Starting phenix.real_space_refine on Sat Mar 7 02:07:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dbq_27298/03_2026/8dbq_27298.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbq_27298/03_2026/8dbq_27298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dbq_27298/03_2026/8dbq_27298.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbq_27298/03_2026/8dbq_27298.map" model { file = "/net/cci-nas-00/data/ceres_data/8dbq_27298/03_2026/8dbq_27298.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbq_27298/03_2026/8dbq_27298.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 178 5.16 5 C 23342 2.51 5 N 6275 2.21 5 O 6921 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36737 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3869 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Chain: "B" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3863 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Chain: "C" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3869 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Chain: "D" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "E" Number of atoms: 3520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3520 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 437} Chain: "F" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "G" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2186 Classifications: {'peptide': 284} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 274} Chain: "H" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "I" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "J" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "L" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "M" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "N" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "O" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "P" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Q" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "R" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 552 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "S" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "W" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1320 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 3, 'TRANS': 169} Chain: "X" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "Y" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "a" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2104 Classifications: {'peptide': 266} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 250} 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: "B" 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" 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: 8.21, per 1000 atoms: 0.22 Number of scatterers: 36737 At special positions: 0 Unit cell: (180.193, 223.353, 137.033, 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 178 16.00 P 16 15.00 Mg 5 11.99 O 6921 8.00 N 6275 7.00 C 23342 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: 2.85 Conformation dependent library (CDL) restraints added in 1.5 seconds 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8756 Finding SS restraints... Secondary structure from input PDB file: 194 helices and 21 sheets defined 61.8% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 4 through 19 Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 185 Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 231 through 252 Proline residue: A 239 - end of helix removed outlier: 3.691A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.745A pdb=" N ALA A 380 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 404 removed outlier: 4.032A pdb=" N GLY A 391 " --> pdb=" O LYS A 387 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLY A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 394 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.291A pdb=" N GLN A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 409' Processing helix chain 'A' and resid 415 through 431 Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 460 through 479 removed outlier: 4.067A pdb=" N GLY A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 490 removed outlier: 3.559A pdb=" N MET A 483 " --> pdb=" O HIS A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 511 Processing helix chain 'B' and resid 4 through 19 removed outlier: 3.844A pdb=" N ILE B 8 " --> pdb=" O ASN B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.510A pdb=" N ARG B 139 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 156 removed outlier: 3.680A pdb=" N ASP B 154 " --> pdb=" O TYR B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 231 through 252 Proline residue: B 239 - end of helix removed outlier: 3.967A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 removed outlier: 3.512A pdb=" N GLN B 266 " --> pdb=" O ASP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 287 Proline residue: B 287 - end of helix Processing helix chain 'B' and resid 288 through 299 removed outlier: 4.360A pdb=" N TYR B 292 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 313 Processing helix chain 'B' and resid 333 through 336 Processing helix chain 'B' and resid 339 through 347 Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 378 through 382 removed outlier: 3.678A pdb=" N ALA B 381 " --> pdb=" O GLY B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 391 Processing helix chain 'B' and resid 392 through 410 removed outlier: 3.916A pdb=" N ALA B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 432 removed outlier: 3.593A pdb=" N LYS B 432 " --> pdb=" O THR B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 453 Processing helix chain 'B' and resid 460 through 462 No H-bonds generated for 'chain 'B' and resid 460 through 462' Processing helix chain 'B' and resid 463 through 478 Processing helix chain 'B' and resid 479 through 489 removed outlier: 3.776A pdb=" N MET B 483 " --> pdb=" O HIS B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 511 Processing helix chain 'C' and resid 8 through 18 Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.540A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.549A pdb=" N ARG C 139 " --> pdb=" O VAL C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.524A pdb=" N GLN C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 189 No H-bonds generated for 'chain 'C' and resid 187 through 189' Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 216 through 219 removed outlier: 3.767A pdb=" N ALA C 219 " --> pdb=" O GLY C 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 216 through 219' Processing helix chain 'C' and resid 231 through 251 Proline residue: C 239 - end of helix removed outlier: 3.755A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 277 removed outlier: 3.970A pdb=" N ALA C 269 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 290 through 299 Processing helix chain 'C' and resid 305 through 313 Processing helix chain 'C' and resid 339 through 349 Processing helix chain 'C' and resid 356 through 362 Processing helix chain 'C' and resid 377 through 382 removed outlier: 4.011A pdb=" N ALA C 380 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 411 removed outlier: 4.348A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR C 395 " --> pdb=" O GLY C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 431 removed outlier: 3.891A pdb=" N LYS C 426 " --> pdb=" O ASP C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 453 Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 463 through 479 Processing helix chain 'C' and resid 479 through 490 Processing helix chain 'C' and resid 493 through 511 Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 115 through 119 Processing helix chain 'D' and resid 130 through 137 Processing helix chain 'D' and resid 154 through 169 Processing helix chain 'D' and resid 182 through 195 Processing helix chain 'D' and resid 196 through 197 No H-bonds generated for 'chain 'D' and resid 196 through 197' Processing helix chain 'D' and resid 198 through 200 No H-bonds generated for 'chain 'D' and resid 198 through 200' Processing helix chain 'D' and resid 212 through 233 removed outlier: 4.162A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 259 removed outlier: 3.733A pdb=" N TYR D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 280 Processing helix chain 'D' and resid 298 through 302 Processing helix chain 'D' and resid 305 through 312 Processing helix chain 'D' and resid 322 through 328 Processing helix chain 'D' and resid 345 through 350 Processing helix chain 'D' and resid 350 through 378 Processing helix chain 'D' and resid 379 through 382 Processing helix chain 'D' and resid 383 through 400 Processing helix chain 'D' and resid 407 through 412 Processing helix chain 'D' and resid 419 through 432 Processing helix chain 'D' and resid 439 through 443 Processing helix chain 'D' and resid 448 through 457 Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.582A pdb=" N LEU E 84 " --> pdb=" O LYS E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 119 removed outlier: 3.532A pdb=" N LEU E 119 " --> pdb=" O TYR E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 137 removed outlier: 3.512A pdb=" N ASP E 134 " --> pdb=" O ILE E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 170 removed outlier: 3.791A pdb=" N MET E 159 " --> pdb=" O LYS E 155 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE E 168 " --> pdb=" O ARG E 164 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU E 169 " --> pdb=" O ASN E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 196 removed outlier: 3.675A pdb=" N GLY E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 200 No H-bonds generated for 'chain 'E' and resid 198 through 200' Processing helix chain 'E' and resid 212 through 233 removed outlier: 4.611A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 256 removed outlier: 3.727A pdb=" N THR E 248 " --> pdb=" O ILE E 244 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA E 256 " --> pdb=" O THR E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 259 No H-bonds generated for 'chain 'E' and resid 257 through 259' Processing helix chain 'E' and resid 270 through 280 removed outlier: 3.599A pdb=" N LEU E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 302 Processing helix chain 'E' and resid 305 through 313 removed outlier: 4.157A pdb=" N ALA E 313 " --> pdb=" O ALA E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 327 Processing helix chain 'E' and resid 345 through 378 removed outlier: 7.087A pdb=" N GLN E 351 " --> pdb=" O LEU E 347 " (cutoff:3.500A) removed outlier: 9.474A pdb=" N GLU E 352 " --> pdb=" O VAL E 348 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N HIS E 353 " --> pdb=" O VAL E 349 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA E 357 " --> pdb=" O HIS E 353 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ILE E 373 " --> pdb=" O GLU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 382 Processing helix chain 'E' and resid 385 through 400 Processing helix chain 'E' and resid 419 through 432 removed outlier: 4.735A pdb=" N ARG E 425 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 448 through 458 Processing helix chain 'F' and resid 80 through 84 Processing helix chain 'F' and resid 115 through 119 Processing helix chain 'F' and resid 130 through 137 Processing helix chain 'F' and resid 154 through 171 removed outlier: 3.630A pdb=" N ILE F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU F 169 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER F 171 " --> pdb=" O ALA F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 196 Processing helix chain 'F' and resid 198 through 200 No H-bonds generated for 'chain 'F' and resid 198 through 200' Processing helix chain 'F' and resid 212 through 233 removed outlier: 4.644A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 259 removed outlier: 3.594A pdb=" N THR F 248 " --> pdb=" O ILE F 244 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY F 259 " --> pdb=" O SER F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 267 Processing helix chain 'F' and resid 270 through 280 Processing helix chain 'F' and resid 299 through 302 Processing helix chain 'F' and resid 305 through 313 removed outlier: 4.249A pdb=" N ALA F 313 " --> pdb=" O ALA F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 328 Processing helix chain 'F' and resid 345 through 350 Processing helix chain 'F' and resid 350 through 378 removed outlier: 4.001A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA F 375 " --> pdb=" O LYS F 371 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE F 376 " --> pdb=" O ASP F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 401 removed outlier: 3.915A pdb=" N SER F 401 " --> pdb=" O GLN F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 412 Processing helix chain 'F' and resid 419 through 432 Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 448 through 459 Processing helix chain 'G' and resid 2 through 40 Processing helix chain 'G' and resid 41 through 57 removed outlier: 3.863A pdb=" N ALA G 45 " --> pdb=" O SER G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 108 removed outlier: 3.594A pdb=" N LYS G 108 " --> pdb=" O THR G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 129 removed outlier: 3.643A pdb=" N VAL G 122 " --> pdb=" O GLY G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 161 removed outlier: 3.749A pdb=" N LEU G 148 " --> pdb=" O SER G 144 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLY G 150 " --> pdb=" O SER G 146 " (cutoff:3.500A) Proline residue: G 151 - end of helix Processing helix chain 'G' and resid 198 through 202 Processing helix chain 'G' and resid 210 through 283 removed outlier: 3.822A pdb=" N GLU G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 103 Processing helix chain 'I' and resid 4 through 42 removed outlier: 3.750A pdb=" N LEU I 9 " --> pdb=" O ASN I 5 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N MET I 11 " --> pdb=" O ASP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 61 removed outlier: 3.797A pdb=" N THR I 51 " --> pdb=" O PRO I 47 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY I 58 " --> pdb=" O PHE I 54 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU I 59 " --> pdb=" O ILE I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 77 removed outlier: 3.720A pdb=" N ILE I 66 " --> pdb=" O ALA I 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 42 removed outlier: 4.001A pdb=" N LEU J 8 " --> pdb=" O LEU J 4 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET J 11 " --> pdb=" O ASP J 7 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 61 removed outlier: 3.610A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 77 Processing helix chain 'L' and resid 4 through 42 removed outlier: 4.112A pdb=" N LEU L 8 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU L 9 " --> pdb=" O ASN L 5 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR L 10 " --> pdb=" O MET L 6 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET L 11 " --> pdb=" O ASP L 7 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS L 34 " --> pdb=" O ILE L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 61 removed outlier: 3.686A pdb=" N THR L 51 " --> pdb=" O PRO L 47 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU L 59 " --> pdb=" O ILE L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 77 Processing helix chain 'M' and resid 4 through 42 removed outlier: 3.656A pdb=" N MET M 11 " --> pdb=" O ASP M 7 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG M 41 " --> pdb=" O GLU M 37 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLN M 42 " --> pdb=" O GLY M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 61 removed outlier: 3.739A pdb=" N THR M 51 " --> pdb=" O PRO M 47 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE M 54 " --> pdb=" O ARG M 50 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU M 59 " --> pdb=" O ILE M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 78 removed outlier: 3.540A pdb=" N MET M 65 " --> pdb=" O ASP M 61 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE M 66 " --> pdb=" O ALA M 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 42 removed outlier: 4.977A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET N 16 " --> pdb=" O ALA N 12 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA N 21 " --> pdb=" O MET N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 61 removed outlier: 3.655A pdb=" N THR N 51 " --> pdb=" O PRO N 47 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY N 58 " --> pdb=" O PHE N 54 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU N 59 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL N 60 " --> pdb=" O VAL N 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 77 removed outlier: 3.760A pdb=" N ILE N 66 " --> pdb=" O ALA N 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 42 removed outlier: 4.117A pdb=" N LEU O 9 " --> pdb=" O ASN O 5 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR O 10 " --> pdb=" O MET O 6 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE O 28 " --> pdb=" O ALA O 24 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG O 41 " --> pdb=" O GLU O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 61 removed outlier: 3.800A pdb=" N THR O 51 " --> pdb=" O PRO O 47 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE O 54 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU O 59 " --> pdb=" O ILE O 55 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP O 61 " --> pdb=" O MET O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 77 Processing helix chain 'P' and resid 5 through 42 removed outlier: 3.643A pdb=" N LEU P 9 " --> pdb=" O ASN P 5 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA P 21 " --> pdb=" O MET P 17 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE P 28 " --> pdb=" O ALA P 24 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS P 34 " --> pdb=" O ILE P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 77 removed outlier: 4.040A pdb=" N LEU P 59 " --> pdb=" O ILE P 55 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) Proline residue: P 64 - end of helix removed outlier: 3.851A pdb=" N ALA P 67 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 42 removed outlier: 3.781A pdb=" N LEU Q 8 " --> pdb=" O LEU Q 4 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR Q 10 " --> pdb=" O MET Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 77 removed outlier: 3.851A pdb=" N THR Q 51 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE Q 55 " --> pdb=" O THR Q 51 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY Q 58 " --> pdb=" O PHE Q 54 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU Q 59 " --> pdb=" O ILE Q 55 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE Q 63 " --> pdb=" O LEU Q 59 " (cutoff:3.500A) Proline residue: Q 64 - end of helix Processing helix chain 'R' and resid 4 through 42 removed outlier: 3.628A pdb=" N LEU R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE R 28 " --> pdb=" O ALA R 24 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS R 34 " --> pdb=" O ILE R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 61 removed outlier: 3.568A pdb=" N THR R 51 " --> pdb=" O PRO R 47 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU R 59 " --> pdb=" O ILE R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 76 removed outlier: 3.659A pdb=" N ILE R 66 " --> pdb=" O ALA R 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 7 No H-bonds generated for 'chain 'S' and resid 5 through 7' Processing helix chain 'S' and resid 8 through 42 removed outlier: 3.603A pdb=" N MET S 16 " --> pdb=" O ALA S 12 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE S 35 " --> pdb=" O LEU S 31 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG S 41 " --> pdb=" O GLU S 37 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN S 42 " --> pdb=" O GLY S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 61 removed outlier: 3.517A pdb=" N GLN S 52 " --> pdb=" O LEU S 48 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE S 54 " --> pdb=" O ARG S 50 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE S 55 " --> pdb=" O THR S 51 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU S 59 " --> pdb=" O ILE S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 78 removed outlier: 3.650A pdb=" N MET S 65 " --> pdb=" O ASP S 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 7 through 21 Processing helix chain 'W' and resid 23 through 39 removed outlier: 3.628A pdb=" N LYS W 39 " --> pdb=" O ALA W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 47 removed outlier: 3.578A pdb=" N GLU W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU W 46 " --> pdb=" O GLN W 42 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 64 Processing helix chain 'W' and resid 71 through 83 Processing helix chain 'W' and resid 84 through 86 No H-bonds generated for 'chain 'W' and resid 84 through 86' Processing helix chain 'W' and resid 87 through 103 removed outlier: 3.943A pdb=" N GLU W 93 " --> pdb=" O PRO W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 117 through 132 Processing helix chain 'W' and resid 144 through 147 Processing helix chain 'W' and resid 163 through 174 removed outlier: 4.069A pdb=" N ASP W 172 " --> pdb=" O GLU W 168 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL W 173 " --> pdb=" O ARG W 169 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU W 174 " --> pdb=" O LEU W 170 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 23 removed outlier: 4.165A pdb=" N GLY X 9 " --> pdb=" O ALA X 5 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA X 11 " --> pdb=" O ILE X 7 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 136 removed outlier: 3.678A pdb=" N ILE X 40 " --> pdb=" O ARG X 36 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA X 59 " --> pdb=" O ASP X 55 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS X 122 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) Processing helix chain 'X' and resid 145 through 156 removed outlier: 3.615A pdb=" N LEU X 156 " --> pdb=" O LEU X 152 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 25 Processing helix chain 'Y' and resid 27 through 38 removed outlier: 4.065A pdb=" N ALA Y 31 " --> pdb=" O PRO Y 27 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA Y 32 " --> pdb=" O PRO Y 28 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 140 removed outlier: 3.947A pdb=" N ALA Y 103 " --> pdb=" O THR Y 99 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG Y 138 " --> pdb=" O LYS Y 134 " (cutoff:3.500A) Processing helix chain 'Y' and resid 143 through 156 Processing helix chain 'a' and resid 7 through 16 removed outlier: 3.639A pdb=" N HIS a 14 " --> pdb=" O ASP a 10 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS a 15 " --> pdb=" O TYR a 11 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 67 removed outlier: 3.509A pdb=" N LYS a 66 " --> pdb=" O SER a 62 " (cutoff:3.500A) Processing helix chain 'a' and resid 73 through 94 removed outlier: 3.606A pdb=" N ALA a 78 " --> pdb=" O LYS a 74 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP a 92 " --> pdb=" O GLY a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 118 removed outlier: 3.557A pdb=" N MET a 118 " --> pdb=" O LEU a 114 " (cutoff:3.500A) Processing helix chain 'a' and resid 119 through 121 No H-bonds generated for 'chain 'a' and resid 119 through 121' Processing helix chain 'a' and resid 124 through 132 Processing helix chain 'a' and resid 142 through 145 Processing helix chain 'a' and resid 146 through 181 removed outlier: 4.035A pdb=" N THR a 150 " --> pdb=" O ASP a 146 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE a 171 " --> pdb=" O LYS a 167 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N GLY a 172 " --> pdb=" O MET a 168 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY a 173 " --> pdb=" O LYS a 169 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS a 176 " --> pdb=" O GLY a 172 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN a 181 " --> pdb=" O GLU a 177 " (cutoff:3.500A) Processing helix chain 'a' and resid 185 through 187 No H-bonds generated for 'chain 'a' and resid 185 through 187' Processing helix chain 'a' and resid 188 through 229 removed outlier: 3.772A pdb=" N ILE a 194 " --> pdb=" O PRO a 190 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU a 195 " --> pdb=" O VAL a 191 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL a 198 " --> pdb=" O ILE a 194 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS a 203 " --> pdb=" O SER a 199 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 3.757A pdb=" N LEU a 229 " --> pdb=" O ILE a 225 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 269 removed outlier: 3.785A pdb=" N ILE a 236 " --> pdb=" O TRP a 232 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 3.875A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 35 removed outlier: 6.396A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 43 current: chain 'A' and resid 59 through 66 removed outlier: 6.078A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 71 through 75 current: chain 'D' and resid 12 through 16 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 12 through 16 current: chain 'D' and resid 36 through 45 removed outlier: 6.686A pdb=" N ARG D 52 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLN D 45 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE D 50 " --> pdb=" O GLN D 45 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 50 through 55 current: chain 'F' and resid 12 through 16 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 12 through 16 current: chain 'F' and resid 36 through 46 removed outlier: 6.772A pdb=" N ARG F 52 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N GLN F 45 " --> pdb=" O ILE F 50 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ILE F 50 " --> pdb=" O GLN F 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 3.751A pdb=" N GLY A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 109 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 107 through 109 current: chain 'A' and resid 221 through 226 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 221 through 226 current: chain 'A' and resid 322 through 331 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 322 through 331 current: chain 'A' and resid 374 through 375 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 26 through 35 removed outlier: 6.562A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 43 current: chain 'B' and resid 60 through 66 removed outlier: 6.491A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 71 through 75 current: chain 'E' and resid 12 through 16 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 12 through 16 current: chain 'E' and resid 36 through 45 removed outlier: 6.890A pdb=" N ARG E 52 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLN E 45 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE E 50 " --> pdb=" O GLN E 45 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 50 through 55 current: chain 'W' and resid 135 through 142 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 135 through 142 current: chain 'W' and resid 157 through 162 Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 109 removed outlier: 6.467A pdb=" N LYS B 192 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ILE B 259 " --> pdb=" O LYS B 192 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE B 194 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 28 through 35 removed outlier: 6.508A pdb=" N ARG C 40 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL C 34 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 98 Processing sheet with id=AA9, first strand: chain 'C' and resid 107 through 109 removed outlier: 6.530A pdb=" N LYS C 192 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ILE C 259 " --> pdb=" O LYS C 192 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE C 194 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ASP C 261 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL C 196 " --> pdb=" O ASP C 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 329 through 331 removed outlier: 6.500A pdb=" N ILE C 167 " --> pdb=" O ILE C 330 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU C 166 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N LEU C 355 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE C 168 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.706A pdb=" N GLU D 105 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 87 through 88 removed outlier: 6.453A pdb=" N MET D 88 " --> pdb=" O TYR D 206 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLN D 208 " --> pdb=" O MET D 88 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL D 237 " --> pdb=" O THR D 291 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL D 293 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU D 239 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ALA D 295 " --> pdb=" O LEU D 239 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL D 241 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL D 145 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS D 144 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N VAL D 319 " --> pdb=" O LYS D 144 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLY D 146 " --> pdb=" O VAL D 319 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 125 through 126 removed outlier: 4.535A pdb=" N PHE D 139 " --> pdb=" O LEU D 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.572A pdb=" N GLU E 105 " --> pdb=" O VAL E 79 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 87 through 88 removed outlier: 6.117A pdb=" N MET E 88 " --> pdb=" O TYR E 206 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL E 237 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL E 293 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU E 239 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ALA E 295 " --> pdb=" O LEU E 239 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL E 241 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N TYR E 297 " --> pdb=" O VAL E 241 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL E 145 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL E 296 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU E 147 " --> pdb=" O VAL E 296 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 76 through 78 Processing sheet with id=AB8, first strand: chain 'F' and resid 87 through 88 removed outlier: 6.129A pdb=" N MET F 88 " --> pdb=" O TYR F 206 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLN F 208 " --> pdb=" O MET F 88 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL F 145 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL F 296 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU F 147 " --> pdb=" O VAL F 296 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 125 through 126 removed outlier: 4.123A pdb=" N PHE F 139 " --> pdb=" O LEU F 126 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 132 through 136 removed outlier: 7.848A pdb=" N VAL G 133 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LEU G 114 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLN G 135 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N MET G 116 " --> pdb=" O GLN G 135 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL G 75 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N ALA G 115 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TYR G 77 " --> pdb=" O ALA G 115 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ILE G 117 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL G 79 " --> pdb=" O ILE G 117 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ARG G 74 " --> pdb=" O LYS G 166 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N TYR G 168 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY G 76 " --> pdb=" O TYR G 168 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL G 170 " --> pdb=" O GLY G 76 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU G 78 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N ASN G 172 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N VAL G 80 " --> pdb=" O ASN G 172 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE G 169 " --> pdb=" O GLN G 186 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N GLN G 186 " --> pdb=" O ILE G 169 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N SER G 171 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ILE G 184 " --> pdb=" O SER G 171 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LYS G 173 " --> pdb=" O PRO G 182 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 207 through 208 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 207 through 208 current: chain 'H' and resid 16 through 26 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 31 through 34 current: chain 'H' and resid 58 through 64 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 58 through 64 current: chain 'H' and resid 75 through 80 Processing sheet with id=AC3, first strand: chain 'a' and resid 20 through 21 removed outlier: 4.519A pdb=" N GLN a 20 " --> pdb=" O VAL a 29 " (cutoff:3.500A) 2174 hydrogen bonds defined for protein. 6348 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.13 Time building geometry restraints manager: 3.75 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: 6791 1.32 - 1.45: 8377 1.45 - 1.57: 21745 1.57 - 1.69: 25 1.69 - 1.82: 356 Bond restraints: 37294 Sorted by residual: bond pdb=" C PRO E 138 " pdb=" O PRO E 138 " ideal model delta sigma weight residual 1.233 1.202 0.031 1.16e-02 7.43e+03 7.10e+00 bond pdb=" N ARG D 24 " pdb=" CA ARG D 24 " ideal model delta sigma weight residual 1.453 1.487 -0.035 1.31e-02 5.83e+03 7.01e+00 bond pdb=" CA ALA E 137 " pdb=" CB ALA E 137 " ideal model delta sigma weight residual 1.530 1.496 0.034 1.32e-02 5.74e+03 6.52e+00 bond pdb=" N ILE E 130 " pdb=" CA ILE E 130 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.25e-02 6.40e+03 5.95e+00 bond pdb=" N SER E 419 " pdb=" CA SER E 419 " ideal model delta sigma weight residual 1.453 1.482 -0.030 1.31e-02 5.83e+03 5.08e+00 ... (remaining 37289 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 48812 2.26 - 4.51: 1488 4.51 - 6.77: 160 6.77 - 9.02: 17 9.02 - 11.28: 8 Bond angle restraints: 50485 Sorted by residual: angle pdb=" C LYS E 131 " pdb=" CA LYS E 131 " pdb=" CB LYS E 131 " ideal model delta sigma weight residual 110.88 100.86 10.02 1.57e+00 4.06e-01 4.07e+01 angle pdb=" C ALA O 62 " pdb=" N ILE O 63 " pdb=" CA ILE O 63 " ideal model delta sigma weight residual 120.24 123.20 -2.96 6.30e-01 2.52e+00 2.21e+01 angle pdb=" N LEU a 125 " pdb=" CA LEU a 125 " pdb=" C LEU a 125 " ideal model delta sigma weight residual 110.97 115.29 -4.32 1.09e+00 8.42e-01 1.57e+01 angle pdb=" CA ILE Q 63 " pdb=" CB ILE Q 63 " pdb=" CG2 ILE Q 63 " ideal model delta sigma weight residual 110.50 116.96 -6.46 1.70e+00 3.46e-01 1.45e+01 angle pdb=" C1' ADP F 500 " pdb=" C2' ADP F 500 " pdb=" C3' ADP F 500 " ideal model delta sigma weight residual 111.00 99.98 11.02 3.00e+00 1.11e-01 1.35e+01 ... (remaining 50480 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.68: 22006 30.68 - 61.37: 567 61.37 - 92.05: 89 92.05 - 122.73: 2 122.73 - 153.42: 2 Dihedral angle restraints: 22666 sinusoidal: 8977 harmonic: 13689 Sorted by residual: 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 300.00 146.59 153.42 1 2.00e+01 2.50e-03 4.55e+01 dihedral pdb=" O1B ADP F 500 " pdb=" O3A ADP F 500 " pdb=" PB ADP F 500 " pdb=" PA ADP F 500 " ideal model delta sinusoidal sigma weight residual 300.00 167.56 132.44 1 2.00e+01 2.50e-03 4.02e+01 dihedral pdb=" O1B ADP D 500 " pdb=" O3A ADP D 500 " pdb=" PB ADP D 500 " pdb=" PA ADP D 500 " ideal model delta sinusoidal sigma weight residual -60.00 -173.19 113.18 1 2.00e+01 2.50e-03 3.34e+01 ... (remaining 22663 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 5799 0.142 - 0.284: 77 0.284 - 0.426: 4 0.426 - 0.567: 0 0.567 - 0.709: 1 Chirality restraints: 5881 Sorted by residual: chirality pdb=" CB ILE Q 63 " pdb=" CA ILE Q 63 " pdb=" CG1 ILE Q 63 " pdb=" CG2 ILE Q 63 " both_signs ideal model delta sigma weight residual False 2.64 1.94 0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" CA THR E 128 " pdb=" N THR E 128 " pdb=" C THR E 128 " pdb=" CB THR E 128 " both_signs ideal model delta sigma weight residual False 2.53 2.88 -0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA LYS E 131 " pdb=" N LYS E 131 " pdb=" C LYS E 131 " pdb=" CB LYS E 131 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.62e+00 ... (remaining 5878 not shown) Planarity restraints: 6510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR G 207 " -0.003 2.00e-02 2.50e+03 2.77e-02 1.53e+01 pdb=" CG TYR G 207 " 0.000 2.00e-02 2.50e+03 pdb=" CD1 TYR G 207 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR G 207 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR G 207 " 0.039 2.00e-02 2.50e+03 pdb=" CE2 TYR G 207 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR G 207 " 0.038 2.00e-02 2.50e+03 pdb=" OH TYR G 207 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 203 " 0.029 2.00e-02 2.50e+03 2.47e-02 1.52e+01 pdb=" CG TRP G 203 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP G 203 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP G 203 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP G 203 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP G 203 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP G 203 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 203 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 203 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP G 203 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 195 " 0.008 2.00e-02 2.50e+03 2.43e-02 1.18e+01 pdb=" CG TYR B 195 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR B 195 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR B 195 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 195 " -0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR B 195 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 195 " -0.032 2.00e-02 2.50e+03 pdb=" OH TYR B 195 " 0.038 2.00e-02 2.50e+03 ... (remaining 6507 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 49 2.51 - 3.11: 27863 3.11 - 3.70: 55187 3.70 - 4.30: 81220 4.30 - 4.90: 133656 Nonbonded interactions: 297975 Sorted by model distance: nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 601 " model vdw 1.911 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 601 " model vdw 1.945 2.170 nonbonded pdb=" O2G ATP A 600 " pdb="MG MG A 601 " model vdw 1.962 2.170 nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.964 2.170 nonbonded pdb=" O2G ATP E 500 " pdb="MG MG E 501 " model vdw 2.083 2.170 ... (remaining 297970 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 2 through 408 or resid 410 through 601)) selection = (chain 'B' and (resid 2 through 408 or resid 410 through 601)) selection = (chain 'C' and (resid 2 through 408 or resid 410 through 601)) } ncs_group { reference = (chain 'D' and resid 2 through 459) selection = (chain 'E' and resid 2 through 459) selection = (chain 'F' and resid 2 through 459) } ncs_group { reference = (chain 'I' and resid 3 through 78) selection = (chain 'J' and resid 3 through 78) selection = (chain 'L' and resid 3 through 78) selection = (chain 'M' and resid 3 through 78) selection = (chain 'N' and resid 3 through 78) selection = (chain 'O' and resid 3 through 78) selection = (chain 'P' and resid 3 through 78) selection = (chain 'Q' and resid 3 through 78) selection = chain 'R' selection = (chain 'S' and resid 3 through 78) } ncs_group { reference = chain 'X' selection = chain 'Y' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 31.250 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 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 : 0.005 0.076 37294 Z= 0.242 Angle : 0.889 11.281 50485 Z= 0.492 Chirality : 0.053 0.709 5881 Planarity : 0.010 0.113 6510 Dihedral : 14.273 153.417 13910 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.63 % Favored : 98.35 % Rotamer: Outliers : 1.26 % Allowed : 6.51 % Favored : 92.24 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 5.03 % 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: -0.19 (0.11), residues: 4775 helix: 0.22 (0.09), residues: 2582 sheet: 0.15 (0.22), residues: 475 loop : -0.52 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.004 ARG C 139 TYR 0.042 0.007 TYR G 207 PHE 0.026 0.003 PHE a 38 TRP 0.064 0.004 TRP G 203 HIS 0.008 0.002 HIS W 21 Details of bonding type rmsd covalent geometry : bond 0.00462 (37294) covalent geometry : angle 0.88914 (50485) hydrogen bonds : bond 0.15083 ( 2174) hydrogen bonds : angle 6.31513 ( 6348) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 658 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ILE cc_start: 0.8937 (mp) cc_final: 0.8537 (mm) REVERT: A 258 ILE cc_start: 0.9124 (tt) cc_final: 0.8806 (tt) REVERT: C 95 LEU cc_start: 0.8904 (tp) cc_final: 0.8615 (tp) REVERT: C 417 THR cc_start: 0.9027 (m) cc_final: 0.8823 (p) REVERT: D 189 PHE cc_start: 0.8829 (t80) cc_final: 0.8383 (t80) REVERT: D 379 MET cc_start: 0.7500 (tpt) cc_final: 0.7083 (tpt) REVERT: D 382 LEU cc_start: 0.8399 (mt) cc_final: 0.7759 (mt) REVERT: D 445 MET cc_start: 0.8770 (mmm) cc_final: 0.8078 (mmm) REVERT: E 136 MET cc_start: 0.9040 (mmm) cc_final: 0.8645 (mmm) REVERT: E 139 PHE cc_start: 0.7594 (OUTLIER) cc_final: 0.7354 (p90) REVERT: E 209 MET cc_start: 0.8931 (ptp) cc_final: 0.8561 (ptp) REVERT: F 79 VAL cc_start: 0.8351 (m) cc_final: 0.8050 (m) REVERT: F 159 MET cc_start: 0.8607 (mtp) cc_final: 0.8164 (tmm) REVERT: F 254 VAL cc_start: 0.9063 (t) cc_final: 0.8839 (p) REVERT: F 342 ARG cc_start: 0.7921 (mtt-85) cc_final: 0.7708 (tpp-160) REVERT: F 379 MET cc_start: 0.9035 (mtp) cc_final: 0.8431 (tpp) REVERT: F 397 GLN cc_start: 0.8956 (tt0) cc_final: 0.8353 (tm-30) REVERT: G 31 MET cc_start: 0.7653 (ttp) cc_final: 0.6716 (tmm) REVERT: G 32 ARG cc_start: 0.8232 (mmt180) cc_final: 0.8016 (mmt180) REVERT: G 48 MET cc_start: 0.8834 (ttm) cc_final: 0.8493 (ttm) REVERT: G 102 MET cc_start: 0.8749 (ttp) cc_final: 0.7982 (ptm) REVERT: H 8 VAL cc_start: 0.8795 (t) cc_final: 0.7749 (p) REVERT: H 61 PHE cc_start: 0.7931 (m-80) cc_final: 0.7617 (m-10) REVERT: I 16 MET cc_start: 0.7541 (ttm) cc_final: 0.6621 (tpt) REVERT: I 53 PHE cc_start: 0.6100 (t80) cc_final: 0.5582 (t80) REVERT: I 54 PHE cc_start: 0.5537 (m-10) cc_final: 0.5166 (t80) REVERT: J 6 MET cc_start: 0.6977 (mtp) cc_final: 0.6733 (pmm) REVERT: J 15 VAL cc_start: 0.7950 (t) cc_final: 0.7710 (p) REVERT: J 16 MET cc_start: 0.6554 (ttt) cc_final: 0.6152 (tpt) REVERT: J 22 ILE cc_start: 0.6836 (mm) cc_final: 0.6606 (mm) REVERT: L 26 ILE cc_start: 0.8569 (mt) cc_final: 0.8328 (mp) REVERT: L 49 LEU cc_start: 0.8490 (mt) cc_final: 0.8262 (mt) REVERT: L 57 MET cc_start: 0.7724 (tmm) cc_final: 0.6264 (ptm) REVERT: M 53 PHE cc_start: 0.8332 (t80) cc_final: 0.7771 (t80) REVERT: M 65 MET cc_start: 0.6298 (mtp) cc_final: 0.5767 (mmt) REVERT: N 31 LEU cc_start: 0.6701 (tp) cc_final: 0.6214 (mt) REVERT: O 6 MET cc_start: 0.5746 (ttm) cc_final: 0.5371 (pmm) REVERT: P 11 MET cc_start: 0.8422 (tpp) cc_final: 0.8025 (mtp) REVERT: Q 63 ILE cc_start: 0.7590 (tt) cc_final: 0.7163 (tt) REVERT: Q 76 PHE cc_start: 0.6962 (m-80) cc_final: 0.6317 (t80) REVERT: R 6 MET cc_start: 0.5805 (mmt) cc_final: 0.5403 (ttm) REVERT: R 68 VAL cc_start: 0.6051 (t) cc_final: 0.5709 (m) REVERT: S 6 MET cc_start: 0.6404 (mmt) cc_final: 0.6118 (pmm) REVERT: S 75 MET cc_start: 0.5173 (ttt) cc_final: 0.4874 (tpt) REVERT: X 49 ARG cc_start: 0.8437 (mtt180) cc_final: 0.8134 (tpt90) REVERT: X 64 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7793 (mm110) REVERT: Y 62 THR cc_start: 0.5997 (m) cc_final: 0.5746 (p) REVERT: Y 99 THR cc_start: 0.8693 (p) cc_final: 0.8481 (p) REVERT: a 46 MET cc_start: 0.2038 (mmm) cc_final: 0.1712 (mtp) outliers start: 48 outliers final: 9 residues processed: 699 average time/residue: 0.2341 time to fit residues: 261.9230 Evaluate side-chains 374 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 364 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 139 PHE Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain a residue 193 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 432 optimal weight: 30.0000 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 10.0000 chunk 455 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 4.9990 chunk 470 optimal weight: 5.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 HIS B 215 HIS B 294 HIS C 147 GLN ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 GLN E 197 ASN E 294 GLN E 353 HIS E 437 HIS ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 GLN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 67 GLN W 73 GLN X 10 GLN Y 123 GLN a 14 HIS a 132 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.059945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.043606 restraints weight = 244219.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.044389 restraints weight = 138736.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.044831 restraints weight = 83705.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.044957 restraints weight = 68084.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.044997 restraints weight = 58549.693| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 37294 Z= 0.213 Angle : 0.722 11.809 50485 Z= 0.376 Chirality : 0.046 0.467 5881 Planarity : 0.005 0.056 6510 Dihedral : 7.564 134.696 5344 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.45 % Favored : 98.53 % Rotamer: Outliers : 2.10 % Allowed : 10.70 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.42 (0.12), residues: 4775 helix: 0.87 (0.10), residues: 2613 sheet: 0.04 (0.21), residues: 529 loop : -0.44 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG X 113 TYR 0.016 0.002 TYR A 236 PHE 0.023 0.002 PHE Q 53 TRP 0.022 0.002 TRP G 203 HIS 0.007 0.001 HIS X 51 Details of bonding type rmsd covalent geometry : bond 0.00450 (37294) covalent geometry : angle 0.72184 (50485) hydrogen bonds : bond 0.06591 ( 2174) hydrogen bonds : angle 4.93163 ( 6348) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 379 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8241 (mtp) REVERT: A 198 ILE cc_start: 0.9254 (mp) cc_final: 0.8846 (mm) REVERT: B 148 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8517 (t) REVERT: C 262 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.8053 (t0) REVERT: D 136 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8663 (mmm) REVERT: D 274 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7528 (mt-10) REVERT: D 379 MET cc_start: 0.8030 (tpt) cc_final: 0.7673 (tpt) REVERT: D 382 LEU cc_start: 0.8586 (mt) cc_final: 0.8331 (mt) REVERT: D 445 MET cc_start: 0.8922 (mmm) cc_final: 0.8205 (mmm) REVERT: F 79 VAL cc_start: 0.8367 (m) cc_final: 0.7705 (m) REVERT: F 159 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8328 (tmm) REVERT: F 358 ARG cc_start: 0.8220 (ttt180) cc_final: 0.7722 (mmm-85) REVERT: F 379 MET cc_start: 0.9244 (mtp) cc_final: 0.8636 (tpp) REVERT: F 397 GLN cc_start: 0.9006 (tt0) cc_final: 0.8521 (tm-30) REVERT: F 431 MET cc_start: 0.8338 (mtp) cc_final: 0.7359 (ptp) REVERT: G 48 MET cc_start: 0.8811 (ttm) cc_final: 0.8322 (ttm) REVERT: G 78 LEU cc_start: 0.9213 (tp) cc_final: 0.8987 (tp) REVERT: G 102 MET cc_start: 0.8786 (ttp) cc_final: 0.7946 (tmm) REVERT: H 61 PHE cc_start: 0.7991 (m-80) cc_final: 0.7777 (m-10) REVERT: I 10 TYR cc_start: 0.7912 (OUTLIER) cc_final: 0.7382 (m-80) REVERT: I 16 MET cc_start: 0.7402 (ttm) cc_final: 0.6962 (tpt) REVERT: I 53 PHE cc_start: 0.6906 (t80) cc_final: 0.5458 (t80) REVERT: I 54 PHE cc_start: 0.5939 (m-10) cc_final: 0.5193 (t80) REVERT: I 75 MET cc_start: 0.3502 (mmm) cc_final: 0.3278 (mmm) REVERT: J 11 MET cc_start: 0.6328 (tpp) cc_final: 0.6123 (mmp) REVERT: J 16 MET cc_start: 0.6230 (ttt) cc_final: 0.5729 (ttt) REVERT: L 11 MET cc_start: 0.7975 (mtp) cc_final: 0.6286 (tpt) REVERT: L 16 MET cc_start: 0.5774 (mmm) cc_final: 0.5178 (tpt) REVERT: L 49 LEU cc_start: 0.8352 (mt) cc_final: 0.7970 (tp) REVERT: L 57 MET cc_start: 0.7936 (tmm) cc_final: 0.6629 (ptm) REVERT: M 55 ILE cc_start: 0.8448 (mm) cc_final: 0.8158 (pt) REVERT: M 65 MET cc_start: 0.6381 (mtp) cc_final: 0.5935 (mmt) REVERT: M 68 VAL cc_start: 0.7139 (t) cc_final: 0.6358 (p) REVERT: P 11 MET cc_start: 0.8179 (tpp) cc_final: 0.7845 (mtp) REVERT: P 16 MET cc_start: 0.5427 (mtt) cc_final: 0.5014 (mtt) REVERT: Q 76 PHE cc_start: 0.7251 (m-80) cc_final: 0.6341 (t80) REVERT: R 6 MET cc_start: 0.6011 (mmt) cc_final: 0.5510 (ttm) REVERT: S 6 MET cc_start: 0.6367 (mmt) cc_final: 0.6028 (pmm) REVERT: S 75 MET cc_start: 0.5437 (ttt) cc_final: 0.4835 (tpt) REVERT: W 157 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.8051 (mmm) REVERT: X 49 ARG cc_start: 0.8637 (mtt180) cc_final: 0.8193 (tpt90) REVERT: X 64 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7854 (mm-40) REVERT: X 73 GLN cc_start: 0.8728 (mm110) cc_final: 0.8499 (mm-40) REVERT: X 83 ARG cc_start: 0.8443 (ttp80) cc_final: 0.8170 (tmm-80) REVERT: a 89 SER cc_start: 0.7775 (m) cc_final: 0.7385 (p) REVERT: a 155 LEU cc_start: 0.7248 (mt) cc_final: 0.6980 (pp) outliers start: 80 outliers final: 33 residues processed: 432 average time/residue: 0.2156 time to fit residues: 154.5378 Evaluate side-chains 353 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 313 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain I residue 10 TYR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain O residue 5 ASN Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 157 MET Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain a residue 56 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 85 optimal weight: 0.8980 chunk 101 optimal weight: 9.9990 chunk 172 optimal weight: 6.9990 chunk 341 optimal weight: 5.9990 chunk 222 optimal weight: 10.0000 chunk 275 optimal weight: 0.9990 chunk 460 optimal weight: 20.0000 chunk 131 optimal weight: 10.0000 chunk 376 optimal weight: 0.7980 chunk 55 optimal weight: 10.0000 chunk 236 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 HIS A 65 ASN ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 GLN ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 HIS ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 GLN ** X 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.059713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.043249 restraints weight = 245991.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.044033 restraints weight = 148623.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.044871 restraints weight = 87834.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.044943 restraints weight = 62600.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.044949 restraints weight = 53892.026| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 37294 Z= 0.162 Angle : 0.629 9.803 50485 Z= 0.326 Chirality : 0.043 0.281 5881 Planarity : 0.004 0.063 6510 Dihedral : 7.016 129.834 5336 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.45 % Favored : 98.53 % Rotamer: Outliers : 1.92 % Allowed : 12.41 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.87 (0.12), residues: 4775 helix: 1.31 (0.10), residues: 2616 sheet: 0.05 (0.20), residues: 547 loop : -0.32 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 50 TYR 0.017 0.001 TYR J 73 PHE 0.037 0.002 PHE Q 53 TRP 0.015 0.001 TRP a 111 HIS 0.006 0.001 HIS W 21 Details of bonding type rmsd covalent geometry : bond 0.00333 (37294) covalent geometry : angle 0.62863 (50485) hydrogen bonds : bond 0.05866 ( 2174) hydrogen bonds : angle 4.61616 ( 6348) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 337 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 494 ASP cc_start: 0.8521 (m-30) cc_final: 0.7952 (p0) REVERT: C 262 ASP cc_start: 0.8205 (m-30) cc_final: 0.7823 (t0) REVERT: D 274 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7357 (mt-10) REVERT: D 379 MET cc_start: 0.7971 (tpt) cc_final: 0.7612 (tpt) REVERT: D 382 LEU cc_start: 0.8653 (mt) cc_final: 0.8372 (mt) REVERT: D 445 MET cc_start: 0.8913 (mmm) cc_final: 0.8137 (mmm) REVERT: E 209 MET cc_start: 0.9207 (ptp) cc_final: 0.8912 (ptp) REVERT: F 159 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8308 (tmm) REVERT: F 209 MET cc_start: 0.8625 (mtp) cc_final: 0.8143 (mmm) REVERT: F 358 ARG cc_start: 0.8278 (ttt180) cc_final: 0.7840 (mmm-85) REVERT: F 379 MET cc_start: 0.9201 (mtp) cc_final: 0.8492 (tpp) REVERT: F 397 GLN cc_start: 0.9029 (tt0) cc_final: 0.8540 (tm-30) REVERT: F 431 MET cc_start: 0.7630 (mtp) cc_final: 0.7315 (ptp) REVERT: F 445 MET cc_start: 0.7007 (mmt) cc_final: 0.6642 (mmp) REVERT: G 31 MET cc_start: 0.7862 (tmm) cc_final: 0.7626 (ppp) REVERT: G 48 MET cc_start: 0.8833 (ttm) cc_final: 0.8348 (ttm) REVERT: G 78 LEU cc_start: 0.9193 (tp) cc_final: 0.8865 (tt) REVERT: G 102 MET cc_start: 0.8764 (ttp) cc_final: 0.7892 (tmm) REVERT: G 243 MET cc_start: 0.8925 (ttp) cc_final: 0.8699 (ttp) REVERT: H 50 ILE cc_start: 0.9027 (pt) cc_final: 0.8808 (pp) REVERT: I 10 TYR cc_start: 0.7929 (OUTLIER) cc_final: 0.7368 (m-80) REVERT: I 22 ILE cc_start: 0.7178 (mp) cc_final: 0.6863 (mt) REVERT: I 53 PHE cc_start: 0.6450 (t80) cc_final: 0.5515 (t80) REVERT: I 54 PHE cc_start: 0.5980 (m-10) cc_final: 0.5352 (t80) REVERT: I 57 MET cc_start: 0.3940 (mtm) cc_final: 0.3729 (mtp) REVERT: J 11 MET cc_start: 0.6327 (tpp) cc_final: 0.6106 (tpp) REVERT: L 11 MET cc_start: 0.7877 (mtp) cc_final: 0.5908 (tpt) REVERT: L 49 LEU cc_start: 0.8360 (mt) cc_final: 0.8023 (tp) REVERT: L 57 MET cc_start: 0.7797 (tmm) cc_final: 0.6699 (ptm) REVERT: L 75 MET cc_start: 0.8013 (tpp) cc_final: 0.6856 (tpp) REVERT: M 55 ILE cc_start: 0.8458 (mm) cc_final: 0.8194 (pt) REVERT: M 65 MET cc_start: 0.6561 (mtp) cc_final: 0.6114 (mmt) REVERT: M 68 VAL cc_start: 0.6934 (t) cc_final: 0.6604 (p) REVERT: P 57 MET cc_start: 0.4825 (ppp) cc_final: 0.4344 (ttm) REVERT: Q 16 MET cc_start: 0.1887 (tpp) cc_final: 0.1664 (tpp) REVERT: Q 75 MET cc_start: 0.5919 (mmt) cc_final: 0.5585 (mmt) REVERT: Q 76 PHE cc_start: 0.7078 (m-80) cc_final: 0.6146 (t80) REVERT: R 6 MET cc_start: 0.6259 (mmt) cc_final: 0.5697 (ttm) REVERT: S 75 MET cc_start: 0.5394 (ttt) cc_final: 0.4762 (tpt) REVERT: W 157 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7983 (mmm) REVERT: X 49 ARG cc_start: 0.8664 (mtt180) cc_final: 0.8217 (tpt90) REVERT: X 64 GLN cc_start: 0.8085 (mm-40) cc_final: 0.7862 (mm-40) REVERT: X 73 GLN cc_start: 0.8719 (mm110) cc_final: 0.8485 (mm-40) REVERT: X 83 ARG cc_start: 0.8391 (ttp80) cc_final: 0.8180 (ttp80) REVERT: a 46 MET cc_start: 0.2610 (mmm) cc_final: 0.2350 (mmt) REVERT: a 155 LEU cc_start: 0.7255 (mt) cc_final: 0.6637 (tt) outliers start: 73 outliers final: 31 residues processed: 390 average time/residue: 0.2182 time to fit residues: 142.6472 Evaluate side-chains 340 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 306 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain I residue 10 TYR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain O residue 5 ASN Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain W residue 143 ASP Chi-restraints excluded: chain W residue 157 MET Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 149 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 257 optimal weight: 6.9990 chunk 450 optimal weight: 20.0000 chunk 363 optimal weight: 0.0670 chunk 82 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 426 optimal weight: 9.9990 chunk 297 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 408 optimal weight: 20.0000 chunk 220 optimal weight: 3.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 GLN ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 GLN ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 5 ASN S 42 GLN ** X 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.058868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.042335 restraints weight = 245629.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.043452 restraints weight = 135598.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.043616 restraints weight = 86667.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.043961 restraints weight = 60486.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.044016 restraints weight = 55394.962| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 37294 Z= 0.166 Angle : 0.620 9.323 50485 Z= 0.318 Chirality : 0.042 0.286 5881 Planarity : 0.004 0.066 6510 Dihedral : 6.632 110.505 5331 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.84 % Favored : 98.14 % Rotamer: Outliers : 2.33 % Allowed : 13.12 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 1.11 (0.12), residues: 4775 helix: 1.53 (0.10), residues: 2622 sheet: 0.11 (0.21), residues: 524 loop : -0.26 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 140 TYR 0.024 0.001 TYR S 73 PHE 0.025 0.002 PHE Q 53 TRP 0.012 0.001 TRP a 111 HIS 0.006 0.001 HIS W 21 Details of bonding type rmsd covalent geometry : bond 0.00350 (37294) covalent geometry : angle 0.62026 (50485) hydrogen bonds : bond 0.05475 ( 2174) hydrogen bonds : angle 4.47988 ( 6348) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 320 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.9381 (mmt) cc_final: 0.8943 (mmt) REVERT: A 225 VAL cc_start: 0.8379 (OUTLIER) cc_final: 0.8145 (m) REVERT: B 494 ASP cc_start: 0.8603 (m-30) cc_final: 0.7940 (p0) REVERT: C 262 ASP cc_start: 0.8182 (m-30) cc_final: 0.7902 (t0) REVERT: D 274 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7349 (mt-10) REVERT: D 379 MET cc_start: 0.8121 (tpt) cc_final: 0.7807 (tpt) REVERT: D 382 LEU cc_start: 0.8644 (mt) cc_final: 0.8397 (mt) REVERT: D 445 MET cc_start: 0.8865 (mmm) cc_final: 0.8176 (mmm) REVERT: F 159 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8299 (tmm) REVERT: F 379 MET cc_start: 0.9103 (mtp) cc_final: 0.8497 (tpp) REVERT: F 397 GLN cc_start: 0.9004 (tt0) cc_final: 0.8487 (tm-30) REVERT: F 431 MET cc_start: 0.7610 (mtp) cc_final: 0.7369 (mtm) REVERT: F 445 MET cc_start: 0.7111 (mmt) cc_final: 0.6735 (mmm) REVERT: G 31 MET cc_start: 0.7966 (tmm) cc_final: 0.7762 (tmm) REVERT: G 48 MET cc_start: 0.8971 (ttm) cc_final: 0.8421 (ttm) REVERT: G 78 LEU cc_start: 0.9127 (tp) cc_final: 0.8779 (tt) REVERT: G 102 MET cc_start: 0.8766 (ttp) cc_final: 0.8010 (tmm) REVERT: H 49 MET cc_start: 0.6978 (tpp) cc_final: 0.6618 (tpp) REVERT: I 10 TYR cc_start: 0.8151 (OUTLIER) cc_final: 0.7639 (m-80) REVERT: I 53 PHE cc_start: 0.6360 (t80) cc_final: 0.5404 (t80) REVERT: I 54 PHE cc_start: 0.6014 (m-10) cc_final: 0.5229 (t80) REVERT: I 57 MET cc_start: 0.4147 (mtm) cc_final: 0.3941 (mtp) REVERT: I 75 MET cc_start: 0.3875 (mmm) cc_final: 0.3487 (mmm) REVERT: J 16 MET cc_start: 0.5562 (ttt) cc_final: 0.5326 (ttt) REVERT: J 37 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8285 (mm-30) REVERT: L 11 MET cc_start: 0.7766 (mtp) cc_final: 0.6126 (tpt) REVERT: L 16 MET cc_start: 0.4149 (tpt) cc_final: 0.3735 (tpp) REVERT: L 49 LEU cc_start: 0.8431 (mt) cc_final: 0.8080 (tp) REVERT: L 57 MET cc_start: 0.7708 (tmm) cc_final: 0.6666 (ptm) REVERT: L 75 MET cc_start: 0.7937 (tpp) cc_final: 0.7711 (mmt) REVERT: M 17 MET cc_start: 0.5424 (tpp) cc_final: 0.5039 (tpp) REVERT: M 53 PHE cc_start: 0.7953 (t80) cc_final: 0.7732 (t80) REVERT: M 55 ILE cc_start: 0.8573 (mm) cc_final: 0.8357 (pt) REVERT: M 65 MET cc_start: 0.6515 (mtp) cc_final: 0.5982 (mmp) REVERT: M 68 VAL cc_start: 0.6765 (t) cc_final: 0.6349 (p) REVERT: N 11 MET cc_start: 0.7344 (mmm) cc_final: 0.7019 (mmm) REVERT: N 16 MET cc_start: 0.3053 (tpp) cc_final: 0.2820 (tpp) REVERT: O 11 MET cc_start: 0.5649 (tpp) cc_final: 0.5268 (tpp) REVERT: O 16 MET cc_start: 0.8446 (tpt) cc_final: 0.7833 (tpt) REVERT: P 11 MET cc_start: 0.7440 (mtt) cc_final: 0.6816 (tpp) REVERT: P 17 MET cc_start: 0.3771 (mmt) cc_final: 0.2923 (ttm) REVERT: P 57 MET cc_start: 0.5185 (ppp) cc_final: 0.4351 (ttm) REVERT: R 6 MET cc_start: 0.6074 (mmt) cc_final: 0.5578 (ttm) REVERT: S 57 MET cc_start: 0.7910 (tpt) cc_final: 0.7132 (tmm) REVERT: S 75 MET cc_start: 0.5554 (ttt) cc_final: 0.4954 (tpp) REVERT: X 49 ARG cc_start: 0.8619 (mtt180) cc_final: 0.8176 (tpt90) REVERT: X 62 THR cc_start: 0.7612 (m) cc_final: 0.7254 (m) REVERT: X 64 GLN cc_start: 0.8228 (mm-40) cc_final: 0.8013 (mm-40) REVERT: a 114 LEU cc_start: 0.8377 (mt) cc_final: 0.7892 (tp) REVERT: a 115 MET cc_start: 0.6523 (ttp) cc_final: 0.6088 (ttp) REVERT: a 155 LEU cc_start: 0.7652 (mt) cc_final: 0.7214 (tt) REVERT: a 257 MET cc_start: 0.6839 (tmm) cc_final: 0.6469 (tmm) outliers start: 89 outliers final: 47 residues processed: 390 average time/residue: 0.2110 time to fit residues: 139.3410 Evaluate side-chains 344 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 294 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain I residue 10 TYR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain O residue 5 ASN Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain W residue 143 ASP Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain Y residue 55 ASP Chi-restraints excluded: chain Y residue 99 THR Chi-restraints excluded: chain a residue 37 THR Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 89 SER Chi-restraints excluded: chain a residue 139 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 452 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 372 optimal weight: 30.0000 chunk 195 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 346 optimal weight: 3.9990 chunk 459 optimal weight: 0.8980 chunk 183 optimal weight: 0.2980 chunk 150 optimal weight: 10.0000 chunk 284 optimal weight: 0.9980 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 HIS ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 GLN D 208 GLN ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 GLN W 71 ASN ** X 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 18 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.059007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.042405 restraints weight = 246192.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.043578 restraints weight = 135164.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.043711 restraints weight = 83844.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.043986 restraints weight = 61732.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.044147 restraints weight = 55138.794| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 37294 Z= 0.137 Angle : 0.595 11.366 50485 Z= 0.302 Chirality : 0.042 0.282 5881 Planarity : 0.004 0.068 6510 Dihedral : 6.351 97.810 5330 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.65 % Favored : 98.32 % Rotamer: Outliers : 1.94 % Allowed : 13.90 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.12), residues: 4775 helix: 1.75 (0.10), residues: 2610 sheet: 0.17 (0.22), residues: 506 loop : -0.22 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG X 83 TYR 0.013 0.001 TYR H 35 PHE 0.034 0.001 PHE J 54 TRP 0.008 0.001 TRP a 232 HIS 0.006 0.001 HIS W 21 Details of bonding type rmsd covalent geometry : bond 0.00284 (37294) covalent geometry : angle 0.59486 (50485) hydrogen bonds : bond 0.05181 ( 2174) hydrogen bonds : angle 4.32989 ( 6348) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 310 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8408 (mp) REVERT: A 156 MET cc_start: 0.9400 (mmt) cc_final: 0.9062 (mmt) REVERT: B 439 MET cc_start: 0.8215 (tmm) cc_final: 0.7993 (ppp) REVERT: C 262 ASP cc_start: 0.8151 (m-30) cc_final: 0.7847 (t0) REVERT: D 274 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7327 (mt-10) REVERT: D 445 MET cc_start: 0.8844 (mmm) cc_final: 0.8196 (mmm) REVERT: E 445 MET cc_start: 0.7952 (mmm) cc_final: 0.7548 (mmm) REVERT: F 159 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8314 (tmm) REVERT: F 379 MET cc_start: 0.9111 (mtp) cc_final: 0.8549 (tpp) REVERT: F 397 GLN cc_start: 0.8988 (tt0) cc_final: 0.8439 (tm-30) REVERT: F 445 MET cc_start: 0.7099 (mmt) cc_final: 0.6799 (mmm) REVERT: G 48 MET cc_start: 0.8930 (ttm) cc_final: 0.8375 (ttm) REVERT: G 78 LEU cc_start: 0.9105 (tp) cc_final: 0.8770 (tt) REVERT: G 102 MET cc_start: 0.8733 (ttp) cc_final: 0.7909 (tmm) REVERT: H 49 MET cc_start: 0.6748 (tpp) cc_final: 0.6499 (tpp) REVERT: I 6 MET cc_start: 0.6099 (mmt) cc_final: 0.5090 (tmm) REVERT: I 10 TYR cc_start: 0.8142 (OUTLIER) cc_final: 0.7357 (m-80) REVERT: I 45 LEU cc_start: 0.6066 (tp) cc_final: 0.5735 (mm) REVERT: I 54 PHE cc_start: 0.5928 (m-10) cc_final: 0.5498 (t80) REVERT: I 75 MET cc_start: 0.3508 (mmm) cc_final: 0.3160 (mmm) REVERT: J 11 MET cc_start: 0.3659 (mmp) cc_final: 0.1831 (tpp) REVERT: J 16 MET cc_start: 0.5589 (ttt) cc_final: 0.5240 (ttt) REVERT: J 65 MET cc_start: 0.7496 (mmt) cc_final: 0.7096 (mtt) REVERT: L 11 MET cc_start: 0.7671 (mtp) cc_final: 0.6032 (tpt) REVERT: L 49 LEU cc_start: 0.8479 (mt) cc_final: 0.8171 (tp) REVERT: L 57 MET cc_start: 0.7697 (tmm) cc_final: 0.6702 (ptm) REVERT: M 35 PHE cc_start: 0.6424 (t80) cc_final: 0.6113 (t80) REVERT: M 53 PHE cc_start: 0.8035 (t80) cc_final: 0.7791 (t80) REVERT: M 55 ILE cc_start: 0.8591 (mm) cc_final: 0.8342 (pt) REVERT: M 65 MET cc_start: 0.6533 (mtp) cc_final: 0.6088 (mmp) REVERT: M 68 VAL cc_start: 0.7035 (t) cc_final: 0.6649 (t) REVERT: N 11 MET cc_start: 0.7437 (mmm) cc_final: 0.7158 (mmm) REVERT: P 57 MET cc_start: 0.5300 (ppp) cc_final: 0.4558 (ttm) REVERT: Q 34 LYS cc_start: 0.6318 (mmpt) cc_final: 0.6111 (mmmt) REVERT: R 6 MET cc_start: 0.5926 (mmt) cc_final: 0.5406 (ttm) REVERT: S 16 MET cc_start: 0.7531 (tpt) cc_final: 0.7262 (mmm) REVERT: S 57 MET cc_start: 0.8013 (tpt) cc_final: 0.7277 (tmm) REVERT: S 75 MET cc_start: 0.5642 (ttt) cc_final: 0.5098 (tpp) REVERT: X 49 ARG cc_start: 0.8579 (mtt180) cc_final: 0.8151 (tpt90) REVERT: a 46 MET cc_start: 0.2816 (mmm) cc_final: 0.2586 (mmt) REVERT: a 155 LEU cc_start: 0.7774 (mt) cc_final: 0.7399 (tt) REVERT: a 201 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7761 (pp) REVERT: a 257 MET cc_start: 0.6931 (tmm) cc_final: 0.6709 (tmm) outliers start: 74 outliers final: 41 residues processed: 368 average time/residue: 0.1999 time to fit residues: 127.0546 Evaluate side-chains 337 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 292 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain I residue 10 TYR Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain O residue 5 ASN Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain Y residue 99 THR Chi-restraints excluded: chain a residue 37 THR Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 89 SER Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain a residue 149 VAL Chi-restraints excluded: chain a residue 201 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 146 optimal weight: 6.9990 chunk 418 optimal weight: 6.9990 chunk 296 optimal weight: 10.0000 chunk 372 optimal weight: 20.0000 chunk 210 optimal weight: 9.9990 chunk 424 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 269 optimal weight: 5.9990 chunk 358 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 442 optimal weight: 0.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 GLN C 358 ASN D 32 GLN G 57 HIS H 5 HIS ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN ** Y 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.057050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.040650 restraints weight = 250493.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.041673 restraints weight = 146259.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.042076 restraints weight = 81699.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.042192 restraints weight = 65642.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.042185 restraints weight = 60840.957| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 37294 Z= 0.223 Angle : 0.674 13.661 50485 Z= 0.343 Chirality : 0.043 0.284 5881 Planarity : 0.005 0.072 6510 Dihedral : 6.477 104.640 5330 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.41 % Allowed : 14.43 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 1.11 (0.12), residues: 4775 helix: 1.61 (0.10), residues: 2607 sheet: -0.05 (0.21), residues: 525 loop : -0.34 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 246 TYR 0.027 0.002 TYR L 10 PHE 0.029 0.002 PHE Q 53 TRP 0.015 0.002 TRP a 232 HIS 0.008 0.001 HIS W 21 Details of bonding type rmsd covalent geometry : bond 0.00482 (37294) covalent geometry : angle 0.67360 (50485) hydrogen bonds : bond 0.05462 ( 2174) hydrogen bonds : angle 4.56911 ( 6348) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 290 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8583 (mp) REVERT: A 156 MET cc_start: 0.9447 (mmt) cc_final: 0.9008 (mmt) REVERT: C 262 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7962 (t0) REVERT: D 379 MET cc_start: 0.8270 (tpt) cc_final: 0.8070 (tpt) REVERT: D 445 MET cc_start: 0.8898 (mmm) cc_final: 0.8113 (mmm) REVERT: F 159 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8327 (tmm) REVERT: F 379 MET cc_start: 0.9319 (mtp) cc_final: 0.8417 (tpp) REVERT: F 397 GLN cc_start: 0.8915 (tt0) cc_final: 0.8357 (tm-30) REVERT: G 25 MET cc_start: 0.8231 (tpp) cc_final: 0.7932 (tpp) REVERT: G 48 MET cc_start: 0.9060 (ttm) cc_final: 0.8425 (ttm) REVERT: G 78 LEU cc_start: 0.9148 (tp) cc_final: 0.8773 (tt) REVERT: G 102 MET cc_start: 0.8780 (ttp) cc_final: 0.8039 (tmm) REVERT: G 243 MET cc_start: 0.9272 (tpp) cc_final: 0.8885 (tpp) REVERT: H 49 MET cc_start: 0.7169 (tpp) cc_final: 0.6892 (tpp) REVERT: I 6 MET cc_start: 0.5700 (mmt) cc_final: 0.5488 (mpp) REVERT: I 10 TYR cc_start: 0.8083 (OUTLIER) cc_final: 0.7594 (m-80) REVERT: I 54 PHE cc_start: 0.6054 (m-10) cc_final: 0.5649 (t80) REVERT: I 75 MET cc_start: 0.3446 (mmm) cc_final: 0.3180 (mmm) REVERT: J 11 MET cc_start: 0.3638 (mmp) cc_final: 0.1848 (tpp) REVERT: J 17 MET cc_start: 0.8298 (ptp) cc_final: 0.7679 (mpp) REVERT: J 65 MET cc_start: 0.7738 (mmt) cc_final: 0.7336 (mmt) REVERT: L 11 MET cc_start: 0.7722 (mtp) cc_final: 0.6026 (tpt) REVERT: L 49 LEU cc_start: 0.8449 (mt) cc_final: 0.8155 (tp) REVERT: L 57 MET cc_start: 0.7730 (tmm) cc_final: 0.6653 (ptm) REVERT: M 65 MET cc_start: 0.6620 (mtp) cc_final: 0.6047 (mmp) REVERT: M 68 VAL cc_start: 0.6898 (t) cc_final: 0.6606 (t) REVERT: N 11 MET cc_start: 0.7403 (mmm) cc_final: 0.7061 (mmp) REVERT: N 65 MET cc_start: 0.6632 (mmp) cc_final: 0.5532 (tpt) REVERT: O 16 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7853 (tpt) REVERT: P 11 MET cc_start: 0.7396 (mtp) cc_final: 0.6990 (tpp) REVERT: P 57 MET cc_start: 0.5088 (ppp) cc_final: 0.4324 (ttm) REVERT: R 6 MET cc_start: 0.6078 (mmt) cc_final: 0.5515 (ttm) REVERT: R 65 MET cc_start: 0.5020 (OUTLIER) cc_final: 0.4488 (mtt) REVERT: S 57 MET cc_start: 0.7993 (tpt) cc_final: 0.7209 (tmm) REVERT: S 75 MET cc_start: 0.5395 (ttt) cc_final: 0.4758 (tpp) REVERT: X 49 ARG cc_start: 0.8644 (mtt180) cc_final: 0.8157 (ttp80) REVERT: X 53 ASP cc_start: 0.7944 (t0) cc_final: 0.7683 (t0) REVERT: X 141 ASP cc_start: 0.8490 (p0) cc_final: 0.8163 (t0) REVERT: a 93 MET cc_start: 0.7977 (tmm) cc_final: 0.7467 (tmm) REVERT: a 155 LEU cc_start: 0.7926 (mt) cc_final: 0.7676 (tt) REVERT: a 201 LEU cc_start: 0.8307 (tt) cc_final: 0.7943 (pp) REVERT: a 215 MET cc_start: 0.6231 (mmm) cc_final: 0.5959 (mmm) REVERT: a 257 MET cc_start: 0.7370 (tmm) cc_final: 0.7141 (tmm) outliers start: 92 outliers final: 57 residues processed: 361 average time/residue: 0.1995 time to fit residues: 125.1078 Evaluate side-chains 332 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 269 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain I residue 10 TYR Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 73 TYR Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain O residue 5 ASN Chi-restraints excluded: chain O residue 16 MET Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 65 MET Chi-restraints excluded: chain W residue 12 LYS Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain Y residue 39 GLU Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain a residue 11 TYR Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 89 SER Chi-restraints excluded: chain a residue 111 TRP Chi-restraints excluded: chain a residue 139 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 220 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 287 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 244 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 186 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 252 optimal weight: 9.9990 chunk 367 optimal weight: 7.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 HIS ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.057512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.041168 restraints weight = 247207.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.042399 restraints weight = 135993.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.042318 restraints weight = 84888.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.042692 restraints weight = 64603.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.042738 restraints weight = 54212.833| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 37294 Z= 0.156 Angle : 0.622 13.565 50485 Z= 0.314 Chirality : 0.042 0.414 5881 Planarity : 0.004 0.072 6510 Dihedral : 6.318 98.043 5330 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.97 % Allowed : 15.22 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 1.24 (0.12), residues: 4775 helix: 1.76 (0.10), residues: 2595 sheet: -0.01 (0.22), residues: 519 loop : -0.34 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 41 TYR 0.037 0.001 TYR a 94 PHE 0.034 0.001 PHE Q 53 TRP 0.010 0.001 TRP a 232 HIS 0.006 0.001 HIS W 21 Details of bonding type rmsd covalent geometry : bond 0.00333 (37294) covalent geometry : angle 0.62183 (50485) hydrogen bonds : bond 0.05187 ( 2174) hydrogen bonds : angle 4.41582 ( 6348) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 286 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8584 (mp) REVERT: A 156 MET cc_start: 0.9464 (mmt) cc_final: 0.9043 (mmt) REVERT: C 262 ASP cc_start: 0.8204 (m-30) cc_final: 0.7931 (t0) REVERT: D 136 MET cc_start: 0.9295 (mmm) cc_final: 0.9092 (mmm) REVERT: D 209 MET cc_start: 0.8651 (mpp) cc_final: 0.8371 (mpp) REVERT: D 445 MET cc_start: 0.8921 (mmm) cc_final: 0.8212 (mmm) REVERT: E 275 MET cc_start: 0.8232 (mmm) cc_final: 0.8025 (tpp) REVERT: F 159 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8281 (tmm) REVERT: F 311 THR cc_start: 0.9605 (OUTLIER) cc_final: 0.9375 (t) REVERT: F 379 MET cc_start: 0.9197 (mtp) cc_final: 0.8377 (tpp) REVERT: F 397 GLN cc_start: 0.8933 (tt0) cc_final: 0.8361 (tm-30) REVERT: F 431 MET cc_start: 0.7543 (mtm) cc_final: 0.7320 (ptt) REVERT: G 25 MET cc_start: 0.8202 (tpp) cc_final: 0.7855 (tpp) REVERT: G 48 MET cc_start: 0.9078 (ttm) cc_final: 0.8427 (ttm) REVERT: G 78 LEU cc_start: 0.9081 (tp) cc_final: 0.8689 (tt) REVERT: G 102 MET cc_start: 0.8775 (ttp) cc_final: 0.8063 (tmm) REVERT: G 116 MET cc_start: 0.8571 (mmp) cc_final: 0.8320 (mmp) REVERT: G 243 MET cc_start: 0.9279 (tpp) cc_final: 0.9057 (tpp) REVERT: H 23 ILE cc_start: 0.9045 (tt) cc_final: 0.8691 (mp) REVERT: H 49 MET cc_start: 0.7141 (tpp) cc_final: 0.6898 (tpp) REVERT: I 6 MET cc_start: 0.5661 (mmt) cc_final: 0.4953 (mpp) REVERT: I 54 PHE cc_start: 0.6056 (m-10) cc_final: 0.5623 (t80) REVERT: J 11 MET cc_start: 0.3483 (mmp) cc_final: 0.1922 (tpp) REVERT: J 16 MET cc_start: 0.8361 (tpt) cc_final: 0.7976 (mmm) REVERT: J 17 MET cc_start: 0.8040 (ptp) cc_final: 0.7759 (ptt) REVERT: J 65 MET cc_start: 0.7502 (mmt) cc_final: 0.7228 (tpp) REVERT: L 11 MET cc_start: 0.7637 (mtp) cc_final: 0.5984 (tpt) REVERT: L 16 MET cc_start: 0.4762 (tpt) cc_final: 0.4517 (tpt) REVERT: L 49 LEU cc_start: 0.8470 (mt) cc_final: 0.8190 (tp) REVERT: L 57 MET cc_start: 0.7669 (tmm) cc_final: 0.6646 (ptm) REVERT: M 35 PHE cc_start: 0.7001 (t80) cc_final: 0.6783 (t80) REVERT: M 65 MET cc_start: 0.6574 (mtp) cc_final: 0.6015 (mmp) REVERT: N 11 MET cc_start: 0.7554 (mmm) cc_final: 0.7267 (mmt) REVERT: N 16 MET cc_start: 0.2503 (tpp) cc_final: 0.2245 (tpp) REVERT: N 65 MET cc_start: 0.6478 (mmp) cc_final: 0.5396 (mmm) REVERT: P 11 MET cc_start: 0.7338 (mtp) cc_final: 0.6998 (tpp) REVERT: P 57 MET cc_start: 0.4914 (ppp) cc_final: 0.4152 (ttm) REVERT: R 6 MET cc_start: 0.6064 (mmt) cc_final: 0.5508 (ttm) REVERT: R 65 MET cc_start: 0.4981 (OUTLIER) cc_final: 0.4439 (mtt) REVERT: S 57 MET cc_start: 0.8005 (tpt) cc_final: 0.7284 (tmm) REVERT: S 75 MET cc_start: 0.5599 (ttt) cc_final: 0.5075 (tpt) REVERT: W 147 MET cc_start: 0.9028 (mtm) cc_final: 0.8597 (mpp) REVERT: X 49 ARG cc_start: 0.8620 (mtt180) cc_final: 0.8283 (ttp80) REVERT: X 83 ARG cc_start: 0.8016 (ttp-110) cc_final: 0.7726 (ttp-110) REVERT: a 93 MET cc_start: 0.8009 (tmm) cc_final: 0.7594 (ppp) REVERT: a 94 TYR cc_start: 0.5922 (t80) cc_final: 0.5427 (t80) REVERT: a 155 LEU cc_start: 0.8161 (mt) cc_final: 0.7911 (tt) REVERT: a 201 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7930 (pp) REVERT: a 215 MET cc_start: 0.6189 (mmm) cc_final: 0.5977 (mmm) REVERT: a 257 MET cc_start: 0.7510 (tmm) cc_final: 0.7296 (tmm) outliers start: 75 outliers final: 51 residues processed: 344 average time/residue: 0.2009 time to fit residues: 118.4353 Evaluate side-chains 330 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 274 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain O residue 5 ASN Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 65 MET Chi-restraints excluded: chain W residue 23 SER Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain Y residue 39 GLU Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 111 TRP Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain a residue 201 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 453 optimal weight: 9.9990 chunk 153 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 257 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 169 optimal weight: 8.9990 chunk 197 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 416 optimal weight: 8.9990 chunk 244 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 GLN E 121 ASN G 226 GLN ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.056289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.040163 restraints weight = 250238.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.041303 restraints weight = 137150.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.041382 restraints weight = 86290.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.041564 restraints weight = 60678.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.041694 restraints weight = 59609.508| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.5812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 37294 Z= 0.220 Angle : 0.677 14.200 50485 Z= 0.344 Chirality : 0.044 0.397 5881 Planarity : 0.004 0.073 6510 Dihedral : 6.447 95.415 5330 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.18 % Allowed : 15.27 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 1.03 (0.12), residues: 4775 helix: 1.61 (0.10), residues: 2600 sheet: -0.13 (0.22), residues: 534 loop : -0.46 (0.16), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 41 TYR 0.043 0.002 TYR I 10 PHE 0.029 0.002 PHE Q 53 TRP 0.015 0.001 TRP a 232 HIS 0.008 0.001 HIS W 21 Details of bonding type rmsd covalent geometry : bond 0.00477 (37294) covalent geometry : angle 0.67670 (50485) hydrogen bonds : bond 0.05397 ( 2174) hydrogen bonds : angle 4.56833 ( 6348) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 276 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8593 (mp) REVERT: A 156 MET cc_start: 0.9466 (mmt) cc_final: 0.9016 (mmt) REVERT: D 209 MET cc_start: 0.8784 (mpp) cc_final: 0.8516 (mpp) REVERT: D 273 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8430 (tm-30) REVERT: D 445 MET cc_start: 0.8859 (mmm) cc_final: 0.8106 (mmm) REVERT: E 459 LEU cc_start: 0.8351 (mp) cc_final: 0.8072 (tt) REVERT: F 159 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8345 (tmm) REVERT: F 379 MET cc_start: 0.9230 (mtp) cc_final: 0.8239 (tpp) REVERT: F 397 GLN cc_start: 0.8941 (tt0) cc_final: 0.8300 (tm-30) REVERT: F 431 MET cc_start: 0.7738 (mtm) cc_final: 0.7421 (ptt) REVERT: G 25 MET cc_start: 0.8198 (tpp) cc_final: 0.7876 (tpp) REVERT: G 48 MET cc_start: 0.9099 (ttm) cc_final: 0.8424 (ttm) REVERT: G 102 MET cc_start: 0.8726 (ttp) cc_final: 0.8078 (tmm) REVERT: G 116 MET cc_start: 0.8719 (mmp) cc_final: 0.8475 (mmp) REVERT: G 155 MET cc_start: 0.9214 (mmm) cc_final: 0.8929 (mmt) REVERT: I 17 MET cc_start: 0.8364 (tmm) cc_final: 0.7830 (mtt) REVERT: I 54 PHE cc_start: 0.6391 (m-10) cc_final: 0.5625 (t80) REVERT: J 11 MET cc_start: 0.3342 (mmp) cc_final: 0.2193 (tpp) REVERT: L 11 MET cc_start: 0.7394 (mtp) cc_final: 0.5741 (tpt) REVERT: L 16 MET cc_start: 0.4677 (tpt) cc_final: 0.3973 (tpt) REVERT: L 31 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.7888 (mm) REVERT: L 49 LEU cc_start: 0.8398 (mt) cc_final: 0.8108 (tp) REVERT: L 57 MET cc_start: 0.7644 (tmm) cc_final: 0.6725 (ptm) REVERT: M 17 MET cc_start: 0.6038 (tpp) cc_final: 0.5784 (tpp) REVERT: M 65 MET cc_start: 0.6262 (mtp) cc_final: 0.5723 (mmp) REVERT: M 68 VAL cc_start: 0.7142 (t) cc_final: 0.6477 (p) REVERT: N 11 MET cc_start: 0.7535 (mmm) cc_final: 0.7044 (mmt) REVERT: N 65 MET cc_start: 0.6563 (mmp) cc_final: 0.5658 (mmm) REVERT: O 75 MET cc_start: 0.2765 (tpp) cc_final: 0.2304 (ttt) REVERT: P 11 MET cc_start: 0.7389 (mtp) cc_final: 0.7144 (tmm) REVERT: P 57 MET cc_start: 0.5051 (ppp) cc_final: 0.4153 (ttm) REVERT: Q 16 MET cc_start: 0.1011 (mmm) cc_final: -0.0338 (tpp) REVERT: R 6 MET cc_start: 0.6352 (mmt) cc_final: 0.5798 (ttm) REVERT: R 11 MET cc_start: 0.6431 (ppp) cc_final: 0.4902 (tpt) REVERT: R 65 MET cc_start: 0.4943 (OUTLIER) cc_final: 0.4412 (mtt) REVERT: S 57 MET cc_start: 0.8117 (tpt) cc_final: 0.7478 (tmm) REVERT: S 75 MET cc_start: 0.5692 (ttt) cc_final: 0.5131 (tpt) REVERT: W 147 MET cc_start: 0.9033 (mtm) cc_final: 0.8594 (mpp) REVERT: X 40 ILE cc_start: 0.6994 (OUTLIER) cc_final: 0.6498 (pt) REVERT: X 49 ARG cc_start: 0.8648 (mtt180) cc_final: 0.8310 (ttp80) REVERT: X 141 ASP cc_start: 0.8318 (p0) cc_final: 0.7949 (t0) REVERT: a 94 TYR cc_start: 0.6116 (t80) cc_final: 0.5858 (t80) REVERT: a 155 LEU cc_start: 0.8224 (mt) cc_final: 0.7984 (tp) REVERT: a 201 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7910 (pp) outliers start: 83 outliers final: 55 residues processed: 338 average time/residue: 0.1965 time to fit residues: 115.5290 Evaluate side-chains 330 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 269 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain I residue 53 PHE Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain O residue 5 ASN Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 65 MET Chi-restraints excluded: chain W residue 23 SER Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain a residue 11 TYR Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 111 TRP Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain a residue 201 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 165 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 359 optimal weight: 6.9990 chunk 469 optimal weight: 8.9990 chunk 171 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 200 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 ASN ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 51 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.057273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.041086 restraints weight = 249964.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.041996 restraints weight = 142723.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.042612 restraints weight = 82287.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.042642 restraints weight = 66713.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.042649 restraints weight = 58385.403| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.5956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 37294 Z= 0.141 Angle : 0.639 14.823 50485 Z= 0.319 Chirality : 0.042 0.408 5881 Planarity : 0.004 0.073 6510 Dihedral : 6.278 92.177 5330 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.68 % Allowed : 15.79 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 1.26 (0.12), residues: 4775 helix: 1.79 (0.10), residues: 2609 sheet: -0.02 (0.22), residues: 528 loop : -0.37 (0.16), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 41 TYR 0.020 0.001 TYR a 94 PHE 0.043 0.001 PHE J 54 TRP 0.009 0.001 TRP a 232 HIS 0.006 0.001 HIS W 21 Details of bonding type rmsd covalent geometry : bond 0.00297 (37294) covalent geometry : angle 0.63872 (50485) hydrogen bonds : bond 0.05025 ( 2174) hydrogen bonds : angle 4.39958 ( 6348) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 282 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8649 (mp) REVERT: A 156 MET cc_start: 0.9484 (mmt) cc_final: 0.9078 (mmt) REVERT: D 160 MET cc_start: 0.8993 (mtm) cc_final: 0.8767 (mtm) REVERT: D 193 MET cc_start: 0.8324 (mmm) cc_final: 0.7961 (mmm) REVERT: D 209 MET cc_start: 0.8676 (mpp) cc_final: 0.8385 (mpp) REVERT: D 273 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8428 (tm-30) REVERT: D 445 MET cc_start: 0.8987 (mmm) cc_final: 0.8228 (mmm) REVERT: E 459 LEU cc_start: 0.8366 (mp) cc_final: 0.8090 (tt) REVERT: F 56 MET cc_start: 0.9205 (mmp) cc_final: 0.8893 (mmp) REVERT: F 159 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8292 (tmm) REVERT: F 311 THR cc_start: 0.9543 (OUTLIER) cc_final: 0.9266 (t) REVERT: F 379 MET cc_start: 0.9301 (mtp) cc_final: 0.8390 (tpp) REVERT: F 397 GLN cc_start: 0.8871 (tt0) cc_final: 0.8226 (tm-30) REVERT: F 431 MET cc_start: 0.7786 (mtm) cc_final: 0.7501 (ptt) REVERT: G 25 MET cc_start: 0.8455 (tpp) cc_final: 0.8079 (tpp) REVERT: G 48 MET cc_start: 0.9007 (ttm) cc_final: 0.8345 (ttm) REVERT: G 78 LEU cc_start: 0.9175 (tp) cc_final: 0.8832 (tp) REVERT: G 102 MET cc_start: 0.8748 (ttp) cc_final: 0.8085 (tmm) REVERT: G 125 PHE cc_start: 0.8733 (m-80) cc_final: 0.8504 (m-80) REVERT: G 243 MET cc_start: 0.9201 (tpp) cc_final: 0.8852 (tpp) REVERT: I 54 PHE cc_start: 0.6328 (m-10) cc_final: 0.5552 (t80) REVERT: J 11 MET cc_start: 0.2807 (mmp) cc_final: 0.1826 (tpp) REVERT: L 7 ASP cc_start: 0.5299 (OUTLIER) cc_final: 0.4727 (p0) REVERT: L 11 MET cc_start: 0.7403 (mtp) cc_final: 0.5740 (tpt) REVERT: L 49 LEU cc_start: 0.8470 (mt) cc_final: 0.8203 (tp) REVERT: L 57 MET cc_start: 0.7642 (tmm) cc_final: 0.6700 (ptm) REVERT: M 17 MET cc_start: 0.6354 (tpp) cc_final: 0.5679 (tpp) REVERT: M 65 MET cc_start: 0.6190 (mtp) cc_final: 0.5612 (mmp) REVERT: M 68 VAL cc_start: 0.7134 (t) cc_final: 0.6511 (p) REVERT: N 11 MET cc_start: 0.7484 (mmm) cc_final: 0.7127 (mmm) REVERT: N 16 MET cc_start: 0.2892 (tpp) cc_final: 0.2604 (tpp) REVERT: N 65 MET cc_start: 0.6727 (mmp) cc_final: 0.5846 (mmm) REVERT: O 75 MET cc_start: 0.2944 (tpp) cc_final: 0.2326 (ttt) REVERT: P 57 MET cc_start: 0.5021 (ppp) cc_final: 0.4041 (ttm) REVERT: R 6 MET cc_start: 0.6112 (mmt) cc_final: 0.5565 (ttm) REVERT: R 11 MET cc_start: 0.6370 (ppp) cc_final: 0.4865 (tpt) REVERT: R 65 MET cc_start: 0.5016 (OUTLIER) cc_final: 0.4507 (mtt) REVERT: S 57 MET cc_start: 0.8077 (tpt) cc_final: 0.7485 (tmm) REVERT: S 75 MET cc_start: 0.5685 (ttt) cc_final: 0.5150 (tpt) REVERT: W 147 MET cc_start: 0.9121 (mtm) cc_final: 0.8632 (mpp) REVERT: X 40 ILE cc_start: 0.6891 (OUTLIER) cc_final: 0.6377 (pt) REVERT: X 49 ARG cc_start: 0.8668 (mtt180) cc_final: 0.8187 (ttp80) REVERT: X 53 ASP cc_start: 0.7694 (t0) cc_final: 0.7459 (t0) REVERT: X 83 ARG cc_start: 0.8041 (ttp-110) cc_final: 0.7757 (ttp-110) REVERT: X 141 ASP cc_start: 0.8474 (p0) cc_final: 0.8086 (t0) REVERT: a 201 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7963 (pp) outliers start: 64 outliers final: 49 residues processed: 327 average time/residue: 0.2031 time to fit residues: 115.0054 Evaluate side-chains 328 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 272 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain O residue 5 ASN Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 65 MET Chi-restraints excluded: chain W residue 23 SER Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 111 TRP Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain a residue 201 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 305 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 375 optimal weight: 5.9990 chunk 234 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 299 optimal weight: 6.9990 chunk 345 optimal weight: 20.0000 chunk 412 optimal weight: 8.9990 chunk 267 optimal weight: 9.9990 chunk 291 optimal weight: 0.9980 chunk 407 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.056523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.040581 restraints weight = 251575.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.041381 restraints weight = 160899.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.041701 restraints weight = 94865.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.041838 restraints weight = 72431.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.041888 restraints weight = 64745.772| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.6165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 37294 Z= 0.184 Angle : 0.675 15.072 50485 Z= 0.335 Chirality : 0.043 0.387 5881 Planarity : 0.004 0.076 6510 Dihedral : 6.314 93.378 5330 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.65 % Allowed : 16.00 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.12), residues: 4775 helix: 1.74 (0.10), residues: 2610 sheet: -0.09 (0.22), residues: 533 loop : -0.43 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 41 TYR 0.017 0.001 TYR B 150 PHE 0.043 0.002 PHE Q 53 TRP 0.012 0.001 TRP a 232 HIS 0.007 0.001 HIS W 21 Details of bonding type rmsd covalent geometry : bond 0.00399 (37294) covalent geometry : angle 0.67516 (50485) hydrogen bonds : bond 0.05093 ( 2174) hydrogen bonds : angle 4.47778 ( 6348) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 278 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8824 (mp) REVERT: A 156 MET cc_start: 0.9444 (mmt) cc_final: 0.9025 (mmt) REVERT: C 52 MET cc_start: 0.9075 (OUTLIER) cc_final: 0.8810 (mmm) REVERT: C 95 LEU cc_start: 0.8790 (tt) cc_final: 0.8582 (tt) REVERT: D 193 MET cc_start: 0.8277 (mmm) cc_final: 0.7975 (mmm) REVERT: D 209 MET cc_start: 0.8682 (mpp) cc_final: 0.8410 (mpp) REVERT: D 273 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8381 (tm-30) REVERT: D 445 MET cc_start: 0.8919 (mmm) cc_final: 0.8093 (mmm) REVERT: E 136 MET cc_start: 0.9276 (mmm) cc_final: 0.9054 (mmm) REVERT: E 459 LEU cc_start: 0.8348 (mp) cc_final: 0.8091 (tt) REVERT: F 159 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8340 (tmm) REVERT: F 379 MET cc_start: 0.9231 (mtp) cc_final: 0.8208 (tpp) REVERT: F 397 GLN cc_start: 0.8888 (tt0) cc_final: 0.8244 (tm-30) REVERT: F 431 MET cc_start: 0.7725 (mtm) cc_final: 0.7361 (ptt) REVERT: G 25 MET cc_start: 0.8226 (tpp) cc_final: 0.7886 (tpp) REVERT: G 48 MET cc_start: 0.9087 (ttm) cc_final: 0.8460 (ttm) REVERT: G 78 LEU cc_start: 0.9040 (tp) cc_final: 0.8682 (tp) REVERT: G 102 MET cc_start: 0.8689 (ttp) cc_final: 0.8084 (tmm) REVERT: G 125 PHE cc_start: 0.8823 (m-80) cc_final: 0.8565 (m-80) REVERT: G 155 MET cc_start: 0.9145 (mmm) cc_final: 0.8864 (mmt) REVERT: G 243 MET cc_start: 0.9179 (tpp) cc_final: 0.8893 (tpp) REVERT: I 54 PHE cc_start: 0.6402 (m-10) cc_final: 0.5586 (t80) REVERT: J 11 MET cc_start: 0.2088 (mmp) cc_final: 0.1204 (tpp) REVERT: J 16 MET cc_start: 0.7790 (mmm) cc_final: 0.7087 (mmm) REVERT: J 17 MET cc_start: 0.7788 (ptp) cc_final: 0.7209 (mpp) REVERT: L 7 ASP cc_start: 0.5344 (OUTLIER) cc_final: 0.4860 (p0) REVERT: L 11 MET cc_start: 0.7422 (mtp) cc_final: 0.5781 (tpt) REVERT: L 49 LEU cc_start: 0.8375 (mt) cc_final: 0.8128 (tp) REVERT: L 57 MET cc_start: 0.7596 (tmm) cc_final: 0.6625 (ptm) REVERT: M 65 MET cc_start: 0.6292 (mtp) cc_final: 0.5548 (mmp) REVERT: N 11 MET cc_start: 0.7650 (mmm) cc_final: 0.7239 (mmt) REVERT: N 65 MET cc_start: 0.6637 (mmp) cc_final: 0.5690 (mmm) REVERT: O 75 MET cc_start: 0.3324 (tpp) cc_final: 0.2510 (ttt) REVERT: P 11 MET cc_start: 0.7949 (tmm) cc_final: 0.7319 (mtp) REVERT: P 57 MET cc_start: 0.5057 (ppp) cc_final: 0.3933 (ttm) REVERT: R 6 MET cc_start: 0.6457 (mmt) cc_final: 0.5834 (ttm) REVERT: R 11 MET cc_start: 0.6172 (ppp) cc_final: 0.4724 (tpt) REVERT: R 53 PHE cc_start: 0.7726 (OUTLIER) cc_final: 0.6851 (t80) REVERT: R 65 MET cc_start: 0.5091 (OUTLIER) cc_final: 0.4535 (mtt) REVERT: R 75 MET cc_start: 0.6633 (ptm) cc_final: 0.6378 (ppp) REVERT: S 57 MET cc_start: 0.8033 (tpt) cc_final: 0.7497 (tmm) REVERT: S 75 MET cc_start: 0.5744 (ttt) cc_final: 0.5283 (tpt) REVERT: W 147 MET cc_start: 0.8998 (mtm) cc_final: 0.8603 (mpp) REVERT: X 40 ILE cc_start: 0.6791 (OUTLIER) cc_final: 0.6214 (pt) REVERT: X 49 ARG cc_start: 0.8701 (mtt180) cc_final: 0.8215 (ttp80) REVERT: X 53 ASP cc_start: 0.7709 (t0) cc_final: 0.7495 (t0) REVERT: X 83 ARG cc_start: 0.8063 (ttp-110) cc_final: 0.7738 (ttp-110) REVERT: X 141 ASP cc_start: 0.8401 (p0) cc_final: 0.8011 (t0) REVERT: a 201 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7913 (pp) outliers start: 63 outliers final: 48 residues processed: 323 average time/residue: 0.2038 time to fit residues: 114.1694 Evaluate side-chains 327 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 271 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 449 ILE Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain O residue 5 ASN Chi-restraints excluded: chain Q residue 53 PHE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 65 MET Chi-restraints excluded: chain W residue 23 SER Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 117 SER Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain Y residue 54 LEU Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 111 TRP Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain a residue 201 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 264 optimal weight: 10.0000 chunk 363 optimal weight: 6.9990 chunk 210 optimal weight: 10.0000 chunk 145 optimal weight: 0.0470 chunk 47 optimal weight: 6.9990 chunk 347 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 270 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 189 optimal weight: 0.8980 chunk 421 optimal weight: 8.9990 overall best weight: 2.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 GLN E 294 GLN ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.057026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.041070 restraints weight = 248424.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.041737 restraints weight = 150441.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.042431 restraints weight = 94373.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.042426 restraints weight = 63349.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.042474 restraints weight = 61094.845| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.6269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37294 Z= 0.144 Angle : 0.653 14.757 50485 Z= 0.322 Chirality : 0.042 0.396 5881 Planarity : 0.004 0.074 6510 Dihedral : 6.214 92.393 5330 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.42 % Allowed : 16.45 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 1.28 (0.12), residues: 4775 helix: 1.84 (0.10), residues: 2602 sheet: 0.00 (0.22), residues: 516 loop : -0.40 (0.16), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 41 TYR 0.014 0.001 TYR I 10 PHE 0.046 0.001 PHE Q 53 TRP 0.009 0.001 TRP a 232 HIS 0.006 0.001 HIS W 21 Details of bonding type rmsd covalent geometry : bond 0.00307 (37294) covalent geometry : angle 0.65269 (50485) hydrogen bonds : bond 0.04914 ( 2174) hydrogen bonds : angle 4.36980 ( 6348) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5977.88 seconds wall clock time: 104 minutes 5.68 seconds (6245.68 seconds total)