Starting phenix.real_space_refine on Sun Aug 24 10:28:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pto_17876/08_2025/8pto_17876.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pto_17876/08_2025/8pto_17876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pto_17876/08_2025/8pto_17876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pto_17876/08_2025/8pto_17876.map" model { file = "/net/cci-nas-00/data/ceres_data/8pto_17876/08_2025/8pto_17876.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pto_17876/08_2025/8pto_17876.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 97 5.16 5 C 11989 2.51 5 N 3372 2.21 5 O 3660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19124 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "B" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "C" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "D" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "E" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "b" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "c" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "d" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "a" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.21, per 1000 atoms: 0.22 Number of scatterers: 19124 At special positions: 0 Unit cell: (118.144, 134.784, 161.408, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 97 16.00 P 6 15.00 O 3660 8.00 N 3372 7.00 C 11989 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 564.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4522 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 23 sheets defined 46.8% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 removed outlier: 3.630A pdb=" N LEU A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A 8 " --> pdb=" O THR A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 22 removed outlier: 3.655A pdb=" N ASN A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 46 Processing helix chain 'A' and resid 82 through 89 Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 155 through 166 removed outlier: 3.893A pdb=" N ALA A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 199 Processing helix chain 'A' and resid 212 through 223 Processing helix chain 'A' and resid 235 through 255 removed outlier: 3.676A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 285 through 289 removed outlier: 4.197A pdb=" N VAL A 289 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 293 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 325 through 335 removed outlier: 4.043A pdb=" N GLU A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 339 removed outlier: 4.277A pdb=" N GLY A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 336 through 339' Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.146A pdb=" N LEU A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 388 removed outlier: 3.623A pdb=" N GLN A 378 " --> pdb=" O GLN A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 405 removed outlier: 3.588A pdb=" N MET A 396 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N MET A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 417 Processing helix chain 'B' and resid 2 through 7 removed outlier: 3.684A pdb=" N LEU B 6 " --> pdb=" O ASN B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 22 Processing helix chain 'B' and resid 30 through 44 Processing helix chain 'B' and resid 82 through 89 Processing helix chain 'B' and resid 123 through 128 removed outlier: 3.744A pdb=" N ARG B 128 " --> pdb=" O PRO B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 155 through 166 removed outlier: 4.280A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 Processing helix chain 'B' and resid 212 through 223 Processing helix chain 'B' and resid 235 through 255 removed outlier: 3.504A pdb=" N HIS B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 325 through 335 Processing helix chain 'B' and resid 336 through 339 removed outlier: 4.495A pdb=" N GLY B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 336 through 339' Processing helix chain 'B' and resid 346 through 352 Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.260A pdb=" N LEU B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 388 removed outlier: 3.518A pdb=" N LEU B 377 " --> pdb=" O THR B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 406 removed outlier: 3.563A pdb=" N MET B 396 " --> pdb=" O GLU B 392 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR B 406 " --> pdb=" O LYS B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 418 Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 10 through 22 Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 82 through 89 Processing helix chain 'C' and resid 123 through 128 removed outlier: 3.803A pdb=" N ARG C 128 " --> pdb=" O PRO C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 155 through 166 removed outlier: 4.114A pdb=" N ALA C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 199 Processing helix chain 'C' and resid 212 through 223 removed outlier: 3.566A pdb=" N THR C 217 " --> pdb=" O PRO C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 255 Processing helix chain 'C' and resid 266 through 278 Processing helix chain 'C' and resid 294 through 302 Processing helix chain 'C' and resid 325 through 333 Processing helix chain 'C' and resid 334 through 339 removed outlier: 5.369A pdb=" N GLY C 337 " --> pdb=" O GLU C 334 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR C 338 " --> pdb=" O PHE C 335 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 334 through 339' Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 367 through 372 removed outlier: 4.305A pdb=" N LEU C 371 " --> pdb=" O LYS C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 388 Processing helix chain 'C' and resid 391 through 405 removed outlier: 3.597A pdb=" N MET C 396 " --> pdb=" O GLU C 392 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 418 Processing helix chain 'D' and resid 2 through 7 removed outlier: 3.565A pdb=" N LEU D 6 " --> pdb=" O ASN D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 20 Processing helix chain 'D' and resid 30 through 44 Processing helix chain 'D' and resid 82 through 89 Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 155 through 166 removed outlier: 4.297A pdb=" N ALA D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 199 Processing helix chain 'D' and resid 212 through 223 removed outlier: 3.611A pdb=" N THR D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 255 Processing helix chain 'D' and resid 266 through 278 Processing helix chain 'D' and resid 285 through 289 removed outlier: 3.968A pdb=" N VAL D 289 " --> pdb=" O THR D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 293 No H-bonds generated for 'chain 'D' and resid 291 through 293' Processing helix chain 'D' and resid 294 through 302 Processing helix chain 'D' and resid 325 through 334 removed outlier: 3.531A pdb=" N GLU D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 352 removed outlier: 3.653A pdb=" N LYS D 352 " --> pdb=" O LYS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 372 removed outlier: 4.276A pdb=" N LEU D 371 " --> pdb=" O LYS D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 388 Processing helix chain 'D' and resid 391 through 406 removed outlier: 3.872A pdb=" N THR D 406 " --> pdb=" O LYS D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 418 Processing helix chain 'E' and resid 2 through 8 Processing helix chain 'E' and resid 10 through 21 Processing helix chain 'E' and resid 30 through 46 removed outlier: 3.735A pdb=" N SER E 45 " --> pdb=" O GLN E 41 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY E 46 " --> pdb=" O HIS E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 89 removed outlier: 3.532A pdb=" N PHE E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 128 Processing helix chain 'E' and resid 155 through 166 removed outlier: 3.997A pdb=" N ALA E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 199 Processing helix chain 'E' and resid 212 through 223 removed outlier: 3.597A pdb=" N THR E 217 " --> pdb=" O PRO E 213 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU E 218 " --> pdb=" O GLU E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 256 Processing helix chain 'E' and resid 266 through 278 Processing helix chain 'E' and resid 290 through 303 removed outlier: 4.223A pdb=" N ARG E 296 " --> pdb=" O ASN E 292 " (cutoff:3.500A) Proline residue: E 297 - end of helix Processing helix chain 'E' and resid 326 through 335 removed outlier: 3.674A pdb=" N VAL E 330 " --> pdb=" O LYS E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 352 removed outlier: 3.559A pdb=" N ALA E 350 " --> pdb=" O SER E 346 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 371 Processing helix chain 'E' and resid 373 through 388 removed outlier: 3.742A pdb=" N GLN E 378 " --> pdb=" O GLN E 374 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS E 379 " --> pdb=" O GLU E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 405 removed outlier: 3.534A pdb=" N GLU E 397 " --> pdb=" O ILE E 393 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N MET E 405 " --> pdb=" O ASN E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 418 Processing helix chain 'b' and resid 9 through 23 Processing helix chain 'b' and resid 56 through 59 Processing helix chain 'c' and resid 9 through 22 removed outlier: 3.677A pdb=" N HIS c 22 " --> pdb=" O LEU c 18 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 23 Processing helix chain 'a' and resid 9 through 22 removed outlier: 3.707A pdb=" N HIS a 22 " --> pdb=" O LEU a 18 " (cutoff:3.500A) Processing helix chain 'a' and resid 56 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 7.793A pdb=" N TYR A 80 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE A 79 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A 63 " --> pdb=" O VAL A 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139 removed outlier: 3.634A pdb=" N ASN A 306 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU A 204 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL A 228 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N VAL A 206 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N SER A 230 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 208 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 139 removed outlier: 3.634A pdb=" N ASN A 306 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLY A 174 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ALA A 319 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE A 176 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET A 341 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 49 through 57 removed outlier: 7.540A pdb=" N TYR B 80 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N LYS B 115 " --> pdb=" O TYR B 80 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS B 100 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N VAL B 116 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N SER B 98 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU B 118 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR B 96 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE B 49 " --> pdb=" O ILE B 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 138 through 139 removed outlier: 3.536A pdb=" N ASN B 306 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 226 through 231 removed outlier: 6.302A pdb=" N VAL B 203 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU B 263 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET B 205 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ASP B 265 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU B 207 " --> pdb=" O ASP B 265 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE B 316 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE B 262 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N THR B 318 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU B 264 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N LEU B 320 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG B 173 " --> pdb=" O MET B 341 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N LEU B 343 " --> pdb=" O ARG B 173 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU B 175 " --> pdb=" O LEU B 343 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 49 through 57 removed outlier: 3.882A pdb=" N ILE C 79 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS C 100 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N VAL C 116 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N SER C 98 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLU C 118 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR C 96 " --> pdb=" O GLU C 118 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE C 49 " --> pdb=" O ILE C 101 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.624A pdb=" N ASN C 306 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL C 203 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU C 263 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N MET C 205 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ASP C 265 " --> pdb=" O MET C 205 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU C 207 " --> pdb=" O ASP C 265 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.624A pdb=" N ASN C 306 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLY C 174 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ALA C 319 " --> pdb=" O GLY C 174 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE C 176 " --> pdb=" O ALA C 319 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 284 through 285 removed outlier: 3.790A pdb=" N VAL C 289 " --> pdb=" O LEU C 285 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 49 through 57 removed outlier: 3.863A pdb=" N ILE D 79 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYS D 100 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N VAL D 116 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N SER D 98 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU D 118 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR D 96 " --> pdb=" O GLU D 118 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE D 49 " --> pdb=" O ILE D 101 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 138 through 139 removed outlier: 6.323A pdb=" N VAL D 203 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N LEU D 263 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N MET D 205 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ASP D 265 " --> pdb=" O MET D 205 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU D 207 " --> pdb=" O ASP D 265 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 138 through 139 removed outlier: 6.381A pdb=" N GLY D 174 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ALA D 319 " --> pdb=" O GLY D 174 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE D 176 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 144 through 145 removed outlier: 4.374A pdb=" N ILE D 168 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 49 through 57 removed outlier: 3.876A pdb=" N ILE E 79 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU E 114 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ARG E 102 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL E 116 " --> pdb=" O LYS E 100 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LYS E 100 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILE E 49 " --> pdb=" O ILE E 101 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 138 through 139 removed outlier: 3.579A pdb=" N ASN E 306 " --> pdb=" O LEU E 139 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 226 through 231 removed outlier: 6.613A pdb=" N LEU E 204 " --> pdb=" O GLU E 226 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL E 228 " --> pdb=" O LEU E 204 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL E 206 " --> pdb=" O VAL E 228 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N SER E 230 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU E 208 " --> pdb=" O SER E 230 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLY E 174 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ALA E 319 " --> pdb=" O GLY E 174 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE E 176 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'b' and resid 35 through 37 removed outlier: 6.550A pdb=" N THR b 27 " --> pdb=" O PHE b 71 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE b 71 " --> pdb=" O THR b 27 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLU b 29 " --> pdb=" O THR b 69 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'b' and resid 40 through 46 removed outlier: 4.072A pdb=" N ASP b 42 " --> pdb=" O VAL b 53 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL b 53 " --> pdb=" O ASP b 42 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'c' and resid 61 through 64 removed outlier: 6.041A pdb=" N VAL c 49 " --> pdb=" O SER c 45 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N SER c 45 " --> pdb=" O VAL c 49 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR c 51 " --> pdb=" O LEU c 43 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LEU c 43 " --> pdb=" O TYR c 51 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL c 53 " --> pdb=" O SER c 41 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS c 39 " --> pdb=" O GLU c 55 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR c 27 " --> pdb=" O PHE c 71 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N PHE c 71 " --> pdb=" O THR c 27 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLU c 29 " --> pdb=" O THR c 69 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE c 71 " --> pdb=" O VAL c 79 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL c 79 " --> pdb=" O PHE c 71 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'd' and resid 61 through 64 removed outlier: 3.679A pdb=" N VAL d 53 " --> pdb=" O ASP d 42 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP d 42 " --> pdb=" O VAL d 53 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU d 55 " --> pdb=" O ALA d 40 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ALA d 40 " --> pdb=" O GLU d 55 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR d 27 " --> pdb=" O SER d 72 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER d 72 " --> pdb=" O THR d 27 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE d 71 " --> pdb=" O VAL d 79 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'a' and resid 35 through 38 removed outlier: 3.593A pdb=" N ALA a 38 " --> pdb=" O LEU a 26 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU a 26 " --> pdb=" O ALA a 38 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR a 27 " --> pdb=" O PHE a 71 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N PHE a 71 " --> pdb=" O THR a 27 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N GLU a 29 " --> pdb=" O THR a 69 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'a' and resid 40 through 46 removed outlier: 4.369A pdb=" N ASP a 42 " --> pdb=" O VAL a 53 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL a 53 " --> pdb=" O ASP a 42 " (cutoff:3.500A) 902 hydrogen bonds defined for protein. 2538 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.27 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6505 1.34 - 1.46: 2616 1.46 - 1.57: 10096 1.57 - 1.69: 9 1.69 - 1.81: 181 Bond restraints: 19407 Sorted by residual: bond pdb=" C4 ADP B1000 " pdb=" C5 ADP B1000 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 9.87e-01 bond pdb=" C4 ADP C1000 " pdb=" C5 ADP C1000 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 9.56e-01 bond pdb=" C4 ADP D1000 " pdb=" C5 ADP D1000 " ideal model delta sigma weight residual 1.490 1.471 0.019 2.00e-02 2.50e+03 9.18e-01 bond pdb=" CB THR C 365 " pdb=" CG2 THR C 365 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.18e-01 bond pdb=" CB VAL C 260 " pdb=" CG2 VAL C 260 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 4.98e-01 ... (remaining 19402 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 25734 1.18 - 2.36: 273 2.36 - 3.53: 114 3.53 - 4.71: 24 4.71 - 5.89: 23 Bond angle restraints: 26168 Sorted by residual: angle pdb=" O1B ADP D1000 " pdb=" PB ADP D1000 " pdb=" O3B ADP D1000 " ideal model delta sigma weight residual 119.90 114.01 5.89 3.00e+00 1.11e-01 3.85e+00 angle pdb=" O1B ADP B1000 " pdb=" PB ADP B1000 " pdb=" O3B ADP B1000 " ideal model delta sigma weight residual 119.90 114.08 5.82 3.00e+00 1.11e-01 3.76e+00 angle pdb=" C ILE E 321 " pdb=" N ASP E 322 " pdb=" CA ASP E 322 " ideal model delta sigma weight residual 121.54 125.17 -3.63 1.91e+00 2.74e-01 3.60e+00 angle pdb=" C ASP C 265 " pdb=" N SER C 266 " pdb=" CA SER C 266 " ideal model delta sigma weight residual 121.70 125.08 -3.38 1.80e+00 3.09e-01 3.52e+00 angle pdb=" O1B ADP B1000 " pdb=" PB ADP B1000 " pdb=" O2B ADP B1000 " ideal model delta sigma weight residual 119.90 114.29 5.61 3.00e+00 1.11e-01 3.50e+00 ... (remaining 26163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.18: 11653 23.18 - 46.37: 353 46.37 - 69.55: 16 69.55 - 92.73: 2 92.73 - 115.91: 4 Dihedral angle restraints: 12028 sinusoidal: 5050 harmonic: 6978 Sorted by residual: dihedral pdb=" O1B ADP B1000 " pdb=" O3A ADP B1000 " pdb=" PB ADP B1000 " pdb=" PA ADP B1000 " ideal model delta sinusoidal sigma weight residual -60.00 -175.92 115.91 1 2.00e+01 2.50e-03 3.45e+01 dihedral pdb=" O1B ADP D1000 " pdb=" O3A ADP D1000 " pdb=" PB ADP D1000 " pdb=" PA ADP D1000 " ideal model delta sinusoidal sigma weight residual -60.00 -170.28 110.28 1 2.00e+01 2.50e-03 3.23e+01 dihedral pdb=" O1B ADP C1000 " pdb=" O3A ADP C1000 " pdb=" PB ADP C1000 " pdb=" PA ADP C1000 " ideal model delta sinusoidal sigma weight residual -60.00 -162.91 102.90 1 2.00e+01 2.50e-03 2.94e+01 ... (remaining 12025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1709 0.025 - 0.049: 743 0.049 - 0.074: 294 0.074 - 0.098: 127 0.098 - 0.123: 119 Chirality restraints: 2992 Sorted by residual: chirality pdb=" CA PRO B 180 " pdb=" N PRO B 180 " pdb=" C PRO B 180 " pdb=" CB PRO B 180 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.77e-01 chirality pdb=" CA ILE E 261 " pdb=" N ILE E 261 " pdb=" C ILE E 261 " pdb=" CB ILE E 261 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.50e-01 chirality pdb=" CA ILE C 261 " pdb=" N ILE C 261 " pdb=" C ILE C 261 " pdb=" CB ILE C 261 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.40e-01 ... (remaining 2989 not shown) Planarity restraints: 3402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS b 73 " 0.023 5.00e-02 4.00e+02 3.54e-02 2.00e+00 pdb=" N PRO b 74 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO b 74 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO b 74 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 179 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO B 180 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 180 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 180 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 179 " -0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO A 180 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 180 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 180 " -0.017 5.00e-02 4.00e+02 ... (remaining 3399 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2326 2.75 - 3.29: 19334 3.29 - 3.82: 30739 3.82 - 4.36: 38377 4.36 - 4.90: 65013 Nonbonded interactions: 155789 Sorted by model distance: nonbonded pdb=" OG1 THR E 323 " pdb=" OD2 ASP E 328 " model vdw 2.212 3.040 nonbonded pdb=" NH1 ARG E 66 " pdb=" OD2 ASP E 78 " model vdw 2.232 3.120 nonbonded pdb=" OG1 THR D 408 " pdb=" OD1 ASP D 410 " model vdw 2.235 3.040 nonbonded pdb=" NH1 ARG D 66 " pdb=" OD2 ASP D 78 " model vdw 2.240 3.120 nonbonded pdb=" OG SER D 84 " pdb=" OD1 ASP d 14 " model vdw 2.245 3.040 ... (remaining 155784 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 418) selection = (chain 'C' and resid 1 through 418) selection = (chain 'D' and resid 1 through 418) selection = chain 'E' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.660 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 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 19407 Z= 0.125 Angle : 0.432 5.890 26168 Z= 0.206 Chirality : 0.039 0.123 2992 Planarity : 0.003 0.035 3402 Dihedral : 10.473 115.914 7506 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.40 % Allowed : 5.90 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.17), residues: 2400 helix: 1.31 (0.17), residues: 962 sheet: 0.59 (0.27), residues: 451 loop : 0.77 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 353 TYR 0.005 0.001 TYR B 110 PHE 0.008 0.001 PHE D 89 TRP 0.003 0.001 TRP D 381 HIS 0.003 0.001 HIS c 73 Details of bonding type rmsd covalent geometry : bond 0.00289 (19407) covalent geometry : angle 0.43183 (26168) hydrogen bonds : bond 0.24513 ( 892) hydrogen bonds : angle 7.04464 ( 2538) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 311 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.8988 (pm20) cc_final: 0.8653 (pm20) REVERT: A 42 HIS cc_start: 0.8557 (m-70) cc_final: 0.8283 (m-70) REVERT: A 333 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8452 (tm-30) REVERT: A 415 MET cc_start: 0.8737 (tmm) cc_final: 0.8495 (tmm) REVERT: B 134 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8457 (mp0) REVERT: B 378 GLN cc_start: 0.8811 (mm-40) cc_final: 0.8235 (mm110) REVERT: C 334 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8173 (mp0) REVERT: C 378 GLN cc_start: 0.8907 (mm-40) cc_final: 0.8703 (mm-40) REVERT: D 244 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8409 (mm-30) REVERT: D 284 VAL cc_start: 0.8998 (OUTLIER) cc_final: 0.8734 (t) REVERT: D 285 LEU cc_start: 0.9159 (mt) cc_final: 0.8930 (mp) REVERT: D 329 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8280 (mm-30) REVERT: E 42 HIS cc_start: 0.8273 (t70) cc_final: 0.7964 (t70) REVERT: E 211 GLU cc_start: 0.8606 (tp30) cc_final: 0.8295 (tp30) REVERT: E 341 MET cc_start: 0.7341 (tpt) cc_final: 0.6460 (tmm) REVERT: b 5 TYR cc_start: 0.8469 (t80) cc_final: 0.8130 (t80) REVERT: b 12 ASP cc_start: 0.8753 (m-30) cc_final: 0.8533 (m-30) REVERT: b 46 ARG cc_start: 0.8462 (mtm-85) cc_final: 0.8175 (mtm-85) REVERT: b 73 HIS cc_start: 0.8193 (t-90) cc_final: 0.7443 (t70) REVERT: b 79 VAL cc_start: 0.9003 (t) cc_final: 0.8767 (m) REVERT: b 82 SER cc_start: 0.8805 (p) cc_final: 0.8533 (p) REVERT: d 47 LYS cc_start: 0.8900 (mptp) cc_final: 0.8627 (tptp) REVERT: d 65 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8677 (mm) outliers start: 50 outliers final: 14 residues processed: 350 average time/residue: 0.7288 time to fit residues: 281.5838 Evaluate side-chains 271 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 255 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain c residue 26 LEU Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 73 HIS Chi-restraints excluded: chain a residue 24 LEU Chi-restraints excluded: chain a residue 80 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.0050 chunk 235 optimal weight: 4.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN D 2 ASN D 41 GLN D 85 GLN D 193 GLN D 241 GLN E 2 ASN E 140 HIS E 199 HIS E 275 ASN b 23 HIS d 6 GLN d 9 ASN d 21 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.100025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.068817 restraints weight = 42785.487| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.84 r_work: 0.2902 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19407 Z= 0.130 Angle : 0.586 9.994 26168 Z= 0.292 Chirality : 0.042 0.182 2992 Planarity : 0.004 0.041 3402 Dihedral : 6.307 96.680 2678 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.59 % Allowed : 10.79 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.17), residues: 2400 helix: 1.71 (0.17), residues: 1007 sheet: 0.61 (0.26), residues: 420 loop : 0.47 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 362 TYR 0.018 0.001 TYR E 197 PHE 0.016 0.001 PHE A 398 TRP 0.009 0.001 TRP E 381 HIS 0.006 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00284 (19407) covalent geometry : angle 0.58638 (26168) hydrogen bonds : bond 0.04602 ( 892) hydrogen bonds : angle 5.03975 ( 2538) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 273 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.9204 (mmm) cc_final: 0.8766 (mmm) REVERT: A 188 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9119 (mm) REVERT: A 333 GLU cc_start: 0.9013 (tm-30) cc_final: 0.8576 (tm-30) REVERT: A 415 MET cc_start: 0.8738 (tmm) cc_final: 0.8503 (tmm) REVERT: B 1 MET cc_start: 0.8366 (pmm) cc_final: 0.8024 (pmm) REVERT: B 134 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8488 (mp0) REVERT: B 362 ARG cc_start: 0.9185 (mtp85) cc_final: 0.8946 (ttm-80) REVERT: B 374 GLN cc_start: 0.8046 (tp-100) cc_final: 0.7469 (tp-100) REVERT: B 378 GLN cc_start: 0.8830 (mm-40) cc_final: 0.8350 (mm110) REVERT: C 378 GLN cc_start: 0.8922 (mm-40) cc_final: 0.8710 (mm-40) REVERT: D 58 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8478 (mm) REVERT: D 244 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8481 (mm-30) REVERT: D 284 VAL cc_start: 0.8831 (OUTLIER) cc_final: 0.8631 (t) REVERT: D 329 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8280 (mm-30) REVERT: D 341 MET cc_start: 0.8459 (tmt) cc_final: 0.8129 (tmt) REVERT: E 42 HIS cc_start: 0.8278 (t70) cc_final: 0.7965 (t70) REVERT: E 211 GLU cc_start: 0.8457 (tp30) cc_final: 0.8094 (tp30) REVERT: E 234 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8405 (mt-10) REVERT: E 244 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8267 (mm-30) REVERT: E 332 TYR cc_start: 0.9300 (t80) cc_final: 0.9016 (t80) REVERT: E 336 LYS cc_start: 0.8949 (mtmm) cc_final: 0.8553 (mmmm) REVERT: E 341 MET cc_start: 0.7112 (OUTLIER) cc_final: 0.6825 (tmm) REVERT: E 388 HIS cc_start: 0.9157 (t-90) cc_final: 0.8617 (t-90) REVERT: E 396 MET cc_start: 0.8789 (tpp) cc_final: 0.8588 (mmm) REVERT: b 25 MET cc_start: 0.8306 (tpp) cc_final: 0.7885 (tpp) REVERT: b 46 ARG cc_start: 0.8729 (mtm-85) cc_final: 0.8224 (mtm-85) REVERT: b 50 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8172 (mt-10) REVERT: b 51 TYR cc_start: 0.8159 (m-80) cc_final: 0.7890 (m-80) REVERT: b 73 HIS cc_start: 0.7922 (t-90) cc_final: 0.7282 (t-90) REVERT: b 79 VAL cc_start: 0.8498 (t) cc_final: 0.8263 (m) REVERT: d 47 LYS cc_start: 0.9017 (mptp) cc_final: 0.8592 (tptp) outliers start: 54 outliers final: 17 residues processed: 305 average time/residue: 0.7151 time to fit residues: 242.2586 Evaluate side-chains 270 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 248 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain b residue 16 LEU Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 72 SER Chi-restraints excluded: chain c residue 26 LEU Chi-restraints excluded: chain d residue 73 HIS Chi-restraints excluded: chain a residue 24 LEU Chi-restraints excluded: chain a residue 80 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 193 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 214 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 178 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 112 optimal weight: 0.4980 chunk 95 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 193 GLN E 32 GLN E 140 HIS d 9 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.099307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.067998 restraints weight = 43387.712| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.85 r_work: 0.2888 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19407 Z= 0.146 Angle : 0.566 9.747 26168 Z= 0.277 Chirality : 0.041 0.134 2992 Planarity : 0.004 0.043 3402 Dihedral : 6.179 94.367 2671 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.88 % Allowed : 11.36 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.18), residues: 2400 helix: 1.85 (0.17), residues: 1009 sheet: 0.36 (0.26), residues: 436 loop : 0.44 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 109 TYR 0.019 0.001 TYR E 197 PHE 0.015 0.001 PHE A 398 TRP 0.004 0.001 TRP E 381 HIS 0.006 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00337 (19407) covalent geometry : angle 0.56564 (26168) hydrogen bonds : bond 0.04069 ( 892) hydrogen bonds : angle 4.73761 ( 2538) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 268 time to evaluate : 0.884 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 186 MET cc_start: 0.9214 (mmm) cc_final: 0.8827 (mmm) REVERT: A 188 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9160 (mm) REVERT: A 415 MET cc_start: 0.8669 (tmm) cc_final: 0.8466 (tmm) REVERT: B 32 GLN cc_start: 0.9057 (mm-40) cc_final: 0.8785 (mp10) REVERT: B 134 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8478 (mp0) REVERT: B 244 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8324 (mm-30) REVERT: B 374 GLN cc_start: 0.8031 (tp-100) cc_final: 0.7368 (tp-100) REVERT: B 378 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8338 (mm110) REVERT: C 193 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8462 (mp10) REVERT: D 58 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8562 (mm) REVERT: D 234 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8451 (mt-10) REVERT: D 329 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8200 (mm-30) REVERT: D 341 MET cc_start: 0.8548 (tmt) cc_final: 0.8296 (tmt) REVERT: D 405 MET cc_start: 0.8955 (mtm) cc_final: 0.8736 (mtm) REVERT: E 41 GLN cc_start: 0.8633 (tp40) cc_final: 0.8146 (tm-30) REVERT: E 211 GLU cc_start: 0.8488 (tp30) cc_final: 0.8171 (tp30) REVERT: E 234 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8354 (mt-10) REVERT: E 244 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8346 (mm-30) REVERT: E 332 TYR cc_start: 0.9266 (t80) cc_final: 0.8863 (t80) REVERT: E 336 LYS cc_start: 0.8936 (mtmm) cc_final: 0.8552 (mmmm) REVERT: E 341 MET cc_start: 0.7224 (OUTLIER) cc_final: 0.6875 (tmm) REVERT: b 25 MET cc_start: 0.8392 (tpp) cc_final: 0.8027 (tpp) REVERT: b 46 ARG cc_start: 0.8744 (mtm-85) cc_final: 0.8448 (mtm-85) REVERT: b 50 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8140 (mt-10) REVERT: b 73 HIS cc_start: 0.7856 (t-90) cc_final: 0.7144 (t-90) REVERT: b 79 VAL cc_start: 0.8489 (t) cc_final: 0.8243 (m) REVERT: d 46 ARG cc_start: 0.8502 (tpp80) cc_final: 0.7801 (mmt90) REVERT: d 47 LYS cc_start: 0.9044 (mptp) cc_final: 0.8485 (tptp) outliers start: 60 outliers final: 21 residues processed: 305 average time/residue: 0.7221 time to fit residues: 244.8826 Evaluate side-chains 278 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 251 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain c residue 26 LEU Chi-restraints excluded: chain c residue 80 VAL Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain d residue 9 ASN Chi-restraints excluded: chain d residue 73 HIS Chi-restraints excluded: chain a residue 24 LEU Chi-restraints excluded: chain a residue 80 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 177 optimal weight: 0.0010 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 213 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 chunk 111 optimal weight: 0.2980 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 140 HIS E 193 GLN E 374 GLN ** E 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 9 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.099680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.068359 restraints weight = 43021.163| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.86 r_work: 0.2893 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19407 Z= 0.133 Angle : 0.562 10.055 26168 Z= 0.273 Chirality : 0.041 0.133 2992 Planarity : 0.004 0.046 3402 Dihedral : 6.101 95.138 2670 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.25 % Allowed : 12.56 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.18), residues: 2400 helix: 1.92 (0.17), residues: 1009 sheet: 0.26 (0.26), residues: 436 loop : 0.43 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 362 TYR 0.019 0.001 TYR E 197 PHE 0.015 0.001 PHE A 62 TRP 0.002 0.000 TRP E 381 HIS 0.005 0.001 HIS E 140 Details of bonding type rmsd covalent geometry : bond 0.00308 (19407) covalent geometry : angle 0.56221 (26168) hydrogen bonds : bond 0.03616 ( 892) hydrogen bonds : angle 4.53553 ( 2538) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 263 time to evaluate : 0.768 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 186 MET cc_start: 0.9222 (mmm) cc_final: 0.8813 (mmm) REVERT: A 188 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9120 (mm) REVERT: A 329 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8055 (mp0) REVERT: A 342 GLU cc_start: 0.8560 (tt0) cc_final: 0.7744 (tm-30) REVERT: B 1 MET cc_start: 0.8170 (pmm) cc_final: 0.7861 (pmm) REVERT: B 32 GLN cc_start: 0.9031 (mm-40) cc_final: 0.8727 (mp10) REVERT: B 134 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8477 (mp0) REVERT: B 244 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8291 (mm-30) REVERT: B 374 GLN cc_start: 0.7992 (tp-100) cc_final: 0.7298 (tp-100) REVERT: B 378 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8384 (mm110) REVERT: C 58 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8742 (mm) REVERT: C 193 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8464 (mp10) REVERT: C 244 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8278 (mm-30) REVERT: C 326 LYS cc_start: 0.8839 (mmmm) cc_final: 0.8638 (mmmm) REVERT: C 378 GLN cc_start: 0.8913 (mm-40) cc_final: 0.8689 (mm-40) REVERT: D 58 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8548 (mm) REVERT: D 234 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8362 (mt-10) REVERT: D 329 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8172 (mm-30) REVERT: D 341 MET cc_start: 0.8551 (tmt) cc_final: 0.8280 (tmt) REVERT: D 405 MET cc_start: 0.8921 (mtt) cc_final: 0.8682 (mtm) REVERT: E 193 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8197 (pm20) REVERT: E 211 GLU cc_start: 0.8459 (tp30) cc_final: 0.8139 (tp30) REVERT: E 244 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8328 (mm-30) REVERT: E 336 LYS cc_start: 0.8968 (mtmm) cc_final: 0.8604 (mtpp) REVERT: E 341 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6896 (tmm) REVERT: E 396 MET cc_start: 0.8777 (mmm) cc_final: 0.8566 (mmm) REVERT: E 416 MET cc_start: 0.7025 (OUTLIER) cc_final: 0.6671 (ttp) REVERT: b 25 MET cc_start: 0.8446 (tpp) cc_final: 0.8149 (tpp) REVERT: b 46 ARG cc_start: 0.8744 (mtm-85) cc_final: 0.8407 (mtm-85) REVERT: b 50 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8128 (mt-10) REVERT: b 73 HIS cc_start: 0.7807 (t-90) cc_final: 0.7175 (t-90) REVERT: b 79 VAL cc_start: 0.8457 (t) cc_final: 0.8207 (m) REVERT: d 46 ARG cc_start: 0.8582 (tpp80) cc_final: 0.7911 (mmt90) REVERT: d 47 LYS cc_start: 0.9060 (mptp) cc_final: 0.8471 (tptp) outliers start: 47 outliers final: 20 residues processed: 296 average time/residue: 0.7197 time to fit residues: 236.5638 Evaluate side-chains 272 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 244 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 72 SER Chi-restraints excluded: chain c residue 26 LEU Chi-restraints excluded: chain c residue 80 VAL Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain a residue 24 LEU Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 80 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 125 optimal weight: 0.0040 chunk 79 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 235 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 185 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 378 GLN E 140 HIS E 193 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.099873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.068753 restraints weight = 42926.235| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.84 r_work: 0.2903 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19407 Z= 0.118 Angle : 0.565 10.597 26168 Z= 0.271 Chirality : 0.041 0.131 2992 Planarity : 0.003 0.047 3402 Dihedral : 5.941 95.080 2667 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.35 % Allowed : 13.37 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.18), residues: 2400 helix: 2.03 (0.17), residues: 1001 sheet: 0.22 (0.25), residues: 436 loop : 0.39 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 362 TYR 0.020 0.001 TYR E 197 PHE 0.014 0.001 PHE A 398 TRP 0.002 0.000 TRP E 381 HIS 0.004 0.001 HIS E 140 Details of bonding type rmsd covalent geometry : bond 0.00273 (19407) covalent geometry : angle 0.56492 (26168) hydrogen bonds : bond 0.03335 ( 892) hydrogen bonds : angle 4.40036 ( 2538) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 254 time to evaluate : 0.843 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 186 MET cc_start: 0.9200 (mmm) cc_final: 0.8816 (mmm) REVERT: A 188 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9129 (mm) REVERT: A 329 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8123 (mp0) REVERT: A 342 GLU cc_start: 0.8568 (tt0) cc_final: 0.7763 (tm-30) REVERT: B 1 MET cc_start: 0.8219 (pmm) cc_final: 0.7853 (pmm) REVERT: B 32 GLN cc_start: 0.9020 (mm-40) cc_final: 0.8715 (mp10) REVERT: B 134 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8485 (mp0) REVERT: B 244 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8322 (mm-30) REVERT: B 374 GLN cc_start: 0.7947 (tp-100) cc_final: 0.7223 (tp-100) REVERT: B 378 GLN cc_start: 0.8873 (mm-40) cc_final: 0.8364 (mm110) REVERT: B 408 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8513 (t) REVERT: C 193 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8458 (mp10) REVERT: C 244 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8242 (mm-30) REVERT: C 378 GLN cc_start: 0.8877 (mm-40) cc_final: 0.8660 (mm-40) REVERT: D 58 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8557 (mm) REVERT: D 234 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8313 (mt-10) REVERT: D 329 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8310 (mm-30) REVERT: D 405 MET cc_start: 0.8875 (mtt) cc_final: 0.8629 (mtm) REVERT: E 21 MET cc_start: 0.8464 (mtp) cc_final: 0.7792 (ttt) REVERT: E 193 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8353 (pm20) REVERT: E 211 GLU cc_start: 0.8446 (tp30) cc_final: 0.8106 (tp30) REVERT: E 244 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8299 (mm-30) REVERT: E 336 LYS cc_start: 0.8959 (mtmm) cc_final: 0.8549 (mmmm) REVERT: E 341 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.6904 (tmm) REVERT: E 416 MET cc_start: 0.7011 (ttt) cc_final: 0.6656 (ttp) REVERT: b 16 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8223 (mp) REVERT: b 25 MET cc_start: 0.8484 (tpp) cc_final: 0.8233 (tpp) REVERT: b 46 ARG cc_start: 0.8782 (mtm-85) cc_final: 0.8400 (mtm-85) REVERT: b 50 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8157 (mt-10) REVERT: b 73 HIS cc_start: 0.7624 (t-90) cc_final: 0.7045 (t-90) REVERT: b 79 VAL cc_start: 0.8488 (t) cc_final: 0.8236 (m) REVERT: d 46 ARG cc_start: 0.8641 (tpp80) cc_final: 0.8026 (mmt90) REVERT: d 47 LYS cc_start: 0.9077 (mptp) cc_final: 0.8501 (tptp) outliers start: 49 outliers final: 21 residues processed: 286 average time/residue: 0.7369 time to fit residues: 234.0814 Evaluate side-chains 268 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 239 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain b residue 16 LEU Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 72 SER Chi-restraints excluded: chain c residue 26 LEU Chi-restraints excluded: chain c residue 80 VAL Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain a residue 24 LEU Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 80 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 171 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 193 GLN E 140 HIS E 193 GLN E 388 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.098162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.066768 restraints weight = 42481.893| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.80 r_work: 0.2849 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 19407 Z= 0.230 Angle : 0.609 10.162 26168 Z= 0.295 Chirality : 0.042 0.135 2992 Planarity : 0.004 0.046 3402 Dihedral : 6.039 96.817 2667 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.54 % Allowed : 14.00 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.17), residues: 2400 helix: 1.89 (0.17), residues: 1003 sheet: 0.28 (0.26), residues: 423 loop : 0.29 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 362 TYR 0.022 0.001 TYR E 197 PHE 0.013 0.001 PHE E 232 TRP 0.004 0.001 TRP E 381 HIS 0.004 0.001 HIS E 42 Details of bonding type rmsd covalent geometry : bond 0.00542 (19407) covalent geometry : angle 0.60916 (26168) hydrogen bonds : bond 0.03958 ( 892) hydrogen bonds : angle 4.50747 ( 2538) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 240 time to evaluate : 0.840 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 186 MET cc_start: 0.9206 (mmm) cc_final: 0.8878 (mmm) REVERT: A 188 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9168 (mm) REVERT: A 329 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8177 (mp0) REVERT: A 342 GLU cc_start: 0.8599 (tt0) cc_final: 0.8360 (tt0) REVERT: B 1 MET cc_start: 0.8275 (pmm) cc_final: 0.7938 (pmm) REVERT: B 134 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8535 (mp0) REVERT: B 408 THR cc_start: 0.8785 (OUTLIER) cc_final: 0.8563 (t) REVERT: C 58 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8764 (mm) REVERT: C 193 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8524 (mp10) REVERT: C 378 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8693 (mm-40) REVERT: D 58 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8663 (mm) REVERT: D 234 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8491 (mt-10) REVERT: D 289 VAL cc_start: 0.9035 (t) cc_final: 0.8690 (m) REVERT: D 329 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8361 (mm-30) REVERT: D 341 MET cc_start: 0.8614 (tmt) cc_final: 0.8362 (tmt) REVERT: D 405 MET cc_start: 0.8873 (mtt) cc_final: 0.8638 (mtm) REVERT: E 193 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8354 (pm20) REVERT: E 211 GLU cc_start: 0.8489 (tp30) cc_final: 0.8176 (tp30) REVERT: E 244 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8314 (mm-30) REVERT: E 332 TYR cc_start: 0.9198 (t80) cc_final: 0.8808 (t80) REVERT: E 336 LYS cc_start: 0.8983 (mtmm) cc_final: 0.8574 (mmmm) REVERT: E 341 MET cc_start: 0.7267 (OUTLIER) cc_final: 0.6935 (tmm) REVERT: E 384 ARG cc_start: 0.9050 (tmt-80) cc_final: 0.8723 (ttp80) REVERT: E 416 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6728 (ttp) REVERT: b 16 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8272 (mp) REVERT: b 25 MET cc_start: 0.8464 (tpp) cc_final: 0.8154 (tpp) REVERT: b 46 ARG cc_start: 0.8767 (mtm-85) cc_final: 0.8500 (mtm-85) REVERT: b 50 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8173 (mt-10) REVERT: b 73 HIS cc_start: 0.7710 (t-90) cc_final: 0.7043 (t-90) REVERT: b 79 VAL cc_start: 0.8487 (t) cc_final: 0.8218 (m) REVERT: d 46 ARG cc_start: 0.8627 (tpp80) cc_final: 0.7984 (mmt90) REVERT: d 47 LYS cc_start: 0.9088 (mptp) cc_final: 0.8540 (tptp) outliers start: 53 outliers final: 23 residues processed: 277 average time/residue: 0.6975 time to fit residues: 215.4361 Evaluate side-chains 272 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 239 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain b residue 16 LEU Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 72 SER Chi-restraints excluded: chain c residue 26 LEU Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain a residue 24 LEU Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 80 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 167 optimal weight: 0.7980 chunk 171 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 160 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 170 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 32 GLN E 140 HIS E 193 GLN E 198 ASN E 388 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.099402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.068436 restraints weight = 42713.680| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.79 r_work: 0.2885 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19407 Z= 0.125 Angle : 0.581 11.042 26168 Z= 0.278 Chirality : 0.041 0.133 2992 Planarity : 0.003 0.047 3402 Dihedral : 5.934 96.275 2667 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.06 % Allowed : 14.81 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.18), residues: 2400 helix: 1.96 (0.17), residues: 1003 sheet: 0.27 (0.25), residues: 428 loop : 0.31 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 362 TYR 0.023 0.001 TYR E 197 PHE 0.014 0.001 PHE A 398 TRP 0.002 0.000 TRP D 381 HIS 0.003 0.001 HIS E 239 Details of bonding type rmsd covalent geometry : bond 0.00293 (19407) covalent geometry : angle 0.58119 (26168) hydrogen bonds : bond 0.03333 ( 892) hydrogen bonds : angle 4.34296 ( 2538) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 252 time to evaluate : 0.822 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 32 GLN cc_start: 0.9182 (pm20) cc_final: 0.8952 (pm20) REVERT: A 186 MET cc_start: 0.9198 (mmm) cc_final: 0.8874 (mmm) REVERT: A 188 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9148 (mm) REVERT: A 244 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8009 (mp0) REVERT: A 329 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8254 (mp0) REVERT: A 342 GLU cc_start: 0.8600 (tt0) cc_final: 0.8319 (tt0) REVERT: B 1 MET cc_start: 0.8273 (pmm) cc_final: 0.7982 (pmm) REVERT: B 32 GLN cc_start: 0.9042 (mm-40) cc_final: 0.8717 (mp10) REVERT: B 134 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8489 (mp0) REVERT: B 374 GLN cc_start: 0.7960 (tp-100) cc_final: 0.7189 (tp-100) REVERT: B 378 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8353 (mm110) REVERT: B 408 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8538 (t) REVERT: C 58 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8773 (mm) REVERT: C 87 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8246 (ttp80) REVERT: C 193 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8493 (mp10) REVERT: C 378 GLN cc_start: 0.8869 (mm-40) cc_final: 0.8619 (mm-40) REVERT: D 234 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8364 (mt-10) REVERT: D 244 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8413 (mm-30) REVERT: D 289 VAL cc_start: 0.9034 (t) cc_final: 0.8738 (m) REVERT: D 329 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8305 (mm-30) REVERT: D 341 MET cc_start: 0.8555 (tmt) cc_final: 0.8280 (tmt) REVERT: D 374 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8337 (tp40) REVERT: D 405 MET cc_start: 0.8824 (mtt) cc_final: 0.8601 (mtm) REVERT: E 193 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8385 (pm20) REVERT: E 211 GLU cc_start: 0.8483 (tp30) cc_final: 0.8146 (tp30) REVERT: E 244 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8291 (mm-30) REVERT: E 336 LYS cc_start: 0.8965 (mtmm) cc_final: 0.8565 (mmmm) REVERT: E 341 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6908 (tmm) REVERT: E 384 ARG cc_start: 0.9026 (tmt-80) cc_final: 0.8702 (ttp80) REVERT: E 416 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6733 (ttp) REVERT: b 16 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8300 (mp) REVERT: b 25 MET cc_start: 0.8448 (tpp) cc_final: 0.8150 (tpp) REVERT: b 46 ARG cc_start: 0.8766 (mtm-85) cc_final: 0.8487 (mtm-85) REVERT: b 50 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8072 (mt-10) REVERT: b 73 HIS cc_start: 0.7623 (t-90) cc_final: 0.6995 (t-90) REVERT: b 79 VAL cc_start: 0.8499 (t) cc_final: 0.8240 (m) REVERT: d 46 ARG cc_start: 0.8645 (tpp80) cc_final: 0.7967 (mmt90) REVERT: d 47 LYS cc_start: 0.9075 (mptp) cc_final: 0.8530 (tptp) outliers start: 43 outliers final: 21 residues processed: 280 average time/residue: 0.7372 time to fit residues: 229.2517 Evaluate side-chains 270 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 239 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain b residue 16 LEU Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain c residue 26 LEU Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain a residue 24 LEU Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 80 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 31 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 165 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 236 optimal weight: 10.0000 chunk 190 optimal weight: 0.9990 chunk 144 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 378 GLN E 140 HIS E 193 GLN E 388 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.099374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.068441 restraints weight = 42616.321| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.79 r_work: 0.2883 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19407 Z= 0.135 Angle : 0.596 11.467 26168 Z= 0.285 Chirality : 0.041 0.147 2992 Planarity : 0.003 0.047 3402 Dihedral : 5.892 96.366 2667 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.97 % Allowed : 15.58 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.18), residues: 2400 helix: 1.94 (0.17), residues: 1003 sheet: 0.29 (0.25), residues: 428 loop : 0.32 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 362 TYR 0.024 0.001 TYR E 197 PHE 0.013 0.001 PHE A 398 TRP 0.002 0.000 TRP D 381 HIS 0.003 0.001 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00318 (19407) covalent geometry : angle 0.59644 (26168) hydrogen bonds : bond 0.03328 ( 892) hydrogen bonds : angle 4.30962 ( 2538) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 242 time to evaluate : 0.865 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 32 GLN cc_start: 0.9172 (pm20) cc_final: 0.8938 (pm20) REVERT: A 186 MET cc_start: 0.9201 (mmm) cc_final: 0.8874 (mmm) REVERT: A 188 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9169 (mm) REVERT: A 244 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8031 (mp0) REVERT: A 329 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8282 (mp0) REVERT: B 134 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8490 (mp0) REVERT: B 244 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8376 (mm-30) REVERT: C 87 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8310 (ttp80) REVERT: C 193 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8491 (mp10) REVERT: C 244 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8250 (mm-30) REVERT: C 378 GLN cc_start: 0.8869 (mm-40) cc_final: 0.8616 (mm-40) REVERT: D 234 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8346 (mt-10) REVERT: D 244 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8424 (mm-30) REVERT: D 289 VAL cc_start: 0.9027 (t) cc_final: 0.8746 (m) REVERT: D 329 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8309 (mm-30) REVERT: D 341 MET cc_start: 0.8572 (tmt) cc_final: 0.8367 (tmt) REVERT: D 374 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8353 (tp40) REVERT: D 405 MET cc_start: 0.8816 (mtt) cc_final: 0.8601 (mtm) REVERT: E 21 MET cc_start: 0.8896 (mtp) cc_final: 0.7569 (ttt) REVERT: E 41 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.7254 (tt0) REVERT: E 193 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8377 (pm20) REVERT: E 211 GLU cc_start: 0.8483 (tp30) cc_final: 0.8153 (tp30) REVERT: E 244 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8299 (mm-30) REVERT: E 336 LYS cc_start: 0.8966 (mtmm) cc_final: 0.8576 (mmmm) REVERT: E 341 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.6905 (tmm) REVERT: E 384 ARG cc_start: 0.8997 (tmt-80) cc_final: 0.8713 (ttp80) REVERT: E 416 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6722 (ttp) REVERT: b 25 MET cc_start: 0.8460 (tpp) cc_final: 0.8174 (tpp) REVERT: b 46 ARG cc_start: 0.8765 (mtm-85) cc_final: 0.8385 (mtm-85) REVERT: b 50 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8038 (mt-10) REVERT: b 73 HIS cc_start: 0.7587 (t-90) cc_final: 0.6957 (t-90) REVERT: b 79 VAL cc_start: 0.8513 (t) cc_final: 0.8258 (m) REVERT: d 46 ARG cc_start: 0.8635 (tpp80) cc_final: 0.7978 (mmt90) REVERT: d 47 LYS cc_start: 0.9064 (mptp) cc_final: 0.8523 (tptp) outliers start: 41 outliers final: 21 residues processed: 273 average time/residue: 0.7368 time to fit residues: 223.6779 Evaluate side-chains 270 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 241 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain c residue 26 LEU Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain a residue 24 LEU Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 80 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 201 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 1 optimal weight: 9.9990 chunk 102 optimal weight: 0.5980 chunk 221 optimal weight: 8.9990 chunk 57 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 344 HIS E 140 HIS E 193 GLN E 388 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.099544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.068793 restraints weight = 42543.065| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.77 r_work: 0.2889 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19407 Z= 0.127 Angle : 0.605 11.354 26168 Z= 0.290 Chirality : 0.041 0.131 2992 Planarity : 0.003 0.046 3402 Dihedral : 5.843 95.836 2667 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.58 % Allowed : 16.30 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.18), residues: 2400 helix: 1.96 (0.17), residues: 1002 sheet: 0.34 (0.26), residues: 423 loop : 0.30 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 362 TYR 0.024 0.001 TYR E 197 PHE 0.013 0.001 PHE A 398 TRP 0.002 0.000 TRP D 381 HIS 0.003 0.001 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00300 (19407) covalent geometry : angle 0.60522 (26168) hydrogen bonds : bond 0.03197 ( 892) hydrogen bonds : angle 4.26720 ( 2538) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 248 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.9191 (pm20) cc_final: 0.8956 (pm20) REVERT: A 186 MET cc_start: 0.9185 (mmm) cc_final: 0.8786 (mmm) REVERT: A 188 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9167 (mm) REVERT: A 244 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8047 (mp0) REVERT: A 329 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8291 (mp0) REVERT: A 342 GLU cc_start: 0.8455 (tt0) cc_final: 0.7745 (tm-30) REVERT: B 32 GLN cc_start: 0.9038 (mm-40) cc_final: 0.8727 (mp10) REVERT: B 134 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8493 (mp0) REVERT: B 244 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8358 (mm-30) REVERT: B 347 ARG cc_start: 0.8715 (tpt-90) cc_final: 0.8354 (tpp80) REVERT: B 374 GLN cc_start: 0.7964 (tp-100) cc_final: 0.7225 (tp-100) REVERT: B 378 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8406 (mm110) REVERT: C 87 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8336 (ttp80) REVERT: C 193 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8455 (mp10) REVERT: C 244 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8266 (mm-30) REVERT: C 378 GLN cc_start: 0.8874 (mm-40) cc_final: 0.8622 (mm-40) REVERT: D 58 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8719 (mm) REVERT: D 234 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8305 (mt-10) REVERT: D 289 VAL cc_start: 0.9016 (t) cc_final: 0.8734 (m) REVERT: D 329 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8297 (mm-30) REVERT: D 341 MET cc_start: 0.8574 (tmt) cc_final: 0.8307 (tmt) REVERT: D 374 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8363 (tp40) REVERT: D 405 MET cc_start: 0.8808 (mtt) cc_final: 0.8600 (mtm) REVERT: E 193 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8419 (pm20) REVERT: E 211 GLU cc_start: 0.8464 (tp30) cc_final: 0.8126 (tp30) REVERT: E 244 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8300 (mm-30) REVERT: E 326 LYS cc_start: 0.9400 (tppp) cc_final: 0.8877 (tmtt) REVERT: E 336 LYS cc_start: 0.8960 (mtmm) cc_final: 0.8584 (mmmm) REVERT: E 341 MET cc_start: 0.7246 (OUTLIER) cc_final: 0.6903 (tmm) REVERT: E 384 ARG cc_start: 0.8977 (tmt-80) cc_final: 0.8757 (ttp80) REVERT: E 416 MET cc_start: 0.6973 (OUTLIER) cc_final: 0.6619 (ttp) REVERT: b 16 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8296 (mp) REVERT: b 25 MET cc_start: 0.8453 (tpp) cc_final: 0.8161 (tpp) REVERT: b 46 ARG cc_start: 0.8763 (mtm-85) cc_final: 0.8378 (mtm-85) REVERT: b 50 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8084 (mt-10) REVERT: b 73 HIS cc_start: 0.7436 (t-90) cc_final: 0.6826 (t-90) REVERT: b 79 VAL cc_start: 0.8511 (t) cc_final: 0.8280 (m) REVERT: d 46 ARG cc_start: 0.8641 (tpp80) cc_final: 0.7994 (mmt90) REVERT: d 47 LYS cc_start: 0.9085 (mptp) cc_final: 0.8546 (tptp) REVERT: d 73 HIS cc_start: 0.8057 (t-170) cc_final: 0.7476 (t70) outliers start: 33 outliers final: 19 residues processed: 270 average time/residue: 0.7547 time to fit residues: 226.1330 Evaluate side-chains 267 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 239 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain b residue 16 LEU Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain c residue 26 LEU Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 80 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 44 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 210 optimal weight: 30.0000 chunk 166 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 124 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 119 optimal weight: 4.9990 chunk 224 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 344 HIS E 140 HIS E 193 GLN E 388 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.099306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.068302 restraints weight = 42398.287| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.80 r_work: 0.2884 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19407 Z= 0.149 Angle : 0.628 11.763 26168 Z= 0.299 Chirality : 0.042 0.186 2992 Planarity : 0.003 0.046 3402 Dihedral : 5.821 95.686 2665 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.73 % Allowed : 16.63 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.18), residues: 2400 helix: 1.91 (0.17), residues: 1002 sheet: 0.24 (0.26), residues: 431 loop : 0.31 (0.20), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 362 TYR 0.025 0.001 TYR E 197 PHE 0.012 0.001 PHE A 398 TRP 0.002 0.000 TRP D 381 HIS 0.003 0.001 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00355 (19407) covalent geometry : angle 0.62800 (26168) hydrogen bonds : bond 0.03341 ( 892) hydrogen bonds : angle 4.29188 ( 2538) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 242 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.9189 (pm20) cc_final: 0.8955 (pm20) REVERT: A 186 MET cc_start: 0.9176 (mmm) cc_final: 0.8839 (mmm) REVERT: A 188 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9171 (mm) REVERT: A 244 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8006 (mp0) REVERT: A 329 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8301 (mp0) REVERT: A 342 GLU cc_start: 0.8484 (tt0) cc_final: 0.7766 (tm-30) REVERT: B 32 GLN cc_start: 0.9036 (mm-40) cc_final: 0.8724 (mp10) REVERT: B 134 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8493 (mp0) REVERT: B 244 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8358 (mm-30) REVERT: B 347 ARG cc_start: 0.8727 (tpt-90) cc_final: 0.8364 (tpp80) REVERT: B 374 GLN cc_start: 0.8012 (tp-100) cc_final: 0.7297 (tp-100) REVERT: B 378 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8402 (mm110) REVERT: C 87 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8339 (ttp80) REVERT: C 193 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8495 (mp10) REVERT: C 244 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8272 (mm-30) REVERT: C 378 GLN cc_start: 0.8875 (mm-40) cc_final: 0.8624 (mm-40) REVERT: D 58 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8742 (mm) REVERT: D 234 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8362 (mt-10) REVERT: D 244 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8507 (mm-30) REVERT: D 289 VAL cc_start: 0.9003 (t) cc_final: 0.8709 (m) REVERT: D 329 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8313 (mm-30) REVERT: D 341 MET cc_start: 0.8586 (tmt) cc_final: 0.8316 (tmt) REVERT: D 405 MET cc_start: 0.8805 (mtt) cc_final: 0.8601 (mtm) REVERT: E 193 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8378 (mp10) REVERT: E 211 GLU cc_start: 0.8459 (tp30) cc_final: 0.8133 (tp30) REVERT: E 244 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8307 (mm-30) REVERT: E 336 LYS cc_start: 0.8955 (mtmm) cc_final: 0.8600 (mmmm) REVERT: E 341 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.6955 (tmm) REVERT: E 384 ARG cc_start: 0.8980 (tmt-80) cc_final: 0.8770 (ttp80) REVERT: E 416 MET cc_start: 0.6945 (OUTLIER) cc_final: 0.6587 (ttp) REVERT: b 16 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8308 (mp) REVERT: b 25 MET cc_start: 0.8484 (tpp) cc_final: 0.8200 (tpp) REVERT: b 46 ARG cc_start: 0.8780 (mtm-85) cc_final: 0.8383 (mtm-85) REVERT: b 50 GLU cc_start: 0.8724 (mt-10) cc_final: 0.7978 (mt-10) REVERT: b 73 HIS cc_start: 0.7464 (t-90) cc_final: 0.6817 (t-90) REVERT: b 79 VAL cc_start: 0.8519 (t) cc_final: 0.8288 (m) REVERT: d 46 ARG cc_start: 0.8656 (tpp80) cc_final: 0.8020 (mmt90) REVERT: d 47 LYS cc_start: 0.9105 (mptp) cc_final: 0.8556 (tptp) REVERT: d 73 HIS cc_start: 0.8042 (t-170) cc_final: 0.7585 (t70) outliers start: 36 outliers final: 20 residues processed: 267 average time/residue: 0.7436 time to fit residues: 220.5166 Evaluate side-chains 267 residues out of total 2086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 238 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 416 MET Chi-restraints excluded: chain b residue 16 LEU Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain c residue 26 LEU Chi-restraints excluded: chain c residue 81 VAL Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 80 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 182 optimal weight: 0.6980 chunk 174 optimal weight: 0.9990 chunk 225 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 171 optimal weight: 0.6980 chunk 214 optimal weight: 1.9990 chunk 193 optimal weight: 0.0270 chunk 118 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 344 HIS E 32 GLN E 140 HIS E 193 GLN E 388 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.099797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.068883 restraints weight = 42567.414| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.80 r_work: 0.2898 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19407 Z= 0.123 Angle : 0.618 11.820 26168 Z= 0.294 Chirality : 0.041 0.131 2992 Planarity : 0.003 0.052 3402 Dihedral : 5.773 95.296 2665 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.39 % Allowed : 17.02 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.18), residues: 2400 helix: 1.94 (0.17), residues: 1002 sheet: 0.26 (0.26), residues: 431 loop : 0.32 (0.20), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 109 TYR 0.024 0.001 TYR E 197 PHE 0.013 0.001 PHE A 398 TRP 0.002 0.000 TRP D 381 HIS 0.003 0.001 HIS E 239 Details of bonding type rmsd covalent geometry : bond 0.00290 (19407) covalent geometry : angle 0.61776 (26168) hydrogen bonds : bond 0.03137 ( 892) hydrogen bonds : angle 4.23239 ( 2538) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7835.14 seconds wall clock time: 134 minutes 23.10 seconds (8063.10 seconds total)