Starting phenix.real_space_refine on Thu Mar 5 12:24:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lar_0862/03_2026/6lar_0862.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lar_0862/03_2026/6lar_0862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6lar_0862/03_2026/6lar_0862.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lar_0862/03_2026/6lar_0862.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lar_0862/03_2026/6lar_0862.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lar_0862/03_2026/6lar_0862.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 78 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: "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: "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: "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: 4.93, per 1000 atoms: 0.22 Number of scatterers: 22448 At special positions: 0 Unit cell: (183.68, 153.34, 135.3, 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: 1.93 Conformation dependent library (CDL) restraints added in 1.2 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: 120 helices and 17 sheets defined 56.5% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 34 through 49 Processing helix chain 'A' and resid 62 through 87 removed outlier: 3.868A pdb=" N THR A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 47 removed outlier: 4.238A 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 82 through 87 Processing helix chain 'B' and resid 111 through 118 Processing helix chain 'B' and resid 127 through 129 No H-bonds generated for 'chain 'B' and resid 127 through 129' Processing helix chain 'B' and resid 130 through 158 removed outlier: 4.043A pdb=" N ARG B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 181 removed outlier: 4.081A pdb=" N PHE B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 removed outlier: 3.807A pdb=" N SER B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 207 removed outlier: 3.611A pdb=" N VAL B 200 " --> pdb=" O ALA B 196 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 235 removed outlier: 3.777A pdb=" N GLY B 234 " --> pdb=" O ILE B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 263 removed outlier: 3.515A pdb=" N PHE B 244 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 263 " --> pdb=" O GLY B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 285 removed outlier: 3.930A pdb=" N CYS B 273 " --> pdb=" O ASP B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 291 removed outlier: 3.696A pdb=" N ALA B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 319 through 350 removed outlier: 3.924A pdb=" N ARG B 325 " --> pdb=" O PRO B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 372 removed outlier: 3.657A pdb=" N TRP B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL B 364 " --> pdb=" O TRP B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 404 removed outlier: 4.559A pdb=" N SER B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TYR B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 430 removed outlier: 4.173A pdb=" N ASN B 430 " --> pdb=" O VAL B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 455 removed outlier: 4.025A pdb=" N ASP B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 466 removed outlier: 4.333A pdb=" N VAL B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 46 Processing helix chain 'C' and resid 114 through 124 removed outlier: 4.218A pdb=" N ILE C 118 " --> pdb=" O ASP C 114 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE C 119 " --> pdb=" O ALA C 115 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU C 121 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA C 122 " --> pdb=" O ILE C 118 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG C 124 " --> pdb=" O SER C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 158 removed outlier: 4.436A pdb=" N ARG C 134 " --> pdb=" O THR C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 181 removed outlier: 3.852A 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 196 through 207 removed outlier: 3.751A pdb=" N VAL C 200 " --> pdb=" O ALA C 196 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA C 201 " --> pdb=" O LEU C 197 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA C 202 " --> pdb=" O VAL C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 234 removed outlier: 3.633A pdb=" N ALA C 220 " --> pdb=" O ASN C 216 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY C 234 " --> pdb=" O ILE C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 264 removed outlier: 4.098A pdb=" N THR C 245 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 285 Processing helix chain 'C' and resid 286 through 295 removed outlier: 3.709A pdb=" N ARG C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 319 removed outlier: 3.603A pdb=" N LEU C 317 " --> pdb=" O PRO C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 345 removed outlier: 3.834A pdb=" N ARG C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 351 removed outlier: 3.961A pdb=" N VAL C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER C 351 " --> pdb=" O VAL C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 374 removed outlier: 3.718A pdb=" N TRP C 360 " --> pdb=" O SER C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 404 removed outlier: 3.770A pdb=" N HIS C 389 " --> pdb=" O TRP C 385 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SER C 390 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N TYR C 391 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 429 Processing helix chain 'C' and resid 435 through 439 removed outlier: 3.544A pdb=" N TYR C 439 " --> pdb=" O PRO C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 467 removed outlier: 3.796A pdb=" N ASP C 455 " --> pdb=" O ALA C 451 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE C 459 " --> pdb=" O ASP C 455 " (cutoff:3.500A) Proline residue: C 460 - end of helix Processing helix chain 'C' and resid 467 through 472 removed outlier: 4.029A pdb=" N VAL C 472 " --> pdb=" O LEU C 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 41 Processing helix chain 'F' and resid 93 through 130 removed outlier: 3.946A pdb=" N VAL F 97 " --> pdb=" O ARG F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 138 Processing helix chain 'F' and resid 183 through 194 removed outlier: 4.007A pdb=" N ALA F 189 " --> pdb=" O VAL F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 239 removed outlier: 3.553A pdb=" N ALA F 224 " --> pdb=" O GLU F 220 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA F 227 " --> pdb=" O GLU F 223 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TRP F 238 " --> pdb=" O GLN F 234 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS F 239 " --> pdb=" O ALA F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 262 Processing helix chain 'F' and resid 285 through 294 Processing helix chain 'F' and resid 386 through 398 Processing helix chain 'G' and resid 2 through 17 removed outlier: 3.840A pdb=" N LEU G 17 " --> pdb=" O VAL G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 41 removed outlier: 3.747A pdb=" N ILE G 38 " --> pdb=" O ILE G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 62 Processing helix chain 'G' and resid 86 through 89 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 139 removed outlier: 3.624A pdb=" N ARG G 138 " --> pdb=" O ALA G 134 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER G 139 " --> pdb=" O LEU G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 163 Processing helix chain 'G' and resid 206 through 212 Processing helix chain 'G' and resid 265 through 269 removed outlier: 3.726A pdb=" N ALA G 269 " --> pdb=" O PRO G 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 265 through 269' Processing helix chain 'E' and resid 34 through 46 removed outlier: 4.165A pdb=" N ILE E 38 " --> pdb=" O PRO E 34 " (cutoff:3.500A) Proline residue: E 40 - end of helix removed outlier: 3.683A pdb=" N ARG E 44 " --> pdb=" O PRO E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 118 removed outlier: 3.972A pdb=" N VAL E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 121 No H-bonds generated for 'chain 'E' and resid 119 through 121' Processing helix chain 'E' and resid 127 through 131 removed outlier: 4.638A pdb=" N THR E 130 " --> pdb=" O TRP E 127 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS E 131 " --> pdb=" O GLY E 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 127 through 131' Processing helix chain 'E' and resid 132 through 157 removed outlier: 3.690A pdb=" N GLY E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 181 removed outlier: 3.704A pdb=" N LEU E 179 " --> pdb=" O VAL E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 205 removed outlier: 3.531A pdb=" N VAL E 194 " --> pdb=" O THR E 190 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR E 195 " --> pdb=" O SER E 191 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU E 197 " --> pdb=" O ALA E 193 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL E 198 " --> pdb=" O VAL E 194 " (cutoff:3.500A) Proline residue: E 199 - end of helix removed outlier: 3.683A pdb=" N ALA E 205 " --> pdb=" O ALA E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 233 removed outlier: 3.554A pdb=" N ALA E 221 " --> pdb=" O VAL E 217 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA E 225 " --> pdb=" O ALA E 221 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER E 231 " --> pdb=" O TRP E 227 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 263 removed outlier: 4.001A pdb=" N PHE E 244 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL E 257 " --> pdb=" O GLY E 253 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA E 261 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU E 263 " --> pdb=" O GLY E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 285 removed outlier: 4.391A pdb=" N CYS E 273 " --> pdb=" O ASP E 269 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU E 277 " --> pdb=" O CYS E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 293 removed outlier: 3.581A pdb=" N TRP E 293 " --> pdb=" O LEU E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 294 No H-bonds generated for 'chain 'E' and resid 294 through 294' Processing helix chain 'E' and resid 316 through 318 No H-bonds generated for 'chain 'E' and resid 316 through 318' Processing helix chain 'E' and resid 319 through 350 removed outlier: 3.612A pdb=" N ARG E 323 " --> pdb=" O ASP E 319 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG E 325 " --> pdb=" O PRO E 321 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL E 326 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA E 336 " --> pdb=" O THR E 332 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY E 345 " --> pdb=" O LEU E 341 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER E 346 " --> pdb=" O GLY E 342 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ALA E 348 " --> pdb=" O ALA E 344 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL E 350 " --> pdb=" O SER E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 372 removed outlier: 3.677A pdb=" N TYR E 361 " --> pdb=" O PRO E 357 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA E 366 " --> pdb=" O ILE E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 377 removed outlier: 3.778A pdb=" N VAL E 376 " --> pdb=" O ARG E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 388 removed outlier: 3.684A pdb=" N LYS E 383 " --> pdb=" O SER E 379 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU E 386 " --> pdb=" O CYS E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 404 Processing helix chain 'E' and resid 408 through 430 removed outlier: 3.933A pdb=" N TRP E 412 " --> pdb=" O GLN E 408 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA E 418 " --> pdb=" O LEU E 414 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL E 419 " --> pdb=" O ALA E 415 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU E 420 " --> pdb=" O ALA E 416 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASN E 430 " --> pdb=" O VAL E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 453 removed outlier: 3.855A pdb=" N GLY E 448 " --> pdb=" O ARG E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 466 removed outlier: 3.555A pdb=" N LEU E 464 " --> pdb=" O PRO E 460 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL E 466 " --> pdb=" O MET E 462 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 37 removed outlier: 3.591A pdb=" N GLU H 37 " --> pdb=" O PRO H 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 34 through 37' Processing helix chain 'H' and resid 38 through 47 removed outlier: 3.817A pdb=" N VAL H 42 " --> pdb=" O ILE H 38 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE H 45 " --> pdb=" O ALA H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 87 removed outlier: 3.663A pdb=" N VAL H 86 " --> pdb=" O THR H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 124 removed outlier: 4.005A pdb=" N PHE H 119 " --> pdb=" O ALA H 115 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU H 121 " --> pdb=" O VAL H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 156 removed outlier: 3.920A pdb=" N ALA H 133 " --> pdb=" O PRO H 129 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG H 134 " --> pdb=" O THR H 130 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY H 142 " --> pdb=" O LEU H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 181 removed outlier: 3.684A pdb=" N ILE H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL H 167 " --> pdb=" O GLY H 163 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL H 175 " --> pdb=" O ALA H 171 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL H 181 " --> pdb=" O ALA H 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 196 removed outlier: 4.490A pdb=" N THR H 190 " --> pdb=" O ALA H 186 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR H 195 " --> pdb=" O SER H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 208 removed outlier: 3.880A pdb=" N ALA H 202 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE H 204 " --> pdb=" O VAL H 200 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA H 205 " --> pdb=" O ALA H 201 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU H 206 " --> pdb=" O ALA H 202 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL H 208 " --> pdb=" O PHE H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 234 removed outlier: 3.926A pdb=" N LEU H 229 " --> pdb=" O ALA H 225 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA H 233 " --> pdb=" O LEU H 229 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY H 234 " --> pdb=" O ILE H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 264 removed outlier: 3.748A pdb=" N THR H 245 " --> pdb=" O ILE H 241 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR H 247 " --> pdb=" O VAL H 243 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL H 249 " --> pdb=" O THR H 245 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR H 250 " --> pdb=" O ALA H 246 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU H 263 " --> pdb=" O GLY H 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 270 through 285 removed outlier: 3.584A pdb=" N LEU H 277 " --> pdb=" O CYS H 273 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU H 278 " --> pdb=" O ALA H 274 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL H 282 " --> pdb=" O LEU H 278 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN H 285 " --> pdb=" O ILE H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 289 through 294 removed outlier: 3.671A pdb=" N TRP H 293 " --> pdb=" O LEU H 289 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA H 294 " --> pdb=" O SER H 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 289 through 294' Processing helix chain 'H' and resid 316 through 318 No H-bonds generated for 'chain 'H' and resid 316 through 318' Processing helix chain 'H' and resid 319 through 351 removed outlier: 3.994A pdb=" N ARG H 325 " --> pdb=" O PRO H 321 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA H 329 " --> pdb=" O ARG H 325 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR H 332 " --> pdb=" O GLN H 328 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY H 333 " --> pdb=" O ALA H 329 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA H 336 " --> pdb=" O THR H 332 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N SER H 346 " --> pdb=" O GLY H 342 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA H 348 " --> pdb=" O ALA H 344 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU H 349 " --> pdb=" O GLY H 345 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL H 350 " --> pdb=" O SER H 346 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER H 351 " --> pdb=" O VAL H 347 " (cutoff:3.500A) Processing helix chain 'H' and resid 356 through 370 removed outlier: 4.028A pdb=" N VAL H 364 " --> pdb=" O TRP H 360 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA H 367 " --> pdb=" O VAL H 363 " (cutoff:3.500A) Processing helix chain 'H' and resid 379 through 403 removed outlier: 3.707A pdb=" N TRP H 385 " --> pdb=" O ALA H 381 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU H 386 " --> pdb=" O CYS H 382 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS H 389 " --> pdb=" O TRP H 385 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N SER H 390 " --> pdb=" O LEU H 386 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR H 391 " --> pdb=" O LEU H 387 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA H 400 " --> pdb=" O ALA H 396 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 429 removed outlier: 4.128A pdb=" N TRP H 412 " --> pdb=" O GLN H 408 " (cutoff:3.500A) Processing helix chain 'H' and resid 442 through 457 removed outlier: 3.783A pdb=" N GLY H 448 " --> pdb=" O ARG H 444 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE H 449 " --> pdb=" O ARG H 445 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASP H 455 " --> pdb=" O ALA H 451 " (cutoff:3.500A) Processing helix chain 'H' and resid 457 through 467 Processing helix chain 'H' and resid 468 through 471 Processing helix chain 'I' and resid 34 through 55 removed outlier: 3.885A pdb=" N PHE I 43 " --> pdb=" O SER I 39 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ALA I 49 " --> pdb=" O MET I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 87 removed outlier: 3.783A pdb=" N THR I 66 " --> pdb=" O ASP I 62 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL I 71 " --> pdb=" O GLN I 67 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA I 75 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU I 76 " --> pdb=" O LEU I 72 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU I 78 " --> pdb=" O GLY I 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 113 removed outlier: 3.790A pdb=" N VAL J 97 " --> pdb=" O ARG J 93 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA J 99 " --> pdb=" O GLU J 95 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA J 102 " --> pdb=" O ASP J 98 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP J 103 " --> pdb=" O ALA J 99 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG J 106 " --> pdb=" O ALA J 102 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR J 107 " --> pdb=" O ASP J 103 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL J 110 " --> pdb=" O ARG J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 129 removed outlier: 3.769A pdb=" N HIS J 118 " --> pdb=" O ASN J 114 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA J 119 " --> pdb=" O VAL J 115 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU J 127 " --> pdb=" O ARG J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 138 Processing helix chain 'J' and resid 183 through 197 removed outlier: 3.623A pdb=" N ALA J 189 " --> pdb=" O VAL J 185 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU J 190 " --> pdb=" O ALA J 186 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL J 196 " --> pdb=" O GLY J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 208 through 212 removed outlier: 3.846A pdb=" N LYS J 211 " --> pdb=" O ASP J 208 " (cutoff:3.500A) Processing helix chain 'J' and resid 220 through 238 removed outlier: 3.843A pdb=" N ARG J 225 " --> pdb=" O ALA J 221 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ALA J 226 " --> pdb=" O ASP J 222 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE J 228 " --> pdb=" O ALA J 224 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA J 233 " --> pdb=" O ARG J 229 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLN J 234 " --> pdb=" O ALA J 230 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TRP J 238 " --> pdb=" O GLN J 234 " (cutoff:3.500A) Processing helix chain 'J' and resid 257 through 263 removed outlier: 3.582A pdb=" N TRP J 260 " --> pdb=" O ASP J 257 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TRP J 263 " --> pdb=" O TRP J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 285 through 292 removed outlier: 3.517A pdb=" N GLU J 291 " --> pdb=" O ALA J 287 " (cutoff:3.500A) Processing helix chain 'J' and resid 386 through 398 removed outlier: 3.705A pdb=" N HIS J 392 " --> pdb=" O ALA J 388 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE J 393 " --> pdb=" O GLU J 389 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA J 394 " --> pdb=" O ALA J 390 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG J 396 " --> pdb=" O HIS J 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 17 removed outlier: 3.839A pdb=" N LEU D 17 " --> pdb=" O VAL D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 41 removed outlier: 3.746A pdb=" N ILE D 38 " --> pdb=" O ILE D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 62 Processing helix chain 'D' and resid 86 through 89 Processing helix chain 'D' and resid 90 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 139 removed outlier: 3.625A pdb=" N ARG D 138 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER D 139 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 163 Processing helix chain 'D' and resid 206 through 212 Processing helix chain 'D' and resid 265 through 269 removed outlier: 3.725A pdb=" N ALA D 269 " --> pdb=" O PRO D 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 265 through 269' Processing sheet with id=AA1, first strand: chain 'B' and resid 67 through 71 removed outlier: 8.664A pdb=" N LEU B 94 " --> pdb=" O ARG B 11 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ALA B 13 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU B 96 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU B 15 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N ALA B 98 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 14 " --> pdb=" O THR B 25 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR B 25 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA B 16 " --> pdb=" O ARG B 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 25 through 30 removed outlier: 8.592A pdb=" N LEU C 94 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ALA C 13 " --> pdb=" O LEU C 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 67 through 68 removed outlier: 3.550A pdb=" N GLN C 97 " --> pdb=" O SER C 68 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 23 through 24 removed outlier: 3.616A pdb=" N ILE F 24 " --> pdb=" O LYS F 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 157 through 158 Processing sheet with id=AA6, first strand: chain 'F' and resid 202 through 204 Processing sheet with id=AA7, first strand: chain 'F' and resid 244 through 247 removed outlier: 6.035A pdb=" N LEU F 314 " --> pdb=" O THR F 338 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ILE F 340 " --> pdb=" O LEU F 314 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL F 316 " --> pdb=" O ILE F 340 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N LEU F 360 " --> pdb=" O ARG F 214 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR F 216 " --> pdb=" O LEU F 360 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N VAL F 362 " --> pdb=" O THR F 216 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE F 218 " --> pdb=" O VAL F 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 166 through 169 removed outlier: 4.444A pdb=" N VAL G 79 " --> pdb=" O VAL G 169 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA G 76 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL G 82 " --> pdb=" O SER G 120 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER G 120 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR G 125 " --> pdb=" O LYS G 106 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS G 106 " --> pdb=" O THR G 125 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU G 225 " --> pdb=" O THR G 236 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL G 241 " --> pdb=" O ALA G 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 9 through 16 removed outlier: 3.835A pdb=" N THR E 25 " --> pdb=" O VAL E 14 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 67 through 71 Processing sheet with id=AB2, first strand: chain 'H' and resid 25 through 26 removed outlier: 6.078A pdb=" N ALA H 13 " --> pdb=" O LEU H 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 67 through 68 Processing sheet with id=AB4, first strand: chain 'J' and resid 4 through 5 removed outlier: 5.957A pdb=" N LEU J 4 " --> pdb=" O ASP J 401 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'J' and resid 158 through 165 removed outlier: 7.249A pdb=" N THR J 205 " --> pdb=" O ALA J 160 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ARG J 162 " --> pdb=" O ALA J 203 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ALA J 203 " --> pdb=" O ARG J 162 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ASP J 164 " --> pdb=" O ARG J 201 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ARG J 201 " --> pdb=" O ASP J 164 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 342 through 343 removed outlier: 6.516A pdb=" N VAL J 217 " --> pdb=" O THR J 343 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE J 218 " --> pdb=" O VAL J 362 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 244 through 249 Processing sheet with id=AB8, first strand: chain 'D' and resid 166 through 169 removed outlier: 4.444A pdb=" N VAL D 79 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA D 76 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL D 82 " --> pdb=" O SER D 120 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER D 120 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR D 125 " --> pdb=" O LYS D 106 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS D 106 " --> pdb=" O THR D 125 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU D 225 " --> pdb=" O THR D 236 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL D 241 " --> pdb=" O ALA D 195 " (cutoff:3.500A) 1159 hydrogen bonds defined for protein. 3378 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: 3.93 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7128 1.33 - 1.45: 3399 1.45 - 1.57: 12246 1.57 - 1.69: 2 1.69 - 1.81: 96 Bond restraints: 22871 Sorted by residual: bond pdb=" N ILE J 22 " pdb=" CA ILE J 22 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.19e-02 7.06e+03 9.22e+00 bond pdb=" N ILE J 180 " pdb=" CA ILE J 180 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.25e-02 6.40e+03 8.68e+00 bond pdb=" N VAL J 111 " pdb=" CA VAL J 111 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.22e-02 6.72e+03 8.54e+00 bond pdb=" N VAL E 395 " pdb=" CA VAL E 395 " ideal model delta sigma weight residual 1.461 1.495 -0.035 1.19e-02 7.06e+03 8.48e+00 bond pdb=" N VAL A 19 " pdb=" CA VAL A 19 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.36e+00 ... (remaining 22866 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 30812 2.98 - 5.96: 447 5.96 - 8.94: 50 8.94 - 11.93: 6 11.93 - 14.91: 2 Bond angle restraints: 31317 Sorted by residual: angle pdb=" CA GLU G 232 " pdb=" CB GLU G 232 " pdb=" CG GLU G 232 " ideal model delta sigma weight residual 114.10 129.01 -14.91 2.00e+00 2.50e-01 5.56e+01 angle pdb=" CA GLU D 232 " pdb=" CB GLU D 232 " pdb=" CG GLU D 232 " ideal model delta sigma weight residual 114.10 128.94 -14.84 2.00e+00 2.50e-01 5.51e+01 angle pdb=" N VAL E 86 " pdb=" CA VAL E 86 " pdb=" C VAL E 86 " ideal model delta sigma weight residual 112.83 105.95 6.88 9.90e-01 1.02e+00 4.84e+01 angle pdb=" CB GLU D 232 " pdb=" CG GLU D 232 " pdb=" CD GLU D 232 " ideal model delta sigma weight residual 112.60 122.05 -9.45 1.70e+00 3.46e-01 3.09e+01 angle pdb=" CB GLU G 232 " pdb=" CG GLU G 232 " pdb=" CD GLU G 232 " ideal model delta sigma weight residual 112.60 122.02 -9.42 1.70e+00 3.46e-01 3.07e+01 ... (remaining 31312 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 12176 17.94 - 35.89: 1156 35.89 - 53.83: 272 53.83 - 71.77: 70 71.77 - 89.71: 12 Dihedral angle restraints: 13686 sinusoidal: 5053 harmonic: 8633 Sorted by residual: dihedral pdb=" CA ALA J 323 " pdb=" C ALA J 323 " pdb=" N ASP J 324 " pdb=" CA ASP J 324 " ideal model delta harmonic sigma weight residual 180.00 149.27 30.73 0 5.00e+00 4.00e-02 3.78e+01 dihedral pdb=" CA VAL B 208 " pdb=" C VAL B 208 " pdb=" N PRO B 209 " pdb=" CA PRO B 209 " ideal model delta harmonic sigma weight residual 180.00 -152.56 -27.44 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA PRO B 100 " pdb=" C PRO B 100 " pdb=" N SER B 101 " pdb=" CA SER B 101 " ideal model delta harmonic sigma weight residual 180.00 -152.58 -27.42 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 13683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2717 0.048 - 0.096: 921 0.096 - 0.144: 219 0.144 - 0.193: 36 0.193 - 0.241: 3 Chirality restraints: 3896 Sorted by residual: chirality pdb=" CA GLN E 408 " pdb=" N GLN E 408 " pdb=" C GLN E 408 " pdb=" CB GLN E 408 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA ILE J 24 " pdb=" N ILE J 24 " pdb=" C ILE J 24 " pdb=" CB ILE J 24 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA VAL J 173 " pdb=" N VAL J 173 " pdb=" C VAL J 173 " pdb=" CB VAL J 173 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 3893 not shown) Planarity restraints: 3952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU G 232 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.18e+00 pdb=" CD GLU G 232 " -0.052 2.00e-02 2.50e+03 pdb=" OE1 GLU G 232 " 0.019 2.00e-02 2.50e+03 pdb=" OE2 GLU G 232 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 232 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.15e+00 pdb=" CD GLU D 232 " -0.052 2.00e-02 2.50e+03 pdb=" OE1 GLU D 232 " 0.019 2.00e-02 2.50e+03 pdb=" OE2 GLU D 232 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL J 165 " -0.043 5.00e-02 4.00e+02 6.45e-02 6.66e+00 pdb=" N PRO J 166 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO J 166 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO J 166 " -0.036 5.00e-02 4.00e+02 ... (remaining 3949 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 138 2.47 - 3.08: 17190 3.08 - 3.68: 33559 3.68 - 4.29: 45813 4.29 - 4.90: 72711 Nonbonded interactions: 169411 Sorted by model distance: nonbonded pdb=" OG SER E 346 " pdb=" CG1 VAL E 363 " model vdw 1.858 3.460 nonbonded pdb=" NE ARG E 107 " pdb=" NH2 ARG J 116 " model vdw 2.015 3.200 nonbonded pdb=" OG1 THR J 94 " pdb=" OE2 GLU J 95 " model vdw 2.037 3.040 nonbonded pdb=" NE2 HIS J 341 " pdb=" OG1 THR J 343 " model vdw 2.080 3.120 nonbonded pdb=" OE2 GLU F 127 " pdb=" NH2 ARG F 162 " model vdw 2.101 3.120 ... (remaining 169406 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: 8.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.930 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 22871 Z= 0.381 Angle : 0.988 14.907 31317 Z= 0.579 Chirality : 0.051 0.241 3896 Planarity : 0.006 0.065 3952 Dihedral : 15.429 89.714 8062 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.37 % Allowed : 13.22 % Favored : 86.41 % Rotamer: Outliers : 5.47 % Allowed : 12.98 % Favored : 81.55 % 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: -4.82 (0.13), residues: 2936 helix: -2.70 (0.10), residues: 1497 sheet: -2.16 (0.31), residues: 258 loop : -4.04 (0.15), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 198 TYR 0.020 0.002 TYR J 352 PHE 0.021 0.002 PHE A 88 TRP 0.035 0.002 TRP F 231 HIS 0.010 0.002 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00732 (22871) covalent geometry : angle 0.98758 (31317) hydrogen bonds : bond 0.23000 ( 1159) hydrogen bonds : angle 8.77323 ( 3378) *********************** 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 593 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 467 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 MET cc_start: 0.8258 (ptp) cc_final: 0.8029 (ptp) REVERT: B 277 LEU cc_start: 0.8975 (tt) cc_final: 0.8604 (mm) REVERT: B 372 LEU cc_start: 0.8458 (tp) cc_final: 0.8237 (tp) REVERT: B 433 ILE cc_start: 0.8046 (mp) cc_final: 0.7792 (mm) REVERT: C 44 ARG cc_start: 0.6773 (ptp90) cc_final: 0.5966 (mmp-170) REVERT: C 411 LEU cc_start: 0.8090 (pp) cc_final: 0.7189 (tp) REVERT: F 352 TYR cc_start: 0.7666 (m-80) cc_final: 0.7401 (t80) REVERT: F 397 LEU cc_start: 0.8751 (pp) cc_final: 0.8210 (tp) REVERT: G 29 VAL cc_start: 0.6583 (OUTLIER) cc_final: 0.6239 (m) REVERT: G 165 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8284 (p) REVERT: E 277 LEU cc_start: 0.8800 (mt) cc_final: 0.8586 (mt) REVERT: E 407 TYR cc_start: 0.7119 (OUTLIER) cc_final: 0.6647 (m-80) REVERT: E 432 LYS cc_start: 0.8005 (tttt) cc_final: 0.7671 (mmtm) REVERT: E 462 MET cc_start: 0.7897 (tpp) cc_final: 0.7674 (tpt) REVERT: E 469 PHE cc_start: 0.6926 (p90) cc_final: 0.6480 (p90) REVERT: H 120 SER cc_start: 0.8729 (p) cc_final: 0.7264 (t) REVERT: I 45 MET cc_start: 0.7674 (mmm) cc_final: 0.7244 (tmm) REVERT: J 96 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7954 (tp30) REVERT: J 111 VAL cc_start: 0.9166 (OUTLIER) cc_final: 0.8955 (p) REVERT: D 267 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7692 (mp) REVERT: D 276 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7565 (tm-30) outliers start: 126 outliers final: 51 residues processed: 557 average time/residue: 0.1643 time to fit residues: 137.0898 Evaluate side-chains 370 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 313 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain G residue 238 CYS Chi-restraints excluded: chain G residue 274 SER Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 389 HIS Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 405 ASP Chi-restraints excluded: chain E residue 407 TYR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain J residue 112 ARG Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 174 LYS Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 238 CYS Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 276 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 HIS ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN C 131 HIS C 154 HIS ** C 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 HIS F 122 GLN F 371 GLN E 164 GLN H 131 HIS I 55 HIS J 122 GLN J 187 HIS J 271 ASN J 371 GLN J 376 GLN D 162 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.136423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.112326 restraints weight = 67740.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.113705 restraints weight = 38383.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.113865 restraints weight = 27283.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.114162 restraints weight = 26280.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.114270 restraints weight = 24000.932| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3816 r_free = 0.3816 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 = 0.3817 r_free = 0.3817 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 22871 Z= 0.207 Angle : 0.810 10.433 31317 Z= 0.405 Chirality : 0.045 0.287 3896 Planarity : 0.007 0.120 3952 Dihedral : 8.058 59.990 3340 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % Rotamer: Outliers : 5.21 % Allowed : 19.28 % Favored : 75.51 % 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: -3.11 (0.14), residues: 2936 helix: -1.00 (0.12), residues: 1587 sheet: -2.10 (0.28), residues: 285 loop : -3.66 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 123 TYR 0.024 0.002 TYR G 100 PHE 0.016 0.002 PHE C 77 TRP 0.030 0.002 TRP G 21 HIS 0.007 0.001 HIS B 154 Details of bonding type rmsd covalent geometry : bond 0.00471 (22871) covalent geometry : angle 0.81035 (31317) hydrogen bonds : bond 0.06116 ( 1159) hydrogen bonds : angle 5.49474 ( 3378) *********************** 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 491 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 371 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASN cc_start: 0.7882 (m-40) cc_final: 0.7577 (m110) REVERT: C 44 ARG cc_start: 0.6978 (ptp90) cc_final: 0.6109 (mmp-170) REVERT: C 114 ASP cc_start: 0.8228 (t0) cc_final: 0.7990 (t0) REVERT: C 277 LEU cc_start: 0.7982 (mm) cc_final: 0.7662 (mm) REVERT: C 393 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8149 (tp) REVERT: C 411 LEU cc_start: 0.7977 (pp) cc_final: 0.7041 (tp) REVERT: F 127 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7992 (tp30) REVERT: F 318 LEU cc_start: 0.8227 (mp) cc_final: 0.7671 (tp) REVERT: F 352 TYR cc_start: 0.7746 (m-80) cc_final: 0.7413 (t80) REVERT: F 397 LEU cc_start: 0.8751 (pp) cc_final: 0.8399 (tp) REVERT: G 200 LYS cc_start: 0.8201 (tppt) cc_final: 0.7828 (tptp) REVERT: E 212 PHE cc_start: 0.2920 (OUTLIER) cc_final: 0.2469 (m-80) REVERT: E 407 TYR cc_start: 0.7280 (OUTLIER) cc_final: 0.6680 (m-80) REVERT: E 432 LYS cc_start: 0.8013 (tttt) cc_final: 0.7556 (mmtm) REVERT: I 45 MET cc_start: 0.7858 (mmm) cc_final: 0.7334 (tmm) REVERT: J 96 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7424 (tm-30) REVERT: J 364 ASP cc_start: 0.7438 (p0) cc_final: 0.7138 (p0) REVERT: D 267 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7368 (mp) outliers start: 120 outliers final: 79 residues processed: 453 average time/residue: 0.1333 time to fit residues: 97.0146 Evaluate side-chains 391 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 308 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 274 SER Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 402 VAL Chi-restraints excluded: chain E residue 407 TYR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain H residue 148 THR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 273 CYS Chi-restraints excluded: chain H residue 403 ILE Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 429 LEU Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 174 LYS Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 316 VAL Chi-restraints excluded: chain J residue 339 VAL Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 162 GLN Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 238 CYS Chi-restraints excluded: chain D residue 267 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 57 optimal weight: 5.9990 chunk 174 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 188 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 128 optimal weight: 8.9990 chunk 223 optimal weight: 0.7980 chunk 43 optimal weight: 8.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN C 285 GLN C 430 ASN G 22 GLN G 63 ASN H 331 GLN J 130 HIS J 313 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.137222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.114343 restraints weight = 68328.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.115407 restraints weight = 38167.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.115920 restraints weight = 30768.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.116155 restraints weight = 26984.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.116193 restraints weight = 24801.815| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3852 r_free = 0.3852 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3851 r_free = 0.3851 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22871 Z= 0.164 Angle : 0.740 13.488 31317 Z= 0.365 Chirality : 0.043 0.294 3896 Planarity : 0.006 0.086 3952 Dihedral : 6.890 59.784 3294 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 5.34 % Allowed : 22.80 % Favored : 71.86 % 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: -2.17 (0.15), residues: 2936 helix: -0.15 (0.13), residues: 1589 sheet: -1.98 (0.28), residues: 285 loop : -3.31 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 399 TYR 0.014 0.002 TYR J 281 PHE 0.014 0.001 PHE H 165 TRP 0.038 0.002 TRP G 121 HIS 0.012 0.001 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00367 (22871) covalent geometry : angle 0.74026 (31317) hydrogen bonds : bond 0.05181 ( 1159) hydrogen bonds : angle 4.85029 ( 3378) *********************** 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 480 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 357 time to evaluate : 0.841 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: C 27 MET cc_start: 0.3266 (tpt) cc_final: 0.2867 (ttm) REVERT: C 277 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7759 (mm) REVERT: C 392 LEU cc_start: 0.7831 (tt) cc_final: 0.7609 (tt) REVERT: C 411 LEU cc_start: 0.7933 (pp) cc_final: 0.7042 (tp) REVERT: F 127 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7966 (tp30) REVERT: F 318 LEU cc_start: 0.8148 (mp) cc_final: 0.7779 (tp) REVERT: F 370 TRP cc_start: 0.5532 (t-100) cc_final: 0.5159 (t-100) REVERT: F 397 LEU cc_start: 0.8657 (pp) cc_final: 0.8353 (tp) REVERT: G 22 GLN cc_start: 0.7157 (OUTLIER) cc_final: 0.6457 (pm20) REVERT: G 200 LYS cc_start: 0.8416 (tppt) cc_final: 0.7795 (tptp) REVERT: E 212 PHE cc_start: 0.2764 (OUTLIER) cc_final: 0.2331 (m-80) REVERT: E 407 TYR cc_start: 0.7401 (OUTLIER) cc_final: 0.6748 (m-80) REVERT: E 432 LYS cc_start: 0.8044 (tttt) cc_final: 0.7597 (mmtm) REVERT: H 420 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8148 (mm) REVERT: I 45 MET cc_start: 0.7819 (mmm) cc_final: 0.7358 (tmm) REVERT: J 96 GLU cc_start: 0.7355 (tm-30) cc_final: 0.7147 (tm-30) REVERT: J 364 ASP cc_start: 0.7441 (p0) cc_final: 0.7035 (p0) outliers start: 123 outliers final: 82 residues processed: 436 average time/residue: 0.1331 time to fit residues: 94.3483 Evaluate side-chains 391 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 304 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 274 SER Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 407 TYR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 190 THR Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 257 VAL Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 273 CYS Chi-restraints excluded: chain H residue 403 ILE Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 429 LEU Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 209 VAL Chi-restraints excluded: chain J residue 316 VAL Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 283 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 58 optimal weight: 0.0470 chunk 286 optimal weight: 7.9990 chunk 174 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 183 optimal weight: 8.9990 chunk 162 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 245 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 195 optimal weight: 1.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 GLN B 408 GLN D 63 ASN D 162 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.135533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.112515 restraints weight = 68142.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.113536 restraints weight = 38556.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.113986 restraints weight = 31112.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.114195 restraints weight = 27838.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.114264 restraints weight = 25594.358| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3810 r_free = 0.3810 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3810 r_free = 0.3810 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22871 Z= 0.196 Angle : 0.755 12.723 31317 Z= 0.372 Chirality : 0.044 0.288 3896 Planarity : 0.006 0.109 3952 Dihedral : 6.454 59.694 3276 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.63 % Favored : 89.34 % Rotamer: Outliers : 6.30 % Allowed : 24.36 % Favored : 69.34 % 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: -1.87 (0.16), residues: 2936 helix: 0.08 (0.13), residues: 1594 sheet: -1.86 (0.29), residues: 271 loop : -3.15 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 123 TYR 0.014 0.002 TYR G 96 PHE 0.014 0.001 PHE H 165 TRP 0.032 0.002 TRP D 21 HIS 0.009 0.001 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00445 (22871) covalent geometry : angle 0.75474 (31317) hydrogen bonds : bond 0.05057 ( 1159) hydrogen bonds : angle 4.68229 ( 3378) *********************** 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 480 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 335 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 TRP cc_start: 0.6908 (m-90) cc_final: 0.6109 (m-10) REVERT: C 27 MET cc_start: 0.3245 (tpt) cc_final: 0.2961 (ttm) REVERT: C 44 ARG cc_start: 0.6507 (mtm180) cc_final: 0.5353 (mmp-170) REVERT: C 277 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7763 (mm) REVERT: C 392 LEU cc_start: 0.7905 (tt) cc_final: 0.7689 (tt) REVERT: C 411 LEU cc_start: 0.7997 (pp) cc_final: 0.7072 (tp) REVERT: F 127 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8042 (tp30) REVERT: F 318 LEU cc_start: 0.8372 (mp) cc_final: 0.7962 (tp) REVERT: F 370 TRP cc_start: 0.5649 (t-100) cc_final: 0.5408 (t-100) REVERT: F 397 LEU cc_start: 0.8714 (pp) cc_final: 0.8480 (tp) REVERT: G 200 LYS cc_start: 0.8493 (tppt) cc_final: 0.8073 (mmmt) REVERT: E 407 TYR cc_start: 0.7601 (OUTLIER) cc_final: 0.6987 (m-80) REVERT: E 432 LYS cc_start: 0.8021 (tttt) cc_final: 0.7549 (mmtm) REVERT: H 444 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.6980 (ptp-170) REVERT: I 45 MET cc_start: 0.7920 (mmm) cc_final: 0.7359 (tmm) REVERT: J 96 GLU cc_start: 0.7408 (tm-30) cc_final: 0.7148 (tm-30) REVERT: J 364 ASP cc_start: 0.7502 (p0) cc_final: 0.7179 (p0) outliers start: 145 outliers final: 102 residues processed: 438 average time/residue: 0.1313 time to fit residues: 94.7331 Evaluate side-chains 409 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 304 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 408 GLN Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 232 MET Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 407 TYR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 190 THR Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 335 ILE Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 403 ILE Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 419 VAL Chi-restraints excluded: chain H residue 429 LEU Chi-restraints excluded: chain H residue 444 ARG Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 209 VAL Chi-restraints excluded: chain J residue 316 VAL Chi-restraints excluded: chain J residue 386 SER Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 283 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 201 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 69 optimal weight: 0.6980 chunk 222 optimal weight: 0.7980 chunk 199 optimal weight: 10.0000 chunk 187 optimal weight: 6.9990 chunk 284 optimal weight: 10.0000 chunk 57 optimal weight: 0.0070 chunk 205 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 200 optimal weight: 0.1980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 GLN F 163 HIS E 330 HIS J 122 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.138739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.116271 restraints weight = 67576.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.117275 restraints weight = 39443.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.117841 restraints weight = 29638.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.118072 restraints weight = 28135.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.118173 restraints weight = 24538.113| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3882 r_free = 0.3882 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3882 r_free = 0.3882 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22871 Z= 0.130 Angle : 0.702 15.345 31317 Z= 0.340 Chirality : 0.042 0.267 3896 Planarity : 0.005 0.065 3952 Dihedral : 5.934 59.875 3274 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 3.95 % Allowed : 26.70 % Favored : 69.34 % 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: -1.34 (0.16), residues: 2936 helix: 0.57 (0.14), residues: 1572 sheet: -1.65 (0.29), residues: 281 loop : -2.95 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 123 TYR 0.015 0.001 TYR G 96 PHE 0.019 0.001 PHE E 449 TRP 0.025 0.001 TRP J 231 HIS 0.008 0.001 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00282 (22871) covalent geometry : angle 0.70197 (31317) hydrogen bonds : bond 0.04185 ( 1159) hydrogen bonds : angle 4.21274 ( 3378) *********************** 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 443 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 352 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 TRP cc_start: 0.6908 (m-90) cc_final: 0.6249 (m-10) REVERT: C 27 MET cc_start: 0.3466 (tpt) cc_final: 0.3141 (ttm) REVERT: C 44 ARG cc_start: 0.6522 (mtm180) cc_final: 0.5321 (mmp-170) REVERT: C 277 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7826 (mm) REVERT: C 411 LEU cc_start: 0.7821 (pp) cc_final: 0.6933 (tp) REVERT: F 243 MET cc_start: 0.8179 (tpp) cc_final: 0.7944 (ttm) REVERT: F 318 LEU cc_start: 0.8265 (mp) cc_final: 0.7921 (tp) REVERT: F 346 LEU cc_start: 0.6209 (pt) cc_final: 0.5817 (tp) REVERT: G 161 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8329 (tp30) REVERT: G 197 TYR cc_start: 0.6286 (m-80) cc_final: 0.5880 (t80) REVERT: G 200 LYS cc_start: 0.8492 (tppt) cc_final: 0.8107 (mmmt) REVERT: E 212 PHE cc_start: 0.2360 (OUTLIER) cc_final: 0.1891 (m-80) REVERT: E 407 TYR cc_start: 0.7476 (OUTLIER) cc_final: 0.6908 (m-80) REVERT: E 432 LYS cc_start: 0.7992 (tttt) cc_final: 0.7558 (mmtm) REVERT: H 335 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8339 (mt) REVERT: H 420 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8131 (mm) REVERT: I 45 MET cc_start: 0.7890 (mmm) cc_final: 0.7303 (tmm) REVERT: I 72 LEU cc_start: 0.8564 (tp) cc_final: 0.8292 (tt) REVERT: J 364 ASP cc_start: 0.7456 (p0) cc_final: 0.7102 (p0) REVERT: D 59 MET cc_start: 0.4158 (mmm) cc_final: 0.3808 (mmm) outliers start: 91 outliers final: 51 residues processed: 417 average time/residue: 0.1305 time to fit residues: 90.0732 Evaluate side-chains 365 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 309 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 285 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 407 TYR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 335 ILE Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 316 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 238 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 99 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 270 optimal weight: 0.8980 chunk 119 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 chunk 277 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 123 optimal weight: 0.9990 chunk 206 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 HIS F 197 GLN H 331 GLN J 163 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.137407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.114799 restraints weight = 68601.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.115700 restraints weight = 44041.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.116088 restraints weight = 33062.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.116327 restraints weight = 30986.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.116456 restraints weight = 27191.891| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3853 r_free = 0.3853 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3853 r_free = 0.3853 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4208 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= 0.141 Angle : 0.724 15.110 31317 Z= 0.346 Chirality : 0.042 0.265 3896 Planarity : 0.005 0.062 3952 Dihedral : 5.721 56.193 3268 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.26 % Favored : 90.70 % Rotamer: Outliers : 4.73 % Allowed : 26.36 % Favored : 68.91 % 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: -1.18 (0.16), residues: 2936 helix: 0.68 (0.14), residues: 1575 sheet: -1.60 (0.30), residues: 267 loop : -2.82 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 36 TYR 0.018 0.001 TYR G 96 PHE 0.017 0.001 PHE G 226 TRP 0.024 0.001 TRP J 258 HIS 0.006 0.001 HIS J 266 Details of bonding type rmsd covalent geometry : bond 0.00324 (22871) covalent geometry : angle 0.72430 (31317) hydrogen bonds : bond 0.04166 ( 1159) hydrogen bonds : angle 4.18655 ( 3378) *********************** 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 435 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 326 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 138 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8684 (tt) REVERT: B 264 TRP cc_start: 0.6926 (m-90) cc_final: 0.6195 (m-10) REVERT: C 44 ARG cc_start: 0.6546 (mtm180) cc_final: 0.5351 (mmp-170) REVERT: C 277 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7791 (mm) REVERT: C 411 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.6990 (tp) REVERT: F 253 LEU cc_start: 0.1658 (OUTLIER) cc_final: 0.1391 (pt) REVERT: F 318 LEU cc_start: 0.8336 (mp) cc_final: 0.7980 (tp) REVERT: F 346 LEU cc_start: 0.6397 (pt) cc_final: 0.6012 (tp) REVERT: G 200 LYS cc_start: 0.8520 (tppt) cc_final: 0.8137 (mmmt) REVERT: E 407 TYR cc_start: 0.7575 (OUTLIER) cc_final: 0.7099 (m-80) REVERT: E 432 LYS cc_start: 0.7940 (tttt) cc_final: 0.7528 (mmtm) REVERT: E 445 ARG cc_start: 0.8518 (mmp80) cc_final: 0.8126 (mmp80) REVERT: I 45 MET cc_start: 0.7924 (mmm) cc_final: 0.7313 (tmm) REVERT: J 364 ASP cc_start: 0.7491 (p0) cc_final: 0.7188 (p0) REVERT: D 59 MET cc_start: 0.4270 (mmm) cc_final: 0.3930 (mmm) outliers start: 109 outliers final: 78 residues processed: 398 average time/residue: 0.1278 time to fit residues: 85.4245 Evaluate side-chains 391 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 308 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 154 HIS Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 407 TYR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 335 ILE Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 316 VAL Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 238 CYS Chi-restraints excluded: chain D residue 283 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 94 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 297 optimal weight: 6.9990 chunk 106 optimal weight: 0.0470 chunk 100 optimal weight: 4.9990 chunk 263 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 276 optimal weight: 4.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 389 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.133988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.110664 restraints weight = 68359.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.111741 restraints weight = 37646.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.111996 restraints weight = 28647.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.112268 restraints weight = 26890.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.112332 restraints weight = 24084.655| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3784 r_free = 0.3784 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3784 r_free = 0.3784 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 22871 Z= 0.217 Angle : 0.796 15.073 31317 Z= 0.387 Chirality : 0.045 0.284 3896 Planarity : 0.006 0.061 3952 Dihedral : 5.861 52.832 3266 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.83 % Favored : 89.13 % Rotamer: Outliers : 5.95 % Allowed : 26.01 % Favored : 68.04 % 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: -1.32 (0.16), residues: 2936 helix: 0.53 (0.13), residues: 1562 sheet: -1.65 (0.30), residues: 275 loop : -2.79 (0.19), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 445 TYR 0.022 0.002 TYR G 96 PHE 0.013 0.002 PHE B 165 TRP 0.044 0.002 TRP D 21 HIS 0.007 0.001 HIS J 130 Details of bonding type rmsd covalent geometry : bond 0.00493 (22871) covalent geometry : angle 0.79594 (31317) hydrogen bonds : bond 0.05070 ( 1159) hydrogen bonds : angle 4.51653 ( 3378) *********************** 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 447 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 310 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 138 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8479 (tt) REVERT: B 264 TRP cc_start: 0.6929 (m-90) cc_final: 0.6120 (m-10) REVERT: C 27 MET cc_start: 0.3736 (tpt) cc_final: 0.3468 (ttp) REVERT: C 44 ARG cc_start: 0.6579 (mtm180) cc_final: 0.5433 (mmp-170) REVERT: C 277 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7800 (mm) REVERT: C 411 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7060 (tp) REVERT: F 253 LEU cc_start: 0.1791 (OUTLIER) cc_final: 0.1548 (pt) REVERT: F 318 LEU cc_start: 0.8312 (mp) cc_final: 0.8096 (tp) REVERT: G 47 MET cc_start: 0.5859 (tpp) cc_final: 0.4686 (tmm) REVERT: G 197 TYR cc_start: 0.6370 (m-80) cc_final: 0.6128 (t80) REVERT: G 200 LYS cc_start: 0.8485 (tppt) cc_final: 0.8223 (mmmt) REVERT: E 132 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7618 (mt) REVERT: E 212 PHE cc_start: 0.2251 (OUTLIER) cc_final: 0.1424 (m-80) REVERT: E 407 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.7318 (m-80) REVERT: E 432 LYS cc_start: 0.8017 (tttt) cc_final: 0.7566 (mmtm) REVERT: H 444 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7076 (ptp-170) REVERT: I 45 MET cc_start: 0.7968 (mmm) cc_final: 0.7386 (tmm) REVERT: J 364 ASP cc_start: 0.7465 (p0) cc_final: 0.7057 (p0) REVERT: D 96 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.8147 (t80) outliers start: 137 outliers final: 100 residues processed: 407 average time/residue: 0.1294 time to fit residues: 89.0050 Evaluate side-chains 398 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 289 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 11 PHE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 407 TYR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 190 THR Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 335 ILE Chi-restraints excluded: chain H residue 346 SER Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 429 LEU Chi-restraints excluded: chain H residue 444 ARG Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 242 THR Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 316 VAL Chi-restraints excluded: chain J residue 339 VAL Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 238 CYS Chi-restraints excluded: chain D residue 283 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 18 optimal weight: 0.8980 chunk 183 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 223 optimal weight: 0.7980 chunk 219 optimal weight: 2.9990 chunk 185 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 239 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 197 GLN G 74 HIS J 392 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.136619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.113946 restraints weight = 67308.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.114842 restraints weight = 39290.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.115040 restraints weight = 29606.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.115332 restraints weight = 28022.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.115483 restraints weight = 25795.434| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3833 r_free = 0.3833 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3833 r_free = 0.3833 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 22871 Z= 0.136 Angle : 0.738 14.744 31317 Z= 0.353 Chirality : 0.043 0.265 3896 Planarity : 0.005 0.057 3952 Dihedral : 5.480 54.467 3265 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 4.47 % Allowed : 27.92 % Favored : 67.61 % 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: -1.02 (0.16), residues: 2936 helix: 0.82 (0.13), residues: 1562 sheet: -1.52 (0.30), residues: 274 loop : -2.71 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 361 TYR 0.022 0.001 TYR G 96 PHE 0.024 0.001 PHE F 6 TRP 0.034 0.001 TRP D 21 HIS 0.006 0.001 HIS J 341 Details of bonding type rmsd covalent geometry : bond 0.00310 (22871) covalent geometry : angle 0.73847 (31317) hydrogen bonds : bond 0.04212 ( 1159) hydrogen bonds : angle 4.15837 ( 3378) *********************** 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 425 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 322 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 138 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8720 (tt) REVERT: B 264 TRP cc_start: 0.6955 (m-90) cc_final: 0.6243 (m-10) REVERT: B 444 ARG cc_start: 0.5929 (tpp80) cc_final: 0.5593 (mtp180) REVERT: C 44 ARG cc_start: 0.6712 (mtm180) cc_final: 0.5582 (mmp-170) REVERT: C 204 PHE cc_start: 0.8003 (t80) cc_final: 0.7420 (t80) REVERT: C 277 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7844 (mm) REVERT: C 411 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.6875 (tp) REVERT: F 318 LEU cc_start: 0.8297 (mp) cc_final: 0.8078 (tp) REVERT: G 47 MET cc_start: 0.5854 (tpp) cc_final: 0.4716 (tmm) REVERT: G 81 ARG cc_start: 0.6954 (OUTLIER) cc_final: 0.5911 (tpp-160) REVERT: G 197 TYR cc_start: 0.6409 (m-80) cc_final: 0.6199 (t80) REVERT: G 200 LYS cc_start: 0.8458 (tppt) cc_final: 0.8138 (mmmt) REVERT: E 407 TYR cc_start: 0.7674 (OUTLIER) cc_final: 0.7329 (m-80) REVERT: E 432 LYS cc_start: 0.7972 (tttt) cc_final: 0.7539 (mmtm) REVERT: H 443 MET cc_start: 0.6687 (tpp) cc_final: 0.6332 (tpp) REVERT: H 444 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.6751 (ptp-170) REVERT: I 45 MET cc_start: 0.7963 (mmm) cc_final: 0.7325 (tmm) REVERT: J 364 ASP cc_start: 0.7384 (p0) cc_final: 0.6854 (p0) REVERT: D 96 TYR cc_start: 0.8344 (OUTLIER) cc_final: 0.8022 (t80) outliers start: 103 outliers final: 69 residues processed: 390 average time/residue: 0.1320 time to fit residues: 85.8282 Evaluate side-chains 383 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 307 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 81 ARG Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 407 TYR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 335 ILE Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain H residue 444 ARG Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 242 THR Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 316 VAL Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 238 CYS Chi-restraints excluded: chain D residue 283 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 113 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 46 optimal weight: 0.0570 chunk 233 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 206 optimal weight: 0.8980 chunk 176 optimal weight: 0.7980 chunk 229 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 74 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.135669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.111941 restraints weight = 68231.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.112917 restraints weight = 37656.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.113474 restraints weight = 26664.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.113748 restraints weight = 25811.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.113760 restraints weight = 22862.593| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3808 r_free = 0.3808 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3808 r_free = 0.3808 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22871 Z= 0.151 Angle : 0.753 15.289 31317 Z= 0.361 Chirality : 0.043 0.257 3896 Planarity : 0.005 0.058 3952 Dihedral : 5.418 54.781 3265 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 4.26 % Allowed : 28.31 % Favored : 67.43 % 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: -0.91 (0.16), residues: 2936 helix: 0.90 (0.14), residues: 1562 sheet: -1.39 (0.31), residues: 272 loop : -2.70 (0.19), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 325 TYR 0.023 0.002 TYR D 197 PHE 0.016 0.001 PHE C 204 TRP 0.030 0.001 TRP D 21 HIS 0.005 0.001 HIS J 341 Details of bonding type rmsd covalent geometry : bond 0.00351 (22871) covalent geometry : angle 0.75255 (31317) hydrogen bonds : bond 0.04240 ( 1159) hydrogen bonds : angle 4.15810 ( 3378) *********************** 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 414 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 316 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 138 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8645 (tt) REVERT: B 264 TRP cc_start: 0.6904 (m-90) cc_final: 0.6187 (m-10) REVERT: B 444 ARG cc_start: 0.5919 (tpp80) cc_final: 0.5666 (mtp85) REVERT: C 204 PHE cc_start: 0.8062 (OUTLIER) cc_final: 0.7344 (t80) REVERT: C 277 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7758 (mm) REVERT: C 331 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.8068 (pp30) REVERT: C 407 TYR cc_start: 0.7420 (t80) cc_final: 0.7185 (t80) REVERT: C 411 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.6909 (tp) REVERT: F 318 LEU cc_start: 0.8394 (mp) cc_final: 0.8125 (tp) REVERT: F 364 ASP cc_start: 0.6060 (p0) cc_final: 0.5655 (m-30) REVERT: G 47 MET cc_start: 0.5884 (tpp) cc_final: 0.4814 (tmm) REVERT: G 197 TYR cc_start: 0.6479 (m-80) cc_final: 0.6214 (t80) REVERT: G 200 LYS cc_start: 0.8409 (tppt) cc_final: 0.8005 (mmmt) REVERT: E 407 TYR cc_start: 0.7706 (OUTLIER) cc_final: 0.7438 (m-80) REVERT: E 432 LYS cc_start: 0.7991 (tttt) cc_final: 0.7531 (mmtm) REVERT: H 444 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.6793 (ptp-170) REVERT: I 45 MET cc_start: 0.7946 (mmm) cc_final: 0.7347 (tmm) REVERT: J 364 ASP cc_start: 0.7439 (p0) cc_final: 0.6876 (p0) REVERT: D 59 MET cc_start: 0.3396 (mmm) cc_final: 0.3124 (mmm) REVERT: D 96 TYR cc_start: 0.8371 (OUTLIER) cc_final: 0.8005 (t80) REVERT: D 224 LEU cc_start: 0.7217 (pt) cc_final: 0.6060 (tp) outliers start: 98 outliers final: 76 residues processed: 382 average time/residue: 0.1288 time to fit residues: 82.7705 Evaluate side-chains 391 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 307 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 204 PHE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 11 PHE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 407 TYR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 335 ILE Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 444 ARG Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 242 THR Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 316 VAL Chi-restraints excluded: chain J residue 386 SER Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 238 CYS Chi-restraints excluded: chain D residue 283 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 72 optimal weight: 6.9990 chunk 196 optimal weight: 20.0000 chunk 138 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 54 optimal weight: 0.4980 chunk 152 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 252 optimal weight: 8.9990 chunk 226 optimal weight: 0.7980 chunk 175 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.136958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.113414 restraints weight = 68310.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.114528 restraints weight = 38353.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.115220 restraints weight = 26304.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.115437 restraints weight = 25598.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.115498 restraints weight = 22530.732| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3838 r_free = 0.3838 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3838 r_free = 0.3838 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22871 Z= 0.133 Angle : 0.749 15.193 31317 Z= 0.356 Chirality : 0.042 0.253 3896 Planarity : 0.005 0.057 3952 Dihedral : 5.211 55.438 3265 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 3.52 % Allowed : 29.18 % Favored : 67.30 % 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: -0.78 (0.16), residues: 2936 helix: 1.02 (0.14), residues: 1557 sheet: -1.34 (0.30), residues: 276 loop : -2.63 (0.19), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 125 TYR 0.024 0.001 TYR D 197 PHE 0.024 0.001 PHE F 6 TRP 0.027 0.001 TRP D 21 HIS 0.006 0.001 HIS J 341 Details of bonding type rmsd covalent geometry : bond 0.00307 (22871) covalent geometry : angle 0.74927 (31317) hydrogen bonds : bond 0.03929 ( 1159) hydrogen bonds : angle 4.00492 ( 3378) ********************** 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 406 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 325 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 138 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8658 (tt) REVERT: B 264 TRP cc_start: 0.6889 (m-90) cc_final: 0.6199 (m-10) REVERT: B 444 ARG cc_start: 0.5881 (tpp80) cc_final: 0.5668 (mtp85) REVERT: C 204 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.7381 (t80) REVERT: C 277 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7753 (mm) REVERT: C 407 TYR cc_start: 0.7404 (t80) cc_final: 0.7171 (t80) REVERT: C 411 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.6850 (tp) REVERT: F 318 LEU cc_start: 0.8301 (mp) cc_final: 0.8100 (tp) REVERT: F 364 ASP cc_start: 0.5880 (p0) cc_final: 0.5546 (m-30) REVERT: F 375 TRP cc_start: 0.4846 (t60) cc_final: 0.4630 (t60) REVERT: G 47 MET cc_start: 0.5900 (tpp) cc_final: 0.5046 (tmm) REVERT: G 200 LYS cc_start: 0.8407 (tppt) cc_final: 0.8007 (mmmt) REVERT: E 407 TYR cc_start: 0.7709 (OUTLIER) cc_final: 0.7388 (m-80) REVERT: E 432 LYS cc_start: 0.7969 (tttt) cc_final: 0.7540 (mmtm) REVERT: H 444 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.6776 (ptp-170) REVERT: I 72 LEU cc_start: 0.8573 (tp) cc_final: 0.8282 (tt) REVERT: J 341 HIS cc_start: 0.6517 (p-80) cc_final: 0.5435 (p-80) REVERT: J 364 ASP cc_start: 0.7339 (p0) cc_final: 0.6787 (p0) REVERT: D 59 MET cc_start: 0.3623 (mmm) cc_final: 0.3384 (mmm) REVERT: D 96 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.7972 (t80) REVERT: D 224 LEU cc_start: 0.7005 (pt) cc_final: 0.5954 (tp) outliers start: 81 outliers final: 67 residues processed: 377 average time/residue: 0.1302 time to fit residues: 81.9636 Evaluate side-chains 380 residues out of total 2303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 306 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 27 GLN Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 204 PHE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 11 PHE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 159 LEU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 407 TYR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 335 ILE Chi-restraints excluded: chain H residue 403 ILE Chi-restraints excluded: chain H residue 420 LEU Chi-restraints excluded: chain H residue 444 ARG Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 242 THR Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 316 VAL Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 238 CYS Chi-restraints excluded: chain D residue 283 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 174 optimal weight: 9.9990 chunk 176 optimal weight: 5.9990 chunk 218 optimal weight: 0.0570 chunk 246 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 272 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 221 optimal weight: 6.9990 chunk 241 optimal weight: 7.9990 chunk 79 optimal weight: 0.5980 overall best weight: 1.1304 ------------------------------------------------------------------------------- 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** C 328 GLN G 74 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.136405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.113470 restraints weight = 68028.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.115043 restraints weight = 40121.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.115208 restraints weight = 28214.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.115472 restraints weight = 27019.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.115566 restraints weight = 24304.920| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3838 r_free = 0.3838 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3838 r_free = 0.3838 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.5049 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= 0.143 Angle : 0.757 15.596 31317 Z= 0.361 Chirality : 0.043 0.261 3896 Planarity : 0.005 0.057 3952 Dihedral : 5.129 55.386 3261 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 3.78 % Allowed : 29.14 % Favored : 67.09 % 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: -0.72 (0.16), residues: 2936 helix: 1.08 (0.14), residues: 1557 sheet: -1.32 (0.31), residues: 276 loop : -2.63 (0.19), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 361 TYR 0.028 0.001 TYR G 197 PHE 0.016 0.001 PHE H 165 TRP 0.026 0.001 TRP D 21 HIS 0.005 0.001 HIS J 341 Details of bonding type rmsd covalent geometry : bond 0.00331 (22871) covalent geometry : angle 0.75653 (31317) hydrogen bonds : bond 0.03985 ( 1159) hydrogen bonds : angle 4.01884 ( 3378) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4008.01 seconds wall clock time: 69 minutes 44.93 seconds (4184.93 seconds total)