Starting phenix.real_space_refine on Sun Aug 24 16:56:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8spv_40687/08_2025/8spv_40687.cif Found real_map, /net/cci-nas-00/data/ceres_data/8spv_40687/08_2025/8spv_40687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8spv_40687/08_2025/8spv_40687.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8spv_40687/08_2025/8spv_40687.map" model { file = "/net/cci-nas-00/data/ceres_data/8spv_40687/08_2025/8spv_40687.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8spv_40687/08_2025/8spv_40687.cif" } resolution = 3.06 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= 0.001 sd= 0.033 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 69 5.16 5 C 13782 2.51 5 N 3795 2.21 5 O 4158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21804 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3644 Classifications: {'peptide': 475} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 452} Chain: "D" Number of atoms: 3624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3624 Classifications: {'peptide': 470} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Restraints were copied for chains: B, C, E, F Time building chain proxies: 4.02, per 1000 atoms: 0.18 Number of scatterers: 21804 At special positions: 0 Unit cell: (131.88, 125.16, 108.36, 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 69 16.00 O 4158 8.00 N 3795 7.00 C 13782 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: 1.53 Conformation dependent library (CDL) restraints added in 769.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5148 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 24 sheets defined 45.0% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 216 through 219 removed outlier: 4.279A pdb=" N ASP A 219 " --> pdb=" O GLY A 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 219' Processing helix chain 'A' and resid 231 through 251 removed outlier: 3.746A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.763A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 Processing helix chain 'A' and resid 288 through 299 removed outlier: 4.512A pdb=" N TYR A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 336 Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 372 through 397 removed outlier: 4.506A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 420 Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'A' and resid 451 through 467 removed outlier: 4.281A pdb=" N ARG A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 479 Processing helix chain 'A' and resid 483 through 498 Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 216 through 219 removed outlier: 4.280A pdb=" N ASP B 219 " --> pdb=" O GLY B 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 216 through 219' Processing helix chain 'B' and resid 231 through 251 removed outlier: 3.746A pdb=" N LEU B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.762A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 277 Processing helix chain 'B' and resid 288 through 299 removed outlier: 4.512A pdb=" N TYR B 292 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 345 through 352 Processing helix chain 'B' and resid 372 through 397 removed outlier: 4.506A pdb=" N THR B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 420 Processing helix chain 'B' and resid 429 through 442 Processing helix chain 'B' and resid 451 through 467 removed outlier: 4.281A pdb=" N ARG B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 479 Processing helix chain 'B' and resid 483 through 498 Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 216 through 219 removed outlier: 4.280A pdb=" N ASP C 219 " --> pdb=" O GLY C 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 216 through 219' Processing helix chain 'C' and resid 231 through 251 removed outlier: 3.746A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Proline residue: C 239 - end of helix removed outlier: 3.762A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 277 Processing helix chain 'C' and resid 288 through 299 removed outlier: 4.511A pdb=" N TYR C 292 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 336 Processing helix chain 'C' and resid 345 through 352 Processing helix chain 'C' and resid 372 through 397 removed outlier: 4.507A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN C 397 " --> pdb=" O GLU C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 420 Processing helix chain 'C' and resid 429 through 442 Processing helix chain 'C' and resid 451 through 467 removed outlier: 4.282A pdb=" N ARG C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 479 Processing helix chain 'C' and resid 483 through 498 Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.527A pdb=" N THR D 91 " --> pdb=" O GLY D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'D' and resid 163 through 178 Processing helix chain 'D' and resid 191 through 204 Processing helix chain 'D' and resid 205 through 206 No H-bonds generated for 'chain 'D' and resid 205 through 206' Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 221 through 243 removed outlier: 5.311A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 269 removed outlier: 3.759A pdb=" N THR D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 277 Processing helix chain 'D' and resid 280 through 290 Processing helix chain 'D' and resid 315 through 325 removed outlier: 3.795A pdb=" N HIS D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D 325 " --> pdb=" O THR D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 339 removed outlier: 3.688A pdb=" N ALA D 336 " --> pdb=" O GLU D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 360 through 387 removed outlier: 3.523A pdb=" N THR D 373 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 410 removed outlier: 3.702A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 419 removed outlier: 4.002A pdb=" N GLN D 419 " --> pdb=" O VAL D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 443 Processing helix chain 'D' and resid 451 through 455 removed outlier: 4.155A pdb=" N LEU D 455 " --> pdb=" O ALA D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 470 removed outlier: 3.907A pdb=" N VAL D 462 " --> pdb=" O ARG D 458 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 removed outlier: 3.527A pdb=" N THR E 91 " --> pdb=" O GLY E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 163 through 178 Processing helix chain 'E' and resid 191 through 204 Processing helix chain 'E' and resid 205 through 206 No H-bonds generated for 'chain 'E' and resid 205 through 206' Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 221 through 243 removed outlier: 5.312A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 269 removed outlier: 3.760A pdb=" N THR E 258 " --> pdb=" O ILE E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 277 Processing helix chain 'E' and resid 280 through 290 Processing helix chain 'E' and resid 315 through 325 removed outlier: 3.796A pdb=" N HIS E 324 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU E 325 " --> pdb=" O THR E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 339 removed outlier: 3.689A pdb=" N ALA E 336 " --> pdb=" O GLU E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 360 through 387 removed outlier: 3.523A pdb=" N THR E 373 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 410 removed outlier: 3.703A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 419 removed outlier: 4.002A pdb=" N GLN E 419 " --> pdb=" O VAL E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 443 Processing helix chain 'E' and resid 451 through 455 removed outlier: 4.156A pdb=" N LEU E 455 " --> pdb=" O ALA E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 470 removed outlier: 3.907A pdb=" N VAL E 462 " --> pdb=" O ARG E 458 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 removed outlier: 3.527A pdb=" N THR F 91 " --> pdb=" O GLY F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 163 through 178 Processing helix chain 'F' and resid 191 through 204 Processing helix chain 'F' and resid 205 through 206 No H-bonds generated for 'chain 'F' and resid 205 through 206' Processing helix chain 'F' and resid 207 through 209 No H-bonds generated for 'chain 'F' and resid 207 through 209' Processing helix chain 'F' and resid 221 through 243 removed outlier: 5.312A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 269 removed outlier: 3.759A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 277 Processing helix chain 'F' and resid 280 through 290 Processing helix chain 'F' and resid 315 through 325 removed outlier: 3.796A pdb=" N HIS F 324 " --> pdb=" O THR F 320 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU F 325 " --> pdb=" O THR F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 339 removed outlier: 3.688A pdb=" N ALA F 336 " --> pdb=" O GLU F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 360 Processing helix chain 'F' and resid 360 through 387 removed outlier: 3.524A pdb=" N THR F 373 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 410 removed outlier: 3.703A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 419 removed outlier: 4.002A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 443 Processing helix chain 'F' and resid 451 through 455 removed outlier: 4.156A pdb=" N LEU F 455 " --> pdb=" O ALA F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 470 removed outlier: 3.907A pdb=" N VAL F 462 " --> pdb=" O ARG F 458 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 35 removed outlier: 6.522A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN A 65 " --> pdb=" O GLY A 72 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 3.546A pdb=" N GLU A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.537A pdb=" N VAL A 256 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU A 316 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL A 258 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N PHE A 318 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR A 260 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N GLU A 320 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU A 166 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU A 344 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE A 168 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 146 removed outlier: 4.764A pdb=" N ILE A 159 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 28 through 35 removed outlier: 6.522A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN B 65 " --> pdb=" O GLY B 72 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.545A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.537A pdb=" N VAL B 256 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU B 316 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL B 258 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N PHE B 318 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR B 260 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N GLU B 320 " --> pdb=" O TYR B 260 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 145 through 146 removed outlier: 4.765A pdb=" N ILE B 159 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 28 through 35 removed outlier: 6.522A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN C 65 " --> pdb=" O GLY C 72 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU C 52 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.545A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.537A pdb=" N VAL C 256 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU C 316 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL C 258 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N PHE C 318 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR C 260 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N GLU C 320 " --> pdb=" O TYR C 260 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU C 166 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU C 344 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE C 168 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 145 through 146 removed outlier: 4.764A pdb=" N ILE C 159 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 3 through 10 removed outlier: 5.728A pdb=" N VAL D 6 " --> pdb=" O LYS D 17 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LYS D 17 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN D 8 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLN D 33 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLU D 75 " --> pdb=" O GLN D 33 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB6, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.511A pdb=" N PHE D 96 " --> pdb=" O PHE D 215 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL D 184 " --> pdb=" O PHE D 250 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE D 154 " --> pdb=" O GLN D 304 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 134 through 135 removed outlier: 4.451A pdb=" N TYR D 148 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 3 through 10 removed outlier: 5.728A pdb=" N VAL E 6 " --> pdb=" O LYS E 17 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LYS E 17 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN E 8 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AC1, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.511A pdb=" N PHE E 96 " --> pdb=" O PHE E 215 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL E 184 " --> pdb=" O PHE E 250 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE E 154 " --> pdb=" O GLN E 304 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.450A pdb=" N TYR E 148 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 3 through 10 removed outlier: 5.728A pdb=" N VAL F 6 " --> pdb=" O LYS F 17 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LYS F 17 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN F 8 " --> pdb=" O ASP F 15 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AC5, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.512A pdb=" N PHE F 96 " --> pdb=" O PHE F 215 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL F 184 " --> pdb=" O PHE F 250 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE F 154 " --> pdb=" O GLN F 304 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 134 through 135 removed outlier: 4.451A pdb=" N TYR F 148 " --> pdb=" O LEU F 135 " (cutoff:3.500A) 1026 hydrogen bonds defined for protein. 2952 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: 3.75 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7443 1.34 - 1.46: 3000 1.46 - 1.57: 11589 1.57 - 1.69: 0 1.69 - 1.81: 138 Bond restraints: 22170 Sorted by residual: bond pdb=" N GLU C 284 " pdb=" CA GLU C 284 " ideal model delta sigma weight residual 1.457 1.476 -0.018 1.29e-02 6.01e+03 1.97e+00 bond pdb=" N GLU A 284 " pdb=" CA GLU A 284 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.92e+00 bond pdb=" N GLU B 284 " pdb=" CA GLU B 284 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.75e+00 bond pdb=" CA ILE A 94 " pdb=" CB ILE A 94 " ideal model delta sigma weight residual 1.538 1.549 -0.011 1.10e-02 8.26e+03 1.06e+00 bond pdb=" CA ILE B 94 " pdb=" CB ILE B 94 " ideal model delta sigma weight residual 1.538 1.549 -0.011 1.10e-02 8.26e+03 1.05e+00 ... (remaining 22165 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 29671 1.95 - 3.91: 329 3.91 - 5.86: 27 5.86 - 7.81: 0 7.81 - 9.76: 3 Bond angle restraints: 30030 Sorted by residual: angle pdb=" C GLU A 284 " pdb=" N ALA A 285 " pdb=" CA ALA A 285 " ideal model delta sigma weight residual 121.54 131.30 -9.76 1.91e+00 2.74e-01 2.61e+01 angle pdb=" C GLU C 284 " pdb=" N ALA C 285 " pdb=" CA ALA C 285 " ideal model delta sigma weight residual 121.54 131.28 -9.74 1.91e+00 2.74e-01 2.60e+01 angle pdb=" C GLU B 284 " pdb=" N ALA B 285 " pdb=" CA ALA B 285 " ideal model delta sigma weight residual 121.54 131.26 -9.72 1.91e+00 2.74e-01 2.59e+01 angle pdb=" C VAL A 136 " pdb=" N MET A 137 " pdb=" CA MET A 137 " ideal model delta sigma weight residual 121.54 127.04 -5.50 1.91e+00 2.74e-01 8.28e+00 angle pdb=" C VAL C 136 " pdb=" N MET C 137 " pdb=" CA MET C 137 " ideal model delta sigma weight residual 121.54 126.98 -5.44 1.91e+00 2.74e-01 8.12e+00 ... (remaining 30025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 12591 17.53 - 35.07: 687 35.07 - 52.60: 144 52.60 - 70.13: 45 70.13 - 87.67: 12 Dihedral angle restraints: 13479 sinusoidal: 5424 harmonic: 8055 Sorted by residual: dihedral pdb=" CA ALA C 285 " pdb=" C ALA C 285 " pdb=" N TYR C 286 " pdb=" CA TYR C 286 " ideal model delta harmonic sigma weight residual 180.00 159.76 20.24 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA ALA B 285 " pdb=" C ALA B 285 " pdb=" N TYR B 286 " pdb=" CA TYR B 286 " ideal model delta harmonic sigma weight residual 180.00 159.77 20.23 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA ALA A 285 " pdb=" C ALA A 285 " pdb=" N TYR A 286 " pdb=" CA TYR A 286 " ideal model delta harmonic sigma weight residual 180.00 159.82 20.18 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 13476 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1919 0.028 - 0.056: 964 0.056 - 0.084: 277 0.084 - 0.112: 204 0.112 - 0.140: 95 Chirality restraints: 3459 Sorted by residual: chirality pdb=" CA VAL E 14 " pdb=" N VAL E 14 " pdb=" C VAL E 14 " pdb=" CB VAL E 14 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA VAL D 456 " pdb=" N VAL D 456 " pdb=" C VAL D 456 " pdb=" CB VAL D 456 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA VAL D 14 " pdb=" N VAL D 14 " pdb=" C VAL D 14 " pdb=" CB VAL D 14 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.87e-01 ... (remaining 3456 not shown) Planarity restraints: 3957 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 284 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C GLU B 284 " 0.028 2.00e-02 2.50e+03 pdb=" O GLU B 284 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA B 285 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 232 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO B 233 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 233 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 233 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 232 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO A 233 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 233 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 233 " 0.022 5.00e-02 4.00e+02 ... (remaining 3954 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 447 2.71 - 3.26: 21957 3.26 - 3.80: 31944 3.80 - 4.35: 42882 4.35 - 4.90: 72349 Nonbonded interactions: 169579 Sorted by model distance: nonbonded pdb=" OG SER D 411 " pdb=" O ARG D 454 " model vdw 2.159 3.040 nonbonded pdb=" OG SER E 411 " pdb=" O ARG E 454 " model vdw 2.159 3.040 nonbonded pdb=" OG SER F 411 " pdb=" O ARG F 454 " model vdw 2.160 3.040 nonbonded pdb=" O ASP A 170 " pdb=" OG1 THR A 173 " model vdw 2.236 3.040 nonbonded pdb=" O ASP C 170 " pdb=" OG1 THR C 173 " model vdw 2.236 3.040 ... (remaining 169574 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.120 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 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 : 0.003 0.032 22170 Z= 0.141 Angle : 0.568 9.764 30030 Z= 0.323 Chirality : 0.044 0.140 3459 Planarity : 0.004 0.040 3957 Dihedral : 12.146 87.667 8331 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.32 % Allowed : 1.13 % Favored : 98.55 % Rotamer: Outliers : 0.78 % Allowed : 7.63 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.15), residues: 2823 helix: 0.88 (0.15), residues: 1092 sheet: 0.91 (0.25), residues: 426 loop : -0.55 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 213 TYR 0.011 0.002 TYR F 364 PHE 0.022 0.002 PHE B 236 HIS 0.003 0.001 HIS D 401 Details of bonding type rmsd covalent geometry : bond 0.00293 (22170) covalent geometry : angle 0.56808 (30030) hydrogen bonds : bond 0.17163 ( 1026) hydrogen bonds : angle 6.42835 ( 2952) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 594 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.4447 (mpp) cc_final: 0.3243 (pmm) REVERT: A 349 PHE cc_start: 0.4449 (t80) cc_final: 0.4097 (t80) REVERT: A 474 HIS cc_start: 0.7070 (t-90) cc_final: 0.6866 (t70) REVERT: B 137 MET cc_start: 0.4798 (mpp) cc_final: 0.3335 (pmm) REVERT: B 474 HIS cc_start: 0.7113 (t-90) cc_final: 0.6764 (t70) REVERT: C 137 MET cc_start: 0.4823 (mpp) cc_final: 0.3372 (pmm) REVERT: C 349 PHE cc_start: 0.4475 (t80) cc_final: 0.4118 (t80) REVERT: C 460 PHE cc_start: 0.7797 (t80) cc_final: 0.7311 (t80) REVERT: F 234 THR cc_start: 0.7064 (t) cc_final: 0.6855 (p) outliers start: 18 outliers final: 3 residues processed: 603 average time/residue: 0.1608 time to fit residues: 140.0793 Evaluate side-chains 355 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 352 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain E residue 62 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 474 HIS D 253 ASN D 365 GLN D 407 GLN ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 GLN E 253 ASN E 407 GLN F 253 ASN F 365 GLN F 401 HIS F 407 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.218035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.189734 restraints weight = 21343.013| |-----------------------------------------------------------------------------| r_work (start): 0.4290 rms_B_bonded: 1.05 r_work: 0.4049 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3908 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 22170 Z= 0.145 Angle : 0.592 8.215 30030 Z= 0.317 Chirality : 0.046 0.162 3459 Planarity : 0.005 0.062 3957 Dihedral : 5.134 68.946 3090 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.80 % Allowed : 13.50 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.15), residues: 2823 helix: 1.06 (0.15), residues: 1131 sheet: 1.06 (0.25), residues: 414 loop : -0.64 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 454 TYR 0.022 0.002 TYR B 286 PHE 0.022 0.002 PHE B 236 HIS 0.008 0.001 HIS E 401 Details of bonding type rmsd covalent geometry : bond 0.00324 (22170) covalent geometry : angle 0.59158 (30030) hydrogen bonds : bond 0.05290 ( 1026) hydrogen bonds : angle 4.95303 ( 2952) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 368 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6217 (mp0) REVERT: A 137 MET cc_start: 0.4065 (tpp) cc_final: 0.3311 (pmm) REVERT: A 182 THR cc_start: 0.7433 (OUTLIER) cc_final: 0.7084 (p) REVERT: A 250 MET cc_start: 0.6489 (ttp) cc_final: 0.6222 (ttp) REVERT: A 349 PHE cc_start: 0.4505 (t80) cc_final: 0.4160 (t80) REVERT: A 448 ILE cc_start: 0.7350 (OUTLIER) cc_final: 0.6843 (mp) REVERT: A 460 PHE cc_start: 0.7851 (t80) cc_final: 0.7538 (t80) REVERT: A 476 ARG cc_start: 0.7785 (mtm-85) cc_final: 0.7527 (ttm170) REVERT: B 137 MET cc_start: 0.4570 (tpp) cc_final: 0.3433 (pmm) REVERT: B 474 HIS cc_start: 0.7050 (t-90) cc_final: 0.6821 (t70) REVERT: C 349 PHE cc_start: 0.4377 (t80) cc_final: 0.4175 (t80) REVERT: C 460 PHE cc_start: 0.7715 (t80) cc_final: 0.7317 (t80) REVERT: D 237 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6941 (pt0) REVERT: D 248 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8065 (tt) REVERT: D 285 MET cc_start: 0.7062 (ttt) cc_final: 0.6848 (ttm) REVERT: D 402 ARG cc_start: 0.7593 (mtt90) cc_final: 0.7372 (mtt90) REVERT: D 469 MET cc_start: 0.6261 (mmt) cc_final: 0.5678 (ptm) REVERT: E 237 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6664 (pt0) REVERT: E 285 MET cc_start: 0.7284 (ttt) cc_final: 0.6906 (ttm) REVERT: F 22 HIS cc_start: 0.6776 (m-70) cc_final: 0.6504 (t-170) REVERT: F 190 GLU cc_start: 0.5991 (OUTLIER) cc_final: 0.5548 (pm20) REVERT: F 237 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6517 (pt0) REVERT: F 325 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7985 (mp) REVERT: F 469 MET cc_start: 0.6391 (mmt) cc_final: 0.5528 (ptm) outliers start: 65 outliers final: 29 residues processed: 419 average time/residue: 0.1474 time to fit residues: 94.5551 Evaluate side-chains 345 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 307 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain F residue 237 GLU Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 413 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 120 optimal weight: 9.9990 chunk 247 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 177 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 chunk 230 optimal weight: 1.9990 chunk 119 optimal weight: 8.9990 chunk 248 optimal weight: 3.9990 chunk 261 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 HIS ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN D 259 GLN E 179 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.215431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.182319 restraints weight = 21362.370| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 1.35 r_work: 0.3940 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22170 Z= 0.133 Angle : 0.557 9.452 30030 Z= 0.295 Chirality : 0.045 0.164 3459 Planarity : 0.005 0.054 3957 Dihedral : 4.965 68.316 3084 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.45 % Allowed : 16.04 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.16), residues: 2823 helix: 1.22 (0.15), residues: 1134 sheet: 0.96 (0.25), residues: 420 loop : -0.67 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 390 TYR 0.013 0.001 TYR C 240 PHE 0.022 0.001 PHE C 494 HIS 0.006 0.001 HIS E 401 Details of bonding type rmsd covalent geometry : bond 0.00299 (22170) covalent geometry : angle 0.55701 (30030) hydrogen bonds : bond 0.04649 ( 1026) hydrogen bonds : angle 4.72578 ( 2952) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 339 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6179 (mp0) REVERT: A 182 THR cc_start: 0.7270 (OUTLIER) cc_final: 0.6882 (p) REVERT: A 250 MET cc_start: 0.6419 (ttp) cc_final: 0.6172 (ttp) REVERT: A 460 PHE cc_start: 0.7813 (t80) cc_final: 0.7424 (t80) REVERT: A 474 HIS cc_start: 0.6899 (t-170) cc_final: 0.6680 (t70) REVERT: B 57 ASN cc_start: 0.6786 (OUTLIER) cc_final: 0.6547 (p0) REVERT: B 108 VAL cc_start: 0.7858 (p) cc_final: 0.7621 (m) REVERT: B 130 GLU cc_start: 0.5061 (pm20) cc_final: 0.4658 (pm20) REVERT: B 299 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7114 (mm-30) REVERT: B 448 ILE cc_start: 0.7517 (OUTLIER) cc_final: 0.7306 (mm) REVERT: C 448 ILE cc_start: 0.7368 (OUTLIER) cc_final: 0.7112 (mm) REVERT: C 460 PHE cc_start: 0.7672 (t80) cc_final: 0.7068 (t80) REVERT: D 226 MET cc_start: 0.6343 (OUTLIER) cc_final: 0.5860 (mtp) REVERT: D 237 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6820 (pt0) REVERT: D 248 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8064 (tt) REVERT: D 406 ILE cc_start: 0.8607 (tp) cc_final: 0.8337 (tp) REVERT: D 469 MET cc_start: 0.6227 (mmt) cc_final: 0.5630 (ptm) REVERT: E 33 GLN cc_start: 0.6137 (OUTLIER) cc_final: 0.5604 (mp10) REVERT: E 64 MET cc_start: 0.6883 (mmp) cc_final: 0.6611 (mmm) REVERT: E 237 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6616 (pt0) REVERT: E 418 GLU cc_start: 0.6492 (pm20) cc_final: 0.5860 (pm20) REVERT: E 465 LYS cc_start: 0.6662 (tttt) cc_final: 0.6246 (ttmm) REVERT: F 22 HIS cc_start: 0.6656 (m-70) cc_final: 0.6450 (t-170) REVERT: F 237 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6774 (pt0) REVERT: F 325 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7998 (mp) outliers start: 80 outliers final: 36 residues processed: 398 average time/residue: 0.1340 time to fit residues: 82.3839 Evaluate side-chains 354 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 305 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain E residue 33 GLN Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 179 HIS Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 253 ASN Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 237 GLU Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 413 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 48 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 202 optimal weight: 3.9990 chunk 213 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 233 optimal weight: 8.9990 chunk 200 optimal weight: 4.9990 chunk 270 optimal weight: 0.3980 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN B 345 GLN B 474 HIS D 22 HIS ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 GLN F 169 GLN F 179 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.208995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.177006 restraints weight = 21750.954| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 1.37 r_work: 0.3842 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 22170 Z= 0.205 Angle : 0.655 8.276 30030 Z= 0.349 Chirality : 0.049 0.171 3459 Planarity : 0.006 0.058 3957 Dihedral : 5.339 65.244 3084 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.36 % Allowed : 17.03 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.15), residues: 2823 helix: 0.94 (0.15), residues: 1104 sheet: 0.79 (0.24), residues: 420 loop : -0.99 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 193 TYR 0.024 0.002 TYR C 240 PHE 0.017 0.002 PHE C 349 HIS 0.020 0.002 HIS E 179 Details of bonding type rmsd covalent geometry : bond 0.00490 (22170) covalent geometry : angle 0.65480 (30030) hydrogen bonds : bond 0.05816 ( 1026) hydrogen bonds : angle 4.90862 ( 2952) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 322 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6324 (mp0) REVERT: A 95 MET cc_start: 0.7154 (mtp) cc_final: 0.6947 (mmm) REVERT: A 250 MET cc_start: 0.6756 (ttp) cc_final: 0.6552 (ttp) REVERT: A 448 ILE cc_start: 0.7373 (OUTLIER) cc_final: 0.7022 (mp) REVERT: A 460 PHE cc_start: 0.7823 (t80) cc_final: 0.7430 (t80) REVERT: C 460 PHE cc_start: 0.7742 (t80) cc_final: 0.7246 (t80) REVERT: D 237 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6710 (pt0) REVERT: D 248 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8178 (tt) REVERT: D 418 GLU cc_start: 0.6426 (pm20) cc_final: 0.6171 (pm20) REVERT: E 33 GLN cc_start: 0.6012 (OUTLIER) cc_final: 0.5474 (mp10) REVERT: E 237 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6860 (pt0) REVERT: E 285 MET cc_start: 0.7242 (ttt) cc_final: 0.6993 (ttm) REVERT: F 202 MET cc_start: 0.6137 (mmp) cc_final: 0.5689 (mmp) REVERT: F 237 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6778 (pt0) REVERT: F 325 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8193 (mp) REVERT: F 418 GLU cc_start: 0.6377 (pm20) cc_final: 0.6132 (pm20) REVERT: F 469 MET cc_start: 0.6380 (mmt) cc_final: 0.6034 (mpp) outliers start: 101 outliers final: 71 residues processed: 396 average time/residue: 0.1487 time to fit residues: 90.0777 Evaluate side-chains 376 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 297 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 22 HIS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 33 GLN Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 253 ASN Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 375 GLN Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 179 HIS Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 237 GLU Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 413 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 143 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 234 optimal weight: 2.9990 chunk 246 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 200 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 HIS ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 HIS D 22 HIS E 179 HIS F 179 HIS F 259 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.211247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.179050 restraints weight = 21468.153| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 1.32 r_work: 0.3958 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3822 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22170 Z= 0.129 Angle : 0.546 7.151 30030 Z= 0.290 Chirality : 0.045 0.170 3459 Planarity : 0.004 0.045 3957 Dihedral : 4.988 66.433 3084 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.36 % Allowed : 18.89 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.15), residues: 2823 helix: 1.19 (0.16), residues: 1125 sheet: 1.02 (0.25), residues: 399 loop : -0.87 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 415 TYR 0.014 0.001 TYR A 240 PHE 0.038 0.001 PHE E 409 HIS 0.010 0.001 HIS D 22 Details of bonding type rmsd covalent geometry : bond 0.00292 (22170) covalent geometry : angle 0.54606 (30030) hydrogen bonds : bond 0.04445 ( 1026) hydrogen bonds : angle 4.65182 ( 2952) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 308 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6389 (mp0) REVERT: A 236 PHE cc_start: 0.7142 (OUTLIER) cc_final: 0.6588 (p90) REVERT: A 460 PHE cc_start: 0.7799 (t80) cc_final: 0.7393 (t80) REVERT: B 265 LYS cc_start: 0.8144 (mttp) cc_final: 0.7759 (tttm) REVERT: C 187 LYS cc_start: 0.6721 (pttt) cc_final: 0.6508 (pttt) REVERT: C 460 PHE cc_start: 0.7627 (t80) cc_final: 0.7064 (t80) REVERT: D 237 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6442 (pt0) REVERT: D 248 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8225 (tt) REVERT: D 406 ILE cc_start: 0.8705 (tp) cc_final: 0.8375 (tp) REVERT: D 418 GLU cc_start: 0.6337 (pm20) cc_final: 0.6118 (pm20) REVERT: D 469 MET cc_start: 0.6050 (mmp) cc_final: 0.5423 (mpp) REVERT: E 33 GLN cc_start: 0.6031 (OUTLIER) cc_final: 0.5599 (mp10) REVERT: E 64 MET cc_start: 0.7162 (mmp) cc_final: 0.6857 (mmm) REVERT: E 237 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6575 (pt0) REVERT: E 418 GLU cc_start: 0.6575 (pm20) cc_final: 0.6280 (pm20) REVERT: F 202 MET cc_start: 0.6024 (mmp) cc_final: 0.5622 (mmp) REVERT: F 237 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6389 (pt0) REVERT: F 418 GLU cc_start: 0.6360 (pm20) cc_final: 0.6131 (pm20) outliers start: 78 outliers final: 50 residues processed: 367 average time/residue: 0.1433 time to fit residues: 80.8866 Evaluate side-chains 344 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 287 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 33 GLN Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 253 ASN Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 237 GLU Chi-restraints excluded: chain F residue 315 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 10 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 202 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 178 optimal weight: 9.9990 chunk 184 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 HIS F 22 HIS F 179 HIS F 259 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.207812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.177209 restraints weight = 21792.181| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 1.30 r_work: 0.3913 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 22170 Z= 0.219 Angle : 0.660 9.583 30030 Z= 0.351 Chirality : 0.049 0.164 3459 Planarity : 0.005 0.051 3957 Dihedral : 5.314 64.808 3084 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.74 % Allowed : 18.33 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.15), residues: 2823 helix: 0.88 (0.15), residues: 1125 sheet: 0.73 (0.24), residues: 405 loop : -1.09 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 415 TYR 0.022 0.002 TYR C 240 PHE 0.029 0.002 PHE E 409 HIS 0.007 0.002 HIS C 255 Details of bonding type rmsd covalent geometry : bond 0.00530 (22170) covalent geometry : angle 0.65990 (30030) hydrogen bonds : bond 0.05737 ( 1026) hydrogen bonds : angle 4.89379 ( 2952) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 303 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.6472 (mp0) REVERT: A 236 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.6665 (p90) REVERT: A 344 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6841 (mt) REVERT: A 460 PHE cc_start: 0.7791 (t80) cc_final: 0.7350 (t80) REVERT: B 344 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6867 (mt) REVERT: B 460 PHE cc_start: 0.7422 (t80) cc_final: 0.6931 (t80) REVERT: B 476 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7418 (mtm-85) REVERT: C 460 PHE cc_start: 0.7696 (t80) cc_final: 0.7224 (t80) REVERT: D 237 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6733 (pt0) REVERT: D 248 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8258 (tt) REVERT: D 406 ILE cc_start: 0.8745 (tp) cc_final: 0.8371 (tp) REVERT: D 418 GLU cc_start: 0.6432 (pm20) cc_final: 0.6193 (pm20) REVERT: E 33 GLN cc_start: 0.6119 (OUTLIER) cc_final: 0.5523 (mp10) REVERT: E 237 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6900 (pt0) REVERT: E 285 MET cc_start: 0.7426 (ttm) cc_final: 0.7149 (ttt) REVERT: E 418 GLU cc_start: 0.6570 (pm20) cc_final: 0.6199 (pm20) REVERT: F 202 MET cc_start: 0.6244 (mmp) cc_final: 0.5831 (mmp) REVERT: F 237 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6645 (pt0) REVERT: F 418 GLU cc_start: 0.6502 (pm20) cc_final: 0.6229 (pm20) outliers start: 110 outliers final: 76 residues processed: 389 average time/residue: 0.1406 time to fit residues: 84.2324 Evaluate side-chains 371 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 285 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 33 GLN Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 253 ASN Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 179 HIS Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 237 GLU Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 413 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 90 optimal weight: 20.0000 chunk 85 optimal weight: 30.0000 chunk 173 optimal weight: 10.0000 chunk 72 optimal weight: 0.0870 chunk 109 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 223 optimal weight: 0.9990 chunk 204 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 238 optimal weight: 7.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 HIS F 179 HIS F 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.208786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.179599 restraints weight = 21635.096| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 1.24 r_work: 0.3958 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3809 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22170 Z= 0.168 Angle : 0.604 8.489 30030 Z= 0.320 Chirality : 0.047 0.156 3459 Planarity : 0.005 0.048 3957 Dihedral : 5.208 65.548 3084 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.14 % Allowed : 19.45 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.15), residues: 2823 helix: 0.95 (0.15), residues: 1125 sheet: 0.71 (0.24), residues: 405 loop : -1.08 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 415 TYR 0.017 0.002 TYR B 240 PHE 0.040 0.002 PHE D 409 HIS 0.019 0.001 HIS F 179 Details of bonding type rmsd covalent geometry : bond 0.00398 (22170) covalent geometry : angle 0.60374 (30030) hydrogen bonds : bond 0.05047 ( 1026) hydrogen bonds : angle 4.78522 ( 2952) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 296 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.6375 (mp0) REVERT: A 236 PHE cc_start: 0.7118 (OUTLIER) cc_final: 0.6605 (p90) REVERT: A 278 ARG cc_start: 0.7011 (mtp85) cc_final: 0.6010 (mtm-85) REVERT: B 236 PHE cc_start: 0.7093 (OUTLIER) cc_final: 0.6068 (p90) REVERT: B 344 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6744 (mt) REVERT: B 460 PHE cc_start: 0.7316 (t80) cc_final: 0.6851 (t80) REVERT: C 198 ILE cc_start: 0.5727 (mt) cc_final: 0.5185 (mt) REVERT: C 454 ARG cc_start: 0.7188 (tpp80) cc_final: 0.6963 (tpp80) REVERT: C 460 PHE cc_start: 0.7538 (t80) cc_final: 0.7065 (t80) REVERT: C 476 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7526 (mtm-85) REVERT: D 237 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6482 (pt0) REVERT: D 248 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8259 (tt) REVERT: D 418 GLU cc_start: 0.6388 (pm20) cc_final: 0.6109 (pm20) REVERT: E 33 GLN cc_start: 0.5984 (OUTLIER) cc_final: 0.5646 (mp10) REVERT: E 237 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6693 (pt0) REVERT: E 285 MET cc_start: 0.7296 (ttm) cc_final: 0.6984 (ttt) REVERT: E 418 GLU cc_start: 0.6463 (pm20) cc_final: 0.6130 (pm20) REVERT: F 202 MET cc_start: 0.6202 (mmp) cc_final: 0.5801 (mmp) REVERT: F 234 THR cc_start: 0.6925 (OUTLIER) cc_final: 0.6500 (m) REVERT: F 237 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6438 (pt0) REVERT: F 418 GLU cc_start: 0.6424 (pm20) cc_final: 0.6180 (pm20) REVERT: F 439 GLU cc_start: 0.8378 (tp30) cc_final: 0.8105 (tp30) outliers start: 96 outliers final: 73 residues processed: 371 average time/residue: 0.1443 time to fit residues: 81.8352 Evaluate side-chains 373 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 289 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 476 ARG Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 285 MET Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 33 GLN Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 253 ASN Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 237 GLU Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 413 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 162 optimal weight: 0.9980 chunk 166 optimal weight: 0.0970 chunk 193 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 153 optimal weight: 0.6980 chunk 238 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 85 optimal weight: 20.0000 chunk 276 optimal weight: 3.9990 overall best weight: 2.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 HIS F 179 HIS F 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.210317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.180714 restraints weight = 21642.001| |-----------------------------------------------------------------------------| r_work (start): 0.4214 rms_B_bonded: 1.12 r_work: 0.3922 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22170 Z= 0.144 Angle : 0.579 8.356 30030 Z= 0.307 Chirality : 0.045 0.158 3459 Planarity : 0.005 0.046 3957 Dihedral : 5.073 67.564 3084 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.84 % Allowed : 20.01 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.15), residues: 2823 helix: 1.09 (0.15), residues: 1125 sheet: 0.85 (0.25), residues: 399 loop : -1.03 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 415 TYR 0.013 0.001 TYR B 240 PHE 0.023 0.002 PHE E 409 HIS 0.005 0.001 HIS F 401 Details of bonding type rmsd covalent geometry : bond 0.00337 (22170) covalent geometry : angle 0.57858 (30030) hydrogen bonds : bond 0.04606 ( 1026) hydrogen bonds : angle 4.69512 ( 2952) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 300 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6215 (mp0) REVERT: A 236 PHE cc_start: 0.7101 (OUTLIER) cc_final: 0.6609 (p90) REVERT: A 278 ARG cc_start: 0.6835 (mtp85) cc_final: 0.6108 (mtm-85) REVERT: A 344 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6930 (mt) REVERT: A 473 GLU cc_start: 0.7233 (tp30) cc_final: 0.7008 (mm-30) REVERT: B 236 PHE cc_start: 0.7081 (OUTLIER) cc_final: 0.6130 (p90) REVERT: B 344 LEU cc_start: 0.7082 (OUTLIER) cc_final: 0.6867 (mt) REVERT: B 460 PHE cc_start: 0.7397 (t80) cc_final: 0.6913 (t80) REVERT: B 476 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7247 (mtm-85) REVERT: C 198 ILE cc_start: 0.5746 (mt) cc_final: 0.5197 (mt) REVERT: C 460 PHE cc_start: 0.7577 (t80) cc_final: 0.7149 (t80) REVERT: C 476 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7489 (mtm-85) REVERT: D 237 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6627 (pt0) REVERT: D 248 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8214 (tt) REVERT: E 33 GLN cc_start: 0.5848 (OUTLIER) cc_final: 0.5505 (mp10) REVERT: E 64 MET cc_start: 0.7370 (mmp) cc_final: 0.7068 (mmm) REVERT: E 237 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6578 (pt0) REVERT: E 285 MET cc_start: 0.7042 (ttm) cc_final: 0.6763 (ttt) REVERT: E 418 GLU cc_start: 0.6408 (pm20) cc_final: 0.6148 (pm20) REVERT: E 437 PHE cc_start: 0.7756 (m-80) cc_final: 0.7437 (m-80) REVERT: F 202 MET cc_start: 0.6218 (mmp) cc_final: 0.5784 (mmp) REVERT: F 237 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6443 (pt0) outliers start: 89 outliers final: 70 residues processed: 370 average time/residue: 0.1405 time to fit residues: 78.8348 Evaluate side-chains 369 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 287 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 476 ARG Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 285 MET Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 33 GLN Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 253 ASN Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 179 HIS Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 237 GLU Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 359 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 122 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 9 optimal weight: 0.0010 chunk 220 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 233 optimal weight: 8.9990 chunk 239 optimal weight: 0.1980 chunk 54 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 HIS F 179 HIS F 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.210316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.180816 restraints weight = 21720.184| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 1.12 r_work: 0.3912 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22170 Z= 0.147 Angle : 0.590 7.979 30030 Z= 0.312 Chirality : 0.046 0.163 3459 Planarity : 0.005 0.046 3957 Dihedral : 5.066 68.650 3084 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.05 % Allowed : 19.92 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.15), residues: 2823 helix: 1.09 (0.15), residues: 1125 sheet: 0.89 (0.25), residues: 399 loop : -1.03 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 415 TYR 0.013 0.001 TYR A 240 PHE 0.039 0.002 PHE D 409 HIS 0.011 0.001 HIS F 179 Details of bonding type rmsd covalent geometry : bond 0.00345 (22170) covalent geometry : angle 0.59021 (30030) hydrogen bonds : bond 0.04582 ( 1026) hydrogen bonds : angle 4.68144 ( 2952) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 288 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6222 (mp0) REVERT: A 236 PHE cc_start: 0.7104 (OUTLIER) cc_final: 0.6615 (p90) REVERT: A 278 ARG cc_start: 0.6860 (mtp85) cc_final: 0.6123 (mtm-85) REVERT: A 344 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6932 (mt) REVERT: A 473 GLU cc_start: 0.7245 (tp30) cc_final: 0.7014 (mm-30) REVERT: B 236 PHE cc_start: 0.7114 (OUTLIER) cc_final: 0.6116 (p90) REVERT: B 344 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6940 (mt) REVERT: B 476 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7167 (mtm-85) REVERT: C 198 ILE cc_start: 0.5764 (mt) cc_final: 0.5215 (mt) REVERT: C 460 PHE cc_start: 0.7638 (t80) cc_final: 0.7254 (t80) REVERT: C 476 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7486 (mtm-85) REVERT: D 237 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6623 (pt0) REVERT: D 248 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8224 (tt) REVERT: E 33 GLN cc_start: 0.5835 (OUTLIER) cc_final: 0.5490 (mp10) REVERT: E 64 MET cc_start: 0.7386 (mmp) cc_final: 0.7091 (mmm) REVERT: E 237 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6566 (pt0) REVERT: E 285 MET cc_start: 0.7071 (ttm) cc_final: 0.6798 (ttt) REVERT: E 418 GLU cc_start: 0.6447 (pm20) cc_final: 0.6205 (pm20) REVERT: F 202 MET cc_start: 0.6235 (mmp) cc_final: 0.5808 (mmp) REVERT: F 234 THR cc_start: 0.6814 (m) cc_final: 0.6502 (m) REVERT: F 237 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6654 (pt0) REVERT: F 248 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8189 (tt) outliers start: 94 outliers final: 76 residues processed: 363 average time/residue: 0.1404 time to fit residues: 78.5429 Evaluate side-chains 370 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 281 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 476 ARG Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 285 MET Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 33 GLN Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 253 ASN Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 179 HIS Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 237 GLU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 413 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 266 optimal weight: 0.0980 chunk 7 optimal weight: 0.7980 chunk 242 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 263 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 175 optimal weight: 0.0980 chunk 190 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 HIS F 179 HIS F 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.216030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.180882 restraints weight = 21688.773| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 1.59 r_work: 0.4027 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3901 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 22170 Z= 0.108 Angle : 0.554 12.640 30030 Z= 0.289 Chirality : 0.044 0.170 3459 Planarity : 0.005 0.042 3957 Dihedral : 4.753 71.846 3084 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.16 % Allowed : 21.91 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.16), residues: 2823 helix: 1.38 (0.16), residues: 1125 sheet: 1.02 (0.24), residues: 429 loop : -0.84 (0.16), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 3 TYR 0.007 0.001 TYR A 260 PHE 0.023 0.001 PHE D 409 HIS 0.018 0.001 HIS F 179 Details of bonding type rmsd covalent geometry : bond 0.00234 (22170) covalent geometry : angle 0.55353 (30030) hydrogen bonds : bond 0.03509 ( 1026) hydrogen bonds : angle 4.52265 ( 2952) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 301 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6087 (mp0) REVERT: A 198 ILE cc_start: 0.6037 (mt) cc_final: 0.5633 (mt) REVERT: A 236 PHE cc_start: 0.6954 (OUTLIER) cc_final: 0.6448 (p90) REVERT: A 278 ARG cc_start: 0.6830 (mtp85) cc_final: 0.5978 (mtm-85) REVERT: A 460 PHE cc_start: 0.7618 (t80) cc_final: 0.7079 (t80) REVERT: A 473 GLU cc_start: 0.7437 (tp30) cc_final: 0.7233 (mm-30) REVERT: B 198 ILE cc_start: 0.6137 (mt) cc_final: 0.5723 (mt) REVERT: B 236 PHE cc_start: 0.6999 (OUTLIER) cc_final: 0.6082 (p90) REVERT: C 108 VAL cc_start: 0.7814 (p) cc_final: 0.7513 (m) REVERT: C 198 ILE cc_start: 0.5736 (mt) cc_final: 0.5189 (mt) REVERT: C 460 PHE cc_start: 0.7509 (t80) cc_final: 0.7052 (t80) REVERT: C 476 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7413 (mtm-85) REVERT: D 218 MET cc_start: 0.8323 (mtt) cc_final: 0.7852 (mtt) REVERT: D 237 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6304 (pt0) REVERT: D 248 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8209 (tt) REVERT: D 469 MET cc_start: 0.6395 (mpp) cc_final: 0.6072 (ptt) REVERT: E 64 MET cc_start: 0.7118 (mmp) cc_final: 0.6900 (mmm) REVERT: E 165 THR cc_start: 0.6202 (m) cc_final: 0.5995 (p) REVERT: E 234 THR cc_start: 0.6842 (m) cc_final: 0.6381 (m) REVERT: E 285 MET cc_start: 0.7033 (ttm) cc_final: 0.6816 (ttt) REVERT: F 202 MET cc_start: 0.6097 (mmp) cc_final: 0.5662 (mmp) outliers start: 50 outliers final: 25 residues processed: 341 average time/residue: 0.1442 time to fit residues: 74.4406 Evaluate side-chains 311 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 280 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 476 ARG Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 253 ASN Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 308 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 104 optimal weight: 7.9990 chunk 182 optimal weight: 3.9990 chunk 203 optimal weight: 20.0000 chunk 37 optimal weight: 30.0000 chunk 190 optimal weight: 5.9990 chunk 262 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 chunk 277 optimal weight: 0.4980 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 HIS C 474 HIS F 179 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.207734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.177501 restraints weight = 21748.078| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 1.29 r_work: 0.3933 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3784 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 22170 Z= 0.204 Angle : 0.675 11.138 30030 Z= 0.355 Chirality : 0.048 0.157 3459 Planarity : 0.005 0.048 3957 Dihedral : 5.254 69.857 3084 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.29 % Allowed : 21.39 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.15), residues: 2823 helix: 0.97 (0.15), residues: 1125 sheet: 0.88 (0.25), residues: 375 loop : -1.03 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 415 TYR 0.019 0.002 TYR B 240 PHE 0.043 0.002 PHE D 409 HIS 0.006 0.002 HIS C 255 Details of bonding type rmsd covalent geometry : bond 0.00493 (22170) covalent geometry : angle 0.67546 (30030) hydrogen bonds : bond 0.05379 ( 1026) hydrogen bonds : angle 4.83515 ( 2952) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4679.79 seconds wall clock time: 80 minutes 46.91 seconds (4846.91 seconds total)