Starting phenix.real_space_refine on Thu Mar 5 12:10:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sgw_10186/03_2026/6sgw_10186.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sgw_10186/03_2026/6sgw_10186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6sgw_10186/03_2026/6sgw_10186.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sgw_10186/03_2026/6sgw_10186.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6sgw_10186/03_2026/6sgw_10186.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sgw_10186/03_2026/6sgw_10186.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 14396 2.51 5 N 4020 2.21 5 O 3976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 98 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22448 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 642 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "B" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3055 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 21, 'TRANS': 405} Chain breaks: 2 Chain: "C" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3168 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 27, 'TRANS': 414} Chain breaks: 3 Chain: "F" Number of atoms: 2667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2667 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 29, 'TRANS': 306} Chain breaks: 4 Chain: "E" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3055 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 21, 'TRANS': 405} Chain breaks: 2 Chain: "H" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3168 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 27, 'TRANS': 414} Chain breaks: 3 Chain: "I" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 461 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "J" Number of atoms: 2574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2574 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 26, 'TRANS': 297} Chain breaks: 4 Chain: "G" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1829 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 15, 'TRANS': 225} Chain breaks: 7 Chain: "D" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1829 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 15, 'TRANS': 225} Chain breaks: 7 Time building chain proxies: 4.78, per 1000 atoms: 0.21 Number of scatterers: 22448 At special positions: 0 Unit cell: (192.494, 144.636, 155.271, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 3976 8.00 N 4020 7.00 C 14396 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: 1.76 Conformation dependent library (CDL) restraints added in 1.1 seconds 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5624 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 15 sheets defined 55.5% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 34 through 49 removed outlier: 3.894A pdb=" N VAL A 38 " --> pdb=" O THR A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 87 removed outlier: 3.546A pdb=" N THR A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 87 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 46 removed outlier: 4.090A pdb=" N ILE B 38 " --> pdb=" O PRO B 34 " (cutoff:3.500A) Proline residue: B 40 - end of helix Processing helix chain 'B' and resid 111 through 119 removed outlier: 3.601A pdb=" N PHE B 119 " --> pdb=" O ALA B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 158 removed outlier: 3.766A pdb=" N HIS B 131 " --> pdb=" O TRP B 127 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ALA B 133 " --> pdb=" O PRO B 129 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 181 removed outlier: 3.507A pdb=" N PHE B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 196 through 207 removed outlier: 3.741A pdb=" N GLY B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 234 removed outlier: 3.956A pdb=" N LEU B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 263 Processing helix chain 'B' and resid 269 through 285 removed outlier: 4.338A pdb=" N CYS B 273 " --> pdb=" O ASP B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 291 Processing helix chain 'B' and resid 319 through 349 removed outlier: 4.358A pdb=" N ARG B 325 " --> pdb=" O PRO B 321 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY B 342 " --> pdb=" O GLY B 338 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER B 346 " --> pdb=" O GLY B 342 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA B 348 " --> pdb=" O ALA B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 372 removed outlier: 3.527A pdb=" N TRP B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 364 " --> pdb=" O TRP B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 404 removed outlier: 3.779A pdb=" N LYS B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N SER B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 430 removed outlier: 4.075A pdb=" N ASN B 430 " --> pdb=" O VAL B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 455 removed outlier: 3.797A pdb=" N ASP B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 466 removed outlier: 3.557A pdb=" N VAL B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 46 removed outlier: 3.862A pdb=" N ILE C 38 " --> pdb=" O PRO C 34 " (cutoff:3.500A) Proline residue: C 40 - end of helix Processing helix chain 'C' and resid 82 through 87 removed outlier: 3.556A pdb=" N VAL C 86 " --> pdb=" O THR C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 118 Processing helix chain 'C' and resid 129 through 158 removed outlier: 3.804A pdb=" N ALA C 133 " --> pdb=" O PRO C 129 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG C 134 " --> pdb=" O THR C 130 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER C 151 " --> pdb=" O GLY C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 181 removed outlier: 3.632A pdb=" N VAL C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 198 through 207 removed outlier: 4.143A pdb=" N ALA C 205 " --> pdb=" O ALA C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 233 Processing helix chain 'C' and resid 241 through 264 removed outlier: 3.850A pdb=" N THR C 245 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR C 247 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TRP C 264 " --> pdb=" O ALA C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 285 Processing helix chain 'C' and resid 286 through 294 Processing helix chain 'C' and resid 313 through 319 Processing helix chain 'C' and resid 319 through 345 removed outlier: 3.555A pdb=" N ARG C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG C 325 " --> pdb=" O PRO C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 351 removed outlier: 4.247A pdb=" N VAL C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER C 351 " --> pdb=" O VAL C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 373 Processing helix chain 'C' and resid 374 through 376 No H-bonds generated for 'chain 'C' and resid 374 through 376' Processing helix chain 'C' and resid 379 through 388 Processing helix chain 'C' and resid 388 through 404 Processing helix chain 'C' and resid 409 through 429 Processing helix chain 'C' and resid 440 through 467 removed outlier: 4.090A pdb=" N ASP C 455 " --> pdb=" O ALA C 451 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ILE C 459 " --> pdb=" O ASP C 455 " (cutoff:3.500A) Proline residue: C 460 - end of helix Processing helix chain 'F' and resid 37 through 41 Processing helix chain 'F' and resid 93 through 130 removed outlier: 3.905A pdb=" N VAL F 97 " --> pdb=" O ARG F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 142 removed outlier: 3.896A pdb=" N ALA F 137 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE F 139 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Proline residue: F 140 - end of helix Processing helix chain 'F' and resid 185 through 197 removed outlier: 3.630A pdb=" N ASP F 195 " --> pdb=" O ARG F 191 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL F 196 " --> pdb=" O GLY F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 239 removed outlier: 3.792A pdb=" N ALA F 227 " --> pdb=" O GLU F 223 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP F 238 " --> pdb=" O GLN F 234 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS F 239 " --> pdb=" O ALA F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 263 removed outlier: 3.506A pdb=" N TRP F 260 " --> pdb=" O ASP F 257 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TRP F 263 " --> pdb=" O TRP F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 268 removed outlier: 3.973A pdb=" N ASP F 268 " --> pdb=" O PRO F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 294 Processing helix chain 'F' and resid 386 through 398 Processing helix chain 'E' and resid 34 through 47 removed outlier: 3.822A pdb=" N ILE E 38 " --> pdb=" O PRO E 34 " (cutoff:3.500A) Proline residue: E 40 - end of helix removed outlier: 3.627A pdb=" N GLN E 47 " --> pdb=" O GLN E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.879A pdb=" N VAL E 86 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY E 87 " --> pdb=" O ASP E 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 83 through 87' Processing helix chain 'E' and resid 111 through 119 Processing helix chain 'E' and resid 127 through 157 removed outlier: 3.641A pdb=" N HIS E 131 " --> pdb=" O TRP E 127 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE E 132 " --> pdb=" O GLY E 128 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ALA E 133 " --> pdb=" O PRO E 129 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG E 134 " --> pdb=" O THR E 130 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 181 removed outlier: 3.959A pdb=" N VAL E 181 " --> pdb=" O ALA E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 196 Processing helix chain 'E' and resid 198 through 204 Processing helix chain 'E' and resid 214 through 233 removed outlier: 4.017A pdb=" N LEU E 218 " --> pdb=" O ALA E 214 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 263 Processing helix chain 'E' and resid 270 through 285 Processing helix chain 'E' and resid 285 through 293 removed outlier: 3.875A pdb=" N LEU E 289 " --> pdb=" O GLN E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 350 removed outlier: 3.715A pdb=" N ARG E 323 " --> pdb=" O ASP E 319 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL E 324 " --> pdb=" O LEU E 320 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ARG E 325 " --> pdb=" O PRO E 321 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA E 336 " --> pdb=" O THR E 332 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY E 342 " --> pdb=" O GLY E 338 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER E 346 " --> pdb=" O GLY E 342 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA E 348 " --> pdb=" O ALA E 344 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL E 350 " --> pdb=" O SER E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 372 removed outlier: 3.519A pdb=" N TRP E 360 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL E 364 " --> pdb=" O TRP E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 404 removed outlier: 3.975A pdb=" N LYS E 383 " --> pdb=" O SER E 379 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N SER E 390 " --> pdb=" O LEU E 386 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TYR E 391 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 430 removed outlier: 3.587A pdb=" N ASN E 430 " --> pdb=" O VAL E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 439 removed outlier: 3.759A pdb=" N THR E 438 " --> pdb=" O SER E 435 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR E 439 " --> pdb=" O PRO E 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 435 through 439' Processing helix chain 'E' and resid 440 through 456 removed outlier: 4.163A pdb=" N ARG E 445 " --> pdb=" O LEU E 441 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA E 456 " --> pdb=" O THR E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 466 Processing helix chain 'H' and resid 34 through 37 Processing helix chain 'H' and resid 38 through 46 removed outlier: 3.649A pdb=" N VAL H 42 " --> pdb=" O ILE H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 123 removed outlier: 3.717A pdb=" N PHE H 119 " --> pdb=" O ALA H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 158 removed outlier: 3.519A pdb=" N ARG H 134 " --> pdb=" O THR H 130 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER H 151 " --> pdb=" O GLY H 147 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE H 157 " --> pdb=" O ALA H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 179 removed outlier: 3.737A pdb=" N GLN H 164 " --> pdb=" O ASP H 160 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL H 167 " --> pdb=" O GLY H 163 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU H 179 " --> pdb=" O VAL H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 196 Processing helix chain 'H' and resid 198 through 204 Processing helix chain 'H' and resid 215 through 234 removed outlier: 3.576A pdb=" N LEU H 219 " --> pdb=" O PRO H 215 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N MET H 232 " --> pdb=" O SER H 228 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA H 233 " --> pdb=" O LEU H 229 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY H 234 " --> pdb=" O ILE H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 262 removed outlier: 3.833A pdb=" N THR H 245 " --> pdb=" O ILE H 241 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA H 260 " --> pdb=" O LEU H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 270 through 285 Processing helix chain 'H' and resid 287 through 294 removed outlier: 3.844A pdb=" N ALA H 294 " --> pdb=" O SER H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 345 removed outlier: 3.565A pdb=" N ARG H 323 " --> pdb=" O ASP H 319 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG H 325 " --> pdb=" O PRO H 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 345 through 350 removed outlier: 4.143A pdb=" N VAL H 350 " --> pdb=" O SER H 346 " (cutoff:3.500A) Processing helix chain 'H' and resid 356 through 373 Processing helix chain 'H' and resid 374 through 376 No H-bonds generated for 'chain 'H' and resid 374 through 376' Processing helix chain 'H' and resid 379 through 388 Processing helix chain 'H' and resid 388 through 403 Processing helix chain 'H' and resid 408 through 429 removed outlier: 4.024A pdb=" N TRP H 412 " --> pdb=" O GLN H 408 " (cutoff:3.500A) Processing helix chain 'H' and resid 435 through 439 removed outlier: 3.574A pdb=" N TYR H 439 " --> pdb=" O PRO H 436 " (cutoff:3.500A) Processing helix chain 'H' and resid 442 through 466 removed outlier: 4.393A pdb=" N ASP H 455 " --> pdb=" O ALA H 451 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ILE H 459 " --> pdb=" O ASP H 455 " (cutoff:3.500A) Proline residue: H 460 - end of helix Processing helix chain 'H' and resid 467 through 471 removed outlier: 3.923A pdb=" N LEU H 471 " --> pdb=" O LEU H 468 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 55 removed outlier: 3.660A pdb=" N VAL I 38 " --> pdb=" O THR I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 88 Processing helix chain 'J' and resid 93 through 130 removed outlier: 3.548A pdb=" N VAL J 97 " --> pdb=" O ARG J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 197 removed outlier: 3.528A pdb=" N SER J 188 " --> pdb=" O PRO J 184 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU J 190 " --> pdb=" O ALA J 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 208 through 212 removed outlier: 3.905A pdb=" N LEU J 212 " --> pdb=" O VAL J 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 220 through 238 removed outlier: 3.889A pdb=" N ALA J 224 " --> pdb=" O GLU J 220 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG J 225 " --> pdb=" O ALA J 221 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA J 226 " --> pdb=" O ASP J 222 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TRP J 238 " --> pdb=" O GLN J 234 " (cutoff:3.500A) Processing helix chain 'J' and resid 257 through 264 removed outlier: 3.525A pdb=" N TRP J 263 " --> pdb=" O TRP J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 285 through 293 Processing helix chain 'J' and resid 386 through 398 Processing helix chain 'G' and resid 2 through 17 Processing helix chain 'G' and resid 27 through 41 removed outlier: 3.777A pdb=" N ILE G 38 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL G 39 " --> pdb=" O ALA G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 63 removed outlier: 3.592A pdb=" N ASN G 63 " --> pdb=" O MET G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 95 Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'G' and resid 131 through 137 removed outlier: 3.507A pdb=" N ALA G 137 " --> pdb=" O ALA G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 162 removed outlier: 3.572A pdb=" N GLN G 162 " --> pdb=" O HIS G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 212 Processing helix chain 'G' and resid 265 through 269 Processing helix chain 'D' and resid 2 through 16 removed outlier: 3.716A pdb=" N ALA D 6 " --> pdb=" O THR D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 41 removed outlier: 3.668A pdb=" N ILE D 38 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU D 40 " --> pdb=" O ALA D 36 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU D 41 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 62 Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 89 through 95 Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'D' and resid 131 through 137 Processing helix chain 'D' and resid 143 through 163 Processing helix chain 'D' and resid 265 through 269 Processing sheet with id=AA1, first strand: chain 'B' and resid 67 through 71 removed outlier: 8.409A pdb=" N LEU B 94 " --> pdb=" O ARG B 11 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ALA B 13 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU B 96 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU B 15 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N ALA B 98 " --> pdb=" O LEU B 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 25 through 30 removed outlier: 8.896A pdb=" N LEU C 94 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ALA C 13 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LEU C 96 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU C 15 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N ALA C 98 " --> pdb=" O LEU C 15 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 23 through 24 removed outlier: 3.577A pdb=" N ILE F 24 " --> pdb=" O LYS F 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'F' and resid 157 through 158 Processing sheet with id=AA5, first strand: chain 'F' and resid 202 through 204 Processing sheet with id=AA6, first strand: chain 'F' and resid 244 through 249 removed outlier: 6.735A pdb=" N GLY F 245 " --> pdb=" O LEU F 315 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N VAL F 317 " --> pdb=" O GLY F 245 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ALA F 247 " --> pdb=" O VAL F 317 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU F 314 " --> pdb=" O THR F 338 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ILE F 340 " --> pdb=" O LEU F 314 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N VAL F 316 " --> pdb=" O ILE F 340 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ARG F 342 " --> pdb=" O VAL F 316 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU F 318 " --> pdb=" O ARG F 342 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLY F 219 " --> pdb=" O THR F 343 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU F 360 " --> pdb=" O THR F 216 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 67 through 71 removed outlier: 8.641A pdb=" N LEU E 94 " --> pdb=" O ARG E 11 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ALA E 13 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU E 96 " --> pdb=" O ALA E 13 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU E 15 " --> pdb=" O LEU E 96 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N ALA E 98 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU E 24 " --> pdb=" O GLU H 110 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU H 110 " --> pdb=" O LEU E 24 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 25 through 30 removed outlier: 8.864A pdb=" N LEU H 94 " --> pdb=" O ARG H 11 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ALA H 13 " --> pdb=" O LEU H 94 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU H 96 " --> pdb=" O ALA H 13 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU H 15 " --> pdb=" O LEU H 96 " (cutoff:3.500A) removed outlier: 8.984A pdb=" N ALA H 98 " --> pdb=" O LEU H 15 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 4 through 5 removed outlier: 6.250A pdb=" N LEU J 4 " --> pdb=" O ASP J 401 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'J' and resid 23 through 24 Processing sheet with id=AB2, first strand: chain 'J' and resid 158 through 164 removed outlier: 5.385A pdb=" N ARG J 159 " --> pdb=" O LEU J 207 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU J 207 " --> pdb=" O ARG J 159 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 339 through 343 removed outlier: 8.213A pdb=" N LEU J 360 " --> pdb=" O ARG J 214 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR J 216 " --> pdb=" O LEU J 360 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL J 362 " --> pdb=" O THR J 216 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE J 218 " --> pdb=" O VAL J 362 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 246 through 249 removed outlier: 6.628A pdb=" N ALA J 247 " --> pdb=" O VAL J 317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'G' and resid 167 through 168 removed outlier: 3.670A pdb=" N LYS G 106 " --> pdb=" O THR G 125 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 166 through 168 removed outlier: 3.918A pdb=" N LYS D 106 " --> pdb=" O THR D 125 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N VAL D 237 " --> pdb=" O VAL D 199 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL D 199 " --> pdb=" O VAL D 237 " (cutoff:3.500A) 1236 hydrogen bonds defined for protein. 3618 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: 3.84 Time building geometry restraints manager: 2.30 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: 7410 1.34 - 1.46: 4434 1.46 - 1.58: 10931 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 22871 Sorted by residual: bond pdb=" C ILE F 139 " pdb=" N PRO F 140 " ideal model delta sigma weight residual 1.337 1.392 -0.055 9.80e-03 1.04e+04 3.20e+01 bond pdb=" CB VAL H 363 " pdb=" CG1 VAL H 363 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.96e+00 bond pdb=" CA THR D 103 " pdb=" CB THR D 103 " ideal model delta sigma weight residual 1.530 1.559 -0.029 1.69e-02 3.50e+03 2.94e+00 bond pdb=" CB PRO C 199 " pdb=" CG PRO C 199 " ideal model delta sigma weight residual 1.492 1.407 0.085 5.00e-02 4.00e+02 2.88e+00 bond pdb=" C ILE J 139 " pdb=" N PRO J 140 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.25e-02 6.40e+03 2.88e+00 ... (remaining 22866 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 30069 2.29 - 4.59: 1008 4.59 - 6.88: 158 6.88 - 9.18: 66 9.18 - 11.47: 16 Bond angle restraints: 31317 Sorted by residual: angle pdb=" N VAL H 270 " pdb=" CA VAL H 270 " pdb=" C VAL H 270 " ideal model delta sigma weight residual 113.71 106.62 7.09 9.50e-01 1.11e+00 5.57e+01 angle pdb=" N ILE C 433 " pdb=" CA ILE C 433 " pdb=" C ILE C 433 " ideal model delta sigma weight residual 112.96 107.00 5.96 1.00e+00 1.00e+00 3.56e+01 angle pdb=" C ASP E 211 " pdb=" N PHE E 212 " pdb=" CA PHE E 212 " ideal model delta sigma weight residual 121.54 131.35 -9.81 1.91e+00 2.74e-01 2.64e+01 angle pdb=" C ALA F 323 " pdb=" N ASP F 324 " pdb=" CA ASP F 324 " ideal model delta sigma weight residual 121.80 133.27 -11.47 2.44e+00 1.68e-01 2.21e+01 angle pdb=" N VAL B 343 " pdb=" CA VAL B 343 " pdb=" C VAL B 343 " ideal model delta sigma weight residual 113.42 107.98 5.44 1.17e+00 7.31e-01 2.16e+01 ... (remaining 31312 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 12289 18.02 - 36.03: 1167 36.03 - 54.05: 189 54.05 - 72.06: 28 72.06 - 90.08: 13 Dihedral angle restraints: 13686 sinusoidal: 5053 harmonic: 8633 Sorted by residual: dihedral pdb=" CA GLY D 171 " pdb=" C GLY D 171 " pdb=" N VAL D 172 " pdb=" CA VAL D 172 " ideal model delta harmonic sigma weight residual -180.00 -139.62 -40.38 0 5.00e+00 4.00e-02 6.52e+01 dihedral pdb=" CA VAL E 99 " pdb=" C VAL E 99 " pdb=" N PRO E 100 " pdb=" CA PRO E 100 " ideal model delta harmonic sigma weight residual -180.00 -143.24 -36.76 0 5.00e+00 4.00e-02 5.41e+01 dihedral pdb=" CA GLY G 171 " pdb=" C GLY G 171 " pdb=" N VAL G 172 " pdb=" CA VAL G 172 " ideal model delta harmonic sigma weight residual -180.00 -147.38 -32.62 0 5.00e+00 4.00e-02 4.26e+01 ... (remaining 13683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3113 0.066 - 0.133: 639 0.133 - 0.199: 118 0.199 - 0.266: 21 0.266 - 0.332: 5 Chirality restraints: 3896 Sorted by residual: chirality pdb=" CB THR F 216 " pdb=" CA THR F 216 " pdb=" OG1 THR F 216 " pdb=" CG2 THR F 216 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CB THR D 117 " pdb=" CA THR D 117 " pdb=" OG1 THR D 117 " pdb=" CG2 THR D 117 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA ARG J 357 " pdb=" N ARG J 357 " pdb=" C ARG J 357 " pdb=" CB ARG J 357 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 3893 not shown) Planarity restraints: 3952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP H 306 " 0.050 5.00e-02 4.00e+02 7.54e-02 9.09e+00 pdb=" N PRO H 307 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO H 307 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO H 307 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 332 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.17e+00 pdb=" C THR B 332 " -0.049 2.00e-02 2.50e+03 pdb=" O THR B 332 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY B 333 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 331 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.65e+00 pdb=" C GLN E 331 " -0.048 2.00e-02 2.50e+03 pdb=" O GLN E 331 " 0.018 2.00e-02 2.50e+03 pdb=" N THR E 332 " 0.016 2.00e-02 2.50e+03 ... (remaining 3949 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5164 2.79 - 3.32: 20854 3.32 - 3.84: 36566 3.84 - 4.37: 39441 4.37 - 4.90: 68642 Nonbonded interactions: 170667 Sorted by model distance: nonbonded pdb=" OG1 THR D 174 " pdb=" O LEU D 176 " model vdw 2.259 3.040 nonbonded pdb=" OG SER H 228 " pdb=" O PHE H 244 " model vdw 2.271 3.040 nonbonded pdb=" O ALA J 233 " pdb=" OG1 THR J 237 " model vdw 2.284 3.040 nonbonded pdb=" OG1 THR C 82 " pdb=" OG1 THR C 85 " model vdw 2.293 3.040 nonbonded pdb=" OG SER G 139 " pdb=" O ARG G 141 " model vdw 2.302 3.040 ... (remaining 170662 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 8 through 16 or resid 21 through 47 or resid 65 through 21 \ 1 or resid 214 through 471)) selection = (chain 'C' and (resid 8 through 294 or resid 316 through 471)) selection = (chain 'E' and (resid 8 through 16 or resid 21 through 47 or resid 65 through 21 \ 1 or resid 214 through 471)) selection = (chain 'H' and (resid 8 through 294 or resid 316 through 471)) } ncs_group { reference = chain 'D' selection = chain 'G' } ncs_group { reference = (chain 'F' and (resid 2 through 32 or resid 92 through 297 or resid 311 through \ 401)) selection = (chain 'J' and resid 2 through 401) } 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=0.91 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.870 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: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.390 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 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 : 0.006 0.085 22871 Z= 0.275 Angle : 1.039 11.475 31317 Z= 0.553 Chirality : 0.058 0.332 3896 Planarity : 0.008 0.075 3952 Dihedral : 14.455 90.078 8062 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.50 % Favored : 90.29 % Rotamer: Outliers : 0.26 % Allowed : 12.42 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.52 (0.12), residues: 2936 helix: -2.68 (0.09), residues: 1571 sheet: -1.70 (0.28), residues: 271 loop : -3.67 (0.16), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 214 TYR 0.015 0.002 TYR F 104 PHE 0.014 0.002 PHE B 165 TRP 0.029 0.002 TRP J 231 HIS 0.006 0.001 HIS F 341 Details of bonding type rmsd covalent geometry : bond 0.00611 (22871) covalent geometry : angle 1.03922 (31317) hydrogen bonds : bond 0.13539 ( 1236) hydrogen bonds : angle 6.45014 ( 3618) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 461 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 232 MET cc_start: 0.8290 (ttp) cc_final: 0.7984 (ttm) REVERT: B 256 LEU cc_start: 0.8509 (tt) cc_final: 0.7901 (mm) REVERT: B 285 GLN cc_start: 0.7493 (mt0) cc_final: 0.7254 (tt0) REVERT: B 328 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8171 (tm-30) REVERT: B 360 TRP cc_start: 0.6944 (m100) cc_final: 0.6731 (m100) REVERT: C 273 CYS cc_start: 0.7692 (m) cc_final: 0.7282 (m) REVERT: C 292 MET cc_start: 0.6915 (mtt) cc_final: 0.6611 (mtt) REVERT: C 378 ASP cc_start: 0.8278 (t0) cc_final: 0.7964 (t0) REVERT: F 231 TRP cc_start: 0.8708 (p90) cc_final: 0.8436 (p90) REVERT: E 43 GLN cc_start: 0.8287 (mt0) cc_final: 0.8037 (mt0) REVERT: E 123 ARG cc_start: 0.5681 (tpt90) cc_final: 0.5114 (ttm-80) REVERT: E 391 TYR cc_start: 0.8401 (t80) cc_final: 0.8030 (t80) REVERT: E 430 ASN cc_start: 0.6262 (t0) cc_final: 0.5513 (m110) REVERT: E 432 LYS cc_start: 0.6788 (tttt) cc_final: 0.6366 (pttm) REVERT: H 27 MET cc_start: 0.6456 (tpt) cc_final: 0.6089 (tpp) REVERT: H 123 ARG cc_start: 0.7621 (mmt180) cc_final: 0.7347 (mpt180) REVERT: H 232 MET cc_start: 0.9122 (ttp) cc_final: 0.8863 (ttp) REVERT: H 420 LEU cc_start: 0.8899 (mt) cc_final: 0.8645 (mp) REVERT: J 29 GLN cc_start: 0.8039 (mt0) cc_final: 0.7590 (tt0) REVERT: J 113 ASP cc_start: 0.7929 (m-30) cc_final: 0.7637 (t0) REVERT: J 357 ARG cc_start: 0.8431 (ptp-170) cc_final: 0.8202 (mtt90) REVERT: G 1 MET cc_start: 0.4974 (ptm) cc_final: 0.4531 (ptt) REVERT: G 55 ARG cc_start: 0.7551 (ttm170) cc_final: 0.7227 (ttm-80) REVERT: G 161 GLU cc_start: 0.8405 (pp20) cc_final: 0.8196 (pp20) REVERT: G 173 ASP cc_start: 0.7699 (t0) cc_final: 0.7452 (t70) REVERT: G 211 GLU cc_start: 0.6177 (tt0) cc_final: 0.5701 (pt0) REVERT: D 47 MET cc_start: 0.1131 (ttt) cc_final: -0.0321 (ptt) REVERT: D 108 ARG cc_start: 0.6345 (ttm170) cc_final: 0.5693 (ttm170) REVERT: D 225 GLU cc_start: 0.6645 (tt0) cc_final: 0.6341 (tt0) REVERT: D 233 PRO cc_start: 0.7255 (Cg_endo) cc_final: 0.6957 (Cg_exo) outliers start: 6 outliers final: 3 residues processed: 465 average time/residue: 0.1560 time to fit residues: 111.1710 Evaluate side-chains 320 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 317 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain D residue 172 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.0870 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.0670 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS A 67 GLN ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 ASN B 330 HIS C 331 GLN F 122 GLN F 341 HIS E 43 GLN E 47 GLN E 331 GLN H 389 HIS I 67 GLN J 122 GLN J 187 HIS G 63 ASN D 74 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.130129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.110799 restraints weight = 51087.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.111952 restraints weight = 34923.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.113191 restraints weight = 25819.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.114025 restraints weight = 20558.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.114246 restraints weight = 18964.708| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3485 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3485 r_free = 0.3485 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3485 r_free = 0.3485 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3485 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 22871 Z= 0.129 Angle : 0.676 9.206 31317 Z= 0.339 Chirality : 0.041 0.185 3896 Planarity : 0.006 0.073 3952 Dihedral : 5.521 40.713 3248 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.75 % Favored : 91.14 % Rotamer: Outliers : 2.48 % Allowed : 16.63 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.15), residues: 2936 helix: -0.78 (0.12), residues: 1598 sheet: -1.42 (0.29), residues: 256 loop : -3.22 (0.17), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 16 TYR 0.013 0.001 TYR F 104 PHE 0.009 0.001 PHE B 165 TRP 0.023 0.001 TRP J 231 HIS 0.010 0.001 HIS F 341 Details of bonding type rmsd covalent geometry : bond 0.00285 (22871) covalent geometry : angle 0.67648 (31317) hydrogen bonds : bond 0.03859 ( 1236) hydrogen bonds : angle 4.45962 ( 3618) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 385 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 232 MET cc_start: 0.8319 (ttp) cc_final: 0.7958 (ttm) REVERT: B 256 LEU cc_start: 0.8507 (tt) cc_final: 0.8015 (mm) REVERT: B 285 GLN cc_start: 0.7645 (mt0) cc_final: 0.7409 (tt0) REVERT: C 127 TRP cc_start: 0.8630 (t-100) cc_final: 0.8379 (t-100) REVERT: C 292 MET cc_start: 0.6893 (mtt) cc_final: 0.6574 (mtt) REVERT: C 378 ASP cc_start: 0.8186 (t0) cc_final: 0.7977 (t0) REVERT: C 465 LEU cc_start: 0.8869 (tp) cc_final: 0.8348 (tp) REVERT: F 143 ARG cc_start: 0.7538 (ptm160) cc_final: 0.6968 (ttt-90) REVERT: F 288 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7069 (tp30) REVERT: E 331 GLN cc_start: 0.8151 (mt0) cc_final: 0.7727 (mp10) REVERT: E 391 TYR cc_start: 0.8398 (t80) cc_final: 0.8029 (t80) REVERT: E 430 ASN cc_start: 0.6289 (t0) cc_final: 0.5655 (m110) REVERT: E 432 LYS cc_start: 0.6764 (tttt) cc_final: 0.6338 (pttm) REVERT: E 446 MET cc_start: 0.5259 (mmm) cc_final: 0.4620 (ttp) REVERT: H 417 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8268 (tt) REVERT: I 41 TRP cc_start: 0.8659 (t-100) cc_final: 0.8450 (t60) REVERT: J 29 GLN cc_start: 0.7958 (mt0) cc_final: 0.7423 (tt0) REVERT: J 113 ASP cc_start: 0.7911 (m-30) cc_final: 0.7637 (t0) REVERT: J 399 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7403 (ttm110) REVERT: G 1 MET cc_start: 0.5140 (ptm) cc_final: 0.4696 (ptt) REVERT: G 4 ARG cc_start: 0.6044 (mmt-90) cc_final: 0.3969 (mmm160) REVERT: G 211 GLU cc_start: 0.6331 (tt0) cc_final: 0.5718 (pt0) REVERT: D 47 MET cc_start: 0.1267 (ttt) cc_final: -0.0372 (ptt) REVERT: D 161 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8177 (tm-30) REVERT: D 233 PRO cc_start: 0.7120 (Cg_endo) cc_final: 0.6832 (Cg_exo) outliers start: 57 outliers final: 33 residues processed: 419 average time/residue: 0.1418 time to fit residues: 94.2068 Evaluate side-chains 351 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 316 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain H residue 395 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 455 ASP Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 399 ARG Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 172 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 57 optimal weight: 0.0170 chunk 174 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 188 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 247 optimal weight: 0.0670 chunk 204 optimal weight: 2.9990 chunk 128 optimal weight: 0.0000 chunk 223 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN A 27 GLN ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 HIS F 163 HIS ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.131140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.111261 restraints weight = 51071.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.113822 restraints weight = 33860.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.114171 restraints weight = 21033.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.114831 restraints weight = 20259.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.114819 restraints weight = 17530.569| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3495 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3495 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22871 Z= 0.118 Angle : 0.640 8.202 31317 Z= 0.316 Chirality : 0.041 0.230 3896 Planarity : 0.005 0.063 3952 Dihedral : 5.048 58.548 3248 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.34 % Favored : 91.55 % Rotamer: Outliers : 2.78 % Allowed : 18.71 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.15), residues: 2936 helix: 0.06 (0.13), residues: 1611 sheet: -1.18 (0.30), residues: 251 loop : -2.99 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 23 TYR 0.012 0.001 TYR F 104 PHE 0.014 0.001 PHE D 48 TRP 0.028 0.001 TRP F 231 HIS 0.003 0.001 HIS E 389 Details of bonding type rmsd covalent geometry : bond 0.00261 (22871) covalent geometry : angle 0.63984 (31317) hydrogen bonds : bond 0.03484 ( 1236) hydrogen bonds : angle 4.02340 ( 3618) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 373 time to evaluate : 0.608 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: B 165 PHE cc_start: 0.8243 (t80) cc_final: 0.8014 (t80) REVERT: B 232 MET cc_start: 0.8101 (ttp) cc_final: 0.7763 (ttm) REVERT: B 256 LEU cc_start: 0.8478 (tt) cc_final: 0.8040 (mm) REVERT: B 422 LEU cc_start: 0.8506 (tp) cc_final: 0.8193 (tp) REVERT: B 462 MET cc_start: 0.7855 (ttp) cc_final: 0.7595 (ttp) REVERT: C 126 GLN cc_start: 0.8135 (tp40) cc_final: 0.7907 (tp40) REVERT: C 127 TRP cc_start: 0.8572 (t-100) cc_final: 0.8354 (t-100) REVERT: C 292 MET cc_start: 0.7014 (mtt) cc_final: 0.6713 (mtt) REVERT: C 465 LEU cc_start: 0.8807 (tp) cc_final: 0.8384 (tp) REVERT: F 143 ARG cc_start: 0.7373 (ptm160) cc_final: 0.6876 (ttt-90) REVERT: F 351 GLN cc_start: 0.5203 (OUTLIER) cc_final: 0.4893 (pt0) REVERT: E 232 MET cc_start: 0.8371 (ttp) cc_final: 0.7974 (ttp) REVERT: E 245 THR cc_start: 0.9269 (t) cc_final: 0.9015 (m) REVERT: E 391 TYR cc_start: 0.8268 (t80) cc_final: 0.7991 (t80) REVERT: E 430 ASN cc_start: 0.6336 (t0) cc_final: 0.5545 (m110) REVERT: E 432 LYS cc_start: 0.6748 (tttt) cc_final: 0.6365 (pttm) REVERT: E 446 MET cc_start: 0.5296 (mmm) cc_final: 0.4726 (ttp) REVERT: E 468 LEU cc_start: 0.3375 (OUTLIER) cc_final: 0.2996 (tt) REVERT: H 164 GLN cc_start: 0.7246 (pp30) cc_final: 0.6605 (tm-30) REVERT: H 417 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8236 (tt) REVERT: H 441 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7854 (mm) REVERT: J 9 GLN cc_start: 0.7166 (mt0) cc_final: 0.6915 (mt0) REVERT: J 29 GLN cc_start: 0.7852 (mt0) cc_final: 0.7367 (tt0) REVERT: J 113 ASP cc_start: 0.7961 (m-30) cc_final: 0.7603 (t0) REVERT: G 4 ARG cc_start: 0.6206 (mmt-90) cc_final: 0.4071 (mmm160) REVERT: G 211 GLU cc_start: 0.6234 (tt0) cc_final: 0.5675 (pt0) REVERT: D 47 MET cc_start: 0.0518 (ttt) cc_final: -0.0070 (ptt) REVERT: D 161 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8223 (tm-30) outliers start: 64 outliers final: 35 residues processed: 414 average time/residue: 0.1354 time to fit residues: 90.1389 Evaluate side-chains 354 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 315 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 273 CYS Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain H residue 449 PHE Chi-restraints excluded: chain H residue 455 ASP Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 172 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 58 optimal weight: 1.9990 chunk 286 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 135 optimal weight: 0.6980 chunk 245 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 195 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN A 67 GLN ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS C 164 GLN C 330 HIS F 197 GLN E 47 GLN J 118 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.129275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.109955 restraints weight = 51010.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.110958 restraints weight = 34662.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.112068 restraints weight = 26145.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.112516 restraints weight = 22043.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.112771 restraints weight = 19963.603| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3465 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22871 Z= 0.148 Angle : 0.661 9.566 31317 Z= 0.325 Chirality : 0.042 0.258 3896 Planarity : 0.005 0.063 3952 Dihedral : 4.894 33.505 3248 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.03 % Favored : 90.91 % Rotamer: Outliers : 3.73 % Allowed : 19.54 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.16), residues: 2936 helix: 0.47 (0.13), residues: 1609 sheet: -1.02 (0.32), residues: 244 loop : -2.83 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 23 TYR 0.012 0.001 TYR F 104 PHE 0.027 0.001 PHE C 77 TRP 0.028 0.001 TRP E 293 HIS 0.003 0.001 HIS E 389 Details of bonding type rmsd covalent geometry : bond 0.00339 (22871) covalent geometry : angle 0.66081 (31317) hydrogen bonds : bond 0.03512 ( 1236) hydrogen bonds : angle 3.96477 ( 3618) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 330 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 165 PHE cc_start: 0.8229 (t80) cc_final: 0.8029 (t80) REVERT: B 232 MET cc_start: 0.8398 (ttp) cc_final: 0.8029 (ttm) REVERT: B 256 LEU cc_start: 0.8443 (tt) cc_final: 0.8010 (mm) REVERT: B 289 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8559 (tt) REVERT: C 292 MET cc_start: 0.7015 (mtt) cc_final: 0.6756 (mtt) REVERT: C 465 LEU cc_start: 0.8850 (tp) cc_final: 0.8489 (tp) REVERT: F 248 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7580 (tm) REVERT: F 351 GLN cc_start: 0.5205 (OUTLIER) cc_final: 0.4855 (pt0) REVERT: E 140 LEU cc_start: 0.9127 (tp) cc_final: 0.8699 (tt) REVERT: E 245 THR cc_start: 0.9350 (t) cc_final: 0.9108 (m) REVERT: E 391 TYR cc_start: 0.8307 (t80) cc_final: 0.8003 (t80) REVERT: E 430 ASN cc_start: 0.6435 (t0) cc_final: 0.5645 (m110) REVERT: E 432 LYS cc_start: 0.6825 (tttt) cc_final: 0.6399 (pttm) REVERT: E 446 MET cc_start: 0.5338 (mmm) cc_final: 0.4731 (ttp) REVERT: E 468 LEU cc_start: 0.3632 (OUTLIER) cc_final: 0.3276 (tt) REVERT: H 417 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8370 (tt) REVERT: H 420 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8793 (mp) REVERT: H 441 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7965 (mm) REVERT: I 45 MET cc_start: 0.8528 (tpp) cc_final: 0.8178 (tpp) REVERT: J 29 GLN cc_start: 0.7840 (mt0) cc_final: 0.7338 (tt0) REVERT: J 113 ASP cc_start: 0.7933 (m-30) cc_final: 0.7635 (t0) REVERT: G 4 ARG cc_start: 0.6378 (mmt-90) cc_final: 0.4188 (mmm160) REVERT: G 173 ASP cc_start: 0.7538 (t70) cc_final: 0.6934 (p0) REVERT: D 47 MET cc_start: 0.0652 (ttt) cc_final: -0.0583 (ptt) REVERT: D 161 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8317 (tm-30) outliers start: 86 outliers final: 57 residues processed: 382 average time/residue: 0.1331 time to fit residues: 82.7407 Evaluate side-chains 370 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 306 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 273 CYS Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain H residue 395 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 433 ILE Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain H residue 449 PHE Chi-restraints excluded: chain H residue 455 ASP Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 118 HIS Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 172 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 201 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 chunk 284 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 205 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 200 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN B 126 GLN C 164 GLN ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.129932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.110568 restraints weight = 50457.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.111603 restraints weight = 34717.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.112441 restraints weight = 25684.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.113169 restraints weight = 22923.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.113356 restraints weight = 19878.092| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22871 Z= 0.129 Angle : 0.648 9.745 31317 Z= 0.318 Chirality : 0.041 0.204 3896 Planarity : 0.005 0.060 3952 Dihedral : 4.772 27.843 3248 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.24 % Favored : 91.69 % Rotamer: Outliers : 3.43 % Allowed : 21.10 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.16), residues: 2936 helix: 0.72 (0.13), residues: 1610 sheet: -0.99 (0.32), residues: 249 loop : -2.75 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 143 TYR 0.011 0.001 TYR F 104 PHE 0.020 0.001 PHE C 77 TRP 0.019 0.001 TRP J 231 HIS 0.014 0.001 HIS J 118 Details of bonding type rmsd covalent geometry : bond 0.00296 (22871) covalent geometry : angle 0.64753 (31317) hydrogen bonds : bond 0.03371 ( 1236) hydrogen bonds : angle 3.87377 ( 3618) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 325 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 GLU cc_start: 0.8782 (pm20) cc_final: 0.8526 (pm20) REVERT: B 232 MET cc_start: 0.8374 (ttp) cc_final: 0.7998 (ttm) REVERT: B 256 LEU cc_start: 0.8482 (tt) cc_final: 0.8083 (mm) REVERT: B 289 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8585 (tt) REVERT: C 292 MET cc_start: 0.7013 (mtt) cc_final: 0.6729 (mtt) REVERT: C 462 MET cc_start: 0.7611 (mmm) cc_final: 0.7353 (tpt) REVERT: C 465 LEU cc_start: 0.8874 (tp) cc_final: 0.8490 (tp) REVERT: F 216 THR cc_start: 0.7735 (OUTLIER) cc_final: 0.7452 (t) REVERT: F 351 GLN cc_start: 0.5157 (OUTLIER) cc_final: 0.4834 (pt0) REVERT: E 391 TYR cc_start: 0.8267 (t80) cc_final: 0.8000 (t80) REVERT: E 430 ASN cc_start: 0.6415 (t0) cc_final: 0.5634 (m110) REVERT: E 432 LYS cc_start: 0.6801 (tttt) cc_final: 0.6382 (pttm) REVERT: E 446 MET cc_start: 0.5261 (mmm) cc_final: 0.4632 (ttp) REVERT: E 468 LEU cc_start: 0.3522 (OUTLIER) cc_final: 0.3275 (tt) REVERT: H 164 GLN cc_start: 0.7223 (pp30) cc_final: 0.6577 (tm-30) REVERT: H 417 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8338 (tt) REVERT: H 441 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7945 (mm) REVERT: J 29 GLN cc_start: 0.7826 (mt0) cc_final: 0.7466 (tt0) REVERT: J 113 ASP cc_start: 0.7936 (m-30) cc_final: 0.7677 (t0) REVERT: G 4 ARG cc_start: 0.6494 (mmt-90) cc_final: 0.4200 (mmm160) REVERT: G 22 GLN cc_start: 0.6807 (mp10) cc_final: 0.6389 (tp40) REVERT: D 47 MET cc_start: 0.0367 (ttt) cc_final: -0.0421 (ptt) REVERT: D 161 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8272 (tm-30) outliers start: 79 outliers final: 55 residues processed: 377 average time/residue: 0.1322 time to fit residues: 82.0739 Evaluate side-chains 359 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 298 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 126 GLN Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 273 CYS Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain H residue 395 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 433 ILE Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain H residue 449 PHE Chi-restraints excluded: chain H residue 455 ASP Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 172 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 99 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 270 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 277 optimal weight: 8.9990 chunk 214 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 67 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 HIS J 130 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.127352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.107478 restraints weight = 51416.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.108613 restraints weight = 36354.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.109263 restraints weight = 26390.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.109879 restraints weight = 23473.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.110238 restraints weight = 20475.614| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3427 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3427 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 22871 Z= 0.194 Angle : 0.699 13.134 31317 Z= 0.344 Chirality : 0.043 0.187 3896 Planarity : 0.005 0.061 3952 Dihedral : 4.883 28.043 3246 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.23 % Favored : 90.70 % Rotamer: Outliers : 4.43 % Allowed : 21.32 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.16), residues: 2936 helix: 0.81 (0.13), residues: 1605 sheet: -1.10 (0.31), residues: 276 loop : -2.74 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 11 TYR 0.013 0.001 TYR C 407 PHE 0.017 0.001 PHE C 77 TRP 0.024 0.001 TRP C 127 HIS 0.004 0.001 HIS F 392 Details of bonding type rmsd covalent geometry : bond 0.00449 (22871) covalent geometry : angle 0.69946 (31317) hydrogen bonds : bond 0.03581 ( 1236) hydrogen bonds : angle 4.00159 ( 3618) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 309 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 GLU cc_start: 0.8796 (pm20) cc_final: 0.8580 (pm20) REVERT: B 232 MET cc_start: 0.8509 (ttp) cc_final: 0.8162 (ttm) REVERT: B 256 LEU cc_start: 0.8496 (tt) cc_final: 0.8067 (mm) REVERT: B 289 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8649 (tt) REVERT: C 111 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.8396 (p0) REVERT: C 126 GLN cc_start: 0.8000 (tp40) cc_final: 0.7741 (tp40) REVERT: C 270 VAL cc_start: 0.8045 (OUTLIER) cc_final: 0.7793 (t) REVERT: C 292 MET cc_start: 0.7074 (mtt) cc_final: 0.6800 (mtt) REVERT: C 465 LEU cc_start: 0.8942 (tp) cc_final: 0.8560 (tp) REVERT: F 216 THR cc_start: 0.7816 (OUTLIER) cc_final: 0.7554 (t) REVERT: F 351 GLN cc_start: 0.5334 (OUTLIER) cc_final: 0.5012 (pt0) REVERT: E 391 TYR cc_start: 0.8361 (t80) cc_final: 0.8046 (t80) REVERT: E 430 ASN cc_start: 0.6419 (t0) cc_final: 0.5679 (m110) REVERT: E 432 LYS cc_start: 0.6799 (tttt) cc_final: 0.6364 (pttm) REVERT: E 446 MET cc_start: 0.5293 (mmm) cc_final: 0.4632 (ttp) REVERT: E 468 LEU cc_start: 0.3497 (OUTLIER) cc_final: 0.3133 (tt) REVERT: H 441 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8105 (mm) REVERT: I 45 MET cc_start: 0.8434 (tpp) cc_final: 0.8074 (tpp) REVERT: J 29 GLN cc_start: 0.7991 (mt0) cc_final: 0.7538 (tt0) REVERT: J 113 ASP cc_start: 0.8064 (m-30) cc_final: 0.7719 (t0) REVERT: G 4 ARG cc_start: 0.6486 (mmt-90) cc_final: 0.4144 (mmm160) REVERT: G 89 GLN cc_start: 0.7672 (pp30) cc_final: 0.7410 (pp30) REVERT: G 161 GLU cc_start: 0.8354 (pp20) cc_final: 0.8110 (pp20) REVERT: D 47 MET cc_start: 0.0441 (ttt) cc_final: -0.0216 (ptt) REVERT: D 106 LYS cc_start: 0.7655 (tttt) cc_final: 0.6365 (ttpt) outliers start: 102 outliers final: 78 residues processed: 375 average time/residue: 0.1296 time to fit residues: 80.3849 Evaluate side-chains 375 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 290 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 273 CYS Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain H residue 395 VAL Chi-restraints excluded: chain H residue 433 ILE Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain H residue 449 PHE Chi-restraints excluded: chain H residue 455 ASP Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain J residue 386 SER Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 172 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 94 optimal weight: 0.3980 chunk 111 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 207 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 297 optimal weight: 0.2980 chunk 106 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 263 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 276 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 67 GLN C 164 GLN ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.130264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.111004 restraints weight = 50569.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.112123 restraints weight = 34856.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.113085 restraints weight = 26062.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.113621 restraints weight = 21928.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.113796 restraints weight = 19802.459| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3483 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3483 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22871 Z= 0.122 Angle : 0.644 11.137 31317 Z= 0.315 Chirality : 0.041 0.203 3896 Planarity : 0.005 0.064 3952 Dihedral : 4.660 25.977 3246 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.55 % Favored : 91.38 % Rotamer: Outliers : 3.21 % Allowed : 23.27 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.16), residues: 2936 helix: 1.04 (0.13), residues: 1613 sheet: -0.88 (0.32), residues: 264 loop : -2.64 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 225 TYR 0.010 0.001 TYR C 407 PHE 0.020 0.001 PHE C 77 TRP 0.021 0.001 TRP J 231 HIS 0.003 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00279 (22871) covalent geometry : angle 0.64368 (31317) hydrogen bonds : bond 0.03239 ( 1236) hydrogen bonds : angle 3.77485 ( 3618) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 323 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 232 MET cc_start: 0.8396 (ttp) cc_final: 0.8039 (ttm) REVERT: B 256 LEU cc_start: 0.8470 (tt) cc_final: 0.8095 (mm) REVERT: B 289 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8613 (tt) REVERT: C 126 GLN cc_start: 0.8057 (tp40) cc_final: 0.7791 (tp40) REVERT: C 127 TRP cc_start: 0.8753 (t-100) cc_final: 0.8520 (t-100) REVERT: C 292 MET cc_start: 0.6995 (mtt) cc_final: 0.6722 (mtt) REVERT: C 465 LEU cc_start: 0.8858 (tp) cc_final: 0.8480 (tp) REVERT: F 288 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7151 (tp30) REVERT: E 391 TYR cc_start: 0.8254 (t80) cc_final: 0.7986 (t80) REVERT: E 430 ASN cc_start: 0.6232 (t0) cc_final: 0.5746 (m110) REVERT: E 432 LYS cc_start: 0.6797 (tttt) cc_final: 0.6354 (pttm) REVERT: E 446 MET cc_start: 0.5284 (mmm) cc_final: 0.4608 (ttp) REVERT: E 468 LEU cc_start: 0.3504 (OUTLIER) cc_final: 0.3247 (tt) REVERT: H 441 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7899 (mm) REVERT: J 113 ASP cc_start: 0.8011 (m-30) cc_final: 0.7706 (t0) REVERT: G 4 ARG cc_start: 0.6602 (mmt-90) cc_final: 0.4198 (mmm160) REVERT: G 22 GLN cc_start: 0.6802 (mp10) cc_final: 0.6272 (tp40) REVERT: G 89 GLN cc_start: 0.7650 (pp30) cc_final: 0.7338 (pp30) REVERT: G 161 GLU cc_start: 0.8276 (pp20) cc_final: 0.8049 (pp20) REVERT: D 47 MET cc_start: 0.0286 (ttt) cc_final: -0.0210 (ptm) REVERT: D 276 GLU cc_start: 0.7237 (tp30) cc_final: 0.7007 (tp30) outliers start: 74 outliers final: 50 residues processed: 373 average time/residue: 0.1398 time to fit residues: 83.5164 Evaluate side-chains 354 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 301 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain H residue 449 PHE Chi-restraints excluded: chain H residue 455 ASP Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 172 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 18 optimal weight: 0.0030 chunk 183 optimal weight: 4.9990 chunk 114 optimal weight: 0.0470 chunk 14 optimal weight: 7.9990 chunk 223 optimal weight: 3.9990 chunk 219 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 79 optimal weight: 0.0670 chunk 239 optimal weight: 0.0070 chunk 154 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 overall best weight: 0.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.132077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.112906 restraints weight = 50328.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.113956 restraints weight = 33765.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.114982 restraints weight = 25687.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.115551 restraints weight = 21593.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.115744 restraints weight = 19499.207| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3510 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3510 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 22871 Z= 0.117 Angle : 0.655 17.235 31317 Z= 0.319 Chirality : 0.041 0.178 3896 Planarity : 0.005 0.065 3952 Dihedral : 4.478 25.615 3246 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.38 % Favored : 91.55 % Rotamer: Outliers : 3.21 % Allowed : 23.88 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.16), residues: 2936 helix: 1.19 (0.13), residues: 1610 sheet: -0.77 (0.32), residues: 255 loop : -2.58 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 52 TYR 0.010 0.001 TYR C 407 PHE 0.018 0.001 PHE C 77 TRP 0.024 0.001 TRP J 231 HIS 0.003 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00265 (22871) covalent geometry : angle 0.65530 (31317) hydrogen bonds : bond 0.03157 ( 1236) hydrogen bonds : angle 3.64420 ( 3618) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 325 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 232 MET cc_start: 0.8339 (ttp) cc_final: 0.7966 (ttm) REVERT: B 256 LEU cc_start: 0.8456 (tt) cc_final: 0.8087 (mm) REVERT: C 292 MET cc_start: 0.7110 (mtt) cc_final: 0.6833 (mtt) REVERT: C 465 LEU cc_start: 0.8708 (tp) cc_final: 0.8335 (tp) REVERT: F 151 ARG cc_start: 0.8491 (mtm110) cc_final: 0.8242 (mtm180) REVERT: F 288 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7135 (tp30) REVERT: F 351 GLN cc_start: 0.5250 (OUTLIER) cc_final: 0.4994 (pt0) REVERT: E 126 GLN cc_start: 0.7366 (mm-40) cc_final: 0.6881 (mp10) REVERT: E 391 TYR cc_start: 0.8243 (t80) cc_final: 0.7976 (t80) REVERT: E 430 ASN cc_start: 0.6312 (t0) cc_final: 0.5744 (m110) REVERT: E 432 LYS cc_start: 0.6760 (tttt) cc_final: 0.6331 (pttm) REVERT: E 446 MET cc_start: 0.5242 (mmm) cc_final: 0.4541 (ttp) REVERT: E 468 LEU cc_start: 0.3052 (OUTLIER) cc_final: 0.2578 (tt) REVERT: H 164 GLN cc_start: 0.7250 (pp30) cc_final: 0.6605 (tm-30) REVERT: H 441 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7863 (mm) REVERT: J 211 LYS cc_start: 0.8437 (ptpp) cc_final: 0.8172 (ptpt) REVERT: J 231 TRP cc_start: 0.8704 (p90) cc_final: 0.8483 (p90) REVERT: G 4 ARG cc_start: 0.6598 (mmt-90) cc_final: 0.4253 (mmm160) REVERT: G 22 GLN cc_start: 0.6839 (mp10) cc_final: 0.6429 (tp40) REVERT: D 47 MET cc_start: 0.0275 (ttt) cc_final: -0.0205 (ptm) REVERT: D 106 LYS cc_start: 0.6906 (ttmt) cc_final: 0.6663 (ttpt) outliers start: 74 outliers final: 47 residues processed: 378 average time/residue: 0.1338 time to fit residues: 82.0341 Evaluate side-chains 349 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 299 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 273 CYS Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain H residue 449 PHE Chi-restraints excluded: chain H residue 455 ASP Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 172 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 113 optimal weight: 0.9990 chunk 170 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 46 optimal weight: 0.0030 chunk 233 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 206 optimal weight: 3.9990 chunk 176 optimal weight: 10.0000 chunk 229 optimal weight: 3.9990 chunk 173 optimal weight: 0.6980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 HIS ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.131071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.111781 restraints weight = 50907.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.112879 restraints weight = 35426.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.113825 restraints weight = 25964.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.114308 restraints weight = 22375.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.114421 restraints weight = 19850.638| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22871 Z= 0.124 Angle : 0.662 16.861 31317 Z= 0.321 Chirality : 0.041 0.356 3896 Planarity : 0.005 0.065 3952 Dihedral : 4.449 25.019 3246 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.55 % Favored : 91.38 % Rotamer: Outliers : 2.65 % Allowed : 24.32 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.16), residues: 2936 helix: 1.25 (0.13), residues: 1616 sheet: -0.67 (0.33), residues: 250 loop : -2.54 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 153 TYR 0.016 0.001 TYR J 281 PHE 0.018 0.001 PHE D 226 TRP 0.028 0.001 TRP C 127 HIS 0.003 0.001 HIS J 266 Details of bonding type rmsd covalent geometry : bond 0.00289 (22871) covalent geometry : angle 0.66219 (31317) hydrogen bonds : bond 0.03173 ( 1236) hydrogen bonds : angle 3.63463 ( 3618) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 305 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 232 MET cc_start: 0.8413 (ttp) cc_final: 0.8043 (ttm) REVERT: B 256 LEU cc_start: 0.8448 (tt) cc_final: 0.8090 (mm) REVERT: C 292 MET cc_start: 0.7154 (mtt) cc_final: 0.6887 (mtt) REVERT: C 465 LEU cc_start: 0.8701 (tp) cc_final: 0.8310 (tp) REVERT: F 144 ARG cc_start: 0.7708 (mtp-110) cc_final: 0.7375 (mtm110) REVERT: F 288 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7141 (tp30) REVERT: E 126 GLN cc_start: 0.7400 (mm-40) cc_final: 0.6896 (mp10) REVERT: E 391 TYR cc_start: 0.8243 (t80) cc_final: 0.7962 (t80) REVERT: E 430 ASN cc_start: 0.6351 (t0) cc_final: 0.5786 (m110) REVERT: E 432 LYS cc_start: 0.6761 (tttt) cc_final: 0.6325 (pttm) REVERT: E 446 MET cc_start: 0.5278 (mmm) cc_final: 0.4557 (ttp) REVERT: H 164 GLN cc_start: 0.7274 (pp30) cc_final: 0.6601 (tm-30) REVERT: H 441 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7887 (mm) REVERT: J 113 ASP cc_start: 0.7985 (m-30) cc_final: 0.7675 (t0) REVERT: J 231 TRP cc_start: 0.8779 (p90) cc_final: 0.8516 (p90) REVERT: G 4 ARG cc_start: 0.6703 (mmt-90) cc_final: 0.4292 (mmm160) REVERT: G 22 GLN cc_start: 0.6806 (mp10) cc_final: 0.6414 (tp40) REVERT: D 47 MET cc_start: 0.0268 (ttt) cc_final: -0.0149 (ptm) outliers start: 61 outliers final: 52 residues processed: 347 average time/residue: 0.1273 time to fit residues: 73.2134 Evaluate side-chains 349 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 296 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 273 CYS Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain H residue 449 PHE Chi-restraints excluded: chain H residue 455 ASP Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 172 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 72 optimal weight: 2.9990 chunk 196 optimal weight: 0.0170 chunk 138 optimal weight: 7.9990 chunk 124 optimal weight: 0.4980 chunk 54 optimal weight: 0.2980 chunk 152 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 252 optimal weight: 4.9990 chunk 226 optimal weight: 6.9990 chunk 175 optimal weight: 5.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 GLN C 164 GLN F 163 HIS ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.131039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.111915 restraints weight = 50700.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.113022 restraints weight = 34098.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.113804 restraints weight = 26007.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.114431 restraints weight = 22591.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.114573 restraints weight = 19840.001| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3495 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3495 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22871 Z= 0.126 Angle : 0.663 16.736 31317 Z= 0.321 Chirality : 0.041 0.389 3896 Planarity : 0.005 0.065 3952 Dihedral : 4.422 24.708 3246 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.72 % Favored : 91.21 % Rotamer: Outliers : 2.69 % Allowed : 24.36 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.16), residues: 2936 helix: 1.30 (0.13), residues: 1614 sheet: -0.62 (0.33), residues: 250 loop : -2.51 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 198 TYR 0.016 0.001 TYR J 281 PHE 0.019 0.001 PHE D 226 TRP 0.021 0.001 TRP C 127 HIS 0.003 0.001 HIS J 266 Details of bonding type rmsd covalent geometry : bond 0.00294 (22871) covalent geometry : angle 0.66341 (31317) hydrogen bonds : bond 0.03173 ( 1236) hydrogen bonds : angle 3.62673 ( 3618) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 305 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 232 MET cc_start: 0.8424 (ttp) cc_final: 0.8056 (ttm) REVERT: B 256 LEU cc_start: 0.8449 (tt) cc_final: 0.8095 (mm) REVERT: C 292 MET cc_start: 0.7145 (mtt) cc_final: 0.6864 (mtt) REVERT: C 462 MET cc_start: 0.6966 (tpt) cc_final: 0.6151 (tpt) REVERT: C 465 LEU cc_start: 0.8700 (tp) cc_final: 0.8334 (tp) REVERT: F 144 ARG cc_start: 0.7645 (mtp-110) cc_final: 0.7336 (mtm110) REVERT: F 288 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7131 (tp30) REVERT: E 126 GLN cc_start: 0.7479 (mm-40) cc_final: 0.6898 (mp10) REVERT: E 391 TYR cc_start: 0.8218 (t80) cc_final: 0.7934 (t80) REVERT: E 430 ASN cc_start: 0.6385 (t0) cc_final: 0.5816 (m110) REVERT: E 432 LYS cc_start: 0.6793 (tttt) cc_final: 0.6404 (pttm) REVERT: E 446 MET cc_start: 0.5190 (mmm) cc_final: 0.4423 (ttp) REVERT: H 164 GLN cc_start: 0.7262 (pp30) cc_final: 0.6608 (tm-30) REVERT: J 113 ASP cc_start: 0.7992 (m-30) cc_final: 0.7680 (t0) REVERT: J 231 TRP cc_start: 0.8779 (p90) cc_final: 0.8521 (p90) REVERT: G 4 ARG cc_start: 0.6782 (mmt-90) cc_final: 0.4334 (mmm160) REVERT: G 22 GLN cc_start: 0.6797 (mp10) cc_final: 0.6416 (tp40) REVERT: D 47 MET cc_start: 0.0100 (ttt) cc_final: -0.0159 (ptm) REVERT: D 106 LYS cc_start: 0.7148 (ttpt) cc_final: 0.6948 (ttmt) REVERT: D 225 GLU cc_start: 0.5355 (tt0) cc_final: 0.4936 (tt0) outliers start: 62 outliers final: 55 residues processed: 348 average time/residue: 0.1279 time to fit residues: 73.4216 Evaluate side-chains 345 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 290 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 273 CYS Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain H residue 449 PHE Chi-restraints excluded: chain H residue 455 ASP Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain J residue 173 VAL Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 317 VAL Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain J residue 386 SER Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 172 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 174 optimal weight: 8.9990 chunk 176 optimal weight: 10.0000 chunk 218 optimal weight: 6.9990 chunk 246 optimal weight: 0.5980 chunk 14 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 272 optimal weight: 0.9990 chunk 184 optimal weight: 7.9990 chunk 221 optimal weight: 0.9990 chunk 241 optimal weight: 1.9990 chunk 79 optimal weight: 0.1980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 GLN ** H 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.129922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.110537 restraints weight = 51022.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.111513 restraints weight = 35480.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.112516 restraints weight = 27012.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.113115 restraints weight = 23137.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.113335 restraints weight = 20525.005| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3475 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3475 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22871 Z= 0.140 Angle : 0.672 16.965 31317 Z= 0.327 Chirality : 0.042 0.369 3896 Planarity : 0.005 0.064 3952 Dihedral : 4.468 25.597 3246 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.82 % Favored : 91.11 % Rotamer: Outliers : 2.78 % Allowed : 24.49 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.16), residues: 2936 helix: 1.35 (0.13), residues: 1614 sheet: -0.66 (0.32), residues: 264 loop : -2.51 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 153 TYR 0.014 0.001 TYR J 281 PHE 0.019 0.001 PHE D 226 TRP 0.020 0.001 TRP C 127 HIS 0.004 0.001 HIS J 266 Details of bonding type rmsd covalent geometry : bond 0.00327 (22871) covalent geometry : angle 0.67233 (31317) hydrogen bonds : bond 0.03262 ( 1236) hydrogen bonds : angle 3.66871 ( 3618) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3621.46 seconds wall clock time: 63 minutes 4.02 seconds (3784.02 seconds total)