Starting phenix.real_space_refine on Fri Feb 6 10:24:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nvm_49840/02_2026/9nvm_49840_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nvm_49840/02_2026/9nvm_49840.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nvm_49840/02_2026/9nvm_49840.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nvm_49840/02_2026/9nvm_49840.map" model { file = "/net/cci-nas-00/data/ceres_data/9nvm_49840/02_2026/9nvm_49840_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nvm_49840/02_2026/9nvm_49840_neut.cif" } resolution = 2.58 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= 0.047 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: 6 Type Number sf(0) Gaussians P 11 5.49 5 Mg 4 5.21 5 S 90 5.16 5 C 15324 2.51 5 N 4199 2.21 5 O 4656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 192 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24284 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3661 Classifications: {'peptide': 476} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 453} Chain: "B" Number of atoms: 3655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3655 Classifications: {'peptide': 475} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 452} Chain: "C" Number of atoms: 3655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3655 Classifications: {'peptide': 475} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 452} Chain: "D" Number of atoms: 3660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3660 Classifications: {'peptide': 469} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 441} Chain: "E" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3650 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 440} Chain: "F" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3668 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} Chain: "G" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2211 Classifications: {'peptide': 282} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 271} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.97, per 1000 atoms: 0.20 Number of scatterers: 24284 At special positions: 0 Unit cell: (152.04, 129.36, 126.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 90 16.00 P 11 15.00 Mg 4 11.99 O 4656 8.00 N 4199 7.00 C 15324 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: 2.00 Conformation dependent library (CDL) restraints added in 1.0 seconds 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5702 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 21 sheets defined 47.9% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.630A pdb=" N LEU A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 175 through 186 removed outlier: 3.616A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 216 through 219 Processing helix chain 'A' and resid 231 through 251 Proline residue: A 239 - end of helix removed outlier: 3.665A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG A 250 " --> pdb=" O GLY A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 removed outlier: 4.011A pdb=" N HIS A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 287 through 288 No H-bonds generated for 'chain 'A' and resid 287 through 288' Processing helix chain 'A' and resid 289 through 299 removed outlier: 3.755A pdb=" N HIS A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 322 through 325 Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 372 through 397 removed outlier: 3.578A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LYS A 381 " --> pdb=" O GLN A 377 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 392 " --> pdb=" O GLN A 388 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN A 397 " --> pdb=" O GLN A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 420 Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'A' and resid 452 through 478 removed outlier: 3.644A pdb=" N ASP A 458 " --> pdb=" O LYS A 454 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER A 466 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS A 467 " --> pdb=" O TYR A 463 " (cutoff:3.500A) Proline residue: A 469 - end of helix removed outlier: 3.920A pdb=" N GLU A 473 " --> pdb=" O PRO A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 501 Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.693A pdb=" N ALA B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 216 through 219 removed outlier: 3.595A pdb=" N GLU B 219 " --> pdb=" O GLY B 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 216 through 219' Processing helix chain 'B' and resid 231 through 253 Proline residue: B 239 - end of helix removed outlier: 3.624A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG B 250 " --> pdb=" O GLY B 246 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 removed outlier: 3.542A pdb=" N HIS B 266 " --> pdb=" O ASP B 262 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE B 273 " --> pdb=" O ALA B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.778A pdb=" N HIS B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 322 through 325 removed outlier: 3.588A pdb=" N ASP B 325 " --> pdb=" O GLN B 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 322 through 325' Processing helix chain 'B' and resid 328 through 338 Processing helix chain 'B' and resid 345 through 351 Processing helix chain 'B' and resid 372 through 380 Processing helix chain 'B' and resid 381 through 399 removed outlier: 4.083A pdb=" N PHE B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 420 removed outlier: 4.035A pdb=" N ARG B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA B 408 " --> pdb=" O GLU B 404 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG B 415 " --> pdb=" O GLU B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 442 removed outlier: 3.874A pdb=" N VAL B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 451 No H-bonds generated for 'chain 'B' and resid 449 through 451' Processing helix chain 'B' and resid 452 through 464 removed outlier: 3.503A pdb=" N ILE B 464 " --> pdb=" O PHE B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 467 No H-bonds generated for 'chain 'B' and resid 465 through 467' Processing helix chain 'B' and resid 468 through 479 removed outlier: 3.595A pdb=" N GLU B 474 " --> pdb=" O ASP B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 500 removed outlier: 3.885A pdb=" N GLU B 487 " --> pdb=" O ASP B 483 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS B 490 " --> pdb=" O GLU B 486 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 491 " --> pdb=" O GLU B 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.736A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 185 removed outlier: 3.546A pdb=" N ALA C 179 " --> pdb=" O LYS C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 216 through 219 Processing helix chain 'C' and resid 231 through 253 removed outlier: 3.556A pdb=" N ILE C 237 " --> pdb=" O ALA C 233 " (cutoff:3.500A) Proline residue: C 239 - end of helix removed outlier: 3.627A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 removed outlier: 3.755A pdb=" N GLN C 272 " --> pdb=" O VAL C 268 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE C 273 " --> pdb=" O ALA C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 299 removed outlier: 3.815A pdb=" N HIS C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 309 Processing helix chain 'C' and resid 322 through 325 Processing helix chain 'C' and resid 328 through 338 Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 372 through 380 Processing helix chain 'C' and resid 381 through 400 removed outlier: 4.179A pdb=" N ALA C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE C 398 " --> pdb=" O ALA C 394 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER C 400 " --> pdb=" O ALA C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 420 Processing helix chain 'C' and resid 429 through 442 removed outlier: 4.068A pdb=" N VAL C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 451 No H-bonds generated for 'chain 'C' and resid 449 through 451' Processing helix chain 'C' and resid 452 through 465 removed outlier: 3.527A pdb=" N GLU C 465 " --> pdb=" O LEU C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 479 Processing helix chain 'C' and resid 483 through 498 removed outlier: 3.624A pdb=" N LYS C 494 " --> pdb=" O LYS C 490 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU C 495 " --> pdb=" O LYS C 491 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE C 496 " --> pdb=" O ALA C 492 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS C 497 " --> pdb=" O ILE C 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 123 through 127 removed outlier: 3.860A pdb=" N GLN D 127 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 145 removed outlier: 3.576A pdb=" N LEU D 143 " --> pdb=" O LYS D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 172 Processing helix chain 'D' and resid 174 through 178 removed outlier: 3.523A pdb=" N HIS D 178 " --> pdb=" O ALA D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 removed outlier: 3.575A pdb=" N GLY D 194 " --> pdb=" O ARG D 190 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN D 195 " --> pdb=" O SER D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 241 removed outlier: 5.373A pdb=" N ALA D 228 " --> pdb=" O ARG D 224 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LEU D 229 " --> pdb=" O PHE D 225 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET D 234 " --> pdb=" O THR D 230 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE D 238 " --> pdb=" O MET D 234 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG D 239 " --> pdb=" O ALA D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 268 removed outlier: 4.147A pdb=" N PHE D 256 " --> pdb=" O ASN D 252 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA D 265 " --> pdb=" O SER D 261 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LEU D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY D 268 " --> pdb=" O SER D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 276 Processing helix chain 'D' and resid 279 through 289 removed outlier: 3.655A pdb=" N LEU D 287 " --> pdb=" O GLU D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 321 Processing helix chain 'D' and resid 322 through 324 No H-bonds generated for 'chain 'D' and resid 322 through 324' Processing helix chain 'D' and resid 331 through 336 Processing helix chain 'D' and resid 359 through 387 removed outlier: 4.143A pdb=" N ASP D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE D 382 " --> pdb=" O ASP D 378 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA D 384 " --> pdb=" O GLN D 380 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 391 removed outlier: 3.641A pdb=" N LEU D 391 " --> pdb=" O MET D 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 388 through 391' Processing helix chain 'D' and resid 392 through 409 removed outlier: 3.676A pdb=" N LYS D 404 " --> pdb=" O GLN D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 415 No H-bonds generated for 'chain 'D' and resid 413 through 415' Processing helix chain 'D' and resid 416 through 421 Processing helix chain 'D' and resid 428 through 441 removed outlier: 3.661A pdb=" N ILE D 439 " --> pdb=" O GLY D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 452 removed outlier: 4.136A pdb=" N PHE D 452 " --> pdb=" O GLU D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 468 removed outlier: 4.016A pdb=" N ALA D 461 " --> pdb=" O THR D 457 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL D 462 " --> pdb=" O ILE D 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 138 through 145 Processing helix chain 'E' and resid 162 through 177 removed outlier: 3.534A pdb=" N ALA E 175 " --> pdb=" O ILE E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 204 Processing helix chain 'E' and resid 205 through 208 removed outlier: 3.948A pdb=" N ASP E 208 " --> pdb=" O GLY E 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 205 through 208' Processing helix chain 'E' and resid 220 through 241 removed outlier: 5.218A pdb=" N ALA E 228 " --> pdb=" O ARG E 224 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N LEU E 229 " --> pdb=" O PHE E 225 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR E 230 " --> pdb=" O ARG E 226 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE E 238 " --> pdb=" O MET E 234 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG E 239 " --> pdb=" O ALA E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 268 removed outlier: 3.975A pdb=" N PHE E 256 " --> pdb=" O ASN E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 276 Processing helix chain 'E' and resid 279 through 289 removed outlier: 3.626A pdb=" N LEU E 287 " --> pdb=" O GLU E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 322 removed outlier: 3.516A pdb=" N ALA E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 338 removed outlier: 3.776A pdb=" N ALA E 335 " --> pdb=" O SER E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 354 No H-bonds generated for 'chain 'E' and resid 352 through 354' Processing helix chain 'E' and resid 359 through 386 removed outlier: 4.514A pdb=" N ASP E 381 " --> pdb=" O LYS E 377 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE E 382 " --> pdb=" O ASP E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 391 removed outlier: 3.568A pdb=" N LEU E 391 " --> pdb=" O MET E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 409 removed outlier: 3.729A pdb=" N ARG E 401 " --> pdb=" O LEU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 419 removed outlier: 4.224A pdb=" N HIS E 418 " --> pdb=" O VAL E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 441 removed outlier: 3.541A pdb=" N GLU E 438 " --> pdb=" O ARG E 434 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP E 441 " --> pdb=" O LYS E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 452 Processing helix chain 'E' and resid 457 through 468 removed outlier: 3.804A pdb=" N ALA E 461 " --> pdb=" O THR E 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 138 through 145 Processing helix chain 'F' and resid 162 through 174 Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 190 through 205 removed outlier: 3.578A pdb=" N GLY F 194 " --> pdb=" O ARG F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 220 through 242 removed outlier: 5.249A pdb=" N ALA F 228 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LEU F 229 " --> pdb=" O PHE F 225 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET F 234 " --> pdb=" O THR F 230 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR F 237 " --> pdb=" O THR F 233 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE F 238 " --> pdb=" O MET F 234 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG F 239 " --> pdb=" O ALA F 235 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU F 242 " --> pdb=" O PHE F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 268 removed outlier: 4.099A pdb=" N PHE F 256 " --> pdb=" O ASN F 252 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA F 257 " --> pdb=" O ILE F 253 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU F 266 " --> pdb=" O GLU F 262 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY F 268 " --> pdb=" O SER F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 289 removed outlier: 3.720A pdb=" N LEU F 287 " --> pdb=" O GLU F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 321 removed outlier: 3.786A pdb=" N PHE F 321 " --> pdb=" O PRO F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 324 No H-bonds generated for 'chain 'F' and resid 322 through 324' Processing helix chain 'F' and resid 331 through 338 Processing helix chain 'F' and resid 359 through 387 removed outlier: 3.537A pdb=" N ILE F 372 " --> pdb=" O ARG F 368 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASP F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ILE F 382 " --> pdb=" O ASP F 378 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 409 removed outlier: 3.769A pdb=" N LYS F 404 " --> pdb=" O GLN F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 428 through 442 Processing helix chain 'F' and resid 448 through 453 removed outlier: 3.743A pdb=" N PHE F 452 " --> pdb=" O GLU F 449 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TYR F 453 " --> pdb=" O GLN F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 457 through 469 removed outlier: 3.837A pdb=" N ALA F 461 " --> pdb=" O THR F 457 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 62 removed outlier: 3.506A pdb=" N LYS G 11 " --> pdb=" O LEU G 7 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR G 12 " --> pdb=" O ARG G 8 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG G 13 " --> pdb=" O ASP G 9 " (cutoff:3.500A) Proline residue: G 47 - end of helix Processing helix chain 'G' and resid 88 through 92 removed outlier: 4.293A pdb=" N ALA G 91 " --> pdb=" O ARG G 88 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY G 92 " --> pdb=" O GLY G 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 88 through 92' Processing helix chain 'G' and resid 93 through 110 removed outlier: 3.997A pdb=" N VAL G 98 " --> pdb=" O TYR G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 122 through 131 Processing helix chain 'G' and resid 152 through 165 Processing helix chain 'G' and resid 211 through 287 Proline residue: G 221 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 35 removed outlier: 6.609A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.418A pdb=" N GLU A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 109 removed outlier: 6.423A pdb=" N ILE A 192 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N VAL A 259 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE A 194 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU A 166 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LEU A 344 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE A 168 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 28 through 35 removed outlier: 6.560A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.281A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.440A pdb=" N VAL B 108 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N ILE B 222 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N CYS B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N VAL B 224 " --> pdb=" O CYS B 193 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 28 through 35 removed outlier: 6.503A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU C 52 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.909A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 107 through 108 removed outlier: 8.686A pdb=" N ILE C 222 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N CYS C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N VAL C 224 " --> pdb=" O CYS C 193 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE C 192 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N VAL C 259 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE C 194 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA C 256 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N LEU C 316 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL C 258 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ILE C 318 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR C 260 " --> pdb=" O ILE C 318 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N GLU C 320 " --> pdb=" O TYR C 260 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU C 166 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU C 344 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE C 168 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 10 removed outlier: 6.546A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N GLN D 33 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLU D 75 " --> pdb=" O GLN D 33 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 84 through 87 removed outlier: 4.541A pdb=" N LYS D 113 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 95 through 96 removed outlier: 7.247A pdb=" N PHE D 181 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N PHE D 249 " --> pdb=" O PHE D 181 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL D 183 " --> pdb=" O PHE D 249 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N ASP D 251 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ALA D 185 " --> pdb=" O ASP D 251 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE D 153 " --> pdb=" O GLN D 303 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ILE D 305 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU D 155 " --> pdb=" O ILE D 305 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 133 through 134 removed outlier: 4.310A pdb=" N ILE D 147 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 3 through 10 removed outlier: 6.586A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 84 through 87 removed outlier: 4.566A pdb=" N LYS E 113 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.420A pdb=" N PHE E 96 " --> pdb=" O PHE E 214 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N GLN E 216 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL E 246 " --> pdb=" O THR E 300 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL E 302 " --> pdb=" O VAL E 246 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU E 248 " --> pdb=" O VAL E 302 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ALA E 304 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE E 250 " --> pdb=" O ALA E 304 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LYS E 152 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE E 328 " --> pdb=" O LYS E 152 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLY E 154 " --> pdb=" O ILE E 328 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LEU E 330 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N PHE E 156 " --> pdb=" O LEU E 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 3 through 10 removed outlier: 6.489A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 84 through 87 removed outlier: 4.309A pdb=" N LYS F 113 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.719A pdb=" N PHE F 96 " --> pdb=" O PHE F 214 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N GLN F 216 " --> pdb=" O PHE F 96 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL F 246 " --> pdb=" O THR F 300 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N VAL F 302 " --> pdb=" O VAL F 246 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU F 248 " --> pdb=" O VAL F 302 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N ALA F 304 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILE F 250 " --> pdb=" O ALA F 304 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N TYR F 306 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE F 153 " --> pdb=" O GLN F 303 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ILE F 305 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU F 155 " --> pdb=" O ILE F 305 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS F 152 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE F 328 " --> pdb=" O LYS F 152 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLY F 154 " --> pdb=" O ILE F 328 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 133 through 134 removed outlier: 4.347A pdb=" N ILE F 147 " --> pdb=" O LEU F 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 138 through 140 removed outlier: 3.860A pdb=" N LEU G 138 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR G 79 " --> pdb=" O ALA G 117 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ILE G 119 " --> pdb=" O THR G 79 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR G 81 " --> pdb=" O ILE G 119 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ILE G 121 " --> pdb=" O TYR G 81 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL G 83 " --> pdb=" O ILE G 121 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY G 80 " --> pdb=" O TYR G 172 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N TYR G 174 " --> pdb=" O GLY G 80 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU G 82 " --> pdb=" O TYR G 174 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N ASN G 176 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N ILE G 84 " --> pdb=" O ASN G 176 " (cutoff:3.500A) removed outlier: 11.436A pdb=" N TYR G 178 " --> pdb=" O ILE G 84 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU G 171 " --> pdb=" O LEU G 191 " (cutoff:3.500A) 1102 hydrogen bonds defined for protein. 3159 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: 4.12 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4978 1.32 - 1.45: 5021 1.45 - 1.57: 14508 1.57 - 1.70: 8 1.70 - 1.83: 172 Bond restraints: 24687 Sorted by residual: bond pdb=" CZ ARG B 90 " pdb=" NH1 ARG B 90 " ideal model delta sigma weight residual 1.323 1.216 0.107 1.40e-02 5.10e+03 5.89e+01 bond pdb=" C4 ADP F 500 " pdb=" C5 ADP F 500 " ideal model delta sigma weight residual 1.490 1.350 0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C5 ADP F 500 " pdb=" C6 ADP F 500 " ideal model delta sigma weight residual 1.490 1.388 0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" CB THR E 210 " pdb=" OG1 THR E 210 " ideal model delta sigma weight residual 1.433 1.355 0.078 1.60e-02 3.91e+03 2.37e+01 bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.348 0.040 1.00e-02 1.00e+04 1.64e+01 ... (remaining 24682 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 31729 3.97 - 7.94: 1649 7.94 - 11.90: 17 11.90 - 15.87: 4 15.87 - 19.84: 3 Bond angle restraints: 33402 Sorted by residual: angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 120.03 19.84 1.00e+00 1.00e+00 3.94e+02 angle pdb=" PA ATP D 501 " pdb=" O3A ATP D 501 " pdb=" PB ATP D 501 " ideal model delta sigma weight residual 136.83 120.08 16.75 1.00e+00 1.00e+00 2.81e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 123.53 16.34 1.00e+00 1.00e+00 2.67e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 124.23 15.64 1.00e+00 1.00e+00 2.45e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 122.66 14.17 1.00e+00 1.00e+00 2.01e+02 ... (remaining 33397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.48: 14429 21.48 - 42.97: 639 42.97 - 64.45: 119 64.45 - 85.93: 25 85.93 - 107.42: 4 Dihedral angle restraints: 15216 sinusoidal: 6309 harmonic: 8907 Sorted by residual: dihedral pdb=" C ASP A 261 " pdb=" N ASP A 261 " pdb=" CA ASP A 261 " pdb=" CB ASP A 261 " ideal model delta harmonic sigma weight residual -122.60 -138.77 16.17 0 2.50e+00 1.60e-01 4.19e+01 dihedral pdb=" N ASP A 261 " pdb=" C ASP A 261 " pdb=" CA ASP A 261 " pdb=" CB ASP A 261 " ideal model delta harmonic sigma weight residual 122.80 137.44 -14.64 0 2.50e+00 1.60e-01 3.43e+01 dihedral pdb=" C5' ADP F 500 " pdb=" O5' ADP F 500 " pdb=" PA ADP F 500 " pdb=" O2A ADP F 500 " ideal model delta sinusoidal sigma weight residual -60.00 -167.41 107.42 1 2.00e+01 2.50e-03 3.12e+01 ... (remaining 15213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 2839 0.123 - 0.245: 847 0.245 - 0.367: 89 0.367 - 0.490: 15 0.490 - 0.612: 2 Chirality restraints: 3792 Sorted by residual: chirality pdb=" CA ASP A 261 " pdb=" N ASP A 261 " pdb=" C ASP A 261 " pdb=" CB ASP A 261 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.38e+00 chirality pdb=" CA MET B 95 " pdb=" N MET B 95 " pdb=" C MET B 95 " pdb=" CB MET B 95 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.90e+00 chirality pdb=" CA PHE D 214 " pdb=" N PHE D 214 " pdb=" C PHE D 214 " pdb=" CB PHE D 214 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.90e+00 ... (remaining 3789 not shown) Planarity restraints: 4362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 27 " -0.133 2.00e-02 2.50e+03 7.33e-02 1.07e+02 pdb=" CG TYR D 27 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR D 27 " 0.051 2.00e-02 2.50e+03 pdb=" CD2 TYR D 27 " 0.063 2.00e-02 2.50e+03 pdb=" CE1 TYR D 27 " 0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR D 27 " 0.038 2.00e-02 2.50e+03 pdb=" CZ TYR D 27 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR D 27 " -0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP F 500 " -0.117 2.00e-02 2.50e+03 5.65e-02 8.77e+01 pdb=" C2 ADP F 500 " 0.050 2.00e-02 2.50e+03 pdb=" C4 ADP F 500 " 0.005 2.00e-02 2.50e+03 pdb=" C5 ADP F 500 " -0.010 2.00e-02 2.50e+03 pdb=" C6 ADP F 500 " -0.018 2.00e-02 2.50e+03 pdb=" C8 ADP F 500 " 0.097 2.00e-02 2.50e+03 pdb=" N1 ADP F 500 " 0.006 2.00e-02 2.50e+03 pdb=" N3 ADP F 500 " 0.036 2.00e-02 2.50e+03 pdb=" N6 ADP F 500 " -0.082 2.00e-02 2.50e+03 pdb=" N7 ADP F 500 " 0.030 2.00e-02 2.50e+03 pdb=" N9 ADP F 500 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 248 " -0.095 2.00e-02 2.50e+03 5.51e-02 6.07e+01 pdb=" CG TYR B 248 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR B 248 " 0.055 2.00e-02 2.50e+03 pdb=" CD2 TYR B 248 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR B 248 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR B 248 " 0.041 2.00e-02 2.50e+03 pdb=" CZ TYR B 248 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 248 " -0.090 2.00e-02 2.50e+03 ... (remaining 4359 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 12 2.49 - 3.09: 15098 3.09 - 3.70: 34260 3.70 - 4.30: 52415 4.30 - 4.90: 87467 Nonbonded interactions: 189252 Sorted by model distance: nonbonded pdb=" O1G ATP D 501 " pdb="MG MG D 502 " model vdw 1.892 2.170 nonbonded pdb=" OG1 THR F 164 " pdb="MG MG F 501 " model vdw 1.902 2.170 nonbonded pdb=" O2G ATP A 601 " pdb="MG MG A 602 " model vdw 1.906 2.170 nonbonded pdb=" O2G ATP C 601 " pdb="MG MG C 602 " model vdw 1.914 2.170 nonbonded pdb=" O1A ATP C 601 " pdb="MG MG C 602 " model vdw 1.930 2.170 ... (remaining 189247 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 'A' and resid 27 through 501) selection = chain 'B' selection = (chain 'C' and resid 27 through 501) } ncs_group { reference = (chain 'D' and resid 2 through 468) selection = (chain 'E' and resid 2 through 468) selection = (chain 'F' and resid 2 through 468) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 20.440 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4311 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 : 0.013 0.140 24687 Z= 0.826 Angle : 1.994 19.838 33402 Z= 1.350 Chirality : 0.111 0.612 3792 Planarity : 0.014 0.149 4362 Dihedral : 12.649 107.415 9514 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 0.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.55 % Favored : 97.36 % Rotamer: Outliers : 0.62 % Allowed : 5.75 % Favored : 93.63 % Cbeta Deviations : 0.88 % Peptide Plane: Cis-proline : 4.46 % 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: -1.05 (0.14), residues: 3101 helix: -0.98 (0.13), residues: 1217 sheet: 0.37 (0.23), residues: 441 loop : -0.63 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG F 192 TYR 0.133 0.019 TYR D 27 PHE 0.074 0.013 PHE F 254 TRP 0.072 0.022 TRP D 198 HIS 0.027 0.004 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.01326 (24687) covalent geometry : angle 1.99352 (33402) hydrogen bonds : bond 0.22319 ( 1102) hydrogen bonds : angle 7.27167 ( 3159) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 562 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.6666 (mtm) cc_final: 0.6464 (mtm) REVERT: A 54 GLU cc_start: 0.5029 (pt0) cc_final: 0.4733 (tt0) REVERT: A 68 GLU cc_start: 0.6108 (tt0) cc_final: 0.5233 (tm-30) REVERT: A 278 ARG cc_start: 0.4592 (mtp85) cc_final: 0.4125 (mmp80) REVERT: A 320 GLU cc_start: 0.5003 (tt0) cc_final: 0.4207 (tp30) REVERT: A 354 ARG cc_start: 0.5832 (mtt90) cc_final: 0.5510 (mmm-85) REVERT: A 373 LYS cc_start: 0.7215 (ttpp) cc_final: 0.6774 (tmmt) REVERT: A 415 ARG cc_start: 0.5827 (mtt90) cc_final: 0.5216 (mtp85) REVERT: B 40 ARG cc_start: 0.5744 (mmt90) cc_final: 0.4376 (mmt180) REVERT: B 54 GLU cc_start: 0.5216 (pt0) cc_final: 0.4275 (tt0) REVERT: B 87 GLU cc_start: 0.4915 (tt0) cc_final: 0.4531 (tp30) REVERT: B 172 GLN cc_start: 0.6403 (mt0) cc_final: 0.5951 (mt0) REVERT: B 320 GLU cc_start: 0.5937 (tt0) cc_final: 0.5604 (pp20) REVERT: B 418 GLU cc_start: 0.6823 (mm-30) cc_final: 0.6555 (mm-30) REVERT: C 60 MET cc_start: 0.6030 (mmt) cc_final: 0.5758 (mmm) REVERT: C 90 ARG cc_start: 0.5535 (ttp80) cc_final: 0.4810 (ttt180) REVERT: C 187 LYS cc_start: 0.5275 (tttm) cc_final: 0.4830 (pmtt) REVERT: C 254 LYS cc_start: 0.6865 (mmtm) cc_final: 0.6453 (mtmp) REVERT: C 320 GLU cc_start: 0.5703 (tt0) cc_final: 0.5385 (pp20) REVERT: C 485 LEU cc_start: 0.5540 (mt) cc_final: 0.5154 (mt) REVERT: D 10 MET cc_start: 0.6032 (mtm) cc_final: 0.5498 (mmm) REVERT: D 22 HIS cc_start: 0.6711 (m90) cc_final: 0.5894 (t70) REVERT: D 33 GLN cc_start: 0.5783 (mt0) cc_final: 0.5019 (mp10) REVERT: D 52 LEU cc_start: 0.6505 (tp) cc_final: 0.6046 (mp) REVERT: D 119 ARG cc_start: 0.5058 (mtp-110) cc_final: 0.4816 (mtp85) REVERT: D 149 LYS cc_start: 0.7447 (ttpt) cc_final: 0.6717 (tmtp) REVERT: D 236 GLU cc_start: 0.4272 (mt-10) cc_final: 0.3968 (mt-10) REVERT: D 270 MET cc_start: 0.7387 (mtt) cc_final: 0.6766 (mtp) REVERT: D 284 MET cc_start: 0.5311 (ttm) cc_final: 0.4971 (ttm) REVERT: D 388 MET cc_start: 0.4095 (ttt) cc_final: 0.3788 (mmp) REVERT: D 406 GLN cc_start: 0.5827 (tt0) cc_final: 0.5620 (pt0) REVERT: E 1 MET cc_start: 0.3123 (mmt) cc_final: 0.2341 (tpp) REVERT: E 10 MET cc_start: 0.6577 (ptp) cc_final: 0.6348 (ptp) REVERT: E 33 GLN cc_start: 0.5103 (mt0) cc_final: 0.4889 (mt0) REVERT: E 37 ARG cc_start: 0.6149 (mtm180) cc_final: 0.5913 (mtm-85) REVERT: E 98 VAL cc_start: 0.6853 (t) cc_final: 0.6560 (p) REVERT: E 119 ARG cc_start: 0.5135 (mtp85) cc_final: 0.4712 (mtt-85) REVERT: E 132 GLU cc_start: 0.5301 (mt-10) cc_final: 0.4841 (mp0) REVERT: E 190 ARG cc_start: 0.5510 (mtt90) cc_final: 0.4877 (mtt180) REVERT: E 306 TYR cc_start: 0.5094 (t80) cc_final: 0.4864 (t80) REVERT: F 5 ARG cc_start: 0.4257 (mmt180) cc_final: 0.3702 (mtm110) REVERT: F 10 MET cc_start: 0.5685 (mtm) cc_final: 0.5085 (mmm) REVERT: F 31 LYS cc_start: 0.5985 (mmtp) cc_final: 0.5761 (mptp) REVERT: F 38 ASN cc_start: 0.4774 (t0) cc_final: 0.4086 (p0) REVERT: F 75 GLU cc_start: 0.5683 (tt0) cc_final: 0.4973 (mm-30) REVERT: F 388 MET cc_start: 0.7357 (mtm) cc_final: 0.6964 (mtm) REVERT: F 420 THR cc_start: 0.6446 (m) cc_final: 0.6228 (p) REVERT: G 14 ILE cc_start: 0.5248 (mt) cc_final: 0.5012 (mt) REVERT: G 28 GLU cc_start: 0.6011 (tt0) cc_final: 0.5777 (tt0) REVERT: G 37 ARG cc_start: 0.5563 (ttp80) cc_final: 0.4789 (mtm180) REVERT: G 239 GLU cc_start: 0.5478 (tt0) cc_final: 0.4862 (tt0) REVERT: G 247 MET cc_start: 0.5712 (mmm) cc_final: 0.5086 (mmm) REVERT: G 253 ASN cc_start: 0.5372 (m-40) cc_final: 0.5032 (m-40) outliers start: 16 outliers final: 7 residues processed: 576 average time/residue: 0.8249 time to fit residues: 528.6757 Evaluate side-chains 322 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 315 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 392 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 186 GLN A 442 ASN B 46 ASN B 186 GLN B 202 GLN B 255 HIS B 272 GLN B 397 GLN B 424 GLN C 46 ASN C 333 ASN C 341 GLN C 397 GLN D 33 GLN D 303 GLN D 418 HIS E 33 GLN E 178 HIS F 8 GLN F 22 HIS F 347 GLN G 15 ASN G 183 GLN G 285 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.202694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.153169 restraints weight = 25593.425| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 2.08 r_work: 0.3756 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24687 Z= 0.154 Angle : 0.648 7.927 33402 Z= 0.350 Chirality : 0.048 0.230 3792 Planarity : 0.005 0.049 4362 Dihedral : 7.381 99.567 3518 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.55 % Favored : 98.39 % Rotamer: Outliers : 3.49 % Allowed : 13.74 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.46 % 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: 0.02 (0.15), residues: 3101 helix: 0.39 (0.14), residues: 1258 sheet: 0.47 (0.21), residues: 522 loop : -0.41 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 375 TYR 0.019 0.002 TYR C 350 PHE 0.017 0.002 PHE F 321 TRP 0.013 0.002 TRP E 198 HIS 0.006 0.001 HIS F 362 Details of bonding type rmsd covalent geometry : bond 0.00323 (24687) covalent geometry : angle 0.64793 (33402) hydrogen bonds : bond 0.05299 ( 1102) hydrogen bonds : angle 4.95411 ( 3159) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 365 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.5767 (m-30) cc_final: 0.5544 (m-30) REVERT: A 36 ASP cc_start: 0.7346 (m-30) cc_final: 0.6872 (t0) REVERT: A 68 GLU cc_start: 0.7763 (tt0) cc_final: 0.7489 (tm-30) REVERT: A 278 ARG cc_start: 0.6028 (mtp85) cc_final: 0.5638 (mmt180) REVERT: A 347 ASP cc_start: 0.7472 (p0) cc_final: 0.7259 (m-30) REVERT: A 353 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7419 (mm) REVERT: A 354 ARG cc_start: 0.7082 (mtt90) cc_final: 0.6787 (mtm180) REVERT: A 373 LYS cc_start: 0.8280 (ttpp) cc_final: 0.7632 (tmmt) REVERT: A 415 ARG cc_start: 0.6518 (mtt90) cc_final: 0.5824 (mpp80) REVERT: B 40 ARG cc_start: 0.8484 (mmt90) cc_final: 0.7863 (mmt180) REVERT: B 87 GLU cc_start: 0.7165 (tt0) cc_final: 0.6892 (tp30) REVERT: B 121 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7597 (mm) REVERT: B 156 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.7881 (mmt) REVERT: B 173 THR cc_start: 0.6956 (OUTLIER) cc_final: 0.6717 (p) REVERT: B 418 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7522 (mm-30) REVERT: B 471 ILE cc_start: 0.5638 (OUTLIER) cc_final: 0.5421 (mm) REVERT: B 474 GLU cc_start: 0.6047 (OUTLIER) cc_final: 0.5681 (pp20) REVERT: C 124 LYS cc_start: 0.6922 (mttt) cc_final: 0.6620 (pttm) REVERT: C 131 ARG cc_start: 0.6770 (OUTLIER) cc_final: 0.6268 (ptm160) REVERT: C 156 MET cc_start: 0.8112 (mpp) cc_final: 0.7671 (mmp) REVERT: C 411 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6675 (mm-30) REVERT: C 481 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7469 (tt) REVERT: C 494 LYS cc_start: 0.7794 (mttt) cc_final: 0.7177 (tppt) REVERT: D 10 MET cc_start: 0.7655 (mtm) cc_final: 0.7353 (mmm) REVERT: D 22 HIS cc_start: 0.7392 (m90) cc_final: 0.6917 (t70) REVERT: D 33 GLN cc_start: 0.7412 (mt0) cc_final: 0.7040 (mp10) REVERT: D 149 LYS cc_start: 0.8442 (ttpt) cc_final: 0.7960 (tmtp) REVERT: D 193 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.6276 (mm-30) REVERT: D 236 GLU cc_start: 0.7039 (mt-10) cc_final: 0.6674 (mt-10) REVERT: D 282 THR cc_start: 0.8168 (t) cc_final: 0.7952 (m) REVERT: D 286 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7465 (mm-30) REVERT: D 370 ARG cc_start: 0.6770 (ttm110) cc_final: 0.6566 (mtm110) REVERT: D 388 MET cc_start: 0.3818 (ttt) cc_final: 0.3164 (tmt) REVERT: E 201 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.7072 (mmp) REVERT: E 286 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7263 (tm-30) REVERT: E 305 ILE cc_start: 0.4929 (OUTLIER) cc_final: 0.4684 (mm) REVERT: E 327 THR cc_start: 0.7579 (m) cc_final: 0.7289 (p) REVERT: E 379 LEU cc_start: 0.6225 (OUTLIER) cc_final: 0.5637 (mt) REVERT: E 453 TYR cc_start: 0.7174 (t80) cc_final: 0.6729 (t80) REVERT: F 5 ARG cc_start: 0.7209 (mmt180) cc_final: 0.6783 (mtm110) REVERT: F 75 GLU cc_start: 0.7182 (tt0) cc_final: 0.6816 (mm-30) REVERT: F 282 THR cc_start: 0.8258 (t) cc_final: 0.7988 (p) REVERT: G 25 LYS cc_start: 0.6543 (OUTLIER) cc_final: 0.6207 (tptm) REVERT: G 27 MET cc_start: 0.5519 (mmm) cc_final: 0.5265 (tpt) REVERT: G 37 ARG cc_start: 0.5077 (ttp80) cc_final: 0.4447 (mtm180) REVERT: G 49 MET cc_start: 0.2304 (mmt) cc_final: 0.2070 (ptp) REVERT: G 88 ARG cc_start: 0.5393 (mpp80) cc_final: 0.4087 (mtm110) outliers start: 90 outliers final: 14 residues processed: 427 average time/residue: 0.7971 time to fit residues: 381.8072 Evaluate side-chains 318 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 291 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 425 LYS Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 201 MET Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 392 SER Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 25 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 23 optimal weight: 4.9990 chunk 284 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 228 optimal weight: 5.9990 chunk 149 optimal weight: 0.7980 chunk 133 optimal weight: 6.9990 chunk 216 optimal weight: 9.9990 chunk 305 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 168 optimal weight: 1.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 GLN B 424 GLN C 113 GLN C 341 GLN C 393 GLN D 173 ASN D 216 GLN D 252 ASN D 406 GLN E 33 GLN ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 ASN F 195 ASN F 400 GLN G 253 ASN G 255 ASN G 275 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.200339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.147845 restraints weight = 25549.642| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.22 r_work: 0.3678 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 24687 Z= 0.191 Angle : 0.676 7.826 33402 Z= 0.357 Chirality : 0.049 0.240 3792 Planarity : 0.005 0.060 4362 Dihedral : 7.304 84.223 3515 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.06 % Favored : 96.87 % Rotamer: Outliers : 4.31 % Allowed : 15.72 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.46 % 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: -0.05 (0.15), residues: 3101 helix: 0.47 (0.14), residues: 1249 sheet: 0.40 (0.22), residues: 512 loop : -0.58 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 90 TYR 0.019 0.002 TYR F 27 PHE 0.019 0.002 PHE E 408 TRP 0.014 0.002 TRP D 198 HIS 0.007 0.002 HIS A 468 Details of bonding type rmsd covalent geometry : bond 0.00454 (24687) covalent geometry : angle 0.67625 (33402) hydrogen bonds : bond 0.05623 ( 1102) hydrogen bonds : angle 4.81308 ( 3159) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 301 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7735 (tt0) cc_final: 0.7437 (tm-30) REVERT: A 95 MET cc_start: 0.7115 (mmm) cc_final: 0.6455 (tmm) REVERT: A 278 ARG cc_start: 0.6287 (mtp85) cc_final: 0.5823 (mmt180) REVERT: A 353 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7435 (mm) REVERT: A 354 ARG cc_start: 0.7145 (mtt90) cc_final: 0.6504 (tpp80) REVERT: A 373 LYS cc_start: 0.8261 (ttpp) cc_final: 0.7524 (mppt) REVERT: A 415 ARG cc_start: 0.6543 (mtt90) cc_final: 0.5776 (mpp80) REVERT: B 40 ARG cc_start: 0.8474 (mmt90) cc_final: 0.7691 (mmt180) REVERT: B 68 GLU cc_start: 0.8206 (tt0) cc_final: 0.7907 (tm-30) REVERT: B 87 GLU cc_start: 0.7352 (tt0) cc_final: 0.7136 (tp30) REVERT: B 156 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.7760 (mmt) REVERT: B 320 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6673 (pt0) REVERT: B 418 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7571 (mm-30) REVERT: B 446 ASP cc_start: 0.6989 (OUTLIER) cc_final: 0.6123 (m-30) REVERT: B 474 GLU cc_start: 0.6046 (OUTLIER) cc_final: 0.5652 (pp20) REVERT: C 124 LYS cc_start: 0.7062 (mttt) cc_final: 0.6756 (pttm) REVERT: C 278 ARG cc_start: 0.7165 (mtp85) cc_final: 0.6961 (mmm160) REVERT: D 22 HIS cc_start: 0.7607 (m90) cc_final: 0.7029 (t70) REVERT: D 33 GLN cc_start: 0.7439 (mt0) cc_final: 0.7049 (mp10) REVERT: D 119 ARG cc_start: 0.7308 (mtp85) cc_final: 0.7061 (mtp-110) REVERT: D 149 LYS cc_start: 0.8503 (ttpt) cc_final: 0.7990 (tmtp) REVERT: D 193 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6498 (mm-30) REVERT: D 201 MET cc_start: 0.6862 (mtt) cc_final: 0.6588 (mtm) REVERT: D 236 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6909 (mt-10) REVERT: D 388 MET cc_start: 0.3804 (ttt) cc_final: 0.3135 (tmt) REVERT: E 1 MET cc_start: 0.3668 (mmt) cc_final: 0.2173 (tpt) REVERT: E 5 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.5999 (ptp90) REVERT: E 292 THR cc_start: 0.7096 (p) cc_final: 0.6886 (p) REVERT: E 327 THR cc_start: 0.7511 (OUTLIER) cc_final: 0.7171 (p) REVERT: E 347 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7351 (mt0) REVERT: E 379 LEU cc_start: 0.6035 (OUTLIER) cc_final: 0.5439 (mt) REVERT: E 430 GLU cc_start: 0.7332 (pm20) cc_final: 0.6839 (pm20) REVERT: E 453 TYR cc_start: 0.7313 (t80) cc_final: 0.6999 (t80) REVERT: F 5 ARG cc_start: 0.7510 (mmt180) cc_final: 0.6928 (mtm110) REVERT: F 48 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7059 (mt) REVERT: F 75 GLU cc_start: 0.7408 (tt0) cc_final: 0.6988 (mm-30) REVERT: F 101 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6957 (mm-30) REVERT: F 172 ARG cc_start: 0.6524 (OUTLIER) cc_final: 0.6045 (tpp-160) REVERT: F 360 GLU cc_start: 0.6153 (OUTLIER) cc_final: 0.5323 (tp30) REVERT: F 395 ASP cc_start: 0.6450 (m-30) cc_final: 0.6158 (m-30) REVERT: G 19 LYS cc_start: 0.6170 (mttt) cc_final: 0.5856 (ttmm) REVERT: G 37 ARG cc_start: 0.5287 (ttp80) cc_final: 0.4605 (mtm180) REVERT: G 88 ARG cc_start: 0.5489 (mpp80) cc_final: 0.5153 (mpp80) REVERT: G 248 LYS cc_start: 0.6909 (mtmm) cc_final: 0.6337 (mmtm) outliers start: 111 outliers final: 37 residues processed: 378 average time/residue: 0.7308 time to fit residues: 312.2921 Evaluate side-chains 326 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 275 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 327 THR Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 172 ARG Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 360 GLU Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 280 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 67 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 300 optimal weight: 30.0000 chunk 203 optimal weight: 9.9990 chunk 241 optimal weight: 3.9990 chunk 245 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 206 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 GLN C 186 GLN C 341 GLN D 418 HIS E 33 GLN ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 362 HIS F 38 ASN F 178 HIS F 400 GLN G 255 ASN G 275 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.196249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.143067 restraints weight = 25645.825| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.21 r_work: 0.3668 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 24687 Z= 0.211 Angle : 0.683 8.010 33402 Z= 0.359 Chirality : 0.049 0.237 3792 Planarity : 0.006 0.066 4362 Dihedral : 7.341 85.175 3514 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.55 % Favored : 96.39 % Rotamer: Outliers : 4.62 % Allowed : 17.00 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.46 % 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: -0.21 (0.15), residues: 3101 helix: 0.37 (0.14), residues: 1257 sheet: 0.46 (0.22), residues: 518 loop : -0.79 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 90 TYR 0.018 0.002 TYR F 27 PHE 0.033 0.002 PHE E 408 TRP 0.011 0.002 TRP E 198 HIS 0.007 0.001 HIS F 362 Details of bonding type rmsd covalent geometry : bond 0.00507 (24687) covalent geometry : angle 0.68324 (33402) hydrogen bonds : bond 0.05410 ( 1102) hydrogen bonds : angle 4.78114 ( 3159) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 293 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7772 (tt0) cc_final: 0.7430 (tm-30) REVERT: A 95 MET cc_start: 0.7251 (mmm) cc_final: 0.6592 (tmm) REVERT: A 278 ARG cc_start: 0.6365 (mtp85) cc_final: 0.5860 (mmp80) REVERT: A 353 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7446 (mm) REVERT: A 373 LYS cc_start: 0.8180 (ttpp) cc_final: 0.7464 (mppt) REVERT: A 415 ARG cc_start: 0.6449 (mtt90) cc_final: 0.5731 (mpp80) REVERT: B 40 ARG cc_start: 0.8516 (mmt90) cc_final: 0.7797 (mmt180) REVERT: B 68 GLU cc_start: 0.8226 (tt0) cc_final: 0.7901 (tm-30) REVERT: B 87 GLU cc_start: 0.7251 (tt0) cc_final: 0.7040 (tp30) REVERT: B 156 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.7811 (mmt) REVERT: B 354 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.5775 (mtm-85) REVERT: B 375 MET cc_start: 0.6288 (tpt) cc_final: 0.6079 (tpp) REVERT: B 418 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7577 (mm-30) REVERT: B 446 ASP cc_start: 0.6548 (OUTLIER) cc_final: 0.5955 (m-30) REVERT: C 67 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7627 (mm-30) REVERT: C 124 LYS cc_start: 0.7129 (mttt) cc_final: 0.6751 (pttm) REVERT: C 474 GLU cc_start: 0.6714 (OUTLIER) cc_final: 0.6416 (tm-30) REVERT: D 10 MET cc_start: 0.7861 (mtm) cc_final: 0.7647 (mmm) REVERT: D 22 HIS cc_start: 0.7695 (m90) cc_final: 0.7050 (t70) REVERT: D 33 GLN cc_start: 0.7576 (mt0) cc_final: 0.6957 (mp10) REVERT: D 119 ARG cc_start: 0.7261 (mtp85) cc_final: 0.7049 (mtp-110) REVERT: D 149 LYS cc_start: 0.8502 (ttpt) cc_final: 0.8002 (tmtp) REVERT: D 193 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.5998 (mt-10) REVERT: D 201 MET cc_start: 0.6909 (mtt) cc_final: 0.6648 (mtm) REVERT: D 225 PHE cc_start: 0.7169 (OUTLIER) cc_final: 0.5539 (p90) REVERT: D 333 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6668 (tm-30) REVERT: D 388 MET cc_start: 0.3912 (ttt) cc_final: 0.3191 (mmp) REVERT: D 406 GLN cc_start: 0.6629 (tp40) cc_final: 0.5306 (pt0) REVERT: E 1 MET cc_start: 0.3504 (mmt) cc_final: 0.2178 (tpt) REVERT: E 5 ARG cc_start: 0.7098 (OUTLIER) cc_final: 0.6071 (ptp90) REVERT: E 201 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6929 (mmp) REVERT: E 327 THR cc_start: 0.7559 (OUTLIER) cc_final: 0.7177 (p) REVERT: E 354 ASP cc_start: 0.6732 (m-30) cc_final: 0.5701 (p0) REVERT: E 378 ASP cc_start: 0.6838 (m-30) cc_final: 0.6522 (m-30) REVERT: E 453 TYR cc_start: 0.7612 (t80) cc_final: 0.7291 (t80) REVERT: F 5 ARG cc_start: 0.7543 (mmt180) cc_final: 0.6831 (mtm110) REVERT: F 48 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7033 (mt) REVERT: F 75 GLU cc_start: 0.7494 (tt0) cc_final: 0.7166 (mm-30) REVERT: F 101 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.7025 (mm-30) REVERT: F 172 ARG cc_start: 0.6535 (tpp-160) cc_final: 0.5893 (tpp-160) REVERT: F 189 GLU cc_start: 0.5524 (OUTLIER) cc_final: 0.4770 (mm-30) REVERT: F 395 ASP cc_start: 0.6325 (m-30) cc_final: 0.6051 (m-30) REVERT: G 11 LYS cc_start: 0.6567 (tttp) cc_final: 0.6367 (mttm) REVERT: G 37 ARG cc_start: 0.5223 (ttp80) cc_final: 0.4548 (mtm180) REVERT: G 49 MET cc_start: 0.3876 (mmm) cc_final: 0.3257 (ptp) outliers start: 119 outliers final: 44 residues processed: 385 average time/residue: 0.7153 time to fit residues: 312.7188 Evaluate side-chains 328 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 269 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 354 ARG Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 474 GLU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain D residue 425 LYS Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 201 MET Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 327 THR Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 189 GLU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 280 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 101 optimal weight: 2.9990 chunk 209 optimal weight: 0.9980 chunk 232 optimal weight: 20.0000 chunk 197 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 203 optimal weight: 10.0000 chunk 228 optimal weight: 4.9990 chunk 7 optimal weight: 0.0670 chunk 77 optimal weight: 0.8980 chunk 235 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN B 202 GLN B 341 GLN B 358 ASN C 341 GLN D 34 HIS D 418 HIS E 33 GLN ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 ASN F 400 GLN G 275 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.199830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.146959 restraints weight = 25489.487| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.20 r_work: 0.3717 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24687 Z= 0.117 Angle : 0.554 11.834 33402 Z= 0.290 Chirality : 0.044 0.288 3792 Planarity : 0.005 0.056 4362 Dihedral : 6.917 81.196 3514 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.48 % Favored : 97.45 % Rotamer: Outliers : 3.26 % Allowed : 19.22 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.46 % 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: 0.21 (0.15), residues: 3101 helix: 0.89 (0.15), residues: 1249 sheet: 0.60 (0.22), residues: 508 loop : -0.70 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 365 TYR 0.015 0.001 TYR E 306 PHE 0.031 0.001 PHE E 408 TRP 0.007 0.001 TRP D 198 HIS 0.004 0.001 HIS A 468 Details of bonding type rmsd covalent geometry : bond 0.00255 (24687) covalent geometry : angle 0.55405 (33402) hydrogen bonds : bond 0.04196 ( 1102) hydrogen bonds : angle 4.48723 ( 3159) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 294 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7699 (tt0) cc_final: 0.7386 (tm-30) REVERT: A 95 MET cc_start: 0.7061 (mmm) cc_final: 0.6427 (tmm) REVERT: A 278 ARG cc_start: 0.6358 (mtp85) cc_final: 0.5851 (mmp80) REVERT: A 353 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7517 (mm) REVERT: A 373 LYS cc_start: 0.8103 (ttpp) cc_final: 0.7398 (mppt) REVERT: A 415 ARG cc_start: 0.6341 (mtt90) cc_final: 0.5606 (mpp80) REVERT: B 40 ARG cc_start: 0.8443 (mmt90) cc_final: 0.7619 (mmt180) REVERT: B 68 GLU cc_start: 0.8176 (tt0) cc_final: 0.7892 (tm-30) REVERT: B 156 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.7798 (mmt) REVERT: B 320 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6616 (pt0) REVERT: B 375 MET cc_start: 0.6168 (tpt) cc_final: 0.5964 (tpp) REVERT: B 418 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7613 (mm-30) REVERT: B 474 GLU cc_start: 0.5943 (OUTLIER) cc_final: 0.5631 (pp20) REVERT: C 69 ASN cc_start: 0.7933 (OUTLIER) cc_final: 0.7623 (m-40) REVERT: C 124 LYS cc_start: 0.7091 (mttt) cc_final: 0.6720 (pttm) REVERT: C 156 MET cc_start: 0.8086 (mmp) cc_final: 0.7454 (mmp) REVERT: C 289 ASP cc_start: 0.7600 (m-30) cc_final: 0.7333 (m-30) REVERT: C 474 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6465 (tm-30) REVERT: D 22 HIS cc_start: 0.7625 (m90) cc_final: 0.6960 (t70) REVERT: D 33 GLN cc_start: 0.7563 (mt0) cc_final: 0.6934 (mp10) REVERT: D 101 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6945 (mm-30) REVERT: D 149 LYS cc_start: 0.8477 (ttpt) cc_final: 0.7958 (tmtp) REVERT: D 193 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.5904 (mt-10) REVERT: D 225 PHE cc_start: 0.6901 (OUTLIER) cc_final: 0.5544 (p90) REVERT: D 370 ARG cc_start: 0.6696 (ttm110) cc_final: 0.6262 (mtm110) REVERT: D 388 MET cc_start: 0.3949 (ttt) cc_final: 0.3173 (tmt) REVERT: D 406 GLN cc_start: 0.6521 (tp40) cc_final: 0.5225 (pt0) REVERT: E 5 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.6016 (ptp90) REVERT: E 193 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7011 (mt-10) REVERT: E 327 THR cc_start: 0.7495 (m) cc_final: 0.7151 (p) REVERT: E 378 ASP cc_start: 0.6801 (m-30) cc_final: 0.6456 (m-30) REVERT: E 430 GLU cc_start: 0.7371 (pm20) cc_final: 0.6730 (pm20) REVERT: E 453 TYR cc_start: 0.7584 (t80) cc_final: 0.7301 (t80) REVERT: F 5 ARG cc_start: 0.7499 (mmt180) cc_final: 0.6761 (mtm110) REVERT: F 48 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.6876 (mt) REVERT: F 75 GLU cc_start: 0.7418 (tt0) cc_final: 0.7109 (mm-30) REVERT: F 101 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6964 (mm-30) REVERT: F 172 ARG cc_start: 0.6490 (tpp-160) cc_final: 0.5889 (tpp-160) REVERT: F 189 GLU cc_start: 0.5271 (OUTLIER) cc_final: 0.4510 (mm-30) REVERT: G 37 ARG cc_start: 0.5014 (ttp80) cc_final: 0.4487 (mtm180) REVERT: G 49 MET cc_start: 0.3798 (mmm) cc_final: 0.3226 (ptp) REVERT: G 140 ILE cc_start: 0.3340 (OUTLIER) cc_final: 0.3039 (mt) outliers start: 84 outliers final: 27 residues processed: 356 average time/residue: 0.7220 time to fit residues: 291.6643 Evaluate side-chains 310 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 270 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 474 GLU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 425 LYS Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 189 GLU Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 140 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 123 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 172 optimal weight: 9.9990 chunk 196 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 293 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 264 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN B 202 GLN C 341 GLN D 252 ASN D 418 HIS E 33 GLN ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 ASN F 400 GLN G 275 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.196946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.139099 restraints weight = 25615.394| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.89 r_work: 0.3675 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24687 Z= 0.172 Angle : 0.620 9.318 33402 Z= 0.323 Chirality : 0.047 0.258 3792 Planarity : 0.005 0.061 4362 Dihedral : 7.076 82.545 3514 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.68 % Favored : 96.29 % Rotamer: Outliers : 4.31 % Allowed : 18.71 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.46 % 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: 0.07 (0.15), residues: 3101 helix: 0.72 (0.15), residues: 1263 sheet: 0.52 (0.21), residues: 527 loop : -0.76 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 365 TYR 0.013 0.002 TYR A 236 PHE 0.034 0.002 PHE E 408 TRP 0.009 0.002 TRP D 198 HIS 0.005 0.001 HIS F 418 Details of bonding type rmsd covalent geometry : bond 0.00411 (24687) covalent geometry : angle 0.61961 (33402) hydrogen bonds : bond 0.04856 ( 1102) hydrogen bonds : angle 4.59067 ( 3159) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 282 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7715 (tt0) cc_final: 0.7384 (tm-30) REVERT: A 95 MET cc_start: 0.7108 (mmm) cc_final: 0.6474 (tmm) REVERT: A 278 ARG cc_start: 0.6407 (mtp85) cc_final: 0.5875 (mmt180) REVERT: A 353 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7477 (mm) REVERT: A 373 LYS cc_start: 0.8124 (ttpp) cc_final: 0.7424 (mppt) REVERT: A 415 ARG cc_start: 0.6381 (mtt90) cc_final: 0.5632 (mpp80) REVERT: B 40 ARG cc_start: 0.8504 (mmt90) cc_final: 0.7817 (mmt180) REVERT: B 57 ASN cc_start: 0.7431 (OUTLIER) cc_final: 0.7094 (t0) REVERT: B 68 GLU cc_start: 0.8194 (tt0) cc_final: 0.7908 (tm-30) REVERT: B 87 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6376 (tp30) REVERT: B 95 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7459 (ttm) REVERT: B 156 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.7815 (mmt) REVERT: B 375 MET cc_start: 0.6229 (tpt) cc_final: 0.6029 (tpp) REVERT: B 446 ASP cc_start: 0.6467 (OUTLIER) cc_final: 0.5992 (m-30) REVERT: C 69 ASN cc_start: 0.7957 (OUTLIER) cc_final: 0.7609 (m-40) REVERT: C 124 LYS cc_start: 0.7147 (mttt) cc_final: 0.6716 (pttm) REVERT: C 289 ASP cc_start: 0.7760 (m-30) cc_final: 0.7471 (m-30) REVERT: C 474 GLU cc_start: 0.6700 (OUTLIER) cc_final: 0.6404 (tm-30) REVERT: D 22 HIS cc_start: 0.7708 (m90) cc_final: 0.7045 (t70) REVERT: D 33 GLN cc_start: 0.7541 (mt0) cc_final: 0.6934 (mp10) REVERT: D 149 LYS cc_start: 0.8520 (ttpt) cc_final: 0.8012 (tmtp) REVERT: D 193 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6503 (mt-10) REVERT: D 225 PHE cc_start: 0.7225 (OUTLIER) cc_final: 0.5731 (p90) REVERT: D 333 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6742 (tm-30) REVERT: D 388 MET cc_start: 0.4104 (ttt) cc_final: 0.3266 (tmt) REVERT: D 406 GLN cc_start: 0.6437 (tp40) cc_final: 0.5248 (pt0) REVERT: E 5 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6028 (ptp90) REVERT: E 193 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7074 (mt-10) REVERT: E 201 MET cc_start: 0.7045 (OUTLIER) cc_final: 0.6791 (mmp) REVERT: E 327 THR cc_start: 0.7524 (m) cc_final: 0.7155 (p) REVERT: E 378 ASP cc_start: 0.6670 (m-30) cc_final: 0.6336 (m-30) REVERT: E 404 LYS cc_start: 0.5485 (OUTLIER) cc_final: 0.5279 (mtpt) REVERT: E 406 GLN cc_start: 0.6638 (OUTLIER) cc_final: 0.5955 (tm-30) REVERT: E 430 GLU cc_start: 0.7359 (pm20) cc_final: 0.6738 (pm20) REVERT: E 453 TYR cc_start: 0.7598 (t80) cc_final: 0.7357 (t80) REVERT: F 5 ARG cc_start: 0.7541 (mmt180) cc_final: 0.6797 (mtm110) REVERT: F 48 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7031 (mt) REVERT: F 75 GLU cc_start: 0.7424 (tt0) cc_final: 0.7114 (mm-30) REVERT: F 101 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6985 (mm-30) REVERT: F 172 ARG cc_start: 0.6577 (tpp-160) cc_final: 0.5978 (tpp-160) REVERT: F 189 GLU cc_start: 0.5526 (OUTLIER) cc_final: 0.4833 (mm-30) REVERT: F 360 GLU cc_start: 0.6046 (OUTLIER) cc_final: 0.5139 (tp30) REVERT: G 37 ARG cc_start: 0.5096 (ttp80) cc_final: 0.4538 (mtm180) REVERT: G 49 MET cc_start: 0.3874 (mmm) cc_final: 0.3271 (ptp) REVERT: G 140 ILE cc_start: 0.3413 (OUTLIER) cc_final: 0.3102 (mt) REVERT: G 239 GLU cc_start: 0.6177 (tt0) cc_final: 0.5956 (tt0) outliers start: 111 outliers final: 49 residues processed: 366 average time/residue: 0.7080 time to fit residues: 293.9610 Evaluate side-chains 339 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 269 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 474 GLU Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 193 GLU Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain D residue 425 LYS Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 201 MET Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 404 LYS Chi-restraints excluded: chain E residue 406 GLN Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 189 GLU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 360 GLU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 425 LYS Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 280 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 69 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 301 optimal weight: 8.9990 chunk 284 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 chunk 206 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 195 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN B 202 GLN C 341 GLN D 195 ASN D 252 ASN D 418 HIS E 33 GLN ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 ASN F 323 HIS F 400 GLN G 110 HIS G 275 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.194941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.137137 restraints weight = 25801.135| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.88 r_work: 0.3653 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 24687 Z= 0.223 Angle : 0.695 9.554 33402 Z= 0.363 Chirality : 0.050 0.236 3792 Planarity : 0.006 0.062 4362 Dihedral : 7.340 80.101 3514 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.32 % Favored : 95.65 % Rotamer: Outliers : 4.46 % Allowed : 19.02 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.46 % 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: -0.25 (0.15), residues: 3101 helix: 0.47 (0.14), residues: 1261 sheet: 0.37 (0.22), residues: 527 loop : -0.94 (0.17), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 90 TYR 0.016 0.002 TYR D 426 PHE 0.038 0.002 PHE E 408 TRP 0.011 0.002 TRP D 198 HIS 0.008 0.001 HIS F 418 Details of bonding type rmsd covalent geometry : bond 0.00542 (24687) covalent geometry : angle 0.69535 (33402) hydrogen bonds : bond 0.05453 ( 1102) hydrogen bonds : angle 4.75764 ( 3159) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 267 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7676 (tt0) cc_final: 0.7373 (tm-30) REVERT: A 95 MET cc_start: 0.7209 (mmm) cc_final: 0.6522 (tmm) REVERT: A 278 ARG cc_start: 0.6407 (mtp85) cc_final: 0.5897 (mmt180) REVERT: A 353 ILE cc_start: 0.7787 (OUTLIER) cc_final: 0.7503 (mm) REVERT: A 373 LYS cc_start: 0.8126 (ttpp) cc_final: 0.7410 (mppt) REVERT: A 415 ARG cc_start: 0.6409 (mtt90) cc_final: 0.5586 (mpp80) REVERT: B 40 ARG cc_start: 0.8543 (mmt90) cc_final: 0.7808 (mmt180) REVERT: B 68 GLU cc_start: 0.8206 (tt0) cc_final: 0.7931 (tm-30) REVERT: B 95 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7472 (ttm) REVERT: B 156 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.7833 (mmt) REVERT: B 446 ASP cc_start: 0.6457 (OUTLIER) cc_final: 0.6077 (m-30) REVERT: C 124 LYS cc_start: 0.7188 (mttt) cc_final: 0.6834 (pttm) REVERT: C 156 MET cc_start: 0.8241 (mmp) cc_final: 0.7497 (mmp) REVERT: C 289 ASP cc_start: 0.7831 (m-30) cc_final: 0.7530 (m-30) REVERT: C 474 GLU cc_start: 0.6707 (OUTLIER) cc_final: 0.6442 (tm-30) REVERT: D 22 HIS cc_start: 0.7777 (m90) cc_final: 0.7069 (t70) REVERT: D 33 GLN cc_start: 0.7453 (mt0) cc_final: 0.6824 (mp10) REVERT: D 225 PHE cc_start: 0.7232 (OUTLIER) cc_final: 0.5399 (p90) REVERT: D 333 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6779 (tm-30) REVERT: E 5 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.6079 (ptp90) REVERT: E 201 MET cc_start: 0.7205 (OUTLIER) cc_final: 0.6953 (mmp) REVERT: E 327 THR cc_start: 0.7596 (OUTLIER) cc_final: 0.7212 (p) REVERT: E 354 ASP cc_start: 0.6789 (m-30) cc_final: 0.5741 (p0) REVERT: E 378 ASP cc_start: 0.6558 (m-30) cc_final: 0.6263 (m-30) REVERT: E 404 LYS cc_start: 0.5453 (OUTLIER) cc_final: 0.4925 (mtpt) REVERT: E 406 GLN cc_start: 0.6546 (OUTLIER) cc_final: 0.5846 (tm-30) REVERT: E 453 TYR cc_start: 0.7759 (t80) cc_final: 0.7515 (t80) REVERT: F 5 ARG cc_start: 0.7555 (mmt180) cc_final: 0.6788 (mtm110) REVERT: F 48 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7068 (mt) REVERT: F 75 GLU cc_start: 0.7497 (tt0) cc_final: 0.7175 (mm-30) REVERT: F 101 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.7025 (mm-30) REVERT: F 104 ASP cc_start: 0.6867 (OUTLIER) cc_final: 0.6526 (m-30) REVERT: F 130 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6619 (mp0) REVERT: F 172 ARG cc_start: 0.6577 (tpp-160) cc_final: 0.5984 (tpp-160) REVERT: F 189 GLU cc_start: 0.5714 (OUTLIER) cc_final: 0.5086 (mm-30) REVERT: F 360 GLU cc_start: 0.6135 (OUTLIER) cc_final: 0.5178 (tp30) REVERT: F 397 LEU cc_start: 0.6268 (OUTLIER) cc_final: 0.6042 (mt) REVERT: F 400 GLN cc_start: 0.5839 (OUTLIER) cc_final: 0.5542 (tm130) REVERT: G 37 ARG cc_start: 0.5278 (ttp80) cc_final: 0.4659 (mtm180) REVERT: G 49 MET cc_start: 0.3789 (mmm) cc_final: 0.3222 (ptp) REVERT: G 140 ILE cc_start: 0.3384 (OUTLIER) cc_final: 0.3093 (mt) outliers start: 115 outliers final: 55 residues processed: 353 average time/residue: 0.6393 time to fit residues: 257.4490 Evaluate side-chains 334 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 258 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 474 GLU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain D residue 425 LYS Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 201 MET Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 327 THR Chi-restraints excluded: chain E residue 404 LYS Chi-restraints excluded: chain E residue 406 GLN Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 189 GLU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 360 GLU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 400 GLN Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 280 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 41 optimal weight: 5.9990 chunk 131 optimal weight: 40.0000 chunk 124 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 chunk 151 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 139 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 227 optimal weight: 20.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN B 202 GLN C 57 ASN C 341 GLN E 33 GLN ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 ASN ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 400 GLN G 275 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.195587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.138185 restraints weight = 25679.342| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 1.86 r_work: 0.3667 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24687 Z= 0.186 Angle : 0.649 10.184 33402 Z= 0.340 Chirality : 0.048 0.203 3792 Planarity : 0.005 0.061 4362 Dihedral : 7.236 77.942 3514 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.93 % Favored : 96.03 % Rotamer: Outliers : 3.73 % Allowed : 20.26 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.46 % 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: -0.21 (0.15), residues: 3101 helix: 0.53 (0.15), residues: 1266 sheet: 0.42 (0.22), residues: 527 loop : -0.97 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 401 TYR 0.013 0.002 TYR A 236 PHE 0.037 0.002 PHE E 408 TRP 0.010 0.002 TRP D 198 HIS 0.006 0.001 HIS F 418 Details of bonding type rmsd covalent geometry : bond 0.00446 (24687) covalent geometry : angle 0.64946 (33402) hydrogen bonds : bond 0.05030 ( 1102) hydrogen bonds : angle 4.68876 ( 3159) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 268 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7646 (tt0) cc_final: 0.7337 (tm-30) REVERT: A 95 MET cc_start: 0.7188 (mmm) cc_final: 0.6521 (tmm) REVERT: A 278 ARG cc_start: 0.6401 (mtp85) cc_final: 0.5893 (mmt180) REVERT: A 353 ILE cc_start: 0.7790 (OUTLIER) cc_final: 0.7504 (mm) REVERT: A 373 LYS cc_start: 0.8107 (ttpp) cc_final: 0.7407 (mppt) REVERT: A 415 ARG cc_start: 0.6360 (mtt90) cc_final: 0.5645 (mpp80) REVERT: B 40 ARG cc_start: 0.8511 (mmt90) cc_final: 0.7797 (mmt180) REVERT: B 57 ASN cc_start: 0.7464 (OUTLIER) cc_final: 0.7126 (t0) REVERT: B 68 GLU cc_start: 0.8187 (tt0) cc_final: 0.7912 (tm-30) REVERT: B 95 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7461 (ttm) REVERT: B 156 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8491 (mmt) REVERT: B 375 MET cc_start: 0.6310 (tpt) cc_final: 0.6102 (tpp) REVERT: B 446 ASP cc_start: 0.6510 (OUTLIER) cc_final: 0.6131 (m-30) REVERT: C 124 LYS cc_start: 0.7178 (mttt) cc_final: 0.6797 (pttm) REVERT: C 156 MET cc_start: 0.8204 (mmp) cc_final: 0.7461 (mmp) REVERT: C 289 ASP cc_start: 0.7772 (m-30) cc_final: 0.7476 (m-30) REVERT: C 474 GLU cc_start: 0.6624 (OUTLIER) cc_final: 0.6407 (tm-30) REVERT: D 22 HIS cc_start: 0.7750 (m90) cc_final: 0.7017 (t70) REVERT: D 33 GLN cc_start: 0.7493 (mt0) cc_final: 0.6922 (mp10) REVERT: D 225 PHE cc_start: 0.7167 (OUTLIER) cc_final: 0.5495 (p90) REVERT: D 333 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6802 (tm-30) REVERT: E 5 ARG cc_start: 0.7080 (OUTLIER) cc_final: 0.6068 (ptp90) REVERT: E 201 MET cc_start: 0.7146 (OUTLIER) cc_final: 0.6901 (mmp) REVERT: E 327 THR cc_start: 0.7549 (OUTLIER) cc_final: 0.7181 (p) REVERT: E 354 ASP cc_start: 0.6724 (m-30) cc_final: 0.5684 (p0) REVERT: E 378 ASP cc_start: 0.6369 (m-30) cc_final: 0.6071 (m-30) REVERT: E 430 GLU cc_start: 0.7379 (pm20) cc_final: 0.7123 (mp0) REVERT: E 453 TYR cc_start: 0.7776 (t80) cc_final: 0.7571 (t80) REVERT: F 48 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7069 (mt) REVERT: F 101 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6996 (mm-30) REVERT: F 104 ASP cc_start: 0.6783 (OUTLIER) cc_final: 0.6414 (m-30) REVERT: F 130 GLU cc_start: 0.6848 (pm20) cc_final: 0.6605 (mp0) REVERT: F 172 ARG cc_start: 0.6553 (tpp-160) cc_final: 0.5980 (tpp-160) REVERT: F 189 GLU cc_start: 0.5598 (OUTLIER) cc_final: 0.4952 (mm-30) REVERT: F 354 ASP cc_start: 0.7619 (t0) cc_final: 0.7250 (t0) REVERT: F 356 ARG cc_start: 0.7087 (mpp80) cc_final: 0.6658 (ptp-110) REVERT: F 360 GLU cc_start: 0.6093 (OUTLIER) cc_final: 0.5137 (tp30) REVERT: G 37 ARG cc_start: 0.5153 (ttp80) cc_final: 0.4518 (mtm180) REVERT: G 49 MET cc_start: 0.3805 (mmm) cc_final: 0.3221 (ptp) REVERT: G 88 ARG cc_start: 0.5306 (mpp80) cc_final: 0.4900 (mpp80) REVERT: G 140 ILE cc_start: 0.3469 (OUTLIER) cc_final: 0.3188 (mt) outliers start: 96 outliers final: 50 residues processed: 348 average time/residue: 0.6847 time to fit residues: 271.8829 Evaluate side-chains 329 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 262 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 474 GLU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain D residue 425 LYS Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 201 MET Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 327 THR Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 189 GLU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 360 GLU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 280 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 55 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 284 optimal weight: 0.2980 chunk 42 optimal weight: 7.9990 chunk 271 optimal weight: 7.9990 chunk 249 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 chunk 260 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN B 202 GLN B 442 ASN C 57 ASN C 341 GLN ** D 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 GLN ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 ASN ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 275 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.198238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.140420 restraints weight = 25740.045| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 1.90 r_work: 0.3696 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24687 Z= 0.133 Angle : 0.580 11.018 33402 Z= 0.303 Chirality : 0.045 0.211 3792 Planarity : 0.005 0.060 4362 Dihedral : 6.952 74.150 3514 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.22 % Favored : 96.74 % Rotamer: Outliers : 2.99 % Allowed : 20.81 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.46 % 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: 0.07 (0.15), residues: 3101 helix: 0.83 (0.15), residues: 1266 sheet: 0.50 (0.22), residues: 513 loop : -0.85 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 375 TYR 0.016 0.001 TYR E 306 PHE 0.039 0.001 PHE E 408 TRP 0.009 0.001 TRP D 198 HIS 0.004 0.001 HIS F 418 Details of bonding type rmsd covalent geometry : bond 0.00306 (24687) covalent geometry : angle 0.58040 (33402) hydrogen bonds : bond 0.04282 ( 1102) hydrogen bonds : angle 4.51720 ( 3159) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 268 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7576 (tt0) cc_final: 0.7271 (tm-30) REVERT: A 95 MET cc_start: 0.7075 (mmm) cc_final: 0.6535 (tmm) REVERT: A 278 ARG cc_start: 0.6406 (mtp85) cc_final: 0.5897 (mmt180) REVERT: A 373 LYS cc_start: 0.8091 (ttpp) cc_final: 0.7349 (mppt) REVERT: A 415 ARG cc_start: 0.6212 (mtt90) cc_final: 0.5573 (mpp80) REVERT: B 40 ARG cc_start: 0.8479 (mmt90) cc_final: 0.7799 (mmt180) REVERT: B 68 GLU cc_start: 0.8163 (tt0) cc_final: 0.7896 (tm-30) REVERT: B 95 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7445 (ttm) REVERT: B 156 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.7633 (mmt) REVERT: B 446 ASP cc_start: 0.6426 (OUTLIER) cc_final: 0.6130 (m-30) REVERT: B 494 LYS cc_start: 0.7874 (mttt) cc_final: 0.7568 (mmtp) REVERT: C 124 LYS cc_start: 0.7186 (mttt) cc_final: 0.6767 (pttm) REVERT: C 156 MET cc_start: 0.8163 (mmp) cc_final: 0.7537 (mmp) REVERT: C 289 ASP cc_start: 0.7618 (m-30) cc_final: 0.7365 (m-30) REVERT: C 447 ASP cc_start: 0.7021 (m-30) cc_final: 0.6629 (m-30) REVERT: C 474 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6403 (tm-30) REVERT: D 22 HIS cc_start: 0.7729 (m90) cc_final: 0.6975 (t70) REVERT: D 225 PHE cc_start: 0.7028 (OUTLIER) cc_final: 0.5607 (p90) REVERT: D 333 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6808 (tm-30) REVERT: E 5 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6060 (ptp90) REVERT: E 201 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.6710 (mmp) REVERT: E 327 THR cc_start: 0.7507 (m) cc_final: 0.7156 (p) REVERT: E 388 MET cc_start: 0.6074 (mmp) cc_final: 0.5139 (tpt) REVERT: E 430 GLU cc_start: 0.7374 (pm20) cc_final: 0.6779 (pm20) REVERT: E 453 TYR cc_start: 0.7780 (t80) cc_final: 0.7580 (t80) REVERT: F 48 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.6994 (mt) REVERT: F 101 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6963 (mm-30) REVERT: F 104 ASP cc_start: 0.6719 (OUTLIER) cc_final: 0.6428 (m-30) REVERT: F 130 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6647 (mp0) REVERT: F 172 ARG cc_start: 0.6556 (tpp-160) cc_final: 0.5986 (tpp-160) REVERT: F 189 GLU cc_start: 0.5429 (OUTLIER) cc_final: 0.4742 (mm-30) REVERT: F 354 ASP cc_start: 0.7610 (t0) cc_final: 0.7267 (t0) REVERT: F 356 ARG cc_start: 0.7070 (mpp80) cc_final: 0.6658 (ptp-110) REVERT: G 37 ARG cc_start: 0.5069 (ttp80) cc_final: 0.4477 (mtm180) REVERT: G 49 MET cc_start: 0.3831 (mmm) cc_final: 0.3302 (ptp) REVERT: G 88 ARG cc_start: 0.5258 (mpp80) cc_final: 0.4999 (mpp80) REVERT: G 140 ILE cc_start: 0.3445 (OUTLIER) cc_final: 0.3166 (mt) outliers start: 77 outliers final: 40 residues processed: 332 average time/residue: 0.6639 time to fit residues: 250.7852 Evaluate side-chains 310 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 256 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 474 GLU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain D residue 425 LYS Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 201 MET Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 189 GLU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 188 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 91 optimal weight: 7.9990 chunk 298 optimal weight: 30.0000 chunk 266 optimal weight: 5.9990 chunk 186 optimal weight: 20.0000 chunk 248 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 GLN C 341 GLN D 33 GLN D 252 ASN E 33 GLN ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 ASN ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 400 GLN G 275 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.194895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.136934 restraints weight = 25772.196| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 1.89 r_work: 0.3654 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 24687 Z= 0.214 Angle : 0.684 11.216 33402 Z= 0.357 Chirality : 0.049 0.235 3792 Planarity : 0.006 0.062 4362 Dihedral : 7.250 75.466 3514 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.45 % Favored : 95.52 % Rotamer: Outliers : 3.26 % Allowed : 20.92 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.46 % 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: -0.17 (0.15), residues: 3101 helix: 0.58 (0.15), residues: 1263 sheet: 0.45 (0.22), residues: 516 loop : -0.96 (0.16), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 94 TYR 0.019 0.002 TYR B 240 PHE 0.037 0.002 PHE E 408 TRP 0.011 0.002 TRP D 198 HIS 0.007 0.001 HIS F 418 Details of bonding type rmsd covalent geometry : bond 0.00519 (24687) covalent geometry : angle 0.68430 (33402) hydrogen bonds : bond 0.05282 ( 1102) hydrogen bonds : angle 4.73797 ( 3159) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 262 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7624 (tt0) cc_final: 0.7318 (tm-30) REVERT: A 95 MET cc_start: 0.7132 (mmm) cc_final: 0.6557 (tmm) REVERT: A 278 ARG cc_start: 0.6409 (mtp85) cc_final: 0.6025 (mmt180) REVERT: A 373 LYS cc_start: 0.8130 (ttpp) cc_final: 0.7391 (mppt) REVERT: A 415 ARG cc_start: 0.6305 (mtt90) cc_final: 0.5580 (mpp80) REVERT: B 40 ARG cc_start: 0.8542 (mmt90) cc_final: 0.7819 (mmt180) REVERT: B 68 GLU cc_start: 0.8193 (tt0) cc_final: 0.7918 (tm-30) REVERT: B 95 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7443 (ttm) REVERT: B 156 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.7637 (mmt) REVERT: B 416 MET cc_start: 0.6392 (mpp) cc_final: 0.6088 (mpp) REVERT: B 446 ASP cc_start: 0.6470 (OUTLIER) cc_final: 0.6131 (m-30) REVERT: B 494 LYS cc_start: 0.7886 (mttt) cc_final: 0.7608 (mmtm) REVERT: C 124 LYS cc_start: 0.7144 (mttt) cc_final: 0.6779 (pttm) REVERT: C 156 MET cc_start: 0.8249 (mmp) cc_final: 0.7519 (mmp) REVERT: C 289 ASP cc_start: 0.7818 (m-30) cc_final: 0.7518 (m-30) REVERT: C 447 ASP cc_start: 0.6979 (m-30) cc_final: 0.6612 (m-30) REVERT: C 474 GLU cc_start: 0.6496 (tm-30) cc_final: 0.6258 (tm-30) REVERT: D 22 HIS cc_start: 0.7789 (m90) cc_final: 0.7039 (t70) REVERT: D 225 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.5509 (p90) REVERT: D 333 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6846 (tm-30) REVERT: D 406 GLN cc_start: 0.6387 (tp40) cc_final: 0.4720 (pt0) REVERT: E 1 MET cc_start: 0.3573 (mmt) cc_final: 0.2313 (tpt) REVERT: E 5 ARG cc_start: 0.7102 (OUTLIER) cc_final: 0.6114 (ptp90) REVERT: E 201 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6981 (mmp) REVERT: E 327 THR cc_start: 0.7604 (OUTLIER) cc_final: 0.7223 (p) REVERT: E 430 GLU cc_start: 0.7354 (pm20) cc_final: 0.6764 (pm20) REVERT: E 453 TYR cc_start: 0.7756 (t80) cc_final: 0.7528 (t80) REVERT: F 48 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7080 (mt) REVERT: F 104 ASP cc_start: 0.6824 (OUTLIER) cc_final: 0.6489 (m-30) REVERT: F 130 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6673 (mp0) REVERT: F 172 ARG cc_start: 0.6558 (tpp-160) cc_final: 0.5981 (tpp-160) REVERT: F 189 GLU cc_start: 0.5685 (OUTLIER) cc_final: 0.5050 (mm-30) REVERT: F 354 ASP cc_start: 0.7667 (t0) cc_final: 0.7288 (t0) REVERT: F 356 ARG cc_start: 0.7075 (mpp80) cc_final: 0.6622 (ptp-110) REVERT: F 400 GLN cc_start: 0.5695 (OUTLIER) cc_final: 0.5431 (tm-30) REVERT: G 37 ARG cc_start: 0.5102 (ttp80) cc_final: 0.4484 (mtm180) REVERT: G 49 MET cc_start: 0.3916 (mmm) cc_final: 0.3329 (ptp) REVERT: G 88 ARG cc_start: 0.5266 (mpp80) cc_final: 0.4995 (mpp80) REVERT: G 140 ILE cc_start: 0.3442 (OUTLIER) cc_final: 0.3137 (mt) outliers start: 84 outliers final: 53 residues processed: 328 average time/residue: 0.6722 time to fit residues: 253.0296 Evaluate side-chains 323 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 256 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain D residue 425 LYS Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 201 MET Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 327 THR Chi-restraints excluded: chain E residue 379 LEU Chi-restraints excluded: chain E residue 429 ILE Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 189 GLU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 353 MET Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 400 GLN Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 188 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 129 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 240 optimal weight: 0.9980 chunk 250 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 273 optimal weight: 8.9990 chunk 270 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 424 GLN C 341 GLN E 33 GLN ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 ASN ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 400 GLN G 275 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.198029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.140735 restraints weight = 25663.111| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 1.89 r_work: 0.3702 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24687 Z= 0.124 Angle : 0.571 11.278 33402 Z= 0.299 Chirality : 0.045 0.232 3792 Planarity : 0.005 0.060 4362 Dihedral : 6.906 71.204 3514 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.90 % Favored : 97.07 % Rotamer: Outliers : 2.68 % Allowed : 21.35 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.46 % 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: 0.15 (0.15), residues: 3101 helix: 0.92 (0.15), residues: 1262 sheet: 0.54 (0.22), residues: 516 loop : -0.83 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 89 TYR 0.013 0.001 TYR E 426 PHE 0.035 0.001 PHE E 408 TRP 0.008 0.001 TRP D 198 HIS 0.004 0.001 HIS F 362 Details of bonding type rmsd covalent geometry : bond 0.00278 (24687) covalent geometry : angle 0.57123 (33402) hydrogen bonds : bond 0.04151 ( 1102) hydrogen bonds : angle 4.50301 ( 3159) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11004.03 seconds wall clock time: 187 minutes 8.95 seconds (11228.95 seconds total)