Starting phenix.real_space_refine on Sat Mar 7 02:26:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dbt_27306/03_2026/8dbt_27306.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbt_27306/03_2026/8dbt_27306.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dbt_27306/03_2026/8dbt_27306.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbt_27306/03_2026/8dbt_27306.map" model { file = "/net/cci-nas-00/data/ceres_data/8dbt_27306/03_2026/8dbt_27306.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbt_27306/03_2026/8dbt_27306.cif" } resolution = 3.1 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= 0.002 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 179 5.16 5 C 23463 2.51 5 N 6312 2.21 5 O 6962 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 182 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: 36937 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3826 Classifications: {'peptide': 508} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 489} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 3877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3877 Classifications: {'peptide': 513} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 494} Chain: "C" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3849 Classifications: {'peptide': 510} Link IDs: {'PTRANS': 18, 'TRANS': 491} Chain: "D" 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: "E" 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: "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': 1, 'PTRANS': 8, 'TRANS': 274} Chain: "H" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1021 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} 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: "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: "X" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "Y" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 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: 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: "E" 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} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.14, per 1000 atoms: 0.22 Number of scatterers: 36937 At special positions: 0 Unit cell: (180.193, 219.037, 134.875, 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 179 16.00 P 16 15.00 Mg 5 11.99 O 6962 8.00 N 6312 7.00 C 23463 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: 3.08 Conformation dependent library (CDL) restraints added in 1.5 seconds 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8810 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 23 sheets defined 61.5% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 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 135 through 139 removed outlier: 3.560A pdb=" N ARG A 139 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' 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 253 Proline residue: A 239 - end of helix removed outlier: 3.945A 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 289 through 299 removed outlier: 3.638A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 314 Processing helix chain 'A' and resid 333 through 336 Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 377 through 382 removed outlier: 4.044A pdb=" N ALA A 380 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 391 removed outlier: 3.581A pdb=" N GLY A 391 " --> pdb=" O LYS A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 408 removed outlier: 3.536A pdb=" N GLU A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 432 Processing helix chain 'A' and resid 440 through 453 removed outlier: 3.548A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 479 removed outlier: 3.817A pdb=" N ARG A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP A 478 " --> pdb=" O TYR A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 489 Processing helix chain 'A' and resid 493 through 510 Processing helix chain 'B' and resid 2 through 19 removed outlier: 3.869A pdb=" N GLU B 10 " --> pdb=" O THR B 6 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 11 " --> pdb=" O GLU B 7 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 16 " --> pdb=" O ILE B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.532A pdb=" N ALA B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' 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 237 through 251 removed outlier: 3.611A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 287 through 288 No H-bonds generated for 'chain 'B' and resid 287 through 288' Processing helix chain 'B' and resid 289 through 299 Processing helix chain 'B' and resid 305 through 314 Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 377 through 382 removed outlier: 3.744A pdb=" N ALA B 380 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 408 removed outlier: 4.880A pdb=" N GLY B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG B 394 " --> pdb=" O SER B 390 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 431 Processing helix chain 'B' and resid 440 through 453 Processing helix chain 'B' and resid 460 through 479 removed outlier: 4.079A pdb=" N GLY B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 490 removed outlier: 3.562A 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 20 through 24 Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 237 through 253 removed outlier: 3.740A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 289 through 299 removed outlier: 3.652A pdb=" N HIS C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) 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: 3.711A pdb=" N ALA C 380 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 405 removed outlier: 4.125A pdb=" N GLY C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU C 402 " --> pdb=" O ALA C 398 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.766A pdb=" N ALA C 410 " --> pdb=" O SER C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 432 removed outlier: 3.891A pdb=" N LYS C 432 " --> pdb=" O THR C 428 " (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 removed outlier: 3.504A pdb=" N MET C 483 " --> pdb=" O HIS C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 509 removed outlier: 3.877A pdb=" N LYS C 499 " --> pdb=" O GLU C 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 130 through 137 removed outlier: 3.513A pdb=" N ASP D 134 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 170 removed outlier: 4.065A pdb=" N ILE D 168 " --> pdb=" O ARG D 164 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU D 169 " --> pdb=" O ASN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 196 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: 3.597A pdb=" N ARG D 216 " --> pdb=" O PRO D 212 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 256 removed outlier: 3.891A pdb=" N THR D 248 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL D 254 " --> pdb=" O ALA D 250 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 280 removed outlier: 3.533A pdb=" N LEU D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 302 Processing helix chain 'D' and resid 305 through 313 removed outlier: 4.310A pdb=" N ALA D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 327 Processing helix chain 'D' and resid 345 through 350 Processing helix chain 'D' and resid 350 through 378 removed outlier: 4.338A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE D 376 " --> pdb=" O ASP D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 382 Processing helix chain 'D' and resid 385 through 400 removed outlier: 3.665A pdb=" N LYS D 395 " --> pdb=" O ALA D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 406 No H-bonds generated for 'chain 'D' and resid 404 through 406' Processing helix chain 'D' and resid 407 through 412 Processing helix chain 'D' and resid 419 through 433 Processing helix chain 'D' and resid 439 through 443 Processing helix chain 'D' and resid 448 through 458 removed outlier: 3.869A pdb=" N LYS D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 115 through 119 removed outlier: 3.769A pdb=" N LEU E 119 " --> pdb=" O TYR E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 137 Processing helix chain 'E' and resid 154 through 170 removed outlier: 3.653A pdb=" N ILE E 168 " --> pdb=" O ARG E 164 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU E 169 " --> pdb=" O ASN E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 196 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 234 removed outlier: 3.786A pdb=" N ARG E 216 " --> pdb=" O PRO E 212 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG E 218 " --> pdb=" O GLY E 214 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY E 234 " --> pdb=" O PHE E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 258 removed outlier: 3.594A pdb=" N THR E 248 " --> pdb=" O ILE E 244 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL E 254 " --> pdb=" O ALA E 250 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA E 256 " --> pdb=" O THR E 252 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 280 Processing helix chain 'E' and resid 299 through 302 Processing helix chain 'E' and resid 305 through 312 Processing helix chain 'E' and resid 322 through 327 Processing helix chain 'E' and resid 345 through 378 removed outlier: 7.735A pdb=" N GLN E 351 " --> pdb=" O LEU E 347 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N GLU E 352 " --> pdb=" O VAL E 348 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N HIS E 353 " --> pdb=" O VAL E 349 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE E 373 " --> pdb=" O GLU E 369 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA E 375 " --> pdb=" O LYS E 371 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE E 376 " --> pdb=" O ASP E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 382 Processing helix chain 'E' and resid 383 through 400 removed outlier: 3.593A pdb=" N ARG E 398 " --> pdb=" O ARG E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 412 Processing helix chain 'E' and resid 419 through 432 Processing helix chain 'E' and resid 433 through 436 Processing helix chain 'E' and resid 448 through 450 No H-bonds generated for 'chain 'E' and resid 448 through 450' Processing helix chain 'E' and resid 451 through 459 Processing helix chain 'F' and resid 18 through 22 removed outlier: 4.237A pdb=" N VAL F 22 " --> pdb=" O GLN F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 Processing helix chain 'F' and resid 130 through 137 Processing helix chain 'F' and resid 154 through 169 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: 4.888A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 259 removed outlier: 3.516A pdb=" N TYR F 247 " --> pdb=" O ASN F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 267 Processing helix chain 'F' and resid 270 through 280 removed outlier: 3.518A pdb=" N LEU F 278 " --> pdb=" O GLU F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 313 removed outlier: 3.715A pdb=" N ALA F 313 " --> pdb=" O ALA F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 328 removed outlier: 3.657A pdb=" N LEU F 328 " --> pdb=" O GLN F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 350 Processing helix chain 'F' and resid 350 through 377 removed outlier: 4.084A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 382 Processing helix chain 'F' and resid 385 through 400 removed outlier: 3.646A pdb=" N LYS F 395 " --> pdb=" O ALA F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 412 Processing helix chain 'F' and resid 419 through 433 Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 448 through 457 removed outlier: 3.905A pdb=" N GLU F 454 " --> pdb=" O GLU F 450 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 56 removed outlier: 4.314A pdb=" N GLU G 24 " --> pdb=" O THR G 20 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA G 27 " --> pdb=" O MET G 23 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG G 37 " --> pdb=" O LYS G 33 " (cutoff:3.500A) Proline residue: G 43 - end of helix Processing helix chain 'G' and resid 90 through 108 removed outlier: 3.969A pdb=" N LYS G 97 " --> pdb=" O ASN G 93 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS G 108 " --> pdb=" O THR G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 129 removed outlier: 3.518A pdb=" N VAL G 122 " --> pdb=" O GLY G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 161 Processing helix chain 'G' and resid 197 through 201 Processing helix chain 'G' and resid 210 through 281 Processing helix chain 'H' and resid 54 through 58 removed outlier: 3.736A pdb=" N HIS H 58 " --> pdb=" O GLN H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 108 Processing helix chain 'H' and resid 111 through 134 removed outlier: 3.659A pdb=" N ALA H 119 " --> pdb=" O ALA H 115 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU H 132 " --> pdb=" O LEU H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 136 No H-bonds generated for 'chain 'H' and resid 135 through 136' Processing helix chain 'W' and resid 2 through 2 No H-bonds generated for 'chain 'W' and resid 2 through 2' Processing helix chain 'W' and resid 3 through 21 Proline residue: W 9 - end of helix Processing helix chain 'W' and resid 23 through 40 removed outlier: 3.551A pdb=" N PHE W 33 " --> pdb=" O ASP W 29 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR W 38 " --> pdb=" O ALA W 34 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS W 39 " --> pdb=" O ALA W 35 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN W 40 " --> pdb=" O GLU W 36 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 48 Processing helix chain 'W' and resid 52 through 64 removed outlier: 3.679A pdb=" N VAL W 63 " --> pdb=" O SER W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 82 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 92 Processing helix chain 'W' and resid 93 through 103 Processing helix chain 'W' and resid 118 through 132 Processing helix chain 'W' and resid 162 through 171 Processing helix chain 'I' and resid 4 through 42 removed outlier: 3.642A pdb=" N LEU I 9 " --> pdb=" O ASN I 5 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR I 10 " --> pdb=" O MET I 6 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET I 11 " --> pdb=" O ASP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 61 removed outlier: 3.737A pdb=" N THR I 51 " --> pdb=" O PRO I 47 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU I 59 " --> pdb=" O ILE I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 77 removed outlier: 3.666A pdb=" N ILE I 66 " --> pdb=" O ALA I 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 42 removed outlier: 3.831A pdb=" N LEU J 8 " --> pdb=" O LEU J 4 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA J 25 " --> pdb=" O ALA J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 61 removed outlier: 3.761A 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: 4.214A pdb=" N LEU L 8 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU L 9 " --> pdb=" O ASN L 5 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET L 11 " --> pdb=" O ASP L 7 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET L 16 " --> pdb=" O ALA L 12 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE L 28 " --> pdb=" O ALA L 24 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS L 34 " --> pdb=" O ILE L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 61 removed outlier: 3.814A pdb=" N THR L 51 " --> pdb=" O PRO L 47 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY L 58 " --> pdb=" O PHE L 54 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU L 59 " --> pdb=" O ILE L 55 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL L 60 " --> pdb=" O VAL L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 77 removed outlier: 3.753A pdb=" N ILE L 66 " --> pdb=" O ALA L 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 42 removed outlier: 3.505A pdb=" N LEU M 31 " --> pdb=" O GLY M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 61 removed outlier: 3.813A pdb=" N THR M 51 " --> pdb=" O PRO M 47 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE M 54 " --> pdb=" O ARG M 50 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU M 59 " --> pdb=" O ILE M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 78 Processing helix chain 'N' and resid 4 through 42 removed outlier: 5.022A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET N 16 " --> pdb=" O ALA N 12 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA N 21 " --> pdb=" O MET N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 61 removed outlier: 3.593A pdb=" N THR N 51 " --> pdb=" O PRO N 47 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY N 58 " --> pdb=" O PHE N 54 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU N 59 " --> pdb=" O ILE N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 77 Processing helix chain 'O' and resid 5 through 42 removed outlier: 4.043A pdb=" N LEU O 9 " --> pdb=" O ASN O 5 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR O 10 " --> pdb=" O MET O 6 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE O 28 " --> pdb=" O ALA O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 61 removed outlier: 3.609A pdb=" N PHE O 54 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU O 59 " --> pdb=" O ILE O 55 " (cutoff:3.500A) removed outlier: 3.679A 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 4 through 42 removed outlier: 3.978A pdb=" N LEU P 8 " --> pdb=" O LEU P 4 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU P 9 " --> pdb=" O ASN P 5 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA P 21 " --> pdb=" O MET P 17 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE P 28 " --> pdb=" O ALA P 24 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS P 34 " --> pdb=" O ILE P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 77 removed outlier: 3.978A pdb=" N LEU P 59 " --> pdb=" O ILE P 55 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) Proline residue: P 64 - end of helix removed outlier: 3.744A pdb=" N ALA P 67 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 42 removed outlier: 3.576A pdb=" N LEU Q 8 " --> pdb=" O LEU Q 4 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR Q 10 " --> pdb=" O MET Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 77 removed outlier: 3.741A pdb=" N THR Q 51 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE Q 55 " --> pdb=" O THR Q 51 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU Q 59 " --> pdb=" O ILE Q 55 " (cutoff:3.500A) removed outlier: 4.241A 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: 3.564A pdb=" N LEU R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA R 21 " --> pdb=" O MET R 17 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE R 28 " --> pdb=" O ALA R 24 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS R 34 " --> pdb=" O ILE R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 63 removed outlier: 3.538A pdb=" N THR R 51 " --> pdb=" O PRO R 47 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN R 52 " --> pdb=" O LEU R 48 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU R 59 " --> pdb=" O ILE R 55 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE R 63 " --> pdb=" O LEU R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 77 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: 3.600A pdb=" N MET S 16 " --> pdb=" O ALA S 12 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 61 removed outlier: 3.725A pdb=" N LEU S 59 " --> pdb=" O ILE S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 78 Processing helix chain 'X' and resid 5 through 24 Processing helix chain 'X' and resid 25 through 136 removed outlier: 3.507A pdb=" N GLU X 119 " --> pdb=" O ARG X 115 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS X 122 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) Processing helix chain 'X' and resid 144 through 156 removed outlier: 4.109A pdb=" N ILE X 148 " --> pdb=" O ALA X 144 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU X 156 " --> pdb=" O LEU X 152 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 24 removed outlier: 3.892A pdb=" N THR Y 6 " --> pdb=" O ASN Y 2 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 139 removed outlier: 4.390A pdb=" N LEU Y 29 " --> pdb=" O VAL Y 25 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET Y 30 " --> pdb=" O TRP Y 26 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE Y 109 " --> pdb=" O ALA Y 105 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS Y 114 " --> pdb=" O GLU Y 110 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU Y 120 " --> pdb=" O ALA Y 116 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS Y 134 " --> pdb=" O ALA Y 130 " (cutoff:3.500A) Processing helix chain 'Y' and resid 141 through 156 removed outlier: 3.761A pdb=" N ALA Y 154 " --> pdb=" O ASP Y 150 " (cutoff:3.500A) Processing helix chain 'a' and resid 7 through 16 Processing helix chain 'a' and resid 43 through 65 Processing helix chain 'a' and resid 75 through 94 removed outlier: 3.534A pdb=" N VAL a 82 " --> pdb=" O ALA a 78 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET a 93 " --> pdb=" O SER a 89 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 118 removed outlier: 3.713A 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 133 Processing helix chain 'a' and resid 142 through 145 Processing helix chain 'a' and resid 146 through 181 removed outlier: 3.839A pdb=" N THR a 150 " --> pdb=" O ASP a 146 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS a 169 " --> pdb=" O SER a 165 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE a 171 " --> pdb=" O LYS a 167 " (cutoff:3.500A) removed outlier: 9.538A pdb=" N GLY a 172 " --> pdb=" O MET a 168 " (cutoff:3.500A) removed outlier: 3.707A 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: 4.392A pdb=" N ILE a 194 " --> pdb=" O PRO a 190 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 3.574A pdb=" N LEU a 211 " --> pdb=" O LEU a 207 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN a 214 " --> pdb=" O ARG a 210 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA a 217 " --> pdb=" O GLY a 213 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE a 222 " --> pdb=" O GLY a 218 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 269 removed outlier: 4.629A pdb=" N TRP a 235 " --> pdb=" O TRP a 231 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE a 236 " --> pdb=" O TRP a 232 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU a 237 " --> pdb=" O SER a 233 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 3.585A pdb=" N PHE a 244 " --> pdb=" O PRO a 240 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER a 268 " --> pdb=" O LEU a 264 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 66 removed outlier: 4.315A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ARG A 93 " --> pdb=" O MET A 52 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N SER A 54 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR A 91 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ASP D 67 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLN D 32 " --> pdb=" O ASP D 67 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ARG D 52 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLN D 45 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE D 50 " --> pdb=" O GLN D 45 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASP D 14 " --> pdb=" O VAL D 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 109 removed outlier: 6.610A pdb=" N ALA A 256 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N LEU A 327 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ILE A 258 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE A 329 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N TYR A 260 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N GLU A 331 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU A 166 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LEU A 355 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE A 168 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 146 removed outlier: 4.439A pdb=" N ILE A 159 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 26 through 35 removed outlier: 6.528A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.758A 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 59 through 67 removed outlier: 5.813A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER B 70 " --> pdb=" O GLU B 67 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 70 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 46 removed outlier: 6.695A pdb=" N ARG E 52 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLN E 45 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 7.400A 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 138 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 135 through 138 current: chain 'W' and resid 157 through 160 Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA7, first strand: chain 'B' and resid 107 through 109 removed outlier: 6.387A pdb=" N LYS B 192 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ILE B 259 " --> pdb=" O LYS B 192 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE B 194 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ASP B 261 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL B 196 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA B 256 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY B 322 " --> pdb=" O VAL B 304 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 329 through 331 removed outlier: 6.472A pdb=" N ILE B 167 " --> pdb=" O ILE B 330 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE B 168 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 59 through 66 removed outlier: 4.360A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ARG C 93 " --> pdb=" O MET C 52 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER C 54 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR C 91 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ARG C 40 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL C 34 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ASP F 67 " --> pdb=" O GLN F 32 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N GLN F 32 " --> pdb=" O ASP F 67 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG F 52 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLN F 45 " --> pdb=" O ILE F 50 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE F 50 " --> pdb=" O GLN F 45 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 96 through 98 Processing sheet with id=AB2, first strand: chain 'C' and resid 107 through 109 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 107 through 109 current: chain 'C' and resid 221 through 226 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 221 through 226 current: chain 'C' and resid 322 through 331 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 322 through 331 current: chain 'C' and resid 374 through 375 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 145 through 146 removed outlier: 4.535A pdb=" N ILE C 159 " --> pdb=" O VAL C 146 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 78 Processing sheet with id=AB5, first strand: chain 'D' and resid 87 through 88 removed outlier: 6.392A pdb=" N VAL D 237 " --> pdb=" O THR D 291 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N VAL D 293 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU D 239 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ALA D 295 " --> pdb=" O LEU D 239 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL D 241 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N TYR D 297 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL D 145 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL D 296 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU D 147 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LYS D 144 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL D 319 " --> pdb=" O LYS D 144 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLY D 146 " --> pdb=" O VAL D 319 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 125 through 126 removed outlier: 4.625A pdb=" N PHE D 139 " --> pdb=" O LEU D 126 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 76 through 78 Processing sheet with id=AB8, first strand: chain 'E' and resid 87 through 88 removed outlier: 6.550A pdb=" N MET E 88 " --> pdb=" O TYR E 206 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL E 145 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N VAL E 296 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU E 147 " --> pdb=" O VAL E 296 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS E 144 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL E 319 " --> pdb=" O LYS E 144 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLY E 146 " --> pdb=" O VAL E 319 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 125 through 126 removed outlier: 4.063A pdb=" N PHE E 139 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 76 through 79 removed outlier: 3.505A pdb=" N VAL F 79 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLU F 105 " --> pdb=" O VAL F 79 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 87 through 88 removed outlier: 6.133A pdb=" N MET F 88 " --> pdb=" O TYR F 206 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLN F 208 " --> pdb=" O MET F 88 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER F 174 " --> pdb=" O SER F 203 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N VAL F 205 " --> pdb=" O SER F 174 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE F 176 " --> pdb=" O VAL F 205 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N GLY F 207 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLY F 178 " --> pdb=" O GLY F 207 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL F 237 " --> pdb=" O THR F 291 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL F 293 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU F 239 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ALA F 295 " --> pdb=" O LEU F 239 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL F 241 " --> pdb=" O ALA F 295 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL F 145 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS F 144 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N VAL F 319 " --> pdb=" O LYS F 144 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLY F 146 " --> pdb=" O VAL F 319 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 134 through 136 removed outlier: 4.103A pdb=" N ALA G 134 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL G 75 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ALA G 115 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N TYR G 77 " --> pdb=" O ALA G 115 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ILE G 117 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL G 79 " --> pdb=" O ILE G 117 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS G 166 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ASN G 172 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU G 167 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE G 175 " --> pdb=" O SER G 179 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N SER G 179 " --> pdb=" O ILE G 175 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 206 through 207 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 206 through 207 current: chain 'H' and resid 14 through 20 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 14 through 20 current: chain 'H' and resid 32 through 34 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 32 through 34 current: chain 'H' and resid 61 through 70 removed outlier: 7.004A pdb=" N ILE H 62 " --> pdb=" O ARG H 85 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ARG H 85 " --> pdb=" O ILE H 62 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU H 64 " --> pdb=" O ALA H 83 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA H 83 " --> pdb=" O LEU H 64 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLY H 66 " --> pdb=" O ASP H 81 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'a' and resid 20 through 22 2210 hydrogen bonds defined for protein. 6459 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: 7.53 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6354 1.31 - 1.44: 8780 1.44 - 1.56: 21971 1.56 - 1.69: 30 1.69 - 1.82: 358 Bond restraints: 37493 Sorted by residual: bond pdb=" C VAL a 50 " pdb=" N VAL a 51 " ideal model delta sigma weight residual 1.334 1.426 -0.092 1.26e-02 6.30e+03 5.31e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.06e+01 bond pdb=" C4 ATP D 502 " pdb=" C5 ATP D 502 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.71e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.455 -0.067 1.00e-02 1.00e+04 4.55e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.454 -0.066 1.00e-02 1.00e+04 4.40e+01 ... (remaining 37488 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.43: 50272 4.43 - 8.85: 456 8.85 - 13.28: 15 13.28 - 17.71: 4 17.71 - 22.13: 3 Bond angle restraints: 50750 Sorted by residual: angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 117.74 22.13 1.00e+00 1.00e+00 4.90e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 119.86 20.01 1.00e+00 1.00e+00 4.00e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 120.75 19.12 1.00e+00 1.00e+00 3.66e+02 angle pdb=" PB ATP D 502 " pdb=" O3B ATP D 502 " pdb=" PG ATP D 502 " ideal model delta sigma weight residual 139.87 122.82 17.05 1.00e+00 1.00e+00 2.91e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 121.97 14.86 1.00e+00 1.00e+00 2.21e+02 ... (remaining 50745 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.39: 22333 35.39 - 70.78: 407 70.78 - 106.16: 54 106.16 - 141.55: 3 141.55 - 176.94: 2 Dihedral angle restraints: 22799 sinusoidal: 9027 harmonic: 13772 Sorted by residual: dihedral pdb=" C ARG C 365 " pdb=" N ARG C 365 " pdb=" CA ARG C 365 " pdb=" CB ARG C 365 " ideal model delta harmonic sigma weight residual -122.60 -152.93 30.33 0 2.50e+00 1.60e-01 1.47e+02 dihedral pdb=" N ARG C 365 " pdb=" C ARG C 365 " pdb=" CA ARG C 365 " pdb=" CB ARG C 365 " ideal model delta harmonic sigma weight residual 122.80 152.43 -29.63 0 2.50e+00 1.60e-01 1.40e+02 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 300.00 123.06 176.94 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 22796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.260: 5880 0.260 - 0.520: 35 0.520 - 0.780: 0 0.780 - 1.040: 0 1.040 - 1.300: 1 Chirality restraints: 5916 Sorted by residual: chirality pdb=" CA ARG C 365 " pdb=" N ARG C 365 " pdb=" C ARG C 365 " pdb=" CB ARG C 365 " both_signs ideal model delta sigma weight residual False 2.51 1.21 1.30 2.00e-01 2.50e+01 4.23e+01 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 2.16 0.49 2.00e-01 2.50e+01 5.92e+00 chirality pdb=" CB ILE E 330 " pdb=" CA ILE E 330 " pdb=" CG1 ILE E 330 " pdb=" CG2 ILE E 330 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.04e+00 ... (remaining 5913 not shown) Planarity restraints: 6545 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG X 36 " -0.132 9.50e-02 1.11e+02 7.53e-02 2.91e+01 pdb=" NE ARG X 36 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG X 36 " -0.088 2.00e-02 2.50e+03 pdb=" NH1 ARG X 36 " 0.031 2.00e-02 2.50e+03 pdb=" NH2 ARG X 36 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 41 " -0.277 9.50e-02 1.11e+02 1.28e-01 2.24e+01 pdb=" NE ARG R 41 " -0.004 2.00e-02 2.50e+03 pdb=" CZ ARG R 41 " 0.065 2.00e-02 2.50e+03 pdb=" NH1 ARG R 41 " -0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG R 41 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 281 " -0.124 9.50e-02 1.11e+02 6.89e-02 2.24e+01 pdb=" NE ARG D 281 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG D 281 " -0.077 2.00e-02 2.50e+03 pdb=" NH1 ARG D 281 " 0.027 2.00e-02 2.50e+03 pdb=" NH2 ARG D 281 " 0.021 2.00e-02 2.50e+03 ... (remaining 6542 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 35 2.45 - 3.06: 24229 3.06 - 3.67: 54923 3.67 - 4.29: 84131 4.29 - 4.90: 140519 Nonbonded interactions: 303837 Sorted by model distance: nonbonded pdb=" O2G ATP A 600 " pdb="MG MG A 601 " model vdw 1.833 2.170 nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.854 2.170 nonbonded pdb=" O2G ATP C 600 " pdb="MG MG C 601 " model vdw 1.863 2.170 nonbonded pdb="MG MG D 501 " pdb=" O1G ATP D 502 " model vdw 1.875 2.170 nonbonded pdb="MG MG D 501 " pdb=" O1B ATP D 502 " model vdw 1.899 2.170 ... (remaining 303832 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' selection = (chain 'B' and (resid 4 through 408 or (resid 409 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 through 511 or resid 600 thr \ ough 601)) selection = (chain 'C' and (resid 4 through 408 or (resid 409 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.810 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: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 32.010 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 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 : 0.010 0.103 37493 Z= 0.490 Angle : 1.264 22.133 50750 Z= 0.822 Chirality : 0.073 1.300 5916 Planarity : 0.008 0.128 6545 Dihedral : 14.819 176.941 13989 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.77 % Favored : 97.19 % Rotamer: Outliers : 0.65 % Allowed : 5.19 % Favored : 94.16 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.91 % 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: -1.61 (0.11), residues: 4803 helix: -1.28 (0.08), residues: 2616 sheet: 0.09 (0.21), residues: 547 loop : -0.77 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.090 0.011 ARG X 36 TYR 0.044 0.007 TYR F 26 PHE 0.052 0.004 PHE L 54 TRP 0.053 0.005 TRP a 111 HIS 0.021 0.003 HIS D 191 Details of bonding type rmsd covalent geometry : bond 0.01011 (37493) covalent geometry : angle 1.26443 (50750) hydrogen bonds : bond 0.22529 ( 2210) hydrogen bonds : angle 8.46031 ( 6459) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 395 time to evaluate : 1.091 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 86 MET cc_start: 0.8423 (mtt) cc_final: 0.8124 (mtt) REVERT: A 236 TYR cc_start: 0.9153 (OUTLIER) cc_final: 0.8746 (p90) REVERT: C 386 MET cc_start: 0.9167 (mmm) cc_final: 0.8588 (mmm) REVERT: D 226 MET cc_start: 0.8994 (mtt) cc_final: 0.8766 (mtt) REVERT: E 88 MET cc_start: 0.8826 (mtm) cc_final: 0.8553 (mtp) REVERT: F 261 MET cc_start: 0.8813 (mtt) cc_final: 0.8608 (ttt) REVERT: F 379 MET cc_start: 0.8221 (tpp) cc_final: 0.7812 (tpp) REVERT: G 116 MET cc_start: 0.8867 (mpp) cc_final: 0.8578 (mmt) REVERT: G 215 LEU cc_start: 0.9524 (tp) cc_final: 0.9317 (pp) REVERT: G 224 GLU cc_start: 0.8692 (tt0) cc_final: 0.8395 (pt0) REVERT: G 243 MET cc_start: 0.8694 (ttp) cc_final: 0.8373 (ttp) REVERT: H 13 GLN cc_start: 0.6760 (pt0) cc_final: 0.6491 (pp30) REVERT: H 40 PRO cc_start: 0.6101 (Cg_exo) cc_final: 0.5896 (Cg_exo) REVERT: H 63 TYR cc_start: 0.5439 (t80) cc_final: 0.5132 (t80) REVERT: H 127 GLN cc_start: 0.8912 (mt0) cc_final: 0.8687 (tt0) REVERT: W 30 MET cc_start: 0.8977 (ttp) cc_final: 0.8553 (ttm) REVERT: L 17 MET cc_start: 0.3167 (mtm) cc_final: 0.2006 (ttt) REVERT: L 59 LEU cc_start: 0.2125 (OUTLIER) cc_final: 0.1899 (mt) REVERT: N 17 MET cc_start: 0.2425 (mtp) cc_final: 0.1289 (tpt) REVERT: O 11 MET cc_start: -0.5304 (tpt) cc_final: -0.5511 (tpt) REVERT: O 17 MET cc_start: -0.1743 (ttm) cc_final: -0.2144 (mmm) REVERT: P 6 MET cc_start: 0.3592 (mmt) cc_final: 0.3057 (ppp) REVERT: P 17 MET cc_start: -0.0122 (mtm) cc_final: -0.1372 (mtm) REVERT: Q 28 ILE cc_start: 0.4329 (mt) cc_final: 0.3822 (mt) REVERT: Q 37 GLU cc_start: 0.8714 (tp30) cc_final: 0.8439 (pt0) REVERT: Q 57 MET cc_start: 0.5521 (tmm) cc_final: 0.4395 (ptm) REVERT: Q 65 MET cc_start: 0.5785 (mtt) cc_final: 0.5360 (tpp) REVERT: X 73 GLN cc_start: 0.8968 (mp-120) cc_final: 0.8732 (mm-40) REVERT: X 83 ARG cc_start: 0.8739 (ttp-110) cc_final: 0.8503 (ttp80) REVERT: X 123 GLN cc_start: 0.9360 (mm110) cc_final: 0.9077 (mm110) REVERT: X 127 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8568 (mp) REVERT: Y 117 ARG cc_start: 0.9082 (mtp180) cc_final: 0.8863 (mtm-85) REVERT: a 6 MET cc_start: -0.0629 (mmp) cc_final: -0.0881 (mtt) REVERT: a 68 THR cc_start: 0.5346 (p) cc_final: 0.4944 (t) REVERT: a 92 ASP cc_start: 0.7891 (m-30) cc_final: 0.7456 (t0) outliers start: 25 outliers final: 4 residues processed: 417 average time/residue: 0.2561 time to fit residues: 166.3174 Evaluate side-chains 270 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 263 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain B residue 418 ARG Chi-restraints excluded: chain G residue 57 HIS Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain X residue 127 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 7.9990 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 chunk 470 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 147 GLN A 186 GLN A 484 GLN B 58 ASN C 147 GLN C 344 ASN C 358 ASN D 35 ASN E 210 ASN ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 365 GLN E 368 GLN F 19 GLN F 208 GLN F 365 GLN F 368 GLN G 126 ASN G 135 GLN W 71 ASN W 73 GLN W 82 ASN I 52 GLN M 42 GLN O 3 ASN R 5 ASN R 52 GLN S 5 ASN X 80 ASN X 106 GLN a 17 ASN a 20 GLN ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 42 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.090697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.052664 restraints weight = 143403.791| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.45 r_work: 0.2828 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37493 Z= 0.166 Angle : 0.660 8.709 50750 Z= 0.347 Chirality : 0.045 0.347 5916 Planarity : 0.004 0.049 6545 Dihedral : 8.418 160.254 5376 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.39 % Favored : 98.58 % Rotamer: Outliers : 1.30 % Allowed : 7.44 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % 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: 0.65 (0.12), residues: 4803 helix: 0.87 (0.10), residues: 2636 sheet: 0.61 (0.21), residues: 536 loop : -0.18 (0.16), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 37 TYR 0.024 0.002 TYR S 10 PHE 0.018 0.002 PHE F 189 TRP 0.014 0.002 TRP a 111 HIS 0.012 0.001 HIS a 14 Details of bonding type rmsd covalent geometry : bond 0.00346 (37493) covalent geometry : angle 0.65989 (50750) hydrogen bonds : bond 0.06152 ( 2210) hydrogen bonds : angle 4.99110 ( 6459) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 295 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: A 86 MET cc_start: 0.8680 (mtt) cc_final: 0.8335 (mtt) REVERT: A 289 ASP cc_start: 0.8272 (t0) cc_final: 0.7964 (t0) REVERT: A 488 GLN cc_start: 0.8993 (mm110) cc_final: 0.8577 (mm110) REVERT: C 386 MET cc_start: 0.9493 (mmm) cc_final: 0.9255 (mmm) REVERT: C 484 GLN cc_start: 0.8984 (tp-100) cc_final: 0.8781 (tm-30) REVERT: D 209 MET cc_start: 0.9190 (ptp) cc_final: 0.8815 (ptp) REVERT: D 366 ARG cc_start: 0.9254 (tpt170) cc_final: 0.8987 (tpp80) REVERT: F 0 MET cc_start: 0.7286 (pmm) cc_final: 0.6874 (pmm) REVERT: F 379 MET cc_start: 0.8373 (tpp) cc_final: 0.7969 (tpp) REVERT: W 124 ILE cc_start: 0.9174 (tt) cc_final: 0.8954 (pt) REVERT: W 145 SER cc_start: 0.8855 (p) cc_final: 0.8459 (p) REVERT: W 147 MET cc_start: 0.8841 (mmt) cc_final: 0.8380 (mmp) REVERT: W 157 MET cc_start: 0.7921 (mpp) cc_final: 0.7705 (mpp) REVERT: I 35 PHE cc_start: 0.5495 (t80) cc_final: 0.5285 (t80) REVERT: J 11 MET cc_start: 0.1292 (mmm) cc_final: 0.0625 (ppp) REVERT: L 17 MET cc_start: 0.2930 (mtm) cc_final: 0.2406 (ttm) REVERT: N 65 MET cc_start: 0.1427 (mmt) cc_final: 0.0359 (ttp) REVERT: O 11 MET cc_start: -0.5330 (tpt) cc_final: -0.5604 (tpt) REVERT: P 6 MET cc_start: 0.4435 (mmt) cc_final: 0.3668 (ppp) REVERT: Q 37 GLU cc_start: 0.8688 (tp30) cc_final: 0.8477 (tp30) REVERT: Q 57 MET cc_start: 0.5977 (tmm) cc_final: 0.5225 (ptm) REVERT: Q 65 MET cc_start: 0.5977 (mtt) cc_final: 0.5114 (tpp) REVERT: R 17 MET cc_start: 0.1456 (mtp) cc_final: 0.1054 (mtm) REVERT: S 6 MET cc_start: 0.8400 (ppp) cc_final: 0.8133 (ppp) REVERT: X 85 GLN cc_start: 0.8864 (mm-40) cc_final: 0.8635 (mp10) REVERT: X 123 GLN cc_start: 0.9133 (mm110) cc_final: 0.8848 (mm110) REVERT: Y 1 MET cc_start: 0.1157 (ttp) cc_final: -0.1269 (mmm) REVERT: Y 78 GLN cc_start: 0.7550 (tp40) cc_final: 0.7279 (mm-40) REVERT: Y 98 ARG cc_start: 0.8602 (tpt170) cc_final: 0.8346 (tpp80) REVERT: a 6 MET cc_start: -0.0225 (mmp) cc_final: -0.0600 (mtt) REVERT: a 92 ASP cc_start: 0.7310 (m-30) cc_final: 0.7018 (t70) REVERT: a 168 MET cc_start: 0.6088 (mmp) cc_final: 0.5837 (ttm) outliers start: 50 outliers final: 13 residues processed: 333 average time/residue: 0.2187 time to fit residues: 121.2404 Evaluate side-chains 270 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 257 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain G residue 57 HIS Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain I residue 3 ASN Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain Y residue 56 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 162 optimal weight: 0.8980 chunk 177 optimal weight: 0.1980 chunk 446 optimal weight: 10.0000 chunk 200 optimal weight: 1.9990 chunk 240 optimal weight: 10.0000 chunk 172 optimal weight: 4.9990 chunk 381 optimal weight: 6.9990 chunk 241 optimal weight: 7.9990 chunk 339 optimal weight: 6.9990 chunk 439 optimal weight: 3.9990 chunk 387 optimal weight: 20.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN F 353 HIS X 64 GLN X 104 GLN a 32 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.089412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.051349 restraints weight = 144179.470| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.48 r_work: 0.2785 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 37493 Z= 0.176 Angle : 0.606 10.420 50750 Z= 0.313 Chirality : 0.043 0.259 5916 Planarity : 0.004 0.046 6545 Dihedral : 7.902 149.184 5368 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.12 % Allowed : 8.64 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % 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: 1.17 (0.12), residues: 4803 helix: 1.45 (0.10), residues: 2631 sheet: 0.64 (0.21), residues: 548 loop : -0.17 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 41 TYR 0.033 0.001 TYR a 263 PHE 0.022 0.001 PHE F 189 TRP 0.011 0.001 TRP G 105 HIS 0.005 0.001 HIS a 14 Details of bonding type rmsd covalent geometry : bond 0.00390 (37493) covalent geometry : angle 0.60579 (50750) hydrogen bonds : bond 0.05522 ( 2210) hydrogen bonds : angle 4.66566 ( 6459) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 259 time to evaluate : 1.645 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 86 MET cc_start: 0.8841 (mtt) cc_final: 0.8460 (mtt) REVERT: A 236 TYR cc_start: 0.9561 (OUTLIER) cc_final: 0.9186 (p90) REVERT: A 289 ASP cc_start: 0.8419 (t0) cc_final: 0.8070 (t0) REVERT: B 386 MET cc_start: 0.9454 (mmt) cc_final: 0.9184 (mmt) REVERT: C 365 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7410 (mmt90) REVERT: C 386 MET cc_start: 0.9525 (mmm) cc_final: 0.9296 (mmm) REVERT: D 209 MET cc_start: 0.9230 (ptp) cc_final: 0.9027 (ptp) REVERT: D 366 ARG cc_start: 0.9265 (tpt170) cc_final: 0.8993 (tpp80) REVERT: E 210 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8503 (m-40) REVERT: F 0 MET cc_start: 0.7459 (pmm) cc_final: 0.7168 (pmm) REVERT: F 379 MET cc_start: 0.8403 (tpp) cc_final: 0.8041 (tpp) REVERT: H 7 ASP cc_start: 0.6519 (t0) cc_final: 0.5807 (p0) REVERT: H 15 MET cc_start: 0.0966 (mtp) cc_final: 0.0649 (mtp) REVERT: W 124 ILE cc_start: 0.9143 (tt) cc_final: 0.8894 (pt) REVERT: W 144 LYS cc_start: 0.9370 (mmmt) cc_final: 0.9136 (mmpt) REVERT: W 157 MET cc_start: 0.7892 (mpp) cc_final: 0.7610 (mpp) REVERT: J 11 MET cc_start: 0.1130 (mmm) cc_final: 0.0395 (ppp) REVERT: L 6 MET cc_start: 0.6166 (mpp) cc_final: 0.5820 (ttp) REVERT: L 17 MET cc_start: 0.2988 (mtm) cc_final: 0.1995 (ttt) REVERT: M 75 MET cc_start: 0.2196 (tmm) cc_final: 0.1625 (ttt) REVERT: N 17 MET cc_start: 0.2174 (mtp) cc_final: 0.0558 (tpt) REVERT: N 35 PHE cc_start: 0.5599 (t80) cc_final: 0.5169 (t80) REVERT: O 11 MET cc_start: -0.5180 (tpt) cc_final: -0.5381 (tpt) REVERT: P 6 MET cc_start: 0.4200 (mmt) cc_final: 0.3599 (ppp) REVERT: Q 37 GLU cc_start: 0.8626 (tp30) cc_final: 0.8416 (tp30) REVERT: Q 57 MET cc_start: 0.5662 (tmm) cc_final: 0.4862 (ptm) REVERT: Q 65 MET cc_start: 0.5737 (mtt) cc_final: 0.4977 (tpp) REVERT: R 17 MET cc_start: 0.1395 (mtp) cc_final: 0.1071 (mtm) REVERT: X 85 GLN cc_start: 0.8857 (mm-40) cc_final: 0.8638 (mp10) REVERT: Y 96 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8375 (pp30) REVERT: Y 98 ARG cc_start: 0.8605 (tpt170) cc_final: 0.8363 (tpp80) REVERT: a 168 MET cc_start: 0.6139 (mmp) cc_final: 0.5789 (ttt) outliers start: 43 outliers final: 22 residues processed: 287 average time/residue: 0.2216 time to fit residues: 105.2534 Evaluate side-chains 275 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 250 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain F residue 19 GLN Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 57 HIS Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain I residue 3 ASN Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain X residue 146 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 240 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 187 optimal weight: 6.9990 chunk 383 optimal weight: 40.0000 chunk 51 optimal weight: 5.9990 chunk 265 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 209 optimal weight: 6.9990 chunk 320 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 164 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 52 GLN ** X 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN Y 85 GLN a 17 ASN a 245 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.089212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.051271 restraints weight = 144386.926| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.36 r_work: 0.2781 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 37493 Z= 0.158 Angle : 0.565 8.422 50750 Z= 0.292 Chirality : 0.042 0.251 5916 Planarity : 0.004 0.048 6545 Dihedral : 7.533 144.879 5368 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.38 % Allowed : 9.39 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % 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: 1.45 (0.12), residues: 4803 helix: 1.74 (0.10), residues: 2629 sheet: 0.66 (0.21), residues: 540 loop : -0.13 (0.16), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 15 TYR 0.023 0.001 TYR a 263 PHE 0.022 0.001 PHE I 35 TRP 0.009 0.001 TRP G 105 HIS 0.005 0.001 HIS a 14 Details of bonding type rmsd covalent geometry : bond 0.00347 (37493) covalent geometry : angle 0.56494 (50750) hydrogen bonds : bond 0.05028 ( 2210) hydrogen bonds : angle 4.46532 ( 6459) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 266 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8911 (mtt) cc_final: 0.8538 (mtt) REVERT: A 236 TYR cc_start: 0.9559 (OUTLIER) cc_final: 0.9099 (p90) REVERT: A 289 ASP cc_start: 0.8377 (t0) cc_final: 0.8046 (t0) REVERT: B 236 TYR cc_start: 0.9465 (OUTLIER) cc_final: 0.9011 (t80) REVERT: C 365 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7337 (mmt90) REVERT: C 386 MET cc_start: 0.9515 (mmm) cc_final: 0.9273 (mmm) REVERT: C 409 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.6814 (p90) REVERT: C 484 GLN cc_start: 0.9000 (tp-100) cc_final: 0.8689 (tm-30) REVERT: D 366 ARG cc_start: 0.9278 (tpt170) cc_final: 0.9004 (tpp80) REVERT: D 379 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8511 (ttm) REVERT: E 210 ASN cc_start: 0.8764 (OUTLIER) cc_final: 0.8399 (m-40) REVERT: F 0 MET cc_start: 0.7372 (pmm) cc_final: 0.7143 (pmm) REVERT: F 379 MET cc_start: 0.8433 (tpp) cc_final: 0.8048 (tpp) REVERT: G 31 MET cc_start: 0.9024 (ttp) cc_final: 0.8793 (ttp) REVERT: G 139 MET cc_start: 0.8135 (mmp) cc_final: 0.7757 (mmp) REVERT: H 7 ASP cc_start: 0.6413 (t0) cc_final: 0.5787 (p0) REVERT: W 109 ASP cc_start: 0.8637 (t0) cc_final: 0.8385 (m-30) REVERT: W 124 ILE cc_start: 0.9102 (tt) cc_final: 0.8853 (pt) REVERT: W 147 MET cc_start: 0.8878 (mmt) cc_final: 0.8557 (mmp) REVERT: W 157 MET cc_start: 0.7881 (mpp) cc_final: 0.7544 (mpp) REVERT: I 35 PHE cc_start: 0.5209 (t80) cc_final: 0.4894 (t80) REVERT: J 11 MET cc_start: 0.1219 (mmm) cc_final: 0.0482 (ppp) REVERT: L 6 MET cc_start: 0.6104 (mpp) cc_final: 0.5725 (ttp) REVERT: L 17 MET cc_start: 0.2538 (mtm) cc_final: 0.1808 (ttt) REVERT: M 6 MET cc_start: -0.0566 (mmp) cc_final: -0.0782 (mmm) REVERT: M 75 MET cc_start: 0.2305 (tmm) cc_final: 0.1831 (ttt) REVERT: N 35 PHE cc_start: 0.5383 (t80) cc_final: 0.5004 (t80) REVERT: P 6 MET cc_start: 0.4221 (mmt) cc_final: 0.3567 (ppp) REVERT: P 11 MET cc_start: -0.2074 (tpp) cc_final: -0.2304 (tpp) REVERT: Q 37 GLU cc_start: 0.8549 (tp30) cc_final: 0.8296 (tp30) REVERT: Q 57 MET cc_start: 0.5756 (tmm) cc_final: 0.4998 (ptm) REVERT: Q 65 MET cc_start: 0.5696 (mtt) cc_final: 0.4909 (tpp) REVERT: R 65 MET cc_start: 0.3476 (mmm) cc_final: 0.2625 (tpt) REVERT: Y 3 LEU cc_start: -0.2993 (OUTLIER) cc_final: -0.3300 (tp) REVERT: Y 98 ARG cc_start: 0.8647 (tpt170) cc_final: 0.8409 (tpp80) REVERT: a 168 MET cc_start: 0.6293 (mmp) cc_final: 0.5933 (ttt) outliers start: 53 outliers final: 29 residues processed: 308 average time/residue: 0.2135 time to fit residues: 109.5083 Evaluate side-chains 288 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 252 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 57 HIS Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain I residue 3 ASN Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 78 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 140 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 457 optimal weight: 30.0000 chunk 367 optimal weight: 7.9990 chunk 433 optimal weight: 50.0000 chunk 438 optimal weight: 5.9990 chunk 436 optimal weight: 9.9990 chunk 220 optimal weight: 1.9990 chunk 113 optimal weight: 0.3980 chunk 67 optimal weight: 0.9990 chunk 467 optimal weight: 9.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.089261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.051429 restraints weight = 144531.985| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.47 r_work: 0.2786 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 37493 Z= 0.146 Angle : 0.556 8.875 50750 Z= 0.285 Chirality : 0.042 0.225 5916 Planarity : 0.004 0.048 6545 Dihedral : 7.291 141.638 5368 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.46 % Allowed : 10.17 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % 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: 1.59 (0.12), residues: 4803 helix: 1.90 (0.10), residues: 2631 sheet: 0.68 (0.21), residues: 542 loop : -0.14 (0.16), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 115 TYR 0.023 0.001 TYR a 263 PHE 0.020 0.001 PHE S 35 TRP 0.010 0.001 TRP G 105 HIS 0.004 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00318 (37493) covalent geometry : angle 0.55552 (50750) hydrogen bonds : bond 0.04804 ( 2210) hydrogen bonds : angle 4.36774 ( 6459) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 256 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8937 (mtt) cc_final: 0.8557 (mtt) REVERT: A 236 TYR cc_start: 0.9584 (OUTLIER) cc_final: 0.9137 (p90) REVERT: A 289 ASP cc_start: 0.8281 (t0) cc_final: 0.8041 (t0) REVERT: B 236 TYR cc_start: 0.9461 (OUTLIER) cc_final: 0.8867 (t80) REVERT: C 386 MET cc_start: 0.9494 (mmm) cc_final: 0.9257 (mmm) REVERT: C 409 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.6704 (p90) REVERT: C 484 GLN cc_start: 0.8977 (tp-100) cc_final: 0.8643 (tm-30) REVERT: D 366 ARG cc_start: 0.9278 (tpt170) cc_final: 0.9004 (tpp80) REVERT: E 210 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.8381 (m-40) REVERT: E 330 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8360 (mp) REVERT: F 379 MET cc_start: 0.8404 (tpp) cc_final: 0.8018 (tpp) REVERT: G 139 MET cc_start: 0.8228 (mmp) cc_final: 0.7963 (mmp) REVERT: H 7 ASP cc_start: 0.6092 (t0) cc_final: 0.5579 (p0) REVERT: H 13 GLN cc_start: 0.5172 (pm20) cc_final: 0.4955 (pm20) REVERT: H 15 MET cc_start: 0.2020 (mtp) cc_final: 0.1416 (mtp) REVERT: W 109 ASP cc_start: 0.8659 (t0) cc_final: 0.8368 (m-30) REVERT: W 124 ILE cc_start: 0.9124 (tt) cc_final: 0.8879 (pt) REVERT: W 147 MET cc_start: 0.8904 (mmt) cc_final: 0.8591 (mmp) REVERT: W 157 MET cc_start: 0.7891 (mpp) cc_final: 0.7532 (mpp) REVERT: I 6 MET cc_start: 0.1851 (tmm) cc_final: 0.1560 (tmm) REVERT: I 35 PHE cc_start: 0.4912 (t80) cc_final: 0.4586 (t80) REVERT: J 11 MET cc_start: 0.1129 (mmm) cc_final: 0.0402 (tmm) REVERT: L 6 MET cc_start: 0.6124 (mpp) cc_final: 0.5715 (ttp) REVERT: L 65 MET cc_start: 0.3711 (ptt) cc_final: 0.2150 (mmm) REVERT: M 6 MET cc_start: -0.0563 (mmp) cc_final: -0.0777 (mmm) REVERT: M 75 MET cc_start: 0.2260 (tmm) cc_final: 0.1744 (ttt) REVERT: N 35 PHE cc_start: 0.5355 (t80) cc_final: 0.4983 (t80) REVERT: P 6 MET cc_start: 0.4027 (mmt) cc_final: 0.3426 (ppp) REVERT: Q 37 GLU cc_start: 0.8571 (tp30) cc_final: 0.8368 (tp30) REVERT: Q 57 MET cc_start: 0.5385 (tmm) cc_final: 0.4713 (ptm) REVERT: Q 65 MET cc_start: 0.5812 (mtt) cc_final: 0.5104 (tpp) REVERT: R 65 MET cc_start: 0.3364 (mmm) cc_final: 0.2605 (tpt) REVERT: S 35 PHE cc_start: 0.4355 (t80) cc_final: 0.3806 (t80) REVERT: X 115 ARG cc_start: 0.8896 (mtp180) cc_final: 0.8656 (mtp-110) REVERT: X 123 GLN cc_start: 0.9013 (mm110) cc_final: 0.8700 (mm110) REVERT: Y 3 LEU cc_start: -0.2946 (OUTLIER) cc_final: -0.3198 (tp) REVERT: Y 98 ARG cc_start: 0.8658 (tpt170) cc_final: 0.8444 (tpp80) REVERT: a 168 MET cc_start: 0.6292 (mmp) cc_final: 0.6022 (ttm) outliers start: 56 outliers final: 28 residues processed: 300 average time/residue: 0.2061 time to fit residues: 103.1537 Evaluate side-chains 285 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 251 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain G residue 57 HIS Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain I residue 3 ASN Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Y residue 104 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 40 optimal weight: 0.2980 chunk 147 optimal weight: 0.9990 chunk 170 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 237 optimal weight: 4.9990 chunk 389 optimal weight: 30.0000 chunk 98 optimal weight: 2.9990 chunk 366 optimal weight: 9.9990 chunk 446 optimal weight: 10.0000 chunk 131 optimal weight: 4.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 67 GLN ** X 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.089408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.051576 restraints weight = 145052.564| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.62 r_work: 0.2791 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37493 Z= 0.136 Angle : 0.545 9.811 50750 Z= 0.278 Chirality : 0.041 0.218 5916 Planarity : 0.004 0.047 6545 Dihedral : 7.065 138.952 5368 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.59 % Allowed : 10.67 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % 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: 1.73 (0.12), residues: 4803 helix: 2.03 (0.10), residues: 2619 sheet: 0.73 (0.21), residues: 544 loop : -0.11 (0.16), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 41 TYR 0.024 0.001 TYR H 63 PHE 0.014 0.001 PHE I 35 TRP 0.009 0.001 TRP G 105 HIS 0.004 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00294 (37493) covalent geometry : angle 0.54484 (50750) hydrogen bonds : bond 0.04578 ( 2210) hydrogen bonds : angle 4.28972 ( 6459) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 264 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8969 (mtt) cc_final: 0.8427 (mtt) REVERT: A 236 TYR cc_start: 0.9588 (OUTLIER) cc_final: 0.9158 (p90) REVERT: A 289 ASP cc_start: 0.8232 (t0) cc_final: 0.7953 (t0) REVERT: B 236 TYR cc_start: 0.9449 (OUTLIER) cc_final: 0.8777 (t80) REVERT: C 365 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7248 (mmt90) REVERT: C 386 MET cc_start: 0.9488 (mmm) cc_final: 0.9227 (mmm) REVERT: C 409 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.6621 (p90) REVERT: C 484 GLN cc_start: 0.8975 (tp-100) cc_final: 0.8631 (tm-30) REVERT: E 330 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8359 (mp) REVERT: F 379 MET cc_start: 0.8437 (tpp) cc_final: 0.8063 (tpp) REVERT: G 139 MET cc_start: 0.8224 (mmp) cc_final: 0.8013 (mmp) REVERT: G 155 MET cc_start: 0.9181 (mmt) cc_final: 0.8859 (mmm) REVERT: H 7 ASP cc_start: 0.6168 (t0) cc_final: 0.5709 (p0) REVERT: H 15 MET cc_start: 0.2071 (mtp) cc_final: 0.1853 (mtp) REVERT: H 51 ARG cc_start: 0.6746 (mtm-85) cc_final: 0.6530 (mmm-85) REVERT: W 67 GLN cc_start: 0.8512 (tp-100) cc_final: 0.8104 (mm-40) REVERT: W 109 ASP cc_start: 0.8665 (t0) cc_final: 0.8316 (m-30) REVERT: W 124 ILE cc_start: 0.9137 (tt) cc_final: 0.8884 (pt) REVERT: W 147 MET cc_start: 0.8905 (mmt) cc_final: 0.8607 (mmp) REVERT: I 35 PHE cc_start: 0.5116 (t80) cc_final: 0.4775 (t80) REVERT: J 11 MET cc_start: 0.1191 (mmm) cc_final: 0.0501 (ppp) REVERT: L 6 MET cc_start: 0.6172 (mpp) cc_final: 0.5814 (ttp) REVERT: L 65 MET cc_start: 0.3866 (ptt) cc_final: 0.2486 (mmm) REVERT: M 75 MET cc_start: 0.2034 (tmm) cc_final: 0.1546 (ttt) REVERT: N 35 PHE cc_start: 0.5172 (t80) cc_final: 0.4753 (t80) REVERT: P 6 MET cc_start: 0.3995 (mmt) cc_final: 0.3423 (ppp) REVERT: P 65 MET cc_start: -0.3146 (mmt) cc_final: -0.3431 (ptp) REVERT: Q 17 MET cc_start: 0.2904 (mpp) cc_final: 0.1526 (mmm) REVERT: Q 57 MET cc_start: 0.5084 (tmm) cc_final: 0.4337 (ptm) REVERT: Q 65 MET cc_start: 0.5837 (mtt) cc_final: 0.5135 (tpp) REVERT: R 17 MET cc_start: 0.1901 (mpp) cc_final: 0.1698 (mpp) REVERT: R 65 MET cc_start: 0.3623 (mmm) cc_final: 0.3055 (tpt) REVERT: X 85 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8600 (mt0) REVERT: X 123 GLN cc_start: 0.8968 (mm110) cc_final: 0.8687 (mm110) REVERT: Y 3 LEU cc_start: -0.2748 (OUTLIER) cc_final: -0.2973 (tp) REVERT: Y 98 ARG cc_start: 0.8648 (tpt170) cc_final: 0.8437 (tpp80) REVERT: Y 113 ARG cc_start: 0.8343 (tmt-80) cc_final: 0.8019 (tmt-80) outliers start: 61 outliers final: 32 residues processed: 310 average time/residue: 0.2167 time to fit residues: 111.6098 Evaluate side-chains 286 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 248 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 57 HIS Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain I residue 3 ASN Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 104 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 381 optimal weight: 8.9990 chunk 367 optimal weight: 10.0000 chunk 127 optimal weight: 0.9990 chunk 326 optimal weight: 6.9990 chunk 428 optimal weight: 20.0000 chunk 88 optimal weight: 0.6980 chunk 420 optimal weight: 10.0000 chunk 235 optimal weight: 0.9990 chunk 246 optimal weight: 3.9990 chunk 466 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 GLN B 27 ASN E 210 ASN ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 GLN ** X 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.089438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.051681 restraints weight = 144875.522| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.67 r_work: 0.2792 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37493 Z= 0.132 Angle : 0.556 11.144 50750 Z= 0.281 Chirality : 0.041 0.217 5916 Planarity : 0.004 0.047 6545 Dihedral : 6.902 137.179 5368 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.33 % Allowed : 11.45 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % 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: 1.81 (0.12), residues: 4803 helix: 2.11 (0.10), residues: 2621 sheet: 0.74 (0.21), residues: 558 loop : -0.10 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG X 115 TYR 0.034 0.001 TYR H 63 PHE 0.023 0.001 PHE S 35 TRP 0.010 0.001 TRP G 105 HIS 0.003 0.001 HIS W 21 Details of bonding type rmsd covalent geometry : bond 0.00284 (37493) covalent geometry : angle 0.55623 (50750) hydrogen bonds : bond 0.04446 ( 2210) hydrogen bonds : angle 4.23620 ( 6459) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 260 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8991 (mtt) cc_final: 0.8425 (mtt) REVERT: A 236 TYR cc_start: 0.9578 (OUTLIER) cc_final: 0.9087 (p90) REVERT: A 289 ASP cc_start: 0.8205 (t0) cc_final: 0.7965 (t0) REVERT: A 356 GLU cc_start: 0.8730 (tp30) cc_final: 0.8426 (tt0) REVERT: B 27 ASN cc_start: 0.8373 (OUTLIER) cc_final: 0.8081 (t0) REVERT: B 236 TYR cc_start: 0.9439 (OUTLIER) cc_final: 0.8681 (t80) REVERT: C 86 MET cc_start: 0.9352 (mtt) cc_final: 0.9143 (mtt) REVERT: C 365 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7240 (mmt90) REVERT: C 386 MET cc_start: 0.9476 (mmm) cc_final: 0.9223 (mmm) REVERT: C 409 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.6573 (p90) REVERT: C 484 GLN cc_start: 0.8989 (tp-100) cc_final: 0.8642 (tm-30) REVERT: E 210 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8252 (m-40) REVERT: E 330 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8364 (mp) REVERT: F 379 MET cc_start: 0.8355 (tpp) cc_final: 0.8148 (tpp) REVERT: G 139 MET cc_start: 0.8210 (mmp) cc_final: 0.7975 (mmp) REVERT: G 243 MET cc_start: 0.8749 (ttp) cc_final: 0.8445 (ttp) REVERT: H 7 ASP cc_start: 0.6155 (t0) cc_final: 0.5698 (p0) REVERT: H 51 ARG cc_start: 0.6774 (mtm-85) cc_final: 0.6462 (tpp80) REVERT: W 67 GLN cc_start: 0.8460 (tp-100) cc_final: 0.8157 (mm-40) REVERT: W 109 ASP cc_start: 0.8686 (t0) cc_final: 0.8307 (m-30) REVERT: W 124 ILE cc_start: 0.9105 (tt) cc_final: 0.8857 (pt) REVERT: W 147 MET cc_start: 0.8917 (mmt) cc_final: 0.8627 (mmp) REVERT: I 35 PHE cc_start: 0.5017 (t80) cc_final: 0.4752 (t80) REVERT: J 11 MET cc_start: 0.1142 (mmm) cc_final: 0.0462 (ppp) REVERT: L 65 MET cc_start: 0.4043 (ptt) cc_final: 0.2724 (mmm) REVERT: M 75 MET cc_start: 0.1893 (tmm) cc_final: 0.1499 (ttt) REVERT: N 16 MET cc_start: -0.0134 (mmt) cc_final: -0.0519 (mmm) REVERT: N 35 PHE cc_start: 0.5067 (t80) cc_final: 0.4666 (t80) REVERT: P 6 MET cc_start: 0.3795 (mmt) cc_final: 0.3248 (ppp) REVERT: P 65 MET cc_start: -0.2944 (mmt) cc_final: -0.3170 (ptp) REVERT: Q 57 MET cc_start: 0.5007 (tmm) cc_final: 0.4254 (ptm) REVERT: Q 65 MET cc_start: 0.5873 (mtt) cc_final: 0.5164 (tpp) REVERT: R 65 MET cc_start: 0.3625 (mmm) cc_final: 0.3063 (tpt) REVERT: X 85 GLN cc_start: 0.8864 (mm-40) cc_final: 0.8644 (mt0) REVERT: X 115 ARG cc_start: 0.8880 (mtp-110) cc_final: 0.8660 (mtm110) REVERT: Y 3 LEU cc_start: -0.2680 (OUTLIER) cc_final: -0.2944 (tp) REVERT: Y 82 ARG cc_start: 0.6908 (mmp80) cc_final: 0.6472 (mmp80) REVERT: Y 98 ARG cc_start: 0.8656 (tpt170) cc_final: 0.8441 (tpp80) REVERT: Y 113 ARG cc_start: 0.8424 (tmt-80) cc_final: 0.8146 (tmt-80) outliers start: 51 outliers final: 30 residues processed: 298 average time/residue: 0.2078 time to fit residues: 103.2145 Evaluate side-chains 288 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 250 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 57 HIS Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain I residue 3 ASN Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 75 MET Chi-restraints excluded: chain Y residue 3 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 346 optimal weight: 10.0000 chunk 287 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 193 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 chunk 447 optimal weight: 10.0000 chunk 263 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 444 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 298 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN E 73 HIS E 210 ASN ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN X 78 GLN ** X 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN a 15 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.088012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.050070 restraints weight = 145239.683| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.52 r_work: 0.2742 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 37493 Z= 0.250 Angle : 0.631 11.856 50750 Z= 0.318 Chirality : 0.043 0.266 5916 Planarity : 0.004 0.054 6545 Dihedral : 7.087 136.162 5368 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.30 % Allowed : 12.24 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % 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: 1.70 (0.12), residues: 4803 helix: 2.05 (0.10), residues: 2621 sheet: 0.63 (0.21), residues: 558 loop : -0.18 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Y 82 TYR 0.026 0.001 TYR H 63 PHE 0.023 0.001 PHE S 35 TRP 0.010 0.001 TRP a 231 HIS 0.014 0.001 HIS B 26 Details of bonding type rmsd covalent geometry : bond 0.00575 (37493) covalent geometry : angle 0.63051 (50750) hydrogen bonds : bond 0.04887 ( 2210) hydrogen bonds : angle 4.36988 ( 6459) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 254 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.9040 (mtt) cc_final: 0.8556 (mtt) REVERT: A 236 TYR cc_start: 0.9667 (OUTLIER) cc_final: 0.9065 (p90) REVERT: A 289 ASP cc_start: 0.8466 (t0) cc_final: 0.8158 (t0) REVERT: A 356 GLU cc_start: 0.8751 (tp30) cc_final: 0.8457 (tt0) REVERT: B 236 TYR cc_start: 0.9523 (OUTLIER) cc_final: 0.9239 (t80) REVERT: C 365 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7408 (mmt90) REVERT: C 386 MET cc_start: 0.9522 (mmm) cc_final: 0.9248 (mmm) REVERT: C 409 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.6729 (p90) REVERT: E 330 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8447 (mp) REVERT: F 379 MET cc_start: 0.8417 (tpp) cc_final: 0.8211 (tpp) REVERT: G 139 MET cc_start: 0.8249 (mmp) cc_final: 0.7982 (mmp) REVERT: H 7 ASP cc_start: 0.6166 (t0) cc_final: 0.5673 (p0) REVERT: H 15 MET cc_start: 0.2217 (mtp) cc_final: 0.1942 (mtp) REVERT: H 51 ARG cc_start: 0.6817 (mtm-85) cc_final: 0.6429 (tpp80) REVERT: W 30 MET cc_start: 0.8932 (ttp) cc_final: 0.8719 (ttm) REVERT: W 67 GLN cc_start: 0.8476 (tp-100) cc_final: 0.8124 (mm-40) REVERT: W 124 ILE cc_start: 0.9128 (tt) cc_final: 0.8879 (pt) REVERT: W 147 MET cc_start: 0.8943 (mmt) cc_final: 0.8658 (mmp) REVERT: I 11 MET cc_start: 0.0018 (ppp) cc_final: -0.0240 (ppp) REVERT: I 17 MET cc_start: 0.3508 (ppp) cc_final: 0.2142 (ttp) REVERT: I 35 PHE cc_start: 0.5086 (t80) cc_final: 0.4811 (t80) REVERT: J 11 MET cc_start: 0.1185 (mmm) cc_final: 0.0496 (tmm) REVERT: L 6 MET cc_start: 0.6195 (mpp) cc_final: 0.5857 (ttp) REVERT: L 16 MET cc_start: 0.0456 (OUTLIER) cc_final: -0.0195 (mmt) REVERT: L 65 MET cc_start: 0.3908 (ptt) cc_final: 0.2554 (mmm) REVERT: M 75 MET cc_start: 0.2055 (tmm) cc_final: 0.1567 (ttt) REVERT: N 6 MET cc_start: 0.0851 (ppp) cc_final: -0.0335 (mpp) REVERT: N 16 MET cc_start: -0.0239 (mmt) cc_final: -0.0623 (mmm) REVERT: N 35 PHE cc_start: 0.5231 (t80) cc_final: 0.4844 (t80) REVERT: P 6 MET cc_start: 0.3791 (mmt) cc_final: 0.3209 (ppp) REVERT: P 16 MET cc_start: -0.3802 (ttm) cc_final: -0.4339 (ptp) REVERT: Q 17 MET cc_start: 0.2611 (mmt) cc_final: 0.2263 (mmt) REVERT: Q 57 MET cc_start: 0.5096 (tmm) cc_final: 0.4355 (ptm) REVERT: Q 65 MET cc_start: 0.5865 (mtt) cc_final: 0.5162 (tpp) REVERT: R 65 MET cc_start: 0.3713 (mmm) cc_final: 0.3144 (tpt) REVERT: X 85 GLN cc_start: 0.8844 (mm-40) cc_final: 0.8626 (mt0) REVERT: Y 3 LEU cc_start: -0.2609 (OUTLIER) cc_final: -0.2865 (tp) REVERT: Y 98 ARG cc_start: 0.8647 (tpt170) cc_final: 0.8439 (tpp80) REVERT: Y 113 ARG cc_start: 0.8353 (tmt-80) cc_final: 0.8083 (tmt-80) outliers start: 50 outliers final: 33 residues processed: 293 average time/residue: 0.2022 time to fit residues: 99.2311 Evaluate side-chains 288 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 248 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 57 HIS Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain I residue 3 ASN Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 16 MET Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain N residue 53 PHE Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain X residue 78 GLN Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Y residue 56 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 432 optimal weight: 10.0000 chunk 268 optimal weight: 0.0020 chunk 167 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 164 optimal weight: 6.9990 chunk 328 optimal weight: 30.0000 chunk 31 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN ** X 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN a 15 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.088992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.051289 restraints weight = 145018.931| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.46 r_work: 0.2779 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 37493 Z= 0.137 Angle : 0.584 12.218 50750 Z= 0.293 Chirality : 0.041 0.265 5916 Planarity : 0.004 0.067 6545 Dihedral : 6.858 131.528 5368 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.17 % Allowed : 12.29 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % 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: 1.80 (0.12), residues: 4803 helix: 2.11 (0.10), residues: 2630 sheet: 0.73 (0.21), residues: 552 loop : -0.14 (0.16), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG Y 82 TYR 0.029 0.001 TYR H 63 PHE 0.023 0.001 PHE S 35 TRP 0.008 0.001 TRP B 513 HIS 0.004 0.001 HIS B 479 Details of bonding type rmsd covalent geometry : bond 0.00296 (37493) covalent geometry : angle 0.58399 (50750) hydrogen bonds : bond 0.04486 ( 2210) hydrogen bonds : angle 4.25937 ( 6459) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 253 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.9016 (mtt) cc_final: 0.8465 (mtt) REVERT: A 236 TYR cc_start: 0.9628 (OUTLIER) cc_final: 0.9026 (p90) REVERT: A 289 ASP cc_start: 0.8262 (t0) cc_final: 0.8009 (t0) REVERT: A 356 GLU cc_start: 0.8733 (tp30) cc_final: 0.8454 (tt0) REVERT: B 236 TYR cc_start: 0.9459 (OUTLIER) cc_final: 0.8793 (t80) REVERT: C 86 MET cc_start: 0.9306 (mtt) cc_final: 0.8955 (mtt) REVERT: C 365 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7293 (mmt90) REVERT: C 386 MET cc_start: 0.9475 (mmm) cc_final: 0.9214 (mmm) REVERT: C 409 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.6668 (p90) REVERT: C 484 GLN cc_start: 0.9039 (tp-100) cc_final: 0.8695 (tm-30) REVERT: E 330 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8396 (mp) REVERT: F 379 MET cc_start: 0.8370 (tpp) cc_final: 0.8160 (tpp) REVERT: G 72 VAL cc_start: 0.7847 (OUTLIER) cc_final: 0.7560 (t) REVERT: G 139 MET cc_start: 0.8221 (mmp) cc_final: 0.7948 (mmp) REVERT: G 243 MET cc_start: 0.8766 (ttp) cc_final: 0.8465 (ttp) REVERT: H 7 ASP cc_start: 0.6092 (t0) cc_final: 0.5649 (p0) REVERT: H 15 MET cc_start: 0.2362 (mtp) cc_final: 0.1946 (mtp) REVERT: H 51 ARG cc_start: 0.6887 (mtm-85) cc_final: 0.6491 (tpp80) REVERT: W 67 GLN cc_start: 0.8475 (tp-100) cc_final: 0.8270 (mm-40) REVERT: W 124 ILE cc_start: 0.9119 (tt) cc_final: 0.8876 (pt) REVERT: W 147 MET cc_start: 0.8929 (mmt) cc_final: 0.8642 (mmp) REVERT: I 17 MET cc_start: 0.3522 (ppp) cc_final: 0.2104 (ttp) REVERT: I 35 PHE cc_start: 0.4949 (t80) cc_final: 0.4733 (t80) REVERT: J 11 MET cc_start: 0.1178 (mmm) cc_final: 0.0471 (tmm) REVERT: L 6 MET cc_start: 0.6227 (mpp) cc_final: 0.5862 (ttp) REVERT: L 65 MET cc_start: 0.4223 (ptt) cc_final: 0.3011 (mmm) REVERT: M 75 MET cc_start: 0.2057 (tmm) cc_final: 0.1531 (ttt) REVERT: N 6 MET cc_start: 0.0803 (ppp) cc_final: -0.0372 (mpp) REVERT: N 11 MET cc_start: 0.3482 (mmm) cc_final: 0.1700 (tpp) REVERT: N 35 PHE cc_start: 0.5159 (t80) cc_final: 0.4800 (t80) REVERT: P 6 MET cc_start: 0.3781 (mmt) cc_final: 0.3175 (ppp) REVERT: P 16 MET cc_start: -0.4026 (ttm) cc_final: -0.4479 (ptp) REVERT: Q 17 MET cc_start: 0.2488 (mmt) cc_final: 0.2174 (mmt) REVERT: Q 57 MET cc_start: 0.5107 (tmm) cc_final: 0.4351 (ptm) REVERT: Q 65 MET cc_start: 0.5842 (mtt) cc_final: 0.5161 (tpp) REVERT: R 17 MET cc_start: 0.1930 (mpp) cc_final: 0.1560 (mpp) REVERT: R 65 MET cc_start: 0.3861 (mmm) cc_final: 0.3277 (tpt) REVERT: X 85 GLN cc_start: 0.8845 (mm-40) cc_final: 0.8610 (mt0) REVERT: Y 3 LEU cc_start: -0.2646 (OUTLIER) cc_final: -0.2897 (tp) REVERT: Y 82 ARG cc_start: 0.7186 (mmp80) cc_final: 0.6878 (mmp-170) REVERT: Y 113 ARG cc_start: 0.8425 (tmt-80) cc_final: 0.8157 (tmt-80) outliers start: 45 outliers final: 29 residues processed: 288 average time/residue: 0.2065 time to fit residues: 99.6213 Evaluate side-chains 286 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 250 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain G residue 57 HIS Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain I residue 3 ASN Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 78 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 14 optimal weight: 0.9990 chunk 425 optimal weight: 0.9980 chunk 346 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 270 optimal weight: 0.8980 chunk 260 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN X 78 GLN ** X 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN a 15 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.089415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.051740 restraints weight = 145145.668| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.55 r_work: 0.2799 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 37493 Z= 0.123 Angle : 0.580 12.751 50750 Z= 0.290 Chirality : 0.041 0.271 5916 Planarity : 0.004 0.073 6545 Dihedral : 6.667 126.267 5368 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.10 % Allowed : 12.52 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % 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: 1.88 (0.12), residues: 4803 helix: 2.18 (0.10), residues: 2626 sheet: 0.76 (0.21), residues: 555 loop : -0.08 (0.16), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG X 83 TYR 0.028 0.001 TYR H 63 PHE 0.028 0.001 PHE S 35 TRP 0.011 0.001 TRP B 513 HIS 0.003 0.001 HIS W 21 Details of bonding type rmsd covalent geometry : bond 0.00261 (37493) covalent geometry : angle 0.58011 (50750) hydrogen bonds : bond 0.04323 ( 2210) hydrogen bonds : angle 4.20712 ( 6459) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 254 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.9010 (mtt) cc_final: 0.8458 (mtt) REVERT: A 236 TYR cc_start: 0.9585 (OUTLIER) cc_final: 0.9056 (p90) REVERT: A 289 ASP cc_start: 0.8151 (t0) cc_final: 0.7913 (t0) REVERT: A 356 GLU cc_start: 0.8724 (tp30) cc_final: 0.8414 (tt0) REVERT: B 236 TYR cc_start: 0.9433 (OUTLIER) cc_final: 0.8676 (t80) REVERT: C 86 MET cc_start: 0.9329 (mtt) cc_final: 0.8943 (mtt) REVERT: C 365 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7286 (mmt90) REVERT: C 386 MET cc_start: 0.9468 (mmm) cc_final: 0.9215 (mmm) REVERT: C 409 PHE cc_start: 0.8113 (OUTLIER) cc_final: 0.6627 (p90) REVERT: C 484 GLN cc_start: 0.9046 (tp-100) cc_final: 0.8690 (tm-30) REVERT: E 330 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8378 (mp) REVERT: F 379 MET cc_start: 0.8386 (tpp) cc_final: 0.8169 (tpp) REVERT: G 72 VAL cc_start: 0.7775 (OUTLIER) cc_final: 0.7498 (t) REVERT: G 139 MET cc_start: 0.8177 (mmp) cc_final: 0.7960 (mmp) REVERT: G 243 MET cc_start: 0.8755 (ttp) cc_final: 0.8493 (ttp) REVERT: H 7 ASP cc_start: 0.6149 (t0) cc_final: 0.5774 (p0) REVERT: H 51 ARG cc_start: 0.6798 (mtm-85) cc_final: 0.6416 (tpp80) REVERT: W 124 ILE cc_start: 0.9117 (tt) cc_final: 0.8876 (pt) REVERT: W 147 MET cc_start: 0.8906 (mmt) cc_final: 0.8618 (mmp) REVERT: I 17 MET cc_start: 0.3171 (ppp) cc_final: 0.1901 (ttp) REVERT: I 35 PHE cc_start: 0.4920 (t80) cc_final: 0.4689 (t80) REVERT: J 11 MET cc_start: 0.1292 (mmm) cc_final: 0.0600 (tmm) REVERT: L 6 MET cc_start: 0.6196 (mpp) cc_final: 0.5858 (ttp) REVERT: L 65 MET cc_start: 0.4301 (ptt) cc_final: 0.3157 (mmm) REVERT: M 75 MET cc_start: 0.1933 (tmm) cc_final: 0.1448 (ttt) REVERT: N 6 MET cc_start: 0.0833 (ppp) cc_final: -0.0274 (mpp) REVERT: N 11 MET cc_start: 0.3560 (mmm) cc_final: 0.1774 (tpp) REVERT: N 35 PHE cc_start: 0.5126 (t80) cc_final: 0.4746 (t80) REVERT: P 6 MET cc_start: 0.3786 (mmt) cc_final: 0.3178 (ppp) REVERT: P 16 MET cc_start: -0.4073 (ttm) cc_final: -0.4595 (ptp) REVERT: Q 57 MET cc_start: 0.5053 (tmm) cc_final: 0.4287 (ptm) REVERT: Q 65 MET cc_start: 0.5775 (mtt) cc_final: 0.5089 (tpp) REVERT: R 65 MET cc_start: 0.3389 (mmm) cc_final: 0.2878 (tpt) REVERT: S 17 MET cc_start: 0.5788 (mtt) cc_final: 0.5527 (ptp) REVERT: S 35 PHE cc_start: 0.4346 (t80) cc_final: 0.3669 (t80) REVERT: Y 3 LEU cc_start: -0.2441 (OUTLIER) cc_final: -0.2694 (tp) REVERT: a 168 MET cc_start: 0.6877 (ttm) cc_final: 0.6089 (ppp) outliers start: 42 outliers final: 27 residues processed: 287 average time/residue: 0.2083 time to fit residues: 100.0538 Evaluate side-chains 285 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 251 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 19 GLN Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain G residue 57 HIS Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain X residue 78 GLN Chi-restraints excluded: chain Y residue 3 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 78 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 90 optimal weight: 6.9990 chunk 267 optimal weight: 4.9990 chunk 247 optimal weight: 4.9990 chunk 219 optimal weight: 4.9990 chunk 154 optimal weight: 0.7980 chunk 240 optimal weight: 0.3980 chunk 21 optimal weight: 0.0030 chunk 43 optimal weight: 0.3980 chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 220 ASN ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN X 78 GLN ** X 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.089685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.052317 restraints weight = 144733.584| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 3.49 r_work: 0.2813 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 37493 Z= 0.115 Angle : 0.580 12.580 50750 Z= 0.289 Chirality : 0.041 0.255 5916 Planarity : 0.004 0.056 6545 Dihedral : 6.536 120.195 5368 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.94 % Allowed : 12.60 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % 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: 1.92 (0.12), residues: 4803 helix: 2.19 (0.10), residues: 2629 sheet: 0.81 (0.21), residues: 556 loop : -0.05 (0.16), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG X 83 TYR 0.029 0.001 TYR H 63 PHE 0.026 0.001 PHE S 35 TRP 0.011 0.001 TRP B 513 HIS 0.003 0.001 HIS G 54 Details of bonding type rmsd covalent geometry : bond 0.00238 (37493) covalent geometry : angle 0.57957 (50750) hydrogen bonds : bond 0.04225 ( 2210) hydrogen bonds : angle 4.16870 ( 6459) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13779.81 seconds wall clock time: 234 minutes 20.73 seconds (14060.73 seconds total)