Starting phenix.real_space_refine on Wed May 21 12:59:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8spv_40687/05_2025/8spv_40687.cif Found real_map, /net/cci-nas-00/data/ceres_data/8spv_40687/05_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_40687/05_2025/8spv_40687.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8spv_40687/05_2025/8spv_40687.map" model { file = "/net/cci-nas-00/data/ceres_data/8spv_40687/05_2025/8spv_40687.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8spv_40687/05_2025/8spv_40687.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: "E" 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: D, F, C, B Time building chain proxies: 12.42, per 1000 atoms: 0.57 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: 6.06 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 2.54 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: 7.73 Time building geometry restraints manager: 6.76 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: 0.16 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 49.150 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.810 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 HIS 0.003 0.001 HIS D 401 PHE 0.022 0.002 PHE B 236 TYR 0.011 0.002 TYR F 364 ARG 0.003 0.000 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.17163 ( 1026) hydrogen bonds : angle 6.42835 ( 2952) covalent geometry : bond 0.00293 (22170) covalent geometry : angle 0.56808 (30030) *********************** 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 : 2.373 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: 0.3244 (pmm) REVERT: A 349 PHE cc_start: 0.4449 (t80) cc_final: 0.4100 (t80) REVERT: A 474 HIS cc_start: 0.7070 (t-90) cc_final: 0.6865 (t70) REVERT: B 137 MET cc_start: 0.4798 (mpp) cc_final: 0.3332 (pmm) REVERT: B 474 HIS cc_start: 0.7113 (t-90) cc_final: 0.6765 (t70) REVERT: C 137 MET cc_start: 0.4823 (mpp) cc_final: 0.3370 (pmm) REVERT: C 349 PHE cc_start: 0.4475 (t80) cc_final: 0.4122 (t80) REVERT: C 460 PHE cc_start: 0.7797 (t80) cc_final: 0.7313 (t80) REVERT: F 234 THR cc_start: 0.7064 (t) cc_final: 0.6854 (p) outliers start: 18 outliers final: 3 residues processed: 603 average time/residue: 0.4039 time to fit residues: 349.4091 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 : 2.255 ------------------------------------------------------------------------------- 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 238 optimal weight: 10.0000 chunk 213 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 144 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 221 optimal weight: 10.0000 chunk 85 optimal weight: 30.0000 chunk 134 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 chunk 256 optimal weight: 4.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 HIS A 345 GLN B 255 HIS B 345 GLN C 255 HIS C 345 GLN C 474 HIS D 365 GLN E 169 GLN E 245 GLN F 365 GLN F 401 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.206986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.175438 restraints weight = 21706.845| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 1.33 r_work: 0.3823 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 22170 Z= 0.338 Angle : 0.850 9.874 30030 Z= 0.457 Chirality : 0.058 0.232 3459 Planarity : 0.007 0.069 3957 Dihedral : 6.193 65.205 3090 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.92 % Allowed : 14.10 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 2823 helix: 0.26 (0.15), residues: 1113 sheet: 0.75 (0.25), residues: 384 loop : -1.11 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.003 HIS E 401 PHE 0.019 0.003 PHE B 494 TYR 0.034 0.003 TYR A 240 ARG 0.009 0.001 ARG F 256 Details of bonding type rmsd hydrogen bonds : bond 0.07761 ( 1026) hydrogen bonds : angle 5.48148 ( 2952) covalent geometry : bond 0.00818 (22170) covalent geometry : angle 0.85006 (30030) *********************** 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 472 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 358 time to evaluate : 2.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6297 (mp0) REVERT: A 290 ILE cc_start: 0.6765 (OUTLIER) cc_final: 0.6117 (mm) REVERT: A 448 ILE cc_start: 0.7463 (OUTLIER) cc_final: 0.6978 (mp) REVERT: A 460 PHE cc_start: 0.7844 (t80) cc_final: 0.7270 (t80) REVERT: A 474 HIS cc_start: 0.7332 (t-90) cc_final: 0.7033 (t70) REVERT: B 95 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.7125 (mmm) REVERT: B 448 ILE cc_start: 0.7676 (OUTLIER) cc_final: 0.7255 (mp) REVERT: B 474 HIS cc_start: 0.7125 (t-90) cc_final: 0.6861 (t70) REVERT: C 62 MET cc_start: 0.7338 (OUTLIER) cc_final: 0.7088 (mtm) REVERT: C 95 MET cc_start: 0.7313 (mtp) cc_final: 0.7057 (mmm) REVERT: C 459 GLU cc_start: 0.6789 (mt-10) cc_final: 0.6535 (mt-10) REVERT: C 460 PHE cc_start: 0.7806 (t80) cc_final: 0.7328 (t80) REVERT: C 494 PHE cc_start: 0.7295 (t80) cc_final: 0.7040 (t80) REVERT: D 237 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6905 (pt0) REVERT: D 248 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8226 (tt) REVERT: D 402 ARG cc_start: 0.7730 (mtt90) cc_final: 0.7472 (mtt90) REVERT: D 406 ILE cc_start: 0.8685 (tp) cc_final: 0.8416 (tp) REVERT: D 469 MET cc_start: 0.6325 (mmt) cc_final: 0.5917 (mpp) REVERT: E 237 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7012 (pt0) REVERT: F 237 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6740 (pt0) REVERT: F 285 MET cc_start: 0.7500 (ttm) cc_final: 0.7170 (ttt) REVERT: F 325 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8126 (mp) REVERT: F 333 ARG cc_start: 0.7345 (mtt180) cc_final: 0.7136 (mtt90) REVERT: F 402 ARG cc_start: 0.7786 (mtt90) cc_final: 0.7577 (mtt90) outliers start: 114 outliers final: 77 residues processed: 443 average time/residue: 0.3468 time to fit residues: 232.8243 Evaluate side-chains 388 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 300 time to evaluate : 2.412 ------------------------------------------------------------------------------- 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 115 VAL Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 136 VAL 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 243 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 62 MET 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 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 478 THR Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 141 VAL 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 301 THR Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 47 THR 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 162 VAL Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 237 GLU 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 326 ASP 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 47 THR 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 141 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 237 GLU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 326 ASP Chi-restraints excluded: chain F residue 370 VAL 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 4 optimal weight: 5.9990 chunk 208 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 227 optimal weight: 0.0670 chunk 250 optimal weight: 3.9990 chunk 228 optimal weight: 4.9990 chunk 131 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 HIS D 259 GLN E 259 GLN F 22 HIS F 253 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.215704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.182706 restraints weight = 21424.338| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 1.29 r_work: 0.3952 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22170 Z= 0.119 Angle : 0.548 8.236 30030 Z= 0.293 Chirality : 0.045 0.213 3459 Planarity : 0.005 0.060 3957 Dihedral : 5.334 67.503 3090 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.23 % Allowed : 17.42 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.15), residues: 2823 helix: 1.06 (0.16), residues: 1128 sheet: 0.93 (0.25), residues: 414 loop : -0.83 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 401 PHE 0.036 0.002 PHE F 409 TYR 0.011 0.001 TYR B 240 ARG 0.010 0.000 ARG B 390 Details of bonding type rmsd hydrogen bonds : bond 0.04312 ( 1026) hydrogen bonds : angle 4.74835 ( 2952) covalent geometry : bond 0.00247 (22170) covalent geometry : angle 0.54809 (30030) *********************** 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 407 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 332 time to evaluate : 2.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6167 (mp0) REVERT: A 101 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.6261 (mm-30) REVERT: A 460 PHE cc_start: 0.7757 (t80) cc_final: 0.7352 (t80) REVERT: A 473 GLU cc_start: 0.7326 (tp30) cc_final: 0.7056 (mm-30) REVERT: B 454 ARG cc_start: 0.7157 (tpp80) cc_final: 0.6939 (tpp80) REVERT: C 460 PHE cc_start: 0.7685 (t80) cc_final: 0.7241 (t80) REVERT: C 494 PHE cc_start: 0.7200 (t80) cc_final: 0.6873 (t80) REVERT: D 202 MET cc_start: 0.6332 (mmt) cc_final: 0.5480 (mmp) REVERT: D 237 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6640 (pt0) REVERT: D 248 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8121 (tt) REVERT: D 379 GLU cc_start: 0.6221 (OUTLIER) cc_final: 0.5877 (tt0) REVERT: D 469 MET cc_start: 0.6301 (mmt) cc_final: 0.5767 (ptm) REVERT: E 64 MET cc_start: 0.7075 (mmp) cc_final: 0.6845 (mmm) REVERT: E 237 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6377 (pt0) REVERT: F 226 MET cc_start: 0.6667 (OUTLIER) cc_final: 0.6428 (mtm) REVERT: F 253 ASN cc_start: 0.5586 (OUTLIER) cc_final: 0.5222 (t0) REVERT: F 285 MET cc_start: 0.7226 (ttm) cc_final: 0.6730 (ttt) REVERT: F 418 GLU cc_start: 0.6339 (pm20) cc_final: 0.5714 (pm20) outliers start: 75 outliers final: 29 residues processed: 390 average time/residue: 0.3539 time to fit residues: 207.8953 Evaluate side-chains 324 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 287 time to evaluate : 2.246 ------------------------------------------------------------------------------- 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 129 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain B residue 54 GLU 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 264 SER Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain C residue 62 MET 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 252 LYS 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 62 ILE 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 379 GLU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 237 GLU 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 F residue 59 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 253 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 191 optimal weight: 0.0370 chunk 249 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 222 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 204 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 474 HIS E 33 GLN F 169 GLN F 423 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.210143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.180238 restraints weight = 21912.698| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 1.28 r_work: 0.3895 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22170 Z= 0.170 Angle : 0.600 7.198 30030 Z= 0.318 Chirality : 0.047 0.166 3459 Planarity : 0.005 0.062 3957 Dihedral : 5.279 66.387 3088 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.23 % Allowed : 18.11 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.15), residues: 2823 helix: 1.05 (0.16), residues: 1107 sheet: 0.81 (0.25), residues: 414 loop : -0.92 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 255 PHE 0.020 0.002 PHE F 409 TYR 0.017 0.002 TYR B 240 ARG 0.005 0.000 ARG F 256 Details of bonding type rmsd hydrogen bonds : bond 0.05115 ( 1026) hydrogen bonds : angle 4.73469 ( 2952) covalent geometry : bond 0.00398 (22170) covalent geometry : angle 0.59981 (30030) *********************** 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 381 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 306 time to evaluate : 2.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6327 (mp0) REVERT: A 236 PHE cc_start: 0.7080 (OUTLIER) cc_final: 0.6534 (p90) REVERT: A 448 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7251 (mp) REVERT: A 460 PHE cc_start: 0.7800 (t80) cc_final: 0.7424 (t80) REVERT: B 415 ARG cc_start: 0.8018 (mpt-90) cc_final: 0.7805 (mpt-90) REVERT: B 460 PHE cc_start: 0.7421 (t80) cc_final: 0.6920 (t80) REVERT: C 460 PHE cc_start: 0.7691 (t80) cc_final: 0.7385 (t80) REVERT: C 494 PHE cc_start: 0.7281 (t80) cc_final: 0.6981 (t80) REVERT: D 237 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6649 (pt0) REVERT: D 248 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8213 (tt) REVERT: D 285 MET cc_start: 0.7053 (ttt) cc_final: 0.6828 (ttm) REVERT: E 10 MET cc_start: 0.7664 (mtt) cc_final: 0.7405 (mtt) REVERT: E 64 MET cc_start: 0.7188 (mmp) cc_final: 0.6903 (mmm) REVERT: E 237 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6660 (pt0) REVERT: E 285 MET cc_start: 0.7030 (ttt) cc_final: 0.6822 (ttm) REVERT: E 303 ILE cc_start: 0.6943 (OUTLIER) cc_final: 0.6711 (mm) REVERT: F 202 MET cc_start: 0.6274 (mmp) cc_final: 0.5705 (mmp) REVERT: F 253 ASN cc_start: 0.5722 (OUTLIER) cc_final: 0.5104 (t0) outliers start: 75 outliers final: 46 residues processed: 363 average time/residue: 0.3361 time to fit residues: 184.5903 Evaluate side-chains 342 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 288 time to evaluate : 2.227 ------------------------------------------------------------------------------- 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 146 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 108 VAL 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 264 SER Chi-restraints excluded: chain B residue 342 ILE 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 290 ILE Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 188 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 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 162 VAL Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 253 ASN Chi-restraints excluded: chain F residue 308 VAL 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 162 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 269 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 265 optimal weight: 0.2980 chunk 13 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 264 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 180 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 474 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.211130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.179539 restraints weight = 21627.764| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 1.31 r_work: 0.3956 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3818 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22170 Z= 0.128 Angle : 0.547 9.024 30030 Z= 0.290 Chirality : 0.045 0.217 3459 Planarity : 0.005 0.046 3957 Dihedral : 5.013 67.276 3088 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.98 % Allowed : 19.53 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.15), residues: 2823 helix: 1.15 (0.16), residues: 1125 sheet: 0.88 (0.25), residues: 414 loop : -0.89 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 401 PHE 0.017 0.001 PHE E 409 TYR 0.020 0.001 TYR E 199 ARG 0.007 0.000 ARG D 3 Details of bonding type rmsd hydrogen bonds : bond 0.04371 ( 1026) hydrogen bonds : angle 4.59202 ( 2952) covalent geometry : bond 0.00291 (22170) covalent geometry : angle 0.54717 (30030) *********************** 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 371 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 302 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6376 (mp0) REVERT: A 236 PHE cc_start: 0.7031 (OUTLIER) cc_final: 0.6484 (p90) REVERT: A 460 PHE cc_start: 0.7744 (t80) cc_final: 0.7340 (t80) REVERT: A 474 HIS cc_start: 0.7217 (t-90) cc_final: 0.6922 (t70) REVERT: B 460 PHE cc_start: 0.7364 (t80) cc_final: 0.6865 (t80) REVERT: C 460 PHE cc_start: 0.7586 (t80) cc_final: 0.7211 (t80) REVERT: D 202 MET cc_start: 0.6337 (mmt) cc_final: 0.5619 (mmp) REVERT: D 237 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6394 (pt0) REVERT: D 248 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8191 (tt) REVERT: D 285 MET cc_start: 0.7220 (ttt) cc_final: 0.6980 (ttm) REVERT: D 406 ILE cc_start: 0.8714 (tp) cc_final: 0.8381 (tp) REVERT: D 469 MET cc_start: 0.6120 (mmp) cc_final: 0.5508 (mpp) REVERT: E 64 MET cc_start: 0.7168 (mmp) cc_final: 0.6923 (mmm) REVERT: E 237 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6633 (pt0) REVERT: F 202 MET cc_start: 0.6209 (mmp) cc_final: 0.5705 (mmp) REVERT: F 285 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.6643 (ttm) REVERT: F 297 LYS cc_start: 0.7311 (OUTLIER) cc_final: 0.6690 (ptpp) REVERT: F 418 GLU cc_start: 0.6202 (pm20) cc_final: 0.5465 (pm20) outliers start: 69 outliers final: 41 residues processed: 355 average time/residue: 0.3476 time to fit residues: 186.8464 Evaluate side-chains 327 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 279 time to evaluate : 2.359 ------------------------------------------------------------------------------- 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 146 LEU Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain B residue 54 GLU 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 262 ASP Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain C residue 62 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 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 103 ILE Chi-restraints excluded: chain D residue 115 ARG 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 359 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 237 GLU 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 359 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 297 LYS Chi-restraints excluded: chain F residue 359 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 245 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 172 optimal weight: 0.2980 chunk 70 optimal weight: 0.7980 chunk 211 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 214 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.215209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.184605 restraints weight = 21584.497| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 1.25 r_work: 0.4005 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3868 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22170 Z= 0.101 Angle : 0.514 10.148 30030 Z= 0.268 Chirality : 0.043 0.185 3459 Planarity : 0.004 0.043 3957 Dihedral : 4.716 69.818 3084 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.03 % Allowed : 20.70 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.16), residues: 2823 helix: 1.40 (0.16), residues: 1128 sheet: 1.06 (0.25), residues: 414 loop : -0.78 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 401 PHE 0.022 0.001 PHE A 349 TYR 0.020 0.001 TYR E 199 ARG 0.006 0.000 ARG D 3 Details of bonding type rmsd hydrogen bonds : bond 0.03585 ( 1026) hydrogen bonds : angle 4.43020 ( 2952) covalent geometry : bond 0.00218 (22170) covalent geometry : angle 0.51365 (30030) *********************** 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 359 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 312 time to evaluate : 2.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6222 (mp0) REVERT: A 236 PHE cc_start: 0.6941 (OUTLIER) cc_final: 0.6431 (p90) REVERT: A 460 PHE cc_start: 0.7757 (t80) cc_final: 0.7368 (t80) REVERT: A 474 HIS cc_start: 0.7234 (t-90) cc_final: 0.6970 (t70) REVERT: B 198 ILE cc_start: 0.6079 (mt) cc_final: 0.5640 (mt) REVERT: B 460 PHE cc_start: 0.7387 (t80) cc_final: 0.6866 (t80) REVERT: B 474 HIS cc_start: 0.7061 (t-90) cc_final: 0.6802 (t-90) REVERT: C 60 MET cc_start: 0.6417 (mmp) cc_final: 0.6117 (mmp) REVERT: C 108 VAL cc_start: 0.7796 (p) cc_final: 0.7474 (m) REVERT: C 198 ILE cc_start: 0.5691 (mt) cc_final: 0.5096 (mt) REVERT: C 454 ARG cc_start: 0.7200 (tpp80) cc_final: 0.6978 (tpp80) REVERT: C 460 PHE cc_start: 0.7556 (t80) cc_final: 0.7039 (t80) REVERT: D 202 MET cc_start: 0.6240 (mmt) cc_final: 0.5555 (mmp) REVERT: D 237 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.6315 (pt0) REVERT: D 248 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8085 (tt) REVERT: D 301 THR cc_start: 0.7421 (OUTLIER) cc_final: 0.7203 (m) REVERT: D 406 ILE cc_start: 0.8596 (tp) cc_final: 0.8309 (tp) REVERT: E 33 GLN cc_start: 0.6592 (mt0) cc_final: 0.6280 (mt0) REVERT: E 64 MET cc_start: 0.7069 (mmp) cc_final: 0.6845 (mmm) REVERT: E 237 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.6477 (pt0) REVERT: E 285 MET cc_start: 0.6890 (ttt) cc_final: 0.6588 (ttm) REVERT: E 465 LYS cc_start: 0.6464 (tttt) cc_final: 0.6019 (ttmm) REVERT: F 202 MET cc_start: 0.6143 (mmp) cc_final: 0.5652 (mmp) REVERT: F 418 GLU cc_start: 0.6168 (pm20) cc_final: 0.5513 (pm20) outliers start: 47 outliers final: 31 residues processed: 350 average time/residue: 0.3393 time to fit residues: 181.8299 Evaluate side-chains 322 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 285 time to evaluate : 2.400 ------------------------------------------------------------------------------- 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 136 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain B residue 34 VAL 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 262 ASP Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain C residue 62 MET 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 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 103 ILE Chi-restraints excluded: chain D residue 115 ARG 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 D residue 265 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 359 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 4 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 211 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 HIS D 169 GLN E 179 HIS F 169 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.205963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.174950 restraints weight = 21834.402| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 1.36 r_work: 0.3889 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3748 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 22170 Z= 0.253 Angle : 0.704 9.439 30030 Z= 0.374 Chirality : 0.051 0.197 3459 Planarity : 0.006 0.054 3957 Dihedral : 5.408 65.515 3084 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.36 % Allowed : 19.15 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.15), residues: 2823 helix: 0.77 (0.15), residues: 1134 sheet: 0.58 (0.25), residues: 390 loop : -1.07 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS A 255 PHE 0.025 0.002 PHE D 409 TYR 0.025 0.002 TYR B 240 ARG 0.007 0.001 ARG F 3 Details of bonding type rmsd hydrogen bonds : bond 0.06119 ( 1026) hydrogen bonds : angle 4.92825 ( 2952) covalent geometry : bond 0.00611 (22170) covalent geometry : angle 0.70434 (30030) *********************** 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 404 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 303 time to evaluate : 2.376 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: 0.7543 (OUTLIER) cc_final: 0.6477 (mp0) REVERT: A 236 PHE cc_start: 0.7206 (OUTLIER) cc_final: 0.6737 (p90) REVERT: A 278 ARG cc_start: 0.7011 (mtp85) cc_final: 0.6064 (mtm-85) REVERT: A 344 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6844 (mt) REVERT: B 460 PHE cc_start: 0.7395 (t80) cc_final: 0.6911 (t80) REVERT: B 476 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7351 (mtm-85) REVERT: C 198 ILE cc_start: 0.5708 (mt) cc_final: 0.5159 (mt) REVERT: C 454 ARG cc_start: 0.7253 (tpp80) cc_final: 0.6889 (tpp80) REVERT: C 460 PHE cc_start: 0.7544 (t80) cc_final: 0.7170 (t80) REVERT: C 476 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7477 (mtm-85) REVERT: D 237 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6830 (pt0) REVERT: D 248 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8303 (tt) REVERT: D 285 MET cc_start: 0.7074 (ttt) cc_final: 0.6825 (ttm) REVERT: D 406 ILE cc_start: 0.8643 (tp) cc_final: 0.8371 (tp) REVERT: D 469 MET cc_start: 0.5943 (mmp) cc_final: 0.5345 (mpp) REVERT: E 33 GLN cc_start: 0.6640 (mt0) cc_final: 0.6367 (mt0) REVERT: E 237 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6743 (pt0) REVERT: E 285 MET cc_start: 0.7179 (ttt) cc_final: 0.6903 (ttm) REVERT: E 303 ILE cc_start: 0.7012 (OUTLIER) cc_final: 0.6794 (mm) REVERT: F 202 MET cc_start: 0.6446 (mmp) cc_final: 0.6015 (mmp) REVERT: F 285 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.6900 (ttm) REVERT: F 297 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.6836 (ptpp) REVERT: F 418 GLU cc_start: 0.6494 (pm20) cc_final: 0.6257 (pm20) REVERT: F 439 GLU cc_start: 0.8349 (tp30) cc_final: 0.8075 (tp30) outliers start: 101 outliers final: 72 residues processed: 379 average time/residue: 0.3444 time to fit residues: 196.2655 Evaluate side-chains 373 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 290 time to evaluate : 2.445 ------------------------------------------------------------------------------- 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 166 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 182 THR 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 327 SER Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 54 GLU 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 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 476 ARG Chi-restraints excluded: chain C residue 34 VAL 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 44 ILE 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 188 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 308 VAL Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 59 VAL 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 179 HIS Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 237 GLU 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 303 ILE Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 297 LYS Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 413 ASN Chi-restraints excluded: chain F residue 423 GLN Chi-restraints excluded: chain F residue 456 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 267 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 234 optimal weight: 10.0000 chunk 178 optimal weight: 2.9990 chunk 7 optimal weight: 0.0870 chunk 230 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 195 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- 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 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 HIS F 169 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.211669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.180244 restraints weight = 21630.107| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 1.34 r_work: 0.3952 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3812 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22170 Z= 0.117 Angle : 0.558 8.042 30030 Z= 0.295 Chirality : 0.044 0.197 3459 Planarity : 0.005 0.042 3957 Dihedral : 4.954 68.081 3084 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.59 % Allowed : 21.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 2823 helix: 1.20 (0.15), residues: 1125 sheet: 0.81 (0.25), residues: 384 loop : -0.93 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS E 179 PHE 0.023 0.001 PHE A 349 TYR 0.020 0.001 TYR E 199 ARG 0.008 0.000 ARG D 3 Details of bonding type rmsd hydrogen bonds : bond 0.04109 ( 1026) hydrogen bonds : angle 4.59914 ( 2952) covalent geometry : bond 0.00258 (22170) covalent geometry : angle 0.55842 (30030) *********************** 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 356 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 296 time to evaluate : 2.445 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: 0.7473 (OUTLIER) cc_final: 0.6319 (mp0) REVERT: A 236 PHE cc_start: 0.7042 (OUTLIER) cc_final: 0.6527 (p90) REVERT: A 278 ARG cc_start: 0.6984 (mtp85) cc_final: 0.6006 (mtm-85) REVERT: A 344 LEU cc_start: 0.6971 (OUTLIER) cc_final: 0.6721 (mt) REVERT: B 198 ILE cc_start: 0.6107 (mt) cc_final: 0.5658 (mt) REVERT: B 460 PHE cc_start: 0.7382 (t80) cc_final: 0.6840 (t80) REVERT: B 474 HIS cc_start: 0.7078 (t-90) cc_final: 0.6750 (t70) REVERT: B 476 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7217 (mtm-85) REVERT: C 198 ILE cc_start: 0.5711 (mt) cc_final: 0.5118 (mt) REVERT: C 460 PHE cc_start: 0.7506 (t80) cc_final: 0.7050 (t80) REVERT: C 476 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7433 (mtm-85) REVERT: D 64 MET cc_start: 0.6683 (mmm) cc_final: 0.6414 (mmm) REVERT: D 202 MET cc_start: 0.6313 (mmt) cc_final: 0.5647 (mmp) REVERT: D 237 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6544 (pt0) REVERT: D 406 ILE cc_start: 0.8584 (tp) cc_final: 0.8297 (tp) REVERT: D 469 MET cc_start: 0.6073 (mmp) cc_final: 0.5484 (mpp) REVERT: E 33 GLN cc_start: 0.6642 (mt0) cc_final: 0.6372 (mt0) REVERT: E 64 MET cc_start: 0.7393 (mmp) cc_final: 0.7154 (mmm) REVERT: E 237 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6456 (pt0) REVERT: E 285 MET cc_start: 0.7005 (ttt) cc_final: 0.6700 (ttm) REVERT: F 202 MET cc_start: 0.6286 (mmp) cc_final: 0.5810 (mmp) REVERT: F 285 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.6628 (ttm) REVERT: F 418 GLU cc_start: 0.6284 (pm20) cc_final: 0.5653 (pm20) outliers start: 60 outliers final: 41 residues processed: 346 average time/residue: 0.3449 time to fit residues: 181.4518 Evaluate side-chains 332 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 283 time to evaluate : 2.630 ------------------------------------------------------------------------------- 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 229 SER Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 54 GLU 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 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 476 ARG Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 196 VAL 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 476 ARG Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 90 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 265 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 456 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 231 optimal weight: 4.9990 chunk 202 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 170 optimal weight: 8.9990 chunk 242 optimal weight: 7.9990 chunk 85 optimal weight: 30.0000 chunk 139 optimal weight: 20.0000 chunk 210 optimal weight: 2.9990 chunk 221 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 474 HIS E 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.207900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.177848 restraints weight = 21933.649| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 1.16 r_work: 0.3864 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 22170 Z= 0.200 Angle : 0.655 8.123 30030 Z= 0.346 Chirality : 0.048 0.156 3459 Planarity : 0.005 0.046 3957 Dihedral : 5.240 67.654 3084 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.15 % Allowed : 20.66 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 2823 helix: 0.93 (0.15), residues: 1125 sheet: 0.63 (0.25), residues: 384 loop : -1.06 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 255 PHE 0.029 0.002 PHE D 409 TYR 0.021 0.002 TYR E 199 ARG 0.008 0.001 ARG D 3 Details of bonding type rmsd hydrogen bonds : bond 0.05322 ( 1026) hydrogen bonds : angle 4.80342 ( 2952) covalent geometry : bond 0.00481 (22170) covalent geometry : angle 0.65494 (30030) *********************** 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 361 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 288 time to evaluate : 2.720 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: 0.7430 (OUTLIER) cc_final: 0.6264 (mp0) REVERT: A 236 PHE cc_start: 0.7144 (OUTLIER) cc_final: 0.6636 (p90) REVERT: A 278 ARG cc_start: 0.6889 (mtp85) cc_final: 0.6157 (mtm-85) REVERT: A 344 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6976 (mt) REVERT: B 132 ARG cc_start: 0.7718 (mpp80) cc_final: 0.6787 (tpt170) REVERT: B 198 ILE cc_start: 0.6162 (mt) cc_final: 0.5753 (mt) REVERT: B 460 PHE cc_start: 0.7452 (t80) cc_final: 0.6982 (t80) REVERT: B 476 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7221 (mtm-85) REVERT: C 198 ILE cc_start: 0.5817 (mt) cc_final: 0.5246 (mt) REVERT: C 460 PHE cc_start: 0.7699 (t80) cc_final: 0.7317 (t80) REVERT: C 476 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7455 (mtm-85) REVERT: D 202 MET cc_start: 0.6424 (mmt) cc_final: 0.5694 (mmp) REVERT: D 237 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6740 (pt0) REVERT: D 469 MET cc_start: 0.6098 (mmp) cc_final: 0.5391 (mpp) REVERT: E 33 GLN cc_start: 0.6504 (mt0) cc_final: 0.6247 (mt0) REVERT: E 237 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6787 (pt0) REVERT: F 285 MET cc_start: 0.7294 (OUTLIER) cc_final: 0.6621 (ttm) outliers start: 73 outliers final: 58 residues processed: 345 average time/residue: 0.3589 time to fit residues: 187.9081 Evaluate side-chains 350 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 284 time to evaluate : 2.435 ------------------------------------------------------------------------------- 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 166 LEU 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 342 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 146 LEU 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 262 ASP Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 115 VAL 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 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 44 ILE Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 237 GLU 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 359 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 423 GLN Chi-restraints excluded: chain F residue 456 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 125 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 230 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 474 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.209822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.178718 restraints weight = 21779.877| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 1.31 r_work: 0.3939 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3792 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22170 Z= 0.136 Angle : 0.584 8.149 30030 Z= 0.308 Chirality : 0.045 0.153 3459 Planarity : 0.005 0.043 3957 Dihedral : 5.013 69.783 3084 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.76 % Allowed : 21.35 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 2823 helix: 1.09 (0.15), residues: 1125 sheet: 0.60 (0.25), residues: 399 loop : -0.99 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 401 PHE 0.026 0.002 PHE C 349 TYR 0.020 0.001 TYR E 199 ARG 0.009 0.000 ARG D 3 Details of bonding type rmsd hydrogen bonds : bond 0.04326 ( 1026) hydrogen bonds : angle 4.63914 ( 2952) covalent geometry : bond 0.00316 (22170) covalent geometry : angle 0.58385 (30030) ********************** 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 357 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 293 time to evaluate : 2.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6326 (mp0) REVERT: A 236 PHE cc_start: 0.7072 (OUTLIER) cc_final: 0.6591 (p90) REVERT: A 278 ARG cc_start: 0.7022 (mtp85) cc_final: 0.6050 (mtm-85) REVERT: A 344 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6755 (mt) REVERT: A 474 HIS cc_start: 0.7268 (t-90) cc_final: 0.7008 (t70) REVERT: B 132 ARG cc_start: 0.7932 (mpp80) cc_final: 0.6826 (tpt170) REVERT: B 198 ILE cc_start: 0.6233 (mt) cc_final: 0.5845 (mt) REVERT: B 460 PHE cc_start: 0.7382 (t80) cc_final: 0.6917 (t80) REVERT: B 476 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7204 (mtm-85) REVERT: C 198 ILE cc_start: 0.5824 (mt) cc_final: 0.5234 (mt) REVERT: C 460 PHE cc_start: 0.7559 (t80) cc_final: 0.7152 (t80) REVERT: C 476 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7404 (mtm-85) REVERT: D 64 MET cc_start: 0.6752 (mmm) cc_final: 0.6376 (mmm) REVERT: D 66 SER cc_start: 0.7743 (m) cc_final: 0.7541 (t) REVERT: D 202 MET cc_start: 0.6389 (mmt) cc_final: 0.5703 (mmp) REVERT: D 237 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6550 (pt0) REVERT: D 469 MET cc_start: 0.6226 (mmp) cc_final: 0.5496 (mpp) REVERT: E 33 GLN cc_start: 0.6533 (mt0) cc_final: 0.6256 (mt0) REVERT: E 64 MET cc_start: 0.7418 (mmp) cc_final: 0.7145 (mmm) REVERT: E 165 THR cc_start: 0.6410 (m) cc_final: 0.6203 (p) REVERT: E 237 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6507 (pt0) REVERT: E 303 ILE cc_start: 0.7066 (OUTLIER) cc_final: 0.6833 (mm) REVERT: F 202 MET cc_start: 0.6225 (mmp) cc_final: 0.5730 (mmp) REVERT: F 285 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.6632 (ttm) outliers start: 64 outliers final: 51 residues processed: 347 average time/residue: 0.3526 time to fit residues: 186.4524 Evaluate side-chains 350 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 290 time to evaluate : 2.232 ------------------------------------------------------------------------------- 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 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 344 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 54 GLU 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 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 476 ARG Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 115 VAL 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 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 44 ILE Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 359 VAL 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 90 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 456 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 6 optimal weight: 7.9990 chunk 219 optimal weight: 0.0870 chunk 157 optimal weight: 8.9990 chunk 203 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 220 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 474 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.211932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.182146 restraints weight = 21856.444| |-----------------------------------------------------------------------------| r_work (start): 0.4225 rms_B_bonded: 1.16 r_work: 0.3976 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3844 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22170 Z= 0.128 Angle : 0.573 9.013 30030 Z= 0.300 Chirality : 0.044 0.146 3459 Planarity : 0.005 0.044 3957 Dihedral : 4.911 71.508 3084 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.76 % Allowed : 21.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.15), residues: 2823 helix: 1.20 (0.15), residues: 1125 sheet: 0.62 (0.24), residues: 429 loop : -0.89 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 401 PHE 0.030 0.002 PHE D 409 TYR 0.020 0.001 TYR E 199 ARG 0.009 0.000 ARG D 3 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 1026) hydrogen bonds : angle 4.55962 ( 2952) covalent geometry : bond 0.00296 (22170) covalent geometry : angle 0.57265 (30030) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10807.67 seconds wall clock time: 187 minutes 10.07 seconds (11230.07 seconds total)