180.00 -155.87 -24.13 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 14847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2282 0.041 - 0.082: 1015 0.082 - 0.123: 203 0.123 - 0.164: 106 0.164 - 0.205: 18 Chirality restraints: 3624 Sorted by residual: chirality pdb=" CB ILE C 376 " pdb=" CA ILE C 376 " pdb=" CG1 ILE C 376 " pdb=" CG2 ILE C 376 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE E 376 " pdb=" CA ILE E 376 " pdb=" CG1 ILE E 376 " pdb=" CG2 ILE E 376 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE D 376 " pdb=" CA ILE D 376 " pdb=" CG1 ILE D 376 " pdb=" CG2 ILE D 376 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 3621 not shown) Planarity restraints: 4308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP E 192 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.69e+00 pdb=" CG ASP E 192 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASP E 192 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP E 192 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 192 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.66e+00 pdb=" CG ASP B 192 " -0.041 2.00e-02 2.50e+03 pdb=" OD1 ASP B 192 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP B 192 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 192 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.63e+00 pdb=" CG ASP A 192 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASP A 192 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP A 192 " -0.014 2.00e-02 2.50e+03 ... (remaining 4305 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 677 2.69 - 3.24: 23432 3.24 - 3.79: 41224 3.79 - 4.35: 57559 4.35 - 4.90: 91675 Nonbonded interactions: 214567 Sorted by model distance: nonbonded pdb=" NE2 GLN A 324 " pdb=" OG SER F 290 " model vdw 2.134 3.120 nonbonded pdb=" OG SER B 290 " pdb=" NE2 GLN D 324 " model vdw 2.149 3.120 nonbonded pdb=" OG SER C 290 " pdb=" NE2 GLN F 324 " model vdw 2.160 3.120 nonbonded pdb=" OG SER A 290 " pdb=" NE2 GLN C 324 " model vdw 2.161 3.120 nonbonded pdb=" OG SER D 290 " pdb=" NE2 GLN E 324 " model vdw 2.161 3.120 ... (remaining 214562 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.660 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: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 21.090 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 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:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 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 : 0.007 0.234 24840 Z= 0.256 Angle : 0.997 15.248 33624 Z= 0.554 Chirality : 0.051 0.205 3624 Planarity : 0.007 0.084 4308 Dihedral : 18.967 89.062 9186 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.86 % Favored : 96.94 % Rotamer: Outliers : 7.52 % Allowed : 26.81 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.99 (0.14), residues: 2940 helix: -0.38 (0.11), residues: 1638 sheet: -0.78 (0.37), residues: 216 loop : -0.82 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 134 TYR 0.020 0.003 TYR B 475 PHE 0.034 0.002 PHE B 140 TRP 0.011 0.002 TRP E 471 HIS 0.008 0.002 HIS D 9 Details of bonding type rmsd covalent geometry : bond 0.00651 (24840) covalent geometry : angle 0.99697 (33624) hydrogen bonds : bond 0.18853 ( 1231) hydrogen bonds : angle 6.66645 ( 3639) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 367 time to evaluate : 0.874 Fit side-chains REVERT: A 23 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7795 (mt0) REVERT: A 134 ARG cc_start: 0.6641 (mtm110) cc_final: 0.6332 (ttm-80) REVERT: A 421 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7547 (mp) REVERT: B 23 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7802 (mt0) REVERT: B 134 ARG cc_start: 0.6640 (mtm110) cc_final: 0.6275 (ttm-80) REVERT: B 236 ARG cc_start: 0.8240 (mmt180) cc_final: 0.8002 (mmm160) REVERT: B 276 LYS cc_start: 0.6803 (ptpt) cc_final: 0.6381 (pttm) REVERT: B 421 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.7404 (mp) REVERT: B 450 LYS cc_start: 0.7135 (mmmt) cc_final: 0.6776 (mttt) REVERT: C 23 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7814 (mt0) REVERT: C 58 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7770 (mt0) REVERT: C 421 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7470 (mt) REVERT: D 23 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7833 (mt0) REVERT: D 58 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7765 (mt0) REVERT: D 421 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7318 (mt) REVERT: E 23 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7792 (mt0) REVERT: E 58 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7861 (mm110) REVERT: E 261 MET cc_start: 0.7420 (mmm) cc_final: 0.7053 (mmp) REVERT: F 104 GLU cc_start: 0.7589 (pt0) cc_final: 0.7375 (pt0) REVERT: F 106 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7557 (pp20) REVERT: F 261 MET cc_start: 0.7362 (mmm) cc_final: 0.6961 (mmp) outliers start: 203 outliers final: 117 residues processed: 539 average time/residue: 0.5616 time to fit residues: 355.4459 Evaluate side-chains 400 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 273 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 403 CYS Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 345 ASN Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 403 CYS Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain D residue 23 GLN Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 251 ASP Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 403 CYS Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain E residue 23 GLN Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 293 ASN Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 319 LEU Chi-restraints excluded: chain E residue 345 ASN Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 403 CYS Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain F residue 23 GLN Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 293 ASN Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 345 ASN Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 403 CYS Chi-restraints excluded: chain F residue 419 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.0870 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN A 324 GLN A 392 ASN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 ASN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 ASN ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 ASN ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 ASN F 392 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.164873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.140162 restraints weight = 27742.004| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.78 r_work: 0.3529 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24840 Z= 0.150 Angle : 0.621 7.508 33624 Z= 0.334 Chirality : 0.043 0.158 3624 Planarity : 0.006 0.053 4308 Dihedral : 9.658 79.506 3482 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.31 % Favored : 97.28 % Rotamer: Outliers : 6.93 % Allowed : 26.59 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.40 (0.15), residues: 2940 helix: 0.27 (0.12), residues: 1770 sheet: -0.75 (0.38), residues: 204 loop : -0.95 (0.18), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 134 TYR 0.025 0.002 TYR B 447 PHE 0.017 0.001 PHE D 140 TRP 0.013 0.001 TRP C 363 HIS 0.005 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00335 (24840) covalent geometry : angle 0.62072 (33624) hydrogen bonds : bond 0.04908 ( 1231) hydrogen bonds : angle 4.75534 ( 3639) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 340 time to evaluate : 0.924 Fit side-chains REVERT: A 23 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.6986 (mt0) REVERT: A 246 CYS cc_start: 0.7210 (m) cc_final: 0.7001 (m) REVERT: A 261 MET cc_start: 0.7328 (mmm) cc_final: 0.6847 (mmp) REVERT: A 386 GLU cc_start: 0.5986 (tt0) cc_final: 0.5556 (tp30) REVERT: A 456 SER cc_start: 0.7469 (m) cc_final: 0.7022 (p) REVERT: B 23 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.6975 (mt0) REVERT: B 236 ARG cc_start: 0.8277 (mmt180) cc_final: 0.8072 (mmm160) REVERT: B 261 MET cc_start: 0.7429 (mmm) cc_final: 0.6961 (mmp) REVERT: B 456 SER cc_start: 0.7486 (m) cc_final: 0.7010 (p) REVERT: C 58 GLN cc_start: 0.8570 (mm-40) cc_final: 0.7975 (mt0) REVERT: C 249 HIS cc_start: 0.7127 (OUTLIER) cc_final: 0.6662 (t70) REVERT: C 386 GLU cc_start: 0.6196 (pt0) cc_final: 0.5992 (pt0) REVERT: C 427 GLU cc_start: 0.6758 (tm-30) cc_final: 0.6285 (mt-10) REVERT: D 58 GLN cc_start: 0.8576 (mm-40) cc_final: 0.7976 (mt0) REVERT: D 134 ARG cc_start: 0.5875 (mtm110) cc_final: 0.5661 (tmm-80) REVERT: D 249 HIS cc_start: 0.7068 (OUTLIER) cc_final: 0.6602 (t70) REVERT: D 386 GLU cc_start: 0.6265 (pt0) cc_final: 0.6052 (pt0) REVERT: D 427 GLU cc_start: 0.6745 (tm-30) cc_final: 0.6293 (mt-10) REVERT: E 23 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7166 (mt0) REVERT: E 106 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7335 (pp20) REVERT: E 120 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7604 (pt) REVERT: E 226 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7738 (ttpt) REVERT: E 249 HIS cc_start: 0.6738 (OUTLIER) cc_final: 0.6229 (t70) REVERT: E 261 MET cc_start: 0.7320 (mmm) cc_final: 0.6920 (mmm) REVERT: E 293 ASN cc_start: 0.8116 (OUTLIER) cc_final: 0.7823 (m110) REVERT: E 335 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7693 (mm) REVERT: E 376 ILE cc_start: 0.6316 (OUTLIER) cc_final: 0.6047 (pp) REVERT: F 23 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7140 (mt0) REVERT: F 106 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7622 (pp20) REVERT: F 120 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7609 (pp) REVERT: F 134 ARG cc_start: 0.5707 (mtm110) cc_final: 0.5428 (tmm-80) REVERT: F 249 HIS cc_start: 0.6864 (OUTLIER) cc_final: 0.6224 (t70) REVERT: F 261 MET cc_start: 0.7303 (mmm) cc_final: 0.6946 (mmm) REVERT: F 293 ASN cc_start: 0.8128 (OUTLIER) cc_final: 0.7827 (m110) REVERT: F 376 ILE cc_start: 0.6238 (OUTLIER) cc_final: 0.5970 (pp) outliers start: 187 outliers final: 87 residues processed: 503 average time/residue: 0.5231 time to fit residues: 309.7773 Evaluate side-chains 402 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 297 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 345 ASN Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 140 PHE Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 249 HIS Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 309 LYS Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain E residue 23 GLN Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 226 LYS Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 293 ASN Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 309 LYS Chi-restraints excluded: chain E residue 319 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 345 ASN Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain F residue 23 GLN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 293 ASN Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 345 ASN Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain F residue 425 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 215 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 227 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 277 optimal weight: 0.9980 chunk 271 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 184 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 ASN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN ** F 95 ASN ** 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 = 0.3883 r_free = 0.3883 target = 0.164414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.139450 restraints weight = 27750.588| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.79 r_work: 0.3500 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24840 Z= 0.142 Angle : 0.573 8.077 33624 Z= 0.310 Chirality : 0.042 0.159 3624 Planarity : 0.005 0.057 4308 Dihedral : 8.813 76.402 3397 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.06 % Favored : 96.53 % Rotamer: Outliers : 6.07 % Allowed : 27.67 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.08 (0.15), residues: 2940 helix: 0.70 (0.12), residues: 1770 sheet: -0.84 (0.38), residues: 204 loop : -0.79 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 143 TYR 0.030 0.002 TYR A 447 PHE 0.019 0.001 PHE A 140 TRP 0.010 0.001 TRP F 363 HIS 0.004 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00319 (24840) covalent geometry : angle 0.57332 (33624) hydrogen bonds : bond 0.04639 ( 1231) hydrogen bonds : angle 4.54290 ( 3639) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 333 time to evaluate : 0.916 Fit side-chains REVERT: A 246 CYS cc_start: 0.7219 (m) cc_final: 0.6973 (m) REVERT: A 261 MET cc_start: 0.7167 (mmm) cc_final: 0.6702 (mmp) REVERT: A 386 GLU cc_start: 0.5958 (tt0) cc_final: 0.5536 (tp30) REVERT: A 400 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6858 (tt0) REVERT: A 402 LYS cc_start: 0.7414 (mmtp) cc_final: 0.6852 (mtmm) REVERT: B 236 ARG cc_start: 0.8321 (mmt180) cc_final: 0.8014 (mmm160) REVERT: B 261 MET cc_start: 0.7310 (mmm) cc_final: 0.6804 (mmp) REVERT: B 400 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6780 (tt0) REVERT: B 402 LYS cc_start: 0.7455 (mmtp) cc_final: 0.6904 (mtmm) REVERT: B 456 SER cc_start: 0.7417 (m) cc_final: 0.6936 (p) REVERT: B 490 LYS cc_start: 0.7838 (mmtp) cc_final: 0.7597 (mmmt) REVERT: C 11 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.7274 (t80) REVERT: C 23 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.6659 (mt0) REVERT: C 58 GLN cc_start: 0.8526 (mm-40) cc_final: 0.7964 (mt0) REVERT: C 134 ARG cc_start: 0.5589 (ttp80) cc_final: 0.5232 (tmm-80) REVERT: C 261 MET cc_start: 0.7412 (mmm) cc_final: 0.6941 (mmm) REVERT: C 386 GLU cc_start: 0.6283 (pt0) cc_final: 0.6061 (pt0) REVERT: C 390 LYS cc_start: 0.6431 (OUTLIER) cc_final: 0.6199 (mmmt) REVERT: C 425 VAL cc_start: 0.5929 (OUTLIER) cc_final: 0.5659 (m) REVERT: C 427 GLU cc_start: 0.6508 (tm-30) cc_final: 0.6060 (mt-10) REVERT: D 11 TYR cc_start: 0.8421 (OUTLIER) cc_final: 0.7271 (t80) REVERT: D 23 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.6625 (mt0) REVERT: D 58 GLN cc_start: 0.8529 (mm-40) cc_final: 0.7933 (mt0) REVERT: D 261 MET cc_start: 0.7394 (mmm) cc_final: 0.6919 (mmm) REVERT: D 386 GLU cc_start: 0.6280 (pt0) cc_final: 0.6071 (pt0) REVERT: D 390 LYS cc_start: 0.6406 (OUTLIER) cc_final: 0.6185 (mmmt) REVERT: D 425 VAL cc_start: 0.5947 (OUTLIER) cc_final: 0.5677 (m) REVERT: D 427 GLU cc_start: 0.6534 (tm-30) cc_final: 0.6104 (mt-10) REVERT: E 23 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.6995 (mt0) REVERT: E 58 GLN cc_start: 0.8453 (mm-40) cc_final: 0.7929 (mt0) REVERT: E 120 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7658 (pp) REVERT: E 157 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8186 (mt) REVERT: E 231 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.6965 (t70) REVERT: E 237 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8417 (ttm110) REVERT: E 261 MET cc_start: 0.7264 (mmm) cc_final: 0.6854 (mmm) REVERT: E 293 ASN cc_start: 0.8007 (OUTLIER) cc_final: 0.7745 (m110) REVERT: E 376 ILE cc_start: 0.6289 (OUTLIER) cc_final: 0.5924 (pp) REVERT: E 402 LYS cc_start: 0.7425 (mmtp) cc_final: 0.6950 (mtmm) REVERT: F 23 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.6969 (mt0) REVERT: F 106 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7591 (pp20) REVERT: F 157 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8164 (mt) REVERT: F 231 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.7040 (t70) REVERT: F 237 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8387 (ttm110) REVERT: F 249 HIS cc_start: 0.6990 (OUTLIER) cc_final: 0.6383 (t70) REVERT: F 261 MET cc_start: 0.7258 (mmm) cc_final: 0.6605 (mmt) REVERT: F 293 ASN cc_start: 0.8072 (OUTLIER) cc_final: 0.7822 (m110) REVERT: F 376 ILE cc_start: 0.6198 (OUTLIER) cc_final: 0.5852 (pp) REVERT: F 400 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7162 (tt0) REVERT: F 402 LYS cc_start: 0.7435 (mmtp) cc_final: 0.6818 (mtmm) outliers start: 164 outliers final: 85 residues processed: 467 average time/residue: 0.5398 time to fit residues: 296.1983 Evaluate side-chains 404 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 293 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 309 LYS Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 345 ASN Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 390 LYS Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 23 GLN Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 249 HIS Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 309 LYS Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 390 LYS Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain E residue 23 GLN Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 293 ASN Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 309 LYS Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 319 LEU Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain F residue 23 GLN Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 237 ARG Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 293 ASN Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 312 SER Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 419 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 26 optimal weight: 0.4980 chunk 281 optimal weight: 0.0170 chunk 74 optimal weight: 0.9990 chunk 195 optimal weight: 0.9980 chunk 191 optimal weight: 0.0980 chunk 255 optimal weight: 5.9990 chunk 245 optimal weight: 8.9990 chunk 147 optimal weight: 8.9990 chunk 222 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 overall best weight: 0.5220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 ASN A 392 ASN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN B 392 ASN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 392 ASN ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.166402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.142060 restraints weight = 27572.406| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.76 r_work: 0.3536 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24840 Z= 0.116 Angle : 0.530 7.357 33624 Z= 0.287 Chirality : 0.041 0.162 3624 Planarity : 0.005 0.057 4308 Dihedral : 7.987 73.075 3375 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.65 % Favored : 96.94 % Rotamer: Outliers : 5.85 % Allowed : 26.63 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.27 (0.15), residues: 2940 helix: 0.93 (0.12), residues: 1800 sheet: -1.04 (0.37), residues: 204 loop : -0.87 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 477 TYR 0.028 0.001 TYR A 447 PHE 0.024 0.001 PHE B 140 TRP 0.009 0.001 TRP E 363 HIS 0.003 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00253 (24840) covalent geometry : angle 0.53021 (33624) hydrogen bonds : bond 0.04106 ( 1231) hydrogen bonds : angle 4.36709 ( 3639) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 361 time to evaluate : 0.972 Fit side-chains REVERT: A 23 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.6456 (mt0) REVERT: A 246 CYS cc_start: 0.7214 (m) cc_final: 0.7004 (m) REVERT: A 261 MET cc_start: 0.7208 (mmm) cc_final: 0.6719 (mmp) REVERT: A 311 SER cc_start: 0.7635 (m) cc_final: 0.7431 (t) REVERT: A 400 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6849 (tt0) REVERT: A 402 LYS cc_start: 0.7391 (mmtp) cc_final: 0.6902 (mtmm) REVERT: A 456 SER cc_start: 0.7450 (m) cc_final: 0.6930 (p) REVERT: B 23 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.6470 (mt0) REVERT: B 236 ARG cc_start: 0.8262 (mmt180) cc_final: 0.8027 (mmm160) REVERT: B 261 MET cc_start: 0.7193 (mmm) cc_final: 0.6738 (mmp) REVERT: B 400 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6767 (tt0) REVERT: B 402 LYS cc_start: 0.7435 (mmtp) cc_final: 0.6912 (mtmm) REVERT: B 456 SER cc_start: 0.7390 (m) cc_final: 0.6948 (p) REVERT: C 11 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.7199 (t80) REVERT: C 58 GLN cc_start: 0.8557 (mm-40) cc_final: 0.7992 (mt0) REVERT: C 134 ARG cc_start: 0.5571 (ttp80) cc_final: 0.5347 (tmm-80) REVERT: C 261 MET cc_start: 0.7313 (mmm) cc_final: 0.6865 (mmm) REVERT: C 390 LYS cc_start: 0.6495 (OUTLIER) cc_final: 0.6220 (mmmt) REVERT: C 427 GLU cc_start: 0.6519 (tm-30) cc_final: 0.6069 (mt-10) REVERT: C 490 LYS cc_start: 0.7839 (mmtp) cc_final: 0.7500 (mmmt) REVERT: D 11 TYR cc_start: 0.8398 (OUTLIER) cc_final: 0.7197 (t80) REVERT: D 58 GLN cc_start: 0.8524 (mm-40) cc_final: 0.7951 (mt0) REVERT: D 134 ARG cc_start: 0.5571 (ttp80) cc_final: 0.5314 (tmm-80) REVERT: D 261 MET cc_start: 0.7311 (mmm) cc_final: 0.6866 (mmm) REVERT: D 390 LYS cc_start: 0.6466 (OUTLIER) cc_final: 0.6046 (mmmt) REVERT: D 427 GLU cc_start: 0.6527 (tm-30) cc_final: 0.6086 (mt-10) REVERT: D 490 LYS cc_start: 0.7876 (mmtp) cc_final: 0.7536 (mmmt) REVERT: E 58 GLN cc_start: 0.8441 (mm-40) cc_final: 0.7934 (mt0) REVERT: E 231 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.6976 (t70) REVERT: E 237 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8349 (ttm110) REVERT: E 249 HIS cc_start: 0.6743 (OUTLIER) cc_final: 0.6099 (t70) REVERT: E 261 MET cc_start: 0.7199 (mmm) cc_final: 0.6782 (mmm) REVERT: E 376 ILE cc_start: 0.6128 (OUTLIER) cc_final: 0.5723 (pp) REVERT: E 402 LYS cc_start: 0.7398 (mmtp) cc_final: 0.6883 (mtmm) REVERT: E 428 LYS cc_start: 0.6929 (mttt) cc_final: 0.6692 (mtpm) REVERT: F 120 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7497 (pt) REVERT: F 134 ARG cc_start: 0.5611 (tmm-80) cc_final: 0.5365 (tmm-80) REVERT: F 231 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7023 (t70) REVERT: F 237 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8317 (ttm170) REVERT: F 249 HIS cc_start: 0.6948 (OUTLIER) cc_final: 0.6356 (t70) REVERT: F 261 MET cc_start: 0.7238 (mmm) cc_final: 0.6544 (mmt) REVERT: F 400 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6941 (mm-30) REVERT: F 402 LYS cc_start: 0.7409 (mmtp) cc_final: 0.6753 (mtmt) outliers start: 158 outliers final: 78 residues processed: 489 average time/residue: 0.5016 time to fit residues: 289.9540 Evaluate side-chains 404 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 309 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 309 LYS Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 345 ASN Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 390 LYS Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 249 HIS Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 309 LYS Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 390 LYS Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 309 LYS Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 319 LEU Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 237 ARG Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 309 LYS Chi-restraints excluded: chain F residue 312 SER Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 461 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 39 optimal weight: 0.7980 chunk 212 optimal weight: 0.8980 chunk 262 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 ASN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN F 392 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.162798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.138090 restraints weight = 27741.453| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.77 r_work: 0.3481 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24840 Z= 0.157 Angle : 0.578 8.840 33624 Z= 0.311 Chirality : 0.043 0.146 3624 Planarity : 0.005 0.065 4308 Dihedral : 6.993 59.505 3331 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.23 % Favored : 96.36 % Rotamer: Outliers : 6.81 % Allowed : 25.74 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.40 (0.15), residues: 2940 helix: 1.06 (0.12), residues: 1758 sheet: -1.07 (0.37), residues: 204 loop : -0.80 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 143 TYR 0.028 0.002 TYR B 447 PHE 0.019 0.001 PHE C 140 TRP 0.009 0.001 TRP F 363 HIS 0.006 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00358 (24840) covalent geometry : angle 0.57767 (33624) hydrogen bonds : bond 0.04500 ( 1231) hydrogen bonds : angle 4.34688 ( 3639) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 321 time to evaluate : 0.863 Fit side-chains REVERT: A 23 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.6451 (mt0) REVERT: A 129 GLU cc_start: 0.5142 (OUTLIER) cc_final: 0.4794 (tp30) REVERT: A 134 ARG cc_start: 0.5393 (ttp80) cc_final: 0.5183 (ttp-110) REVERT: A 246 CYS cc_start: 0.7280 (m) cc_final: 0.7027 (m) REVERT: A 261 MET cc_start: 0.7273 (mmm) cc_final: 0.6773 (mmp) REVERT: A 386 GLU cc_start: 0.6443 (pm20) cc_final: 0.6096 (pt0) REVERT: A 400 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6919 (tt0) REVERT: A 402 LYS cc_start: 0.7385 (mmtp) cc_final: 0.6817 (mtmm) REVERT: A 456 SER cc_start: 0.7526 (m) cc_final: 0.6978 (p) REVERT: B 23 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.6460 (mt0) REVERT: B 236 ARG cc_start: 0.8326 (mmt180) cc_final: 0.8011 (mmm160) REVERT: B 261 MET cc_start: 0.7292 (mmm) cc_final: 0.6780 (mmp) REVERT: B 400 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6916 (tt0) REVERT: B 402 LYS cc_start: 0.7447 (mmtp) cc_final: 0.6811 (mtmt) REVERT: B 456 SER cc_start: 0.7446 (m) cc_final: 0.6991 (p) REVERT: C 11 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.7406 (t80) REVERT: C 23 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.6691 (mt0) REVERT: C 58 GLN cc_start: 0.8553 (mm-40) cc_final: 0.7975 (mt0) REVERT: C 261 MET cc_start: 0.7316 (OUTLIER) cc_final: 0.6846 (mmm) REVERT: C 400 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6813 (mm-30) REVERT: C 427 GLU cc_start: 0.6572 (tm-30) cc_final: 0.6104 (mt-10) REVERT: C 428 LYS cc_start: 0.7104 (OUTLIER) cc_final: 0.6389 (mtpp) REVERT: C 490 LYS cc_start: 0.7863 (mmtp) cc_final: 0.7548 (mmmt) REVERT: D 11 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.7385 (t80) REVERT: D 23 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.6633 (mt0) REVERT: D 58 GLN cc_start: 0.8546 (mm-40) cc_final: 0.7971 (mt0) REVERT: D 134 ARG cc_start: 0.5563 (ttp80) cc_final: 0.5287 (tmm-80) REVERT: D 261 MET cc_start: 0.7312 (OUTLIER) cc_final: 0.6800 (mmm) REVERT: D 400 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6745 (mm-30) REVERT: D 427 GLU cc_start: 0.6562 (tm-30) cc_final: 0.6133 (mt-10) REVERT: D 428 LYS cc_start: 0.7133 (OUTLIER) cc_final: 0.6418 (mtpp) REVERT: D 490 LYS cc_start: 0.7885 (mmtp) cc_final: 0.7543 (mmmt) REVERT: E 58 GLN cc_start: 0.8493 (mm-40) cc_final: 0.7966 (mt0) REVERT: E 120 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7592 (pt) REVERT: E 157 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.8049 (mt) REVERT: E 231 ASP cc_start: 0.7572 (m-30) cc_final: 0.7046 (t70) REVERT: E 237 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8435 (ttm110) REVERT: E 261 MET cc_start: 0.7215 (mmm) cc_final: 0.6589 (mmm) REVERT: E 402 LYS cc_start: 0.7373 (mmtp) cc_final: 0.6823 (mtmm) REVERT: E 482 LYS cc_start: 0.7894 (mtpm) cc_final: 0.7366 (mttt) REVERT: F 120 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7531 (pt) REVERT: F 129 GLU cc_start: 0.5363 (OUTLIER) cc_final: 0.5126 (tp30) REVERT: F 157 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.8038 (mt) REVERT: F 231 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.7071 (t70) REVERT: F 237 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8436 (ttm170) REVERT: F 249 HIS cc_start: 0.7157 (OUTLIER) cc_final: 0.6691 (t70) REVERT: F 261 MET cc_start: 0.7231 (mmm) cc_final: 0.6489 (mmt) REVERT: F 293 ASN cc_start: 0.8086 (OUTLIER) cc_final: 0.7734 (m-40) REVERT: F 400 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7015 (mm-30) REVERT: F 402 LYS cc_start: 0.7434 (mmtp) cc_final: 0.6831 (mtmm) REVERT: F 428 LYS cc_start: 0.6678 (mttt) cc_final: 0.6473 (mtpm) REVERT: F 482 LYS cc_start: 0.7899 (mtpm) cc_final: 0.7312 (mttt) outliers start: 184 outliers final: 87 residues processed: 471 average time/residue: 0.5271 time to fit residues: 293.6930 Evaluate side-chains 411 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 298 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 309 LYS Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 23 GLN Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 400 GLU Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 319 LEU Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 237 ARG Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 293 ASN Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 309 LYS Chi-restraints excluded: chain F residue 312 SER Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain F residue 461 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 211 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 257 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 201 optimal weight: 2.9990 chunk 134 optimal weight: 0.0770 chunk 220 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 ASN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 GLN E 201 ASN E 392 ASN ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN F 392 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.160503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.135426 restraints weight = 27653.337| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.78 r_work: 0.3466 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 24840 Z= 0.194 Angle : 0.600 7.458 33624 Z= 0.323 Chirality : 0.044 0.183 3624 Planarity : 0.005 0.069 4308 Dihedral : 7.055 59.851 3328 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.89 % Favored : 96.70 % Rotamer: Outliers : 6.70 % Allowed : 26.30 % Favored : 67.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.10 (0.15), residues: 2940 helix: 0.85 (0.12), residues: 1794 sheet: -1.10 (0.38), residues: 198 loop : -1.06 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 143 TYR 0.034 0.002 TYR B 447 PHE 0.036 0.002 PHE C 140 TRP 0.009 0.001 TRP A 363 HIS 0.008 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00453 (24840) covalent geometry : angle 0.60024 (33624) hydrogen bonds : bond 0.04801 ( 1231) hydrogen bonds : angle 4.39841 ( 3639) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 305 time to evaluate : 1.075 Fit side-chains REVERT: A 11 TYR cc_start: 0.8456 (OUTLIER) cc_final: 0.7933 (t80) REVERT: A 23 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.6558 (mt0) REVERT: A 129 GLU cc_start: 0.5156 (OUTLIER) cc_final: 0.4849 (tp30) REVERT: A 246 CYS cc_start: 0.7301 (m) cc_final: 0.7049 (m) REVERT: A 261 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.7089 (mmm) REVERT: A 386 GLU cc_start: 0.6469 (pm20) cc_final: 0.6108 (pt0) REVERT: A 400 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6969 (tt0) REVERT: A 402 LYS cc_start: 0.7508 (mmtp) cc_final: 0.6902 (mtmm) REVERT: A 456 SER cc_start: 0.7575 (m) cc_final: 0.7041 (p) REVERT: B 11 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.7908 (t80) REVERT: B 23 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.6538 (mt0) REVERT: B 129 GLU cc_start: 0.5174 (OUTLIER) cc_final: 0.4771 (tp30) REVERT: B 346 LEU cc_start: 0.7443 (mt) cc_final: 0.7033 (mp) REVERT: B 400 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6919 (tt0) REVERT: B 402 LYS cc_start: 0.7544 (mmtp) cc_final: 0.6914 (mtmm) REVERT: C 11 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.7356 (t80) REVERT: C 23 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.6694 (mt0) REVERT: C 58 GLN cc_start: 0.8564 (mm-40) cc_final: 0.7956 (mt0) REVERT: C 134 ARG cc_start: 0.5476 (ttp80) cc_final: 0.5205 (tmm-80) REVERT: C 143 ARG cc_start: 0.8066 (mpt-90) cc_final: 0.7863 (mmt90) REVERT: C 185 LYS cc_start: 0.6188 (OUTLIER) cc_final: 0.5883 (ttpp) REVERT: C 261 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6904 (mmm) REVERT: C 390 LYS cc_start: 0.6498 (OUTLIER) cc_final: 0.5410 (mmmt) REVERT: C 400 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6899 (mm-30) REVERT: C 427 GLU cc_start: 0.6735 (tm-30) cc_final: 0.6274 (mt-10) REVERT: C 428 LYS cc_start: 0.7053 (OUTLIER) cc_final: 0.6370 (mtpp) REVERT: D 11 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.7358 (t80) REVERT: D 23 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.6671 (mt0) REVERT: D 58 GLN cc_start: 0.8546 (mm-40) cc_final: 0.7950 (mt0) REVERT: D 185 LYS cc_start: 0.6193 (OUTLIER) cc_final: 0.5891 (ttpp) REVERT: D 261 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.6775 (mmm) REVERT: D 356 ASP cc_start: 0.7194 (m-30) cc_final: 0.6963 (m-30) REVERT: D 390 LYS cc_start: 0.6484 (OUTLIER) cc_final: 0.5398 (mmmt) REVERT: D 400 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6855 (mm-30) REVERT: D 427 GLU cc_start: 0.6750 (tm-30) cc_final: 0.6284 (mt-10) REVERT: D 428 LYS cc_start: 0.7076 (OUTLIER) cc_final: 0.6394 (mtpp) REVERT: E 23 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.6705 (mt0) REVERT: E 120 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7583 (pt) REVERT: E 157 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.8127 (mt) REVERT: E 231 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7022 (t70) REVERT: E 261 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.6882 (mmm) REVERT: E 402 LYS cc_start: 0.7469 (mmtp) cc_final: 0.6868 (mtmm) REVERT: F 11 TYR cc_start: 0.8505 (OUTLIER) cc_final: 0.7415 (t80) REVERT: F 23 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.6641 (mt0) REVERT: F 120 ILE cc_start: 0.7907 (OUTLIER) cc_final: 0.7573 (pt) REVERT: F 157 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8115 (mt) REVERT: F 231 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.7108 (t70) REVERT: F 261 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.6537 (mmt) REVERT: F 276 LYS cc_start: 0.6465 (pttm) cc_final: 0.5503 (pptt) REVERT: F 400 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7090 (mm-30) REVERT: F 402 LYS cc_start: 0.7409 (mmtp) cc_final: 0.6684 (mtmm) outliers start: 181 outliers final: 88 residues processed: 449 average time/residue: 0.5492 time to fit residues: 290.9244 Evaluate side-chains 409 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 286 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 TYR Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 11 TYR Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain C residue 390 LYS Chi-restraints excluded: chain C residue 400 GLU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 11 TYR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 23 GLN Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 185 LYS Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 390 LYS Chi-restraints excluded: chain D residue 400 GLU Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain E residue 23 GLN Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 185 LYS Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 319 LEU Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain F residue 11 TYR Chi-restraints excluded: chain F residue 23 GLN Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 261 MET Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 309 LYS Chi-restraints excluded: chain F residue 312 SER Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain F residue 461 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 140 optimal weight: 2.9990 chunk 231 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 220 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 236 optimal weight: 0.8980 chunk 293 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 ASN ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 ASN ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN E 392 ASN E 417 ASN ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 392 ASN F 417 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.163234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.138304 restraints weight = 27663.729| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.79 r_work: 0.3496 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24840 Z= 0.136 Angle : 0.552 8.326 33624 Z= 0.299 Chirality : 0.042 0.143 3624 Planarity : 0.005 0.062 4308 Dihedral : 6.822 58.175 3326 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.16 % Favored : 96.43 % Rotamer: Outliers : 5.78 % Allowed : 27.56 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.37 (0.15), residues: 2940 helix: 1.06 (0.12), residues: 1740 sheet: -1.24 (0.37), residues: 198 loop : -0.77 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 143 TYR 0.034 0.002 TYR B 447 PHE 0.030 0.001 PHE C 140 TRP 0.010 0.001 TRP E 471 HIS 0.004 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00309 (24840) covalent geometry : angle 0.55183 (33624) hydrogen bonds : bond 0.04310 ( 1231) hydrogen bonds : angle 4.37424 ( 3639) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 286 time to evaluate : 0.894 Fit side-chains REVERT: A 23 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.6416 (mt0) REVERT: A 129 GLU cc_start: 0.5185 (OUTLIER) cc_final: 0.4777 (tp30) REVERT: A 246 CYS cc_start: 0.7253 (m) cc_final: 0.7040 (m) REVERT: A 386 GLU cc_start: 0.6464 (pm20) cc_final: 0.6064 (pt0) REVERT: A 400 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6963 (tt0) REVERT: A 402 LYS cc_start: 0.7365 (mmtp) cc_final: 0.6794 (mtmm) REVERT: A 456 SER cc_start: 0.7526 (m) cc_final: 0.7010 (p) REVERT: B 23 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.6401 (mt0) REVERT: B 129 GLU cc_start: 0.5192 (OUTLIER) cc_final: 0.4790 (tp30) REVERT: B 261 MET cc_start: 0.7258 (mmm) cc_final: 0.6745 (mmp) REVERT: B 400 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6927 (tt0) REVERT: B 402 LYS cc_start: 0.7462 (mmtp) cc_final: 0.6855 (mtmm) REVERT: B 456 SER cc_start: 0.7495 (m) cc_final: 0.7040 (p) REVERT: C 23 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.6626 (mt0) REVERT: C 58 GLN cc_start: 0.8568 (mm-40) cc_final: 0.7970 (mt0) REVERT: C 106 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7588 (pt0) REVERT: C 231 ASP cc_start: 0.7159 (OUTLIER) cc_final: 0.6890 (t70) REVERT: C 261 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.6779 (mmm) REVERT: C 375 LEU cc_start: 0.5595 (OUTLIER) cc_final: 0.5130 (mt) REVERT: C 402 LYS cc_start: 0.7355 (mmtp) cc_final: 0.6550 (mtmm) REVERT: C 427 GLU cc_start: 0.6662 (tm-30) cc_final: 0.6185 (mt-10) REVERT: D 23 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.6591 (mt0) REVERT: D 58 GLN cc_start: 0.8545 (mm-40) cc_final: 0.7955 (mt0) REVERT: D 231 ASP cc_start: 0.7189 (OUTLIER) cc_final: 0.6921 (t70) REVERT: D 261 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6760 (mmm) REVERT: D 375 LEU cc_start: 0.5650 (OUTLIER) cc_final: 0.5160 (mt) REVERT: D 427 GLU cc_start: 0.6732 (tm-30) cc_final: 0.6277 (mt-10) REVERT: E 23 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7804 (mt0) REVERT: E 120 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7532 (pt) REVERT: E 231 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7103 (t70) REVERT: E 261 MET cc_start: 0.7204 (mmm) cc_final: 0.6793 (mmm) REVERT: E 402 LYS cc_start: 0.7414 (mmtp) cc_final: 0.6821 (mtmm) REVERT: F 23 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7793 (mt0) REVERT: F 120 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7522 (pt) REVERT: F 231 ASP cc_start: 0.7555 (OUTLIER) cc_final: 0.7082 (t70) REVERT: F 237 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8377 (ttm170) REVERT: F 261 MET cc_start: 0.7249 (mmm) cc_final: 0.6554 (mmt) REVERT: F 276 LYS cc_start: 0.6552 (pttm) cc_final: 0.5508 (pptt) REVERT: F 400 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7063 (mm-30) REVERT: F 402 LYS cc_start: 0.7387 (mmtp) cc_final: 0.6659 (mtmm) REVERT: F 495 MET cc_start: 0.8134 (mtp) cc_final: 0.7846 (mtm) outliers start: 156 outliers final: 78 residues processed: 409 average time/residue: 0.4666 time to fit residues: 227.7777 Evaluate side-chains 376 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 275 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 23 GLN Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 140 PHE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain E residue 23 GLN Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain F residue 23 GLN Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 237 ARG Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 309 LYS Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 461 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 75 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 270 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 171 optimal weight: 0.9990 chunk 175 optimal weight: 0.9980 chunk 100 optimal weight: 0.0670 chunk 37 optimal weight: 3.9990 chunk 173 optimal weight: 0.9980 chunk 223 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 392 ASN ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN F 353 GLN F 392 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.164381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.139666 restraints weight = 27548.197| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.77 r_work: 0.3507 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24840 Z= 0.129 Angle : 0.545 8.645 33624 Z= 0.295 Chirality : 0.041 0.146 3624 Planarity : 0.005 0.061 4308 Dihedral : 6.554 55.654 3322 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.23 % Favored : 96.36 % Rotamer: Outliers : 5.48 % Allowed : 27.78 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.43 (0.15), residues: 2940 helix: 1.13 (0.12), residues: 1734 sheet: -1.35 (0.36), residues: 198 loop : -0.77 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 143 TYR 0.032 0.001 TYR A 447 PHE 0.029 0.001 PHE C 140 TRP 0.010 0.001 TRP C 363 HIS 0.003 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00289 (24840) covalent geometry : angle 0.54495 (33624) hydrogen bonds : bond 0.04160 ( 1231) hydrogen bonds : angle 4.31104 ( 3639) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 295 time to evaluate : 0.784 Fit side-chains REVERT: A 129 GLU cc_start: 0.5234 (OUTLIER) cc_final: 0.4826 (tp30) REVERT: A 192 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.8015 (t0) REVERT: A 246 CYS cc_start: 0.7233 (m) cc_final: 0.7032 (m) REVERT: A 261 MET cc_start: 0.7255 (mmm) cc_final: 0.6751 (mmp) REVERT: A 386 GLU cc_start: 0.6502 (pm20) cc_final: 0.6086 (pt0) REVERT: A 400 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6945 (tt0) REVERT: A 402 LYS cc_start: 0.7362 (mmtp) cc_final: 0.6803 (mtmm) REVERT: A 456 SER cc_start: 0.7544 (m) cc_final: 0.7027 (p) REVERT: B 129 GLU cc_start: 0.5182 (OUTLIER) cc_final: 0.4776 (tp30) REVERT: B 192 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.8021 (t0) REVERT: B 261 MET cc_start: 0.7277 (mmm) cc_final: 0.6744 (mmp) REVERT: B 400 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6909 (tt0) REVERT: B 402 LYS cc_start: 0.7407 (mmtp) cc_final: 0.6829 (mtmm) REVERT: B 456 SER cc_start: 0.7482 (m) cc_final: 0.7031 (p) REVERT: C 58 GLN cc_start: 0.8568 (mm-40) cc_final: 0.7979 (mt0) REVERT: C 231 ASP cc_start: 0.7164 (OUTLIER) cc_final: 0.6910 (t70) REVERT: C 261 MET cc_start: 0.7278 (OUTLIER) cc_final: 0.6799 (mmm) REVERT: C 375 LEU cc_start: 0.5509 (OUTLIER) cc_final: 0.5284 (mt) REVERT: C 402 LYS cc_start: 0.7376 (mmtp) cc_final: 0.6538 (mtmm) REVERT: C 427 GLU cc_start: 0.6719 (tm-30) cc_final: 0.6234 (mt-10) REVERT: C 428 LYS cc_start: 0.6980 (OUTLIER) cc_final: 0.6301 (mtpp) REVERT: D 58 GLN cc_start: 0.8540 (mm-40) cc_final: 0.7963 (mt0) REVERT: D 143 ARG cc_start: 0.7933 (mmt90) cc_final: 0.7631 (mpt-90) REVERT: D 231 ASP cc_start: 0.7160 (OUTLIER) cc_final: 0.6908 (t70) REVERT: D 261 MET cc_start: 0.7282 (OUTLIER) cc_final: 0.6793 (mmm) REVERT: D 375 LEU cc_start: 0.5529 (OUTLIER) cc_final: 0.5308 (mt) REVERT: D 402 LYS cc_start: 0.7306 (mmtp) cc_final: 0.6521 (mtmm) REVERT: D 427 GLU cc_start: 0.6775 (tm-30) cc_final: 0.6333 (mt-10) REVERT: D 428 LYS cc_start: 0.7003 (OUTLIER) cc_final: 0.6323 (mtpp) REVERT: E 23 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7797 (mt0) REVERT: E 157 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7844 (tt) REVERT: E 231 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.7074 (t70) REVERT: E 237 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8425 (ttm110) REVERT: E 249 HIS cc_start: 0.7149 (OUTLIER) cc_final: 0.6656 (t70) REVERT: E 261 MET cc_start: 0.7240 (OUTLIER) cc_final: 0.6971 (mmm) REVERT: E 293 ASN cc_start: 0.8090 (OUTLIER) cc_final: 0.7808 (m110) REVERT: E 402 LYS cc_start: 0.7422 (mmtp) cc_final: 0.6849 (mtmm) REVERT: E 495 MET cc_start: 0.8258 (mtp) cc_final: 0.7774 (mtm) REVERT: F 23 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7757 (mt0) REVERT: F 120 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7452 (pt) REVERT: F 157 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7838 (tt) REVERT: F 231 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7049 (t70) REVERT: F 237 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8363 (ttm170) REVERT: F 249 HIS cc_start: 0.7266 (OUTLIER) cc_final: 0.6863 (t70) REVERT: F 261 MET cc_start: 0.7229 (OUTLIER) cc_final: 0.6522 (mmt) REVERT: F 276 LYS cc_start: 0.6573 (pttm) cc_final: 0.5553 (pptt) REVERT: F 400 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7104 (mm-30) REVERT: F 402 LYS cc_start: 0.7343 (mmtp) cc_final: 0.6609 (mtmm) REVERT: F 495 MET cc_start: 0.8219 (mtp) cc_final: 0.7834 (mtm) outliers start: 148 outliers final: 86 residues processed: 411 average time/residue: 0.4600 time to fit residues: 225.6472 Evaluate side-chains 389 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 274 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 350 THR Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain C residue 447 TYR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 140 PHE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 309 LYS Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 447 TYR Chi-restraints excluded: chain E residue 23 GLN Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 140 PHE Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 185 LYS Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain E residue 293 ASN Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 309 LYS Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 447 TYR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain F residue 23 GLN Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 237 ARG Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 261 MET Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 309 LYS Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain F residue 447 TYR Chi-restraints excluded: chain F residue 461 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 78 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 284 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 274 optimal weight: 8.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 ASN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 392 ASN ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN F 197 GLN F 201 ASN F 392 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.162417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.137448 restraints weight = 27725.717| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.77 r_work: 0.3476 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24840 Z= 0.165 Angle : 0.586 9.685 33624 Z= 0.316 Chirality : 0.043 0.156 3624 Planarity : 0.005 0.067 4308 Dihedral : 6.497 56.818 3318 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.40 % Favored : 96.19 % Rotamer: Outliers : 4.56 % Allowed : 29.07 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.29 (0.15), residues: 2940 helix: 0.98 (0.12), residues: 1752 sheet: -1.31 (0.36), residues: 198 loop : -0.80 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 143 TYR 0.034 0.002 TYR B 447 PHE 0.030 0.002 PHE C 140 TRP 0.010 0.001 TRP D 363 HIS 0.005 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00383 (24840) covalent geometry : angle 0.58629 (33624) hydrogen bonds : bond 0.04479 ( 1231) hydrogen bonds : angle 4.36512 ( 3639) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 288 time to evaluate : 0.977 Fit side-chains REVERT: A 129 GLU cc_start: 0.5234 (OUTLIER) cc_final: 0.4880 (tp30) REVERT: A 246 CYS cc_start: 0.7234 (m) cc_final: 0.7024 (m) REVERT: A 261 MET cc_start: 0.7268 (mmm) cc_final: 0.6729 (mmp) REVERT: A 346 LEU cc_start: 0.7371 (mt) cc_final: 0.6966 (mp) REVERT: A 386 GLU cc_start: 0.6489 (pm20) cc_final: 0.6079 (pt0) REVERT: A 400 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6997 (tt0) REVERT: A 402 LYS cc_start: 0.7409 (mmtp) cc_final: 0.6839 (mtmm) REVERT: A 456 SER cc_start: 0.7584 (m) cc_final: 0.7065 (p) REVERT: B 129 GLU cc_start: 0.5203 (OUTLIER) cc_final: 0.4767 (tp30) REVERT: B 192 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.8073 (t0) REVERT: B 261 MET cc_start: 0.7335 (mmm) cc_final: 0.6799 (mmp) REVERT: B 400 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6961 (tt0) REVERT: B 402 LYS cc_start: 0.7411 (mmtp) cc_final: 0.6838 (mtmm) REVERT: B 456 SER cc_start: 0.7569 (m) cc_final: 0.7122 (p) REVERT: C 58 GLN cc_start: 0.8554 (mm-40) cc_final: 0.7952 (mt0) REVERT: C 185 LYS cc_start: 0.6050 (OUTLIER) cc_final: 0.5695 (ttpp) REVERT: C 231 ASP cc_start: 0.7196 (OUTLIER) cc_final: 0.6921 (t70) REVERT: C 261 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.6787 (mmm) REVERT: C 375 LEU cc_start: 0.5445 (OUTLIER) cc_final: 0.4982 (mt) REVERT: C 402 LYS cc_start: 0.7338 (mmtp) cc_final: 0.6496 (mtmm) REVERT: C 427 GLU cc_start: 0.6800 (tm-30) cc_final: 0.6358 (mt-10) REVERT: D 58 GLN cc_start: 0.8538 (mm-40) cc_final: 0.7941 (mt0) REVERT: D 185 LYS cc_start: 0.6073 (OUTLIER) cc_final: 0.5723 (ttpp) REVERT: D 231 ASP cc_start: 0.7162 (OUTLIER) cc_final: 0.6893 (t70) REVERT: D 261 MET cc_start: 0.7293 (OUTLIER) cc_final: 0.6807 (mmm) REVERT: D 375 LEU cc_start: 0.5509 (OUTLIER) cc_final: 0.5053 (mt) REVERT: D 402 LYS cc_start: 0.7344 (mmtp) cc_final: 0.6505 (mtmm) REVERT: D 427 GLU cc_start: 0.6805 (tm-30) cc_final: 0.6346 (mt-10) REVERT: E 23 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7838 (mt0) REVERT: E 157 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7940 (mm) REVERT: E 231 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.7118 (t70) REVERT: E 249 HIS cc_start: 0.7285 (OUTLIER) cc_final: 0.6938 (t70) REVERT: E 261 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6960 (mmm) REVERT: E 402 LYS cc_start: 0.7449 (mmtp) cc_final: 0.6851 (mtmm) REVERT: E 495 MET cc_start: 0.8329 (mtp) cc_final: 0.7918 (mtm) REVERT: F 23 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7799 (mt0) REVERT: F 120 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7496 (pt) REVERT: F 157 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7939 (mm) REVERT: F 231 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7079 (t70) REVERT: F 249 HIS cc_start: 0.7293 (OUTLIER) cc_final: 0.6996 (t70) REVERT: F 261 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.6534 (mmt) REVERT: F 276 LYS cc_start: 0.6587 (pttm) cc_final: 0.5564 (pptt) REVERT: F 400 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7134 (mm-30) REVERT: F 402 LYS cc_start: 0.7437 (mmtp) cc_final: 0.6662 (mtmm) REVERT: F 495 MET cc_start: 0.8216 (mtp) cc_final: 0.7921 (mtm) outliers start: 123 outliers final: 71 residues processed: 382 average time/residue: 0.4963 time to fit residues: 225.8048 Evaluate side-chains 370 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 274 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 140 PHE Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 185 LYS Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 309 LYS Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain E residue 23 GLN Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 140 PHE Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 185 LYS Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain F residue 23 GLN Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 140 PHE Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 261 MET Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 309 LYS Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain F residue 461 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 39 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 16 optimal weight: 0.0040 chunk 160 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 112 optimal weight: 0.3980 chunk 194 optimal weight: 0.7980 chunk 277 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 147 optimal weight: 7.9990 overall best weight: 1.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 ASN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN E 392 ASN ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN F 392 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.163853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.138980 restraints weight = 27742.954| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.78 r_work: 0.3500 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24840 Z= 0.144 Angle : 0.572 8.032 33624 Z= 0.308 Chirality : 0.042 0.164 3624 Planarity : 0.005 0.065 4308 Dihedral : 6.279 58.206 3308 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.20 % Favored : 96.46 % Rotamer: Outliers : 4.15 % Allowed : 29.44 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.34 (0.15), residues: 2940 helix: 1.01 (0.12), residues: 1746 sheet: -1.30 (0.36), residues: 198 loop : -0.75 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 143 TYR 0.035 0.002 TYR B 447 PHE 0.029 0.001 PHE C 140 TRP 0.011 0.001 TRP D 363 HIS 0.004 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00330 (24840) covalent geometry : angle 0.57202 (33624) hydrogen bonds : bond 0.04259 ( 1231) hydrogen bonds : angle 4.35906 ( 3639) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 281 time to evaluate : 0.863 Fit side-chains REVERT: A 129 GLU cc_start: 0.5240 (OUTLIER) cc_final: 0.4891 (tp30) REVERT: A 246 CYS cc_start: 0.7182 (m) cc_final: 0.6978 (m) REVERT: A 261 MET cc_start: 0.7290 (mmm) cc_final: 0.6771 (mmp) REVERT: A 386 GLU cc_start: 0.6494 (pm20) cc_final: 0.6118 (pt0) REVERT: A 400 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7040 (mm-30) REVERT: A 402 LYS cc_start: 0.7406 (mmtp) cc_final: 0.6839 (mtmm) REVERT: A 456 SER cc_start: 0.7605 (m) cc_final: 0.7097 (p) REVERT: B 129 GLU cc_start: 0.5243 (OUTLIER) cc_final: 0.4843 (tp30) REVERT: B 261 MET cc_start: 0.7347 (mmm) cc_final: 0.6809 (mmp) REVERT: B 400 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6972 (tt0) REVERT: B 402 LYS cc_start: 0.7448 (mmtp) cc_final: 0.6885 (mtmm) REVERT: B 456 SER cc_start: 0.7526 (m) cc_final: 0.7078 (p) REVERT: C 58 GLN cc_start: 0.8581 (mm-40) cc_final: 0.8007 (mt0) REVERT: C 143 ARG cc_start: 0.8061 (mmt90) cc_final: 0.7671 (mpt-90) REVERT: C 185 LYS cc_start: 0.6083 (OUTLIER) cc_final: 0.5762 (ttpp) REVERT: C 231 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.6961 (t70) REVERT: C 261 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.6833 (mmm) REVERT: C 375 LEU cc_start: 0.5537 (OUTLIER) cc_final: 0.5326 (mt) REVERT: C 402 LYS cc_start: 0.7366 (mmtp) cc_final: 0.6511 (mtmm) REVERT: C 427 GLU cc_start: 0.6850 (tm-30) cc_final: 0.6395 (mt-10) REVERT: C 428 LYS cc_start: 0.6822 (OUTLIER) cc_final: 0.6287 (mtpp) REVERT: D 58 GLN cc_start: 0.8559 (mm-40) cc_final: 0.7993 (mt0) REVERT: D 185 LYS cc_start: 0.6089 (OUTLIER) cc_final: 0.5764 (ttpp) REVERT: D 231 ASP cc_start: 0.7205 (OUTLIER) cc_final: 0.6959 (t70) REVERT: D 261 MET cc_start: 0.7338 (OUTLIER) cc_final: 0.6856 (mmm) REVERT: D 375 LEU cc_start: 0.5499 (OUTLIER) cc_final: 0.5280 (mt) REVERT: D 402 LYS cc_start: 0.7384 (mmtp) cc_final: 0.6561 (mtmm) REVERT: D 427 GLU cc_start: 0.6837 (tm-30) cc_final: 0.6381 (mt-10) REVERT: D 428 LYS cc_start: 0.6826 (OUTLIER) cc_final: 0.6293 (mtpp) REVERT: E 23 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7821 (mt0) REVERT: E 106 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7328 (pp20) REVERT: E 157 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7931 (mm) REVERT: E 231 ASP cc_start: 0.7588 (OUTLIER) cc_final: 0.7140 (t70) REVERT: E 249 HIS cc_start: 0.7249 (OUTLIER) cc_final: 0.6852 (t70) REVERT: E 261 MET cc_start: 0.7316 (OUTLIER) cc_final: 0.7045 (mmm) REVERT: E 293 ASN cc_start: 0.8194 (OUTLIER) cc_final: 0.7896 (m110) REVERT: E 402 LYS cc_start: 0.7436 (mmtp) cc_final: 0.6852 (mtmm) REVERT: E 495 MET cc_start: 0.8356 (mtp) cc_final: 0.7910 (mtm) REVERT: F 23 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7748 (mt0) REVERT: F 120 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7476 (pt) REVERT: F 157 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7945 (mm) REVERT: F 231 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7100 (t70) REVERT: F 249 HIS cc_start: 0.7208 (OUTLIER) cc_final: 0.6918 (t70) REVERT: F 261 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.6566 (mmt) REVERT: F 276 LYS cc_start: 0.6571 (pttm) cc_final: 0.5547 (pptt) REVERT: F 400 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7186 (mm-30) REVERT: F 402 LYS cc_start: 0.7419 (mmtp) cc_final: 0.6668 (mtmm) REVERT: F 495 MET cc_start: 0.8212 (mtp) cc_final: 0.7923 (mtm) outliers start: 112 outliers final: 73 residues processed: 366 average time/residue: 0.5140 time to fit residues: 224.6773 Evaluate side-chains 374 residues out of total 2700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 273 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 400 GLU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 309 LYS Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 261 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 309 LYS Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain C residue 456 SER Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 140 PHE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 185 LYS Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain E residue 23 GLN Chi-restraints excluded: chain E residue 28 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 140 PHE Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 185 LYS Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain E residue 293 ASN Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain F residue 23 GLN Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 185 LYS Chi-restraints excluded: chain F residue 231 ASP Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 261 MET Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 309 LYS Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 457 ASP Chi-restraints excluded: chain F residue 461 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 94 optimal weight: 0.3980 chunk 113 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 208 optimal weight: 0.5980 chunk 173 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 254 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 245 optimal weight: 7.9990 chunk 210 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 ASN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 392 ASN ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN F 392 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.164089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.139192 restraints weight = 27591.423| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.78 r_work: 0.3501 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24840 Z= 0.142 Angle : 0.565 9.261 33624 Z= 0.304 Chirality : 0.042 0.151 3624 Planarity : 0.005 0.065 4308 Dihedral : 6.214 59.807 3308 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.61 % Favored : 96.05 % Rotamer: Outliers : 4.37 % Allowed : 29.37 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.30 (0.15), residues: 2940 helix: 0.98 (0.12), residues: 1758 sheet: -1.26 (0.36), residues: 198 loop : -0.79 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 143 TYR 0.035 0.002 TYR B 447 PHE 0.029 0.001 PHE C 140 TRP 0.012 0.001 TRP D 363 HIS 0.004 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00324 (24840) covalent geometry : angle 0.56480 (33624) hydrogen bonds : bond 0.04210 ( 1231) hydrogen bonds : angle 4.33256 ( 3639) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7999.59 seconds wall clock time: 137 minutes 32.56 seconds (8252.56 seconds total)