Starting phenix.real_space_refine on Sat Mar 7 01:55:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dbr_27303/03_2026/8dbr_27303.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbr_27303/03_2026/8dbr_27303.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dbr_27303/03_2026/8dbr_27303.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbr_27303/03_2026/8dbr_27303.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dbr_27303/03_2026/8dbr_27303.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbr_27303/03_2026/8dbr_27303.map" } resolution = 3.2 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 23302 2.51 5 N 6263 2.21 5 O 6913 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 339 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: 36678 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': 2, 'PTRANS': 7, 'TRANS': 274} Chain: "H" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "I" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "J" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "L" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "M" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "N" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "O" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "P" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Q" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "R" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 552 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "S" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "W" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1320 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 3, 'TRANS': 169} Chain: "X" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1200 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 153} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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: 8.59, per 1000 atoms: 0.23 Number of scatterers: 36678 At special positions: 0 Unit cell: (185.588, 216.879, 133.796, 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 6913 8.00 N 6263 7.00 C 23302 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: 3.20 Conformation dependent library (CDL) restraints added in 1.4 seconds 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8746 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 23 sheets defined 61.3% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 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: 3.553A 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: 3.871A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 removed outlier: 3.583A pdb=" N ILE A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 299 removed outlier: 3.512A pdb=" N HIS A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.567A 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: 3.901A pdb=" N ALA A 380 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 391 removed outlier: 3.649A pdb=" N GLY A 391 " --> pdb=" O LYS A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 408 removed outlier: 3.560A pdb=" N GLU A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.696A 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: 3.561A 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: 3.826A pdb=" N ARG A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 4.070A 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 3 through 19 removed outlier: 4.044A pdb=" N GLU B 7 " --> pdb=" O LEU B 3 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N SER B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU B 10 " --> pdb=" O THR B 6 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG B 15 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ILE B 16 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA B 17 " --> pdb=" O LYS B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.534A pdb=" N LEU B 103 " --> pdb=" O GLY B 100 " (cutoff:3.500A) 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: 3.512A pdb=" N ALA B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 3.653A 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 231 through 252 Proline residue: B 239 - end of helix removed outlier: 3.516A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 3.869A 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 removed outlier: 3.574A pdb=" N ALA B 285 " --> pdb=" O GLY B 282 " (cutoff:3.500A) 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: 3.753A pdb=" N ALA B 380 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 408 removed outlier: 4.886A pdb=" N GLY B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG B 394 " --> pdb=" O SER B 390 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N THR B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 431 removed outlier: 4.409A pdb=" N GLN B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 453 Processing helix chain 'B' and resid 460 through 479 removed outlier: 4.107A pdb=" N GLY B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 490 removed outlier: 3.561A 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 231 through 253 Proline residue: C 239 - end of helix removed outlier: 3.620A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.584A 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: 3.646A pdb=" N HIS C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 3.513A 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 363 Processing helix chain 'C' and resid 377 through 382 removed outlier: 3.729A pdb=" N ALA C 380 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 405 removed outlier: 4.145A pdb=" N GLY C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU C 402 " --> pdb=" O ALA C 398 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.824A pdb=" N ALA C 410 " --> pdb=" O SER C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 432 removed outlier: 3.761A pdb=" N LYS C 426 " --> pdb=" O ASP C 422 " (cutoff:3.500A) removed outlier: 4.096A 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 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 Processing helix chain 'D' and resid 154 through 170 removed outlier: 4.043A pdb=" N ILE D 168 " --> pdb=" O ARG D 164 " (cutoff:3.500A) removed outlier: 3.854A 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: 3.548A pdb=" N ARG D 216 " --> pdb=" O PRO D 212 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 256 removed outlier: 3.871A pdb=" N THR D 248 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL D 254 " --> pdb=" O ALA D 250 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 280 removed outlier: 3.555A 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 314 removed outlier: 4.226A pdb=" N ALA D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N HIS D 314 " --> pdb=" O THR D 310 " (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: 4.324A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ILE D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) removed outlier: 3.808A 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: 3.736A 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 432 Processing helix chain 'D' and resid 439 through 443 Processing helix chain 'D' and resid 448 through 458 removed outlier: 3.863A 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: 3.739A 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: 3.691A pdb=" N ILE E 168 " --> pdb=" O ARG E 164 " (cutoff:3.500A) removed outlier: 3.721A 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: 3.610A pdb=" N ARG E 216 " --> pdb=" O PRO E 212 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 258 removed outlier: 4.238A pdb=" N TYR E 247 " --> pdb=" O ASN E 243 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR E 248 " --> pdb=" O ILE E 244 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA E 256 " --> pdb=" O THR E 252 " (cutoff:3.500A) removed outlier: 4.488A 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 313 through 315 No H-bonds generated for 'chain 'E' and resid 313 through 315' Processing helix chain 'E' and resid 322 through 327 Processing helix chain 'E' and resid 345 through 378 removed outlier: 7.767A pdb=" N GLN E 351 " --> pdb=" O LEU E 347 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N GLU E 352 " --> pdb=" O VAL E 348 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N HIS E 353 " --> pdb=" O VAL E 349 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU E 369 " --> pdb=" O GLN E 365 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE E 373 " --> pdb=" O GLU E 369 " (cutoff:3.500A) removed outlier: 4.024A 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: 3.600A 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 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 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: 3.595A pdb=" N ARG F 216 " --> pdb=" O PRO F 212 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 259 removed outlier: 3.522A 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: 3.503A pdb=" N LEU F 278 " --> pdb=" O GLU F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 313 removed outlier: 3.708A pdb=" N ALA F 313 " --> pdb=" O ALA F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 328 removed outlier: 3.696A 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: 4.096A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 3.597A 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: 3.512A 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: 3.891A pdb=" N GLU F 454 " --> pdb=" O GLU F 450 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 57 removed outlier: 3.561A pdb=" N ALA G 11 " --> pdb=" O ARG G 7 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Proline residue: G 43 - end of helix Processing helix chain 'G' and resid 89 through 108 Processing helix chain 'G' and resid 118 through 129 Processing helix chain 'G' and resid 144 through 161 removed outlier: 3.978A pdb=" N LEU G 148 " --> pdb=" O SER G 144 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLY G 150 " --> pdb=" O SER G 146 " (cutoff:3.500A) Proline residue: G 151 - end of helix Processing helix chain 'G' and resid 198 through 203 Processing helix chain 'G' and resid 212 through 283 removed outlier: 3.695A pdb=" N LEU G 218 " --> pdb=" O LEU G 214 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS G 258 " --> pdb=" O GLY G 254 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE G 272 " --> pdb=" O ARG G 268 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 91 through 103 removed outlier: 3.681A pdb=" N GLU H 96 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA H 97 " --> pdb=" O ARG H 93 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS H 98 " --> pdb=" O ALA H 94 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 42 removed outlier: 3.598A pdb=" N LEU I 9 " --> pdb=" O ASN I 5 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET I 11 " --> pdb=" O ASP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 61 removed outlier: 3.725A pdb=" N THR I 51 " --> pdb=" O PRO I 47 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU I 59 " --> pdb=" O ILE I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 77 Processing helix chain 'J' and resid 4 through 42 removed outlier: 3.990A pdb=" N LEU J 8 " --> pdb=" O LEU J 4 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET J 11 " --> pdb=" O ASP J 7 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA J 25 " --> pdb=" O ALA J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 61 removed outlier: 3.697A 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: 4.157A pdb=" N LEU L 8 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU L 9 " --> pdb=" O ASN L 5 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR L 10 " --> pdb=" O MET L 6 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET L 11 " --> pdb=" O ASP L 7 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET L 16 " --> pdb=" O ALA L 12 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE L 28 " --> pdb=" O ALA L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 61 removed outlier: 3.829A pdb=" N THR L 51 " --> pdb=" O PRO L 47 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY L 58 " --> pdb=" O PHE L 54 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU L 59 " --> pdb=" O ILE L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 77 removed outlier: 3.714A pdb=" N ILE L 66 " --> pdb=" O ALA L 62 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE L 76 " --> pdb=" O LEU L 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 42 removed outlier: 3.532A pdb=" N MET M 11 " --> pdb=" O ASP M 7 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN M 42 " --> pdb=" O GLY M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 61 removed outlier: 3.798A pdb=" N THR M 51 " --> pdb=" O PRO M 47 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU M 59 " --> pdb=" O ILE M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 77 Processing helix chain 'N' and resid 4 through 42 removed outlier: 5.037A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET N 16 " --> pdb=" O ALA N 12 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA N 21 " --> pdb=" O MET N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 61 removed outlier: 3.537A pdb=" N THR N 51 " --> pdb=" O PRO N 47 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY N 58 " --> pdb=" O PHE N 54 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU N 59 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL N 60 " --> pdb=" O VAL N 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 77 Processing helix chain 'O' and resid 5 through 42 removed outlier: 4.062A pdb=" N LEU O 9 " --> pdb=" O ASN O 5 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR O 10 " --> pdb=" O MET O 6 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE O 28 " --> pdb=" O ALA O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 61 removed outlier: 3.796A pdb=" N THR O 51 " --> pdb=" O PRO O 47 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE O 54 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU O 59 " --> pdb=" O ILE O 55 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP O 61 " --> pdb=" O MET O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 77 Processing helix chain 'P' and resid 5 through 42 removed outlier: 3.632A pdb=" N LEU P 9 " --> pdb=" O ASN P 5 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA P 21 " --> pdb=" O MET P 17 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS P 34 " --> pdb=" O ILE P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 77 removed outlier: 3.729A pdb=" N LEU P 59 " --> pdb=" O ILE P 55 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) Proline residue: P 64 - end of helix removed outlier: 3.793A pdb=" N ALA P 67 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 42 removed outlier: 3.726A pdb=" N LEU Q 8 " --> pdb=" O LEU Q 4 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR Q 10 " --> pdb=" O MET Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 77 removed outlier: 3.825A pdb=" N THR Q 51 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE Q 55 " --> pdb=" O THR Q 51 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU Q 59 " --> pdb=" O ILE Q 55 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE Q 63 " --> pdb=" O LEU Q 59 " (cutoff:3.500A) Proline residue: Q 64 - end of helix removed outlier: 3.573A pdb=" N ALA Q 67 " --> pdb=" O ILE Q 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 42 removed outlier: 3.817A pdb=" N LEU R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA R 21 " --> pdb=" O MET R 17 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE R 28 " --> pdb=" O ALA R 24 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS R 34 " --> pdb=" O ILE R 30 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN R 42 " --> pdb=" O GLY R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 61 removed outlier: 3.505A pdb=" N GLN R 52 " --> pdb=" O LEU R 48 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU R 59 " --> pdb=" O ILE R 55 " (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: 3.621A pdb=" N MET S 16 " --> pdb=" O ALA S 12 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 61 removed outlier: 3.547A pdb=" N GLY S 58 " --> pdb=" O PHE S 54 " (cutoff:3.500A) removed outlier: 3.828A 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 'W' and resid 3 through 21 removed outlier: 3.605A pdb=" N ARG W 8 " --> pdb=" O ILE W 4 " (cutoff:3.500A) Proline residue: W 9 - end of helix Processing helix chain 'W' and resid 23 through 38 Processing helix chain 'W' and resid 40 through 49 removed outlier: 3.666A pdb=" N GLU W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 63 removed outlier: 3.580A pdb=" N SER W 59 " --> pdb=" O THR W 55 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL W 63 " --> pdb=" O SER W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 68 through 82 removed outlier: 4.385A pdb=" N ASN W 74 " --> pdb=" O GLU W 70 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN W 82 " --> pdb=" O VAL W 78 " (cutoff:3.500A) Processing helix chain 'W' and resid 83 through 86 removed outlier: 4.932A pdb=" N ASN W 86 " --> pdb=" O GLY W 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 83 through 86' Processing helix chain 'W' and resid 87 through 103 removed outlier: 3.608A pdb=" N GLU W 93 " --> pdb=" O PRO W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 117 through 133 removed outlier: 3.705A pdb=" N LYS W 130 " --> pdb=" O ALA W 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 162 through 172 Processing helix chain 'X' and resid 5 through 24 Processing helix chain 'X' and resid 25 through 124 removed outlier: 3.649A pdb=" N GLU X 39 " --> pdb=" O LYS X 35 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN X 73 " --> pdb=" O LYS X 69 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL X 74 " --> pdb=" O ALA X 70 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN X 96 " --> pdb=" O ALA X 92 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS X 100 " --> pdb=" O GLN X 96 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA X 107 " --> pdb=" O ALA X 103 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA X 111 " --> pdb=" O ALA X 107 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS X 114 " --> pdb=" O GLU X 110 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU X 118 " --> pdb=" O LYS X 114 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU X 119 " --> pdb=" O ARG X 115 " (cutoff:3.500A) Processing helix chain 'X' and resid 127 through 136 removed outlier: 3.744A pdb=" N LYS X 134 " --> pdb=" O ALA X 130 " (cutoff:3.500A) Processing helix chain 'X' and resid 146 through 156 Processing helix chain 'Y' and resid 2 through 25 removed outlier: 3.564A pdb=" N THR Y 6 " --> pdb=" O ASN Y 2 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 138 removed outlier: 3.782A pdb=" N LEU Y 29 " --> pdb=" O VAL Y 25 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU Y 39 " --> pdb=" O LYS Y 35 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE Y 40 " --> pdb=" O ARG Y 36 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP Y 55 " --> pdb=" O HIS Y 51 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS Y 58 " --> pdb=" O LEU Y 54 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLU Y 95 " --> pdb=" O LYS Y 91 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA Y 103 " --> pdb=" O THR Y 99 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE Y 126 " --> pdb=" O LYS Y 122 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU Y 127 " --> pdb=" O GLN Y 123 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS Y 134 " --> pdb=" O ALA Y 130 " (cutoff:3.500A) Processing helix chain 'Y' and resid 141 through 154 removed outlier: 3.507A pdb=" N ALA Y 154 " --> pdb=" O ASP Y 150 " (cutoff:3.500A) Processing helix chain 'a' and resid 7 through 16 removed outlier: 3.550A pdb=" N GLY a 13 " --> pdb=" O GLN a 9 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU a 16 " --> pdb=" O ILE a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 43 through 65 Processing helix chain 'a' and resid 75 through 94 removed outlier: 3.525A pdb=" N VAL a 82 " --> pdb=" O ALA a 78 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET a 93 " --> pdb=" O SER a 89 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 118 removed outlier: 3.599A 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 removed outlier: 3.567A pdb=" N ALA a 145 " --> pdb=" O VAL a 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 142 through 145' Processing helix chain 'a' and resid 146 through 181 removed outlier: 3.826A pdb=" N THR a 150 " --> pdb=" O ASP a 146 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS a 169 " --> pdb=" O SER a 165 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE a 171 " --> pdb=" O LYS a 167 " (cutoff:3.500A) removed outlier: 9.596A pdb=" N GLY a 172 " --> pdb=" O MET a 168 " (cutoff:3.500A) removed outlier: 3.514A 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: 4.064A pdb=" N ILE a 194 " --> pdb=" O PRO a 190 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 4.142A pdb=" N ILE a 221 " --> pdb=" O ALA a 217 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 269 removed outlier: 4.670A pdb=" N TRP a 235 " --> pdb=" O TRP a 231 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE a 236 " --> pdb=" O TRP a 232 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU a 237 " --> pdb=" O SER a 233 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 3.535A pdb=" N PHE a 244 " --> pdb=" O PRO a 240 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR a 250 " --> pdb=" O ILE a 246 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE a 256 " --> pdb=" O GLN a 252 " (cutoff:3.500A) removed outlier: 3.825A 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: 4.329A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ARG A 93 " --> pdb=" O MET A 52 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N SER A 54 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR A 91 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASP D 67 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLN D 32 " --> pdb=" O ASP D 67 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ARG D 52 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N GLN D 45 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ILE D 50 " --> pdb=" O GLN D 45 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.462A 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: 3.506A pdb=" N ILE A 198 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA A 256 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N LEU A 327 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE A 258 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE A 329 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N TYR A 260 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N GLU A 331 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU A 166 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N LEU A 355 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.687A 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: 4.479A pdb=" N ILE A 159 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 25 through 35 removed outlier: 6.449A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.764A 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: 5.822A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 3.708A 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: 6.678A pdb=" N ARG E 52 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLN E 45 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 7.401A 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 140 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 135 through 140 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 Processing sheet with id=AA8, first strand: chain 'B' and resid 329 through 331 removed outlier: 6.482A pdb=" N ILE B 167 " --> pdb=" O ILE B 330 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.387A 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: 4.348A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ARG C 93 " --> pdb=" O MET C 52 " (cutoff:3.500A) removed outlier: 6.449A 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: 6.327A pdb=" N ARG C 40 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL C 34 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASP F 67 " --> pdb=" O GLN F 32 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLN F 32 " --> pdb=" O ASP F 67 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA F 28 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N VAL F 42 " --> pdb=" O ILE F 54 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE F 54 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.530A 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: 4.513A 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: 6.445A pdb=" N VAL D 237 " --> pdb=" O THR D 291 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N VAL D 293 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU D 239 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ALA D 295 " --> pdb=" O LEU D 239 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL D 241 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N TYR D 297 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL D 145 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL D 296 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU D 147 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 125 through 126 removed outlier: 4.636A 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: 6.314A pdb=" N MET E 88 " --> pdb=" O TYR E 206 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL E 145 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL E 296 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU E 147 " --> pdb=" O VAL E 296 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS E 144 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N VAL E 319 " --> pdb=" O LYS E 144 " (cutoff:3.500A) removed outlier: 6.264A 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: 3.978A 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: 3.534A pdb=" N VAL F 79 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 4.729A 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: 6.033A pdb=" N MET F 88 " --> pdb=" O TYR F 206 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N GLN F 208 " --> pdb=" O MET F 88 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N SER F 174 " --> pdb=" O SER F 203 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N VAL F 205 " --> pdb=" O SER F 174 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N PHE F 176 " --> pdb=" O VAL F 205 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N GLY F 207 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLY F 178 " --> pdb=" O GLY F 207 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR F 173 " --> pdb=" O ASP F 236 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL F 237 " --> pdb=" O THR F 291 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N VAL F 293 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU F 239 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ALA F 295 " --> pdb=" O LEU F 239 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL F 241 " --> pdb=" O ALA F 295 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL F 145 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS F 144 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N VAL F 319 " --> pdb=" O LYS F 144 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLY F 146 " --> pdb=" O VAL F 319 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 132 through 136 removed outlier: 6.810A pdb=" N VAL G 132 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU G 114 " --> pdb=" O VAL G 132 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA G 134 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL G 75 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N ALA G 115 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TYR G 77 " --> pdb=" O ALA G 115 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ILE G 117 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL G 79 " --> pdb=" O ILE G 117 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ARG G 74 " --> pdb=" O LYS G 166 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N TYR G 168 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLY G 76 " --> pdb=" O TYR G 168 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL G 170 " --> pdb=" O GLY G 76 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU G 78 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N ASN G 172 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N VAL G 80 " --> pdb=" O ASN G 172 " (cutoff:3.500A) removed outlier: 11.927A pdb=" N PHE G 174 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU G 167 " --> pdb=" O LEU G 187 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 206 through 208 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 206 through 208 current: chain 'H' and resid 13 through 26 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 31 through 34 current: chain 'H' and resid 58 through 64 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 58 through 64 current: chain 'H' and resid 75 through 79 Processing sheet with id=AC5, first strand: chain 'a' and resid 20 through 22 2166 hydrogen bonds defined for protein. 6342 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: 7.01 Time building geometry restraints manager: 4.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 6370 1.31 - 1.44: 8683 1.44 - 1.57: 21794 1.57 - 1.69: 26 1.69 - 1.82: 358 Bond restraints: 37231 Sorted by residual: bond pdb=" C VAL a 50 " pdb=" N VAL a 51 " ideal model delta sigma weight residual 1.334 1.471 -0.137 1.26e-02 6.30e+03 1.19e+02 bond pdb=" C4 ATP D 502 " pdb=" C5 ATP D 502 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.57e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " 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 1.456 -0.068 1.00e-02 1.00e+04 4.60e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.57e+01 ... (remaining 37226 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.18: 50133 5.18 - 10.37: 254 10.37 - 15.55: 7 15.55 - 20.74: 3 20.74 - 25.92: 2 Bond angle restraints: 50399 Sorted by residual: angle pdb=" PB ATP D 502 " pdb=" O3B ATP D 502 " pdb=" PG ATP D 502 " ideal model delta sigma weight residual 139.87 113.95 25.92 1.00e+00 1.00e+00 6.72e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 117.03 22.84 1.00e+00 1.00e+00 5.22e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 119.18 20.69 1.00e+00 1.00e+00 4.28e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 120.53 19.34 1.00e+00 1.00e+00 3.74e+02 angle pdb=" PA ATP D 502 " pdb=" O3A ATP D 502 " pdb=" PB ATP D 502 " ideal model delta sigma weight residual 136.83 119.43 17.40 1.00e+00 1.00e+00 3.03e+02 ... (remaining 50394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.24: 21833 28.24 - 56.48: 674 56.48 - 84.73: 108 84.73 - 112.97: 16 112.97 - 141.21: 3 Dihedral angle restraints: 22634 sinusoidal: 8960 harmonic: 13674 Sorted by residual: 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 300.00 158.79 141.21 1 2.00e+01 2.50e-03 4.27e+01 dihedral pdb=" O1B ADP E 501 " pdb=" O3A ADP E 501 " pdb=" PB ADP E 501 " pdb=" PA ADP E 501 " ideal model delta sinusoidal sigma weight residual -60.00 65.76 -125.76 1 2.00e+01 2.50e-03 3.80e+01 dihedral pdb=" C5' ADP E 501 " pdb=" O5' ADP E 501 " pdb=" PA ADP E 501 " pdb=" O2A ADP E 501 " ideal model delta sinusoidal sigma weight residual -60.00 -179.08 119.08 1 2.00e+01 2.50e-03 3.57e+01 ... (remaining 22631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 4951 0.091 - 0.182: 807 0.182 - 0.274: 92 0.274 - 0.365: 18 0.365 - 0.456: 7 Chirality restraints: 5875 Sorted by residual: chirality pdb=" CB ILE Q 63 " pdb=" CA ILE Q 63 " pdb=" CG1 ILE Q 63 " pdb=" CG2 ILE Q 63 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.46 2.00e-01 2.50e+01 5.20e+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 2.23 0.42 2.00e-01 2.50e+01 4.32e+00 chirality pdb=" CB ILE P 63 " pdb=" CA ILE P 63 " pdb=" CG1 ILE P 63 " pdb=" CG2 ILE P 63 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.80e+00 ... (remaining 5872 not shown) Planarity restraints: 6501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG X 36 " -0.130 9.50e-02 1.11e+02 7.68e-02 3.32e+01 pdb=" NE ARG X 36 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG X 36 " -0.095 2.00e-02 2.50e+03 pdb=" NH1 ARG X 36 " 0.034 2.00e-02 2.50e+03 pdb=" NH2 ARG X 36 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 281 " -0.126 9.50e-02 1.11e+02 6.98e-02 2.29e+01 pdb=" NE ARG D 281 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG D 281 " -0.078 2.00e-02 2.50e+03 pdb=" NH1 ARG D 281 " 0.028 2.00e-02 2.50e+03 pdb=" NH2 ARG D 281 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 268 " -0.022 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" C VAL A 268 " 0.075 2.00e-02 2.50e+03 pdb=" O VAL A 268 " -0.028 2.00e-02 2.50e+03 pdb=" N ALA A 269 " -0.025 2.00e-02 2.50e+03 ... (remaining 6498 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 49 2.49 - 3.09: 26755 3.09 - 3.70: 54342 3.70 - 4.30: 81874 4.30 - 4.90: 137191 Nonbonded interactions: 300211 Sorted by model distance: nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.890 2.170 nonbonded pdb=" O2G ATP C 600 " pdb="MG MG C 601 " model vdw 1.899 2.170 nonbonded pdb=" O2G ATP A 600 " pdb="MG MG A 601 " model vdw 1.899 2.170 nonbonded pdb="MG MG D 501 " pdb=" O1G ATP D 502 " model vdw 1.930 2.170 nonbonded pdb=" O2B ATP A 600 " pdb="MG MG A 601 " model vdw 2.033 2.170 ... (remaining 300206 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' and (resid 1 through 80 or (resid 81 through 82 and (name N or name C \ A or name C or name O or name CB )) or resid 83 through 156)) } 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: 3.590 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: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 32.870 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.110 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:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 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 0.137 37231 Z= 0.495 Angle : 1.284 25.924 50399 Z= 0.833 Chirality : 0.070 0.456 5875 Planarity : 0.008 0.110 6501 Dihedral : 14.490 141.209 13888 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.68 % Favored : 97.25 % Rotamer: Outliers : 0.74 % Allowed : 4.34 % Favored : 94.93 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 4.47 % 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: -1.64 (0.11), residues: 4770 helix: -1.39 (0.09), residues: 2557 sheet: 0.24 (0.21), residues: 525 loop : -0.70 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.097 0.011 ARG X 36 TYR 0.042 0.007 TYR D 26 PHE 0.059 0.005 PHE O 54 TRP 0.047 0.005 TRP a 111 HIS 0.016 0.003 HIS W 21 Details of bonding type rmsd covalent geometry : bond 0.01008 (37231) covalent geometry : angle 1.28435 (50399) hydrogen bonds : bond 0.22877 ( 2166) hydrogen bonds : angle 8.65657 ( 6342) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 571 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 TYR cc_start: 0.9336 (OUTLIER) cc_final: 0.8388 (t80) REVERT: A 289 ASP cc_start: 0.7697 (t0) cc_final: 0.7121 (t0) REVERT: A 468 GLU cc_start: 0.8603 (tt0) cc_final: 0.8360 (tm-30) REVERT: B 456 LEU cc_start: 0.9226 (mt) cc_final: 0.9021 (pp) REVERT: E 88 MET cc_start: 0.8815 (mtm) cc_final: 0.8604 (mtm) REVERT: E 159 MET cc_start: 0.8849 (ttp) cc_final: 0.8633 (ttm) REVERT: E 226 MET cc_start: 0.8728 (mtt) cc_final: 0.8526 (mtp) REVERT: E 445 MET cc_start: 0.8245 (mtt) cc_final: 0.7947 (mpp) REVERT: F 445 MET cc_start: 0.8906 (mmt) cc_final: 0.8680 (mmt) REVERT: G 59 ASN cc_start: 0.4574 (OUTLIER) cc_final: 0.4102 (p0) REVERT: H 24 GLN cc_start: 0.8291 (tt0) cc_final: 0.8074 (tm-30) REVERT: H 61 PHE cc_start: 0.8012 (m-80) cc_final: 0.7801 (m-10) REVERT: H 63 TYR cc_start: 0.8235 (t80) cc_final: 0.8013 (t80) REVERT: H 70 GLU cc_start: 0.8431 (pt0) cc_final: 0.8199 (pp20) REVERT: I 11 MET cc_start: 0.7130 (tpp) cc_final: 0.6728 (tpt) REVERT: I 17 MET cc_start: 0.5177 (ptp) cc_final: 0.4707 (ptm) REVERT: J 54 PHE cc_start: 0.6336 (m-10) cc_final: 0.5758 (t80) REVERT: L 16 MET cc_start: 0.4808 (mtm) cc_final: 0.4137 (mtp) REVERT: L 26 ILE cc_start: 0.4828 (mt) cc_final: 0.4600 (mm) REVERT: M 6 MET cc_start: 0.7059 (mtt) cc_final: 0.6750 (ppp) REVERT: M 53 PHE cc_start: 0.8292 (t80) cc_final: 0.7821 (t80) REVERT: N 16 MET cc_start: -0.2031 (mtp) cc_final: -0.2761 (tpp) REVERT: N 17 MET cc_start: 0.1364 (mtp) cc_final: 0.0916 (tpt) REVERT: N 78 VAL cc_start: 0.0246 (m) cc_final: -0.0303 (t) REVERT: O 37 GLU cc_start: 0.8762 (tt0) cc_final: 0.8547 (tt0) REVERT: P 44 ASP cc_start: 0.8114 (m-30) cc_final: 0.7792 (p0) REVERT: P 49 LEU cc_start: 0.9006 (mt) cc_final: 0.8553 (tp) REVERT: Q 16 MET cc_start: 0.5495 (ttt) cc_final: 0.4756 (tpp) REVERT: R 6 MET cc_start: 0.5680 (mmt) cc_final: 0.5144 (tpp) REVERT: W 68 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8684 (tt) REVERT: W 102 SER cc_start: 0.8394 (t) cc_final: 0.8139 (p) REVERT: W 111 ILE cc_start: 0.9102 (mt) cc_final: 0.8846 (mm) REVERT: X 74 VAL cc_start: 0.8951 (m) cc_final: 0.8601 (p) REVERT: X 135 ILE cc_start: 0.6838 (OUTLIER) cc_final: 0.6400 (pp) REVERT: X 147 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7588 (m-30) REVERT: Y 39 GLU cc_start: 0.7956 (tt0) cc_final: 0.7604 (tm-30) REVERT: a 177 GLU cc_start: 0.4972 (mt-10) cc_final: 0.4595 (tm-30) REVERT: a 219 GLU cc_start: 0.6480 (tt0) cc_final: 0.6199 (tt0) outliers start: 28 outliers final: 5 residues processed: 594 average time/residue: 0.2498 time to fit residues: 234.5642 Evaluate side-chains 350 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 340 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain G residue 59 ASN Chi-restraints excluded: chain W residue 68 LEU Chi-restraints excluded: chain X residue 135 ILE Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain X residue 147 ASP Chi-restraints excluded: chain a residue 20 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 20.0000 chunk 455 optimal weight: 8.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN A 186 GLN B 58 ASN C 147 GLN C 344 ASN C 399 GLN C 479 HIS E 368 GLN F 19 GLN F 45 GLN F 365 GLN F 368 GLN H 5 HIS H 55 GLN I 52 GLN M 5 ASN O 3 ASN O 42 GLN O 52 GLN P 42 GLN Q 52 GLN S 3 ASN S 5 ASN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 37 GLN X 51 HIS a 17 ASN a 20 GLN ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 234 GLN ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.092704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.055450 restraints weight = 123540.799| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.01 r_work: 0.2858 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 37231 Z= 0.169 Angle : 0.678 9.015 50399 Z= 0.359 Chirality : 0.045 0.342 5875 Planarity : 0.005 0.046 6501 Dihedral : 7.835 132.827 5344 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.17 % Favored : 98.81 % Rotamer: Outliers : 1.60 % Allowed : 8.12 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 0.53 (0.12), residues: 4770 helix: 0.68 (0.10), residues: 2609 sheet: 0.74 (0.21), residues: 520 loop : -0.11 (0.16), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 93 TYR 0.031 0.002 TYR R 10 PHE 0.021 0.002 PHE P 53 TRP 0.027 0.002 TRP X 26 HIS 0.012 0.001 HIS a 14 Details of bonding type rmsd covalent geometry : bond 0.00333 (37231) covalent geometry : angle 0.67816 (50399) hydrogen bonds : bond 0.06282 ( 2166) hydrogen bonds : angle 5.07471 ( 6342) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 397 time to evaluate : 1.450 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 236 TYR cc_start: 0.9467 (OUTLIER) cc_final: 0.8568 (t80) REVERT: A 289 ASP cc_start: 0.8397 (t0) cc_final: 0.7762 (t0) REVERT: A 468 GLU cc_start: 0.8762 (tt0) cc_final: 0.8512 (tm-30) REVERT: B 76 MET cc_start: 0.9307 (OUTLIER) cc_final: 0.9046 (mtp) REVERT: E 275 MET cc_start: 0.9103 (tpp) cc_final: 0.8777 (ttp) REVERT: E 379 MET cc_start: 0.8467 (tmm) cc_final: 0.8238 (tmm) REVERT: F 56 MET cc_start: 0.9596 (mmm) cc_final: 0.9354 (mmm) REVERT: F 242 ASP cc_start: 0.8073 (t0) cc_final: 0.7521 (t0) REVERT: F 445 MET cc_start: 0.8957 (mmt) cc_final: 0.8565 (mmt) REVERT: H 13 GLN cc_start: 0.8537 (pt0) cc_final: 0.8136 (pm20) REVERT: H 24 GLN cc_start: 0.8266 (tt0) cc_final: 0.7927 (tm-30) REVERT: H 31 GLU cc_start: 0.6829 (pm20) cc_final: 0.6537 (pm20) REVERT: H 49 MET cc_start: 0.7347 (tpp) cc_final: 0.7125 (tpp) REVERT: H 63 TYR cc_start: 0.8272 (t80) cc_final: 0.7942 (t80) REVERT: H 70 GLU cc_start: 0.8410 (pt0) cc_final: 0.7828 (pp20) REVERT: J 53 PHE cc_start: 0.6933 (t80) cc_final: 0.6145 (t80) REVERT: L 16 MET cc_start: 0.4423 (mtm) cc_final: 0.3968 (mtp) REVERT: L 54 PHE cc_start: 0.6096 (m-10) cc_final: 0.4519 (t80) REVERT: M 6 MET cc_start: 0.7146 (mtt) cc_final: 0.6927 (ppp) REVERT: M 54 PHE cc_start: 0.5375 (m-80) cc_final: 0.4170 (t80) REVERT: N 16 MET cc_start: -0.2297 (mtp) cc_final: -0.2778 (tpp) REVERT: N 17 MET cc_start: 0.1856 (mtp) cc_final: 0.1543 (tpt) REVERT: O 17 MET cc_start: 0.5730 (mtm) cc_final: 0.5370 (mtt) REVERT: P 22 ILE cc_start: 0.8087 (mm) cc_final: 0.7854 (mm) REVERT: P 31 LEU cc_start: 0.8680 (tp) cc_final: 0.8185 (mt) REVERT: P 44 ASP cc_start: 0.7769 (m-30) cc_final: 0.7464 (p0) REVERT: P 49 LEU cc_start: 0.8984 (mt) cc_final: 0.8531 (tp) REVERT: Q 11 MET cc_start: 0.2830 (tpp) cc_final: 0.2543 (mmp) REVERT: Q 16 MET cc_start: 0.5058 (ttt) cc_final: 0.4695 (ttm) REVERT: R 11 MET cc_start: 0.6207 (tpp) cc_final: 0.4935 (mmt) REVERT: S 16 MET cc_start: 0.5583 (ttm) cc_final: 0.5241 (ttt) REVERT: W 67 GLN cc_start: 0.8821 (mt0) cc_final: 0.8502 (tt0) REVERT: W 88 LEU cc_start: 0.9134 (mt) cc_final: 0.8904 (mt) REVERT: W 102 SER cc_start: 0.8708 (t) cc_final: 0.8257 (p) REVERT: W 109 ASP cc_start: 0.8395 (t70) cc_final: 0.8009 (t0) REVERT: W 111 ILE cc_start: 0.9225 (mt) cc_final: 0.8913 (mm) REVERT: X 74 VAL cc_start: 0.8733 (m) cc_final: 0.8432 (p) REVERT: a 61 ARG cc_start: 0.5886 (tpt170) cc_final: 0.5423 (mmm160) REVERT: a 177 GLU cc_start: 0.5114 (mt-10) cc_final: 0.4764 (tm-30) outliers start: 61 outliers final: 21 residues processed: 436 average time/residue: 0.2210 time to fit residues: 159.2053 Evaluate side-chains 342 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 319 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain S residue 3 ASN Chi-restraints excluded: chain W residue 145 SER Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain Y residue 15 VAL Chi-restraints excluded: chain a residue 140 ARG Chi-restraints excluded: chain a residue 216 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 184 optimal weight: 0.9990 chunk 356 optimal weight: 8.9990 chunk 436 optimal weight: 6.9990 chunk 373 optimal weight: 0.5980 chunk 127 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 350 optimal weight: 8.9990 chunk 389 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 386 optimal weight: 6.9990 chunk 270 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 220 ASN H 14 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 5 ASN ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 32 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.092734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.055783 restraints weight = 123705.712| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.96 r_work: 0.2860 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 37231 Z= 0.138 Angle : 0.588 8.979 50399 Z= 0.306 Chirality : 0.043 0.272 5875 Planarity : 0.004 0.046 6501 Dihedral : 7.189 124.980 5330 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.47 % Favored : 98.51 % Rotamer: Outliers : 1.39 % Allowed : 9.62 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 1.07 (0.12), residues: 4770 helix: 1.23 (0.10), residues: 2630 sheet: 0.80 (0.21), residues: 523 loop : -0.03 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 323 TYR 0.018 0.001 TYR A 236 PHE 0.023 0.001 PHE S 53 TRP 0.033 0.002 TRP X 26 HIS 0.007 0.001 HIS a 14 Details of bonding type rmsd covalent geometry : bond 0.00272 (37231) covalent geometry : angle 0.58773 (50399) hydrogen bonds : bond 0.05553 ( 2166) hydrogen bonds : angle 4.71078 ( 6342) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 352 time to evaluate : 1.716 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: A 52 MET cc_start: 0.9189 (mtp) cc_final: 0.8874 (mtm) REVERT: A 236 TYR cc_start: 0.9417 (OUTLIER) cc_final: 0.8819 (t80) REVERT: A 289 ASP cc_start: 0.8357 (t0) cc_final: 0.7726 (t0) REVERT: A 468 GLU cc_start: 0.8760 (tt0) cc_final: 0.8507 (tm-30) REVERT: B 76 MET cc_start: 0.9330 (OUTLIER) cc_final: 0.9083 (mtp) REVERT: B 236 TYR cc_start: 0.9353 (OUTLIER) cc_final: 0.8631 (t80) REVERT: E 275 MET cc_start: 0.9110 (tpp) cc_final: 0.8835 (ttp) REVERT: E 445 MET cc_start: 0.8240 (mmm) cc_final: 0.7785 (mmm) REVERT: F 445 MET cc_start: 0.8904 (mmt) cc_final: 0.8390 (mmt) REVERT: H 13 GLN cc_start: 0.8625 (pt0) cc_final: 0.8254 (pm20) REVERT: H 49 MET cc_start: 0.7497 (tpp) cc_final: 0.7289 (tpp) REVERT: H 63 TYR cc_start: 0.8350 (t80) cc_final: 0.8012 (t80) REVERT: H 70 GLU cc_start: 0.8562 (pt0) cc_final: 0.7981 (pp20) REVERT: L 16 MET cc_start: 0.4476 (mtm) cc_final: 0.4028 (mtp) REVERT: L 54 PHE cc_start: 0.6036 (m-10) cc_final: 0.4596 (t80) REVERT: M 6 MET cc_start: 0.7215 (mtt) cc_final: 0.7013 (ppp) REVERT: M 31 LEU cc_start: 0.5987 (tp) cc_final: 0.5733 (mt) REVERT: M 54 PHE cc_start: 0.5589 (m-80) cc_final: 0.4530 (t80) REVERT: M 65 MET cc_start: 0.7177 (tpp) cc_final: 0.6705 (ptp) REVERT: O 30 ILE cc_start: 0.7349 (tp) cc_final: 0.6963 (pt) REVERT: P 17 MET cc_start: 0.5503 (ttm) cc_final: 0.4885 (tpp) REVERT: P 44 ASP cc_start: 0.7798 (m-30) cc_final: 0.7500 (p0) REVERT: P 49 LEU cc_start: 0.8816 (mt) cc_final: 0.8399 (tp) REVERT: Q 16 MET cc_start: 0.4852 (ttt) cc_final: 0.4244 (tpp) REVERT: R 28 ILE cc_start: 0.7792 (mm) cc_final: 0.7544 (pt) REVERT: W 67 GLN cc_start: 0.8952 (mt0) cc_final: 0.8576 (tt0) REVERT: W 109 ASP cc_start: 0.8420 (t70) cc_final: 0.8199 (t0) REVERT: W 111 ILE cc_start: 0.9180 (mt) cc_final: 0.8866 (mm) REVERT: W 137 LYS cc_start: 0.8215 (tmtt) cc_final: 0.7769 (tmtt) REVERT: a 79 ILE cc_start: 0.2979 (OUTLIER) cc_final: 0.2759 (tt) REVERT: a 119 ASP cc_start: 0.6713 (t0) cc_final: 0.5676 (m-30) REVERT: a 167 LYS cc_start: 0.6992 (tttt) cc_final: 0.6759 (tptt) REVERT: a 177 GLU cc_start: 0.4800 (mt-10) cc_final: 0.4462 (tm-30) REVERT: a 210 ARG cc_start: 0.8577 (ptm-80) cc_final: 0.8297 (ptt-90) REVERT: a 235 TRP cc_start: 0.3269 (p-90) cc_final: 0.3005 (p-90) outliers start: 53 outliers final: 22 residues processed: 390 average time/residue: 0.2258 time to fit residues: 145.8208 Evaluate side-chains 343 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 317 time to evaluate : 1.337 ------------------------------------------------------------------------------- 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 406 PHE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain O residue 3 ASN Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain W residue 145 SER Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 201 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 170 optimal weight: 7.9990 chunk 408 optimal weight: 7.9990 chunk 459 optimal weight: 7.9990 chunk 286 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 277 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 HIS E 365 GLN F 353 HIS G 131 ASN H 38 HIS M 5 ASN ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 14 HIS a 15 HIS a 32 GLN a 116 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.090430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.053432 restraints weight = 123514.230| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.97 r_work: 0.2797 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 37231 Z= 0.191 Angle : 0.621 11.465 50399 Z= 0.319 Chirality : 0.043 0.239 5875 Planarity : 0.004 0.062 6501 Dihedral : 6.950 118.673 5330 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.59 % Favored : 98.39 % Rotamer: Outliers : 1.68 % Allowed : 10.35 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.12), residues: 4770 helix: 1.44 (0.10), residues: 2660 sheet: 0.79 (0.21), residues: 536 loop : -0.10 (0.16), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG a 140 TYR 0.018 0.001 TYR A 236 PHE 0.030 0.002 PHE R 53 TRP 0.015 0.001 TRP G 203 HIS 0.006 0.001 HIS W 21 Details of bonding type rmsd covalent geometry : bond 0.00415 (37231) covalent geometry : angle 0.62103 (50399) hydrogen bonds : bond 0.05393 ( 2166) hydrogen bonds : angle 4.58983 ( 6342) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 333 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.9026 (mtt) cc_final: 0.8684 (mtt) REVERT: A 236 TYR cc_start: 0.9567 (OUTLIER) cc_final: 0.8817 (t80) REVERT: A 289 ASP cc_start: 0.8470 (t0) cc_final: 0.7974 (t0) REVERT: B 76 MET cc_start: 0.9367 (OUTLIER) cc_final: 0.8998 (mtp) REVERT: B 236 TYR cc_start: 0.9525 (OUTLIER) cc_final: 0.9005 (t80) REVERT: E 330 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7843 (mp) REVERT: E 445 MET cc_start: 0.8503 (mmm) cc_final: 0.8050 (mmm) REVERT: F 445 MET cc_start: 0.8966 (mmt) cc_final: 0.8404 (mmt) REVERT: G 38 MET cc_start: 0.8716 (ttm) cc_final: 0.8507 (ttm) REVERT: H 13 GLN cc_start: 0.8727 (pt0) cc_final: 0.8483 (pm20) REVERT: H 22 LYS cc_start: 0.8022 (tmtt) cc_final: 0.7732 (ttmt) REVERT: H 63 TYR cc_start: 0.8282 (t80) cc_final: 0.7962 (t80) REVERT: H 70 GLU cc_start: 0.8468 (pt0) cc_final: 0.7810 (pp20) REVERT: I 65 MET cc_start: 0.4867 (mmp) cc_final: 0.4495 (mmp) REVERT: L 11 MET cc_start: 0.3209 (OUTLIER) cc_final: 0.2859 (mpp) REVERT: L 16 MET cc_start: 0.4571 (mtm) cc_final: 0.4158 (mtp) REVERT: L 54 PHE cc_start: 0.6049 (m-10) cc_final: 0.4633 (t80) REVERT: M 6 MET cc_start: 0.7188 (mtt) cc_final: 0.6983 (ppp) REVERT: M 31 LEU cc_start: 0.6080 (tp) cc_final: 0.5845 (mt) REVERT: M 54 PHE cc_start: 0.5762 (m-80) cc_final: 0.4679 (t80) REVERT: M 65 MET cc_start: 0.7991 (tpp) cc_final: 0.7738 (ttp) REVERT: N 16 MET cc_start: -0.2109 (tpp) cc_final: -0.2348 (tpt) REVERT: N 30 ILE cc_start: 0.5273 (OUTLIER) cc_final: 0.5063 (tt) REVERT: N 65 MET cc_start: 0.2198 (mtt) cc_final: 0.1947 (mmp) REVERT: O 17 MET cc_start: 0.6641 (mtp) cc_final: 0.6255 (mtt) REVERT: O 30 ILE cc_start: 0.7369 (tp) cc_final: 0.7026 (pt) REVERT: O 75 MET cc_start: 0.2233 (ttt) cc_final: 0.1870 (tmm) REVERT: P 17 MET cc_start: 0.5124 (ttm) cc_final: 0.4674 (tpp) REVERT: P 44 ASP cc_start: 0.8257 (m-30) cc_final: 0.7841 (p0) REVERT: Q 16 MET cc_start: 0.4730 (ttt) cc_final: 0.4265 (tpp) REVERT: Q 17 MET cc_start: 0.5174 (mtp) cc_final: 0.4805 (mtt) REVERT: R 28 ILE cc_start: 0.7662 (mm) cc_final: 0.7448 (pt) REVERT: W 67 GLN cc_start: 0.9055 (mt0) cc_final: 0.8732 (tt0) REVERT: W 109 ASP cc_start: 0.8359 (t70) cc_final: 0.8142 (t70) REVERT: W 137 LYS cc_start: 0.8435 (tmtt) cc_final: 0.7935 (tmtt) REVERT: X 30 MET cc_start: 0.2017 (mmt) cc_final: 0.1339 (mmt) REVERT: X 98 ARG cc_start: 0.8883 (ttp80) cc_final: 0.8456 (ttp80) REVERT: a 6 MET cc_start: 0.1513 (ppp) cc_final: 0.0733 (ppp) REVERT: a 119 ASP cc_start: 0.6774 (t0) cc_final: 0.6233 (m-30) REVERT: a 177 GLU cc_start: 0.4937 (mt-10) cc_final: 0.4555 (tm-30) outliers start: 64 outliers final: 34 residues processed: 380 average time/residue: 0.2144 time to fit residues: 137.8551 Evaluate side-chains 341 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 301 time to evaluate : 1.852 ------------------------------------------------------------------------------- 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 A residue 504 LEU Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 56 HIS Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain O residue 3 ASN Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 65 MET Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain W residue 145 SER Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain a residue 201 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 391 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 447 optimal weight: 10.0000 chunk 221 optimal weight: 3.9990 chunk 260 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 300 optimal weight: 20.0000 chunk 467 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 135 GLN G 200 HIS ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 87 ASN a 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.089743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.052895 restraints weight = 122786.175| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.96 r_work: 0.2779 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 37231 Z= 0.194 Angle : 0.599 14.212 50399 Z= 0.309 Chirality : 0.043 0.238 5875 Planarity : 0.004 0.045 6501 Dihedral : 6.804 118.139 5330 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.66 % Allowed : 11.25 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 1.36 (0.12), residues: 4770 helix: 1.61 (0.10), residues: 2653 sheet: 0.80 (0.21), residues: 532 loop : -0.16 (0.16), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 401 TYR 0.030 0.001 TYR a 94 PHE 0.029 0.001 PHE R 53 TRP 0.015 0.001 TRP G 203 HIS 0.005 0.001 HIS W 21 Details of bonding type rmsd covalent geometry : bond 0.00440 (37231) covalent geometry : angle 0.59934 (50399) hydrogen bonds : bond 0.05218 ( 2166) hydrogen bonds : angle 4.53787 ( 6342) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 316 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.9116 (mtt) cc_final: 0.8831 (mtt) REVERT: A 289 ASP cc_start: 0.8514 (t0) cc_final: 0.7974 (t0) REVERT: B 67 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8459 (mt-10) REVERT: B 236 TYR cc_start: 0.9561 (OUTLIER) cc_final: 0.9188 (t80) REVERT: E 330 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7916 (mp) REVERT: E 445 MET cc_start: 0.8536 (mmm) cc_final: 0.8051 (mmm) REVERT: F 445 MET cc_start: 0.8946 (mmt) cc_final: 0.8354 (mmt) REVERT: G 38 MET cc_start: 0.8758 (ttm) cc_final: 0.8443 (ttm) REVERT: H 13 GLN cc_start: 0.8633 (pt0) cc_final: 0.8415 (pm20) REVERT: H 46 LYS cc_start: 0.8791 (mtmt) cc_final: 0.8415 (mtmm) REVERT: H 51 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.8162 (ptm-80) REVERT: H 70 GLU cc_start: 0.8218 (pt0) cc_final: 0.7635 (pp20) REVERT: H 76 VAL cc_start: 0.8122 (m) cc_final: 0.7905 (p) REVERT: I 11 MET cc_start: 0.2856 (mmm) cc_final: 0.2646 (mmm) REVERT: I 61 ASP cc_start: 0.5405 (m-30) cc_final: 0.4979 (t0) REVERT: I 65 MET cc_start: 0.3839 (mmp) cc_final: 0.3400 (mtp) REVERT: L 11 MET cc_start: 0.2517 (OUTLIER) cc_final: 0.2234 (mpp) REVERT: L 16 MET cc_start: 0.4898 (mtm) cc_final: 0.4520 (mtp) REVERT: L 54 PHE cc_start: 0.6054 (m-10) cc_final: 0.4664 (t80) REVERT: M 31 LEU cc_start: 0.6053 (tp) cc_final: 0.5794 (mt) REVERT: M 54 PHE cc_start: 0.5818 (m-80) cc_final: 0.4697 (t80) REVERT: M 65 MET cc_start: 0.7967 (tpp) cc_final: 0.7685 (ttp) REVERT: N 16 MET cc_start: -0.2194 (tpp) cc_final: -0.2589 (tpp) REVERT: N 17 MET cc_start: -0.0091 (mpp) cc_final: -0.0979 (tpt) REVERT: O 17 MET cc_start: 0.6610 (mtp) cc_final: 0.4202 (tpt) REVERT: O 30 ILE cc_start: 0.7471 (tp) cc_final: 0.7134 (pt) REVERT: P 17 MET cc_start: 0.5125 (ttm) cc_final: 0.4820 (tpp) REVERT: P 44 ASP cc_start: 0.8294 (m-30) cc_final: 0.7793 (p0) REVERT: Q 6 MET cc_start: 0.3528 (mpp) cc_final: 0.3304 (mmp) REVERT: Q 16 MET cc_start: 0.4697 (ttt) cc_final: 0.4217 (tpp) REVERT: R 16 MET cc_start: 0.7173 (tpt) cc_final: 0.6798 (tpt) REVERT: S 17 MET cc_start: 0.4958 (mmm) cc_final: 0.3005 (ttt) REVERT: W 67 GLN cc_start: 0.9057 (mt0) cc_final: 0.8770 (tt0) REVERT: W 109 ASP cc_start: 0.8404 (t70) cc_final: 0.8036 (t0) REVERT: W 137 LYS cc_start: 0.8296 (tmtt) cc_final: 0.7715 (tmtt) REVERT: W 142 ILE cc_start: 0.8590 (pt) cc_final: 0.8269 (mp) REVERT: X 98 ARG cc_start: 0.8743 (ttp80) cc_final: 0.8363 (ttt90) REVERT: a 6 MET cc_start: 0.0666 (ppp) cc_final: 0.0303 (ppp) REVERT: a 115 MET cc_start: 0.3575 (mtp) cc_final: 0.3234 (ptm) REVERT: a 119 ASP cc_start: 0.6739 (t0) cc_final: 0.6503 (m-30) REVERT: a 167 LYS cc_start: 0.6928 (tttt) cc_final: 0.6699 (tptt) REVERT: a 177 GLU cc_start: 0.4875 (mt-10) cc_final: 0.4447 (tm-30) REVERT: a 215 MET cc_start: 0.6933 (mmp) cc_final: 0.6632 (mmp) outliers start: 63 outliers final: 32 residues processed: 366 average time/residue: 0.2198 time to fit residues: 134.9413 Evaluate side-chains 334 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 298 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain H residue 56 HIS Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain O residue 3 ASN Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain W residue 145 SER Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain a residue 216 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 139 optimal weight: 1.9990 chunk 320 optimal weight: 8.9990 chunk 422 optimal weight: 8.9990 chunk 297 optimal weight: 5.9990 chunk 423 optimal weight: 5.9990 chunk 300 optimal weight: 6.9990 chunk 198 optimal weight: 5.9990 chunk 251 optimal weight: 4.9990 chunk 459 optimal weight: 7.9990 chunk 284 optimal weight: 0.2980 chunk 420 optimal weight: 7.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 GLN C 369 ASN ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 5 ASN ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 87 ASN ** a 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.088730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.052106 restraints weight = 123656.768| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.85 r_work: 0.2752 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 37231 Z= 0.238 Angle : 0.636 10.208 50399 Z= 0.328 Chirality : 0.044 0.245 5875 Planarity : 0.004 0.055 6501 Dihedral : 6.838 118.694 5330 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.76 % Allowed : 11.59 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 1.31 (0.12), residues: 4770 helix: 1.58 (0.10), residues: 2665 sheet: 0.73 (0.21), residues: 540 loop : -0.21 (0.16), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG X 115 TYR 0.021 0.002 TYR H 63 PHE 0.034 0.002 PHE R 53 TRP 0.016 0.001 TRP G 203 HIS 0.007 0.001 HIS Y 51 Details of bonding type rmsd covalent geometry : bond 0.00549 (37231) covalent geometry : angle 0.63567 (50399) hydrogen bonds : bond 0.05389 ( 2166) hydrogen bonds : angle 4.61003 ( 6342) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 315 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.9022 (mtt) cc_final: 0.8685 (mtt) REVERT: A 289 ASP cc_start: 0.8537 (t0) cc_final: 0.8071 (t0) REVERT: B 67 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8554 (mt-10) REVERT: B 236 TYR cc_start: 0.9608 (OUTLIER) cc_final: 0.9282 (t80) REVERT: C 94 ILE cc_start: 0.9463 (OUTLIER) cc_final: 0.9236 (mm) REVERT: D 224 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9333 (tt) REVERT: E 330 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8070 (mp) REVERT: E 445 MET cc_start: 0.8558 (mmm) cc_final: 0.8111 (mmm) REVERT: G 38 MET cc_start: 0.8835 (ttm) cc_final: 0.8515 (ttm) REVERT: H 22 LYS cc_start: 0.8480 (tmtt) cc_final: 0.8072 (ttmt) REVERT: H 46 LYS cc_start: 0.8655 (mtmt) cc_final: 0.8261 (mtmm) REVERT: H 70 GLU cc_start: 0.8249 (pt0) cc_final: 0.7558 (pp20) REVERT: H 76 VAL cc_start: 0.8146 (m) cc_final: 0.7863 (p) REVERT: I 61 ASP cc_start: 0.5712 (m-30) cc_final: 0.5154 (t0) REVERT: I 65 MET cc_start: 0.3259 (mmp) cc_final: 0.2880 (mtp) REVERT: I 68 VAL cc_start: 0.5006 (t) cc_final: 0.4735 (t) REVERT: L 16 MET cc_start: 0.4798 (mtm) cc_final: 0.4471 (mtp) REVERT: L 54 PHE cc_start: 0.6199 (m-10) cc_final: 0.4826 (t80) REVERT: M 16 MET cc_start: 0.6537 (mmm) cc_final: 0.5886 (mmm) REVERT: M 31 LEU cc_start: 0.6159 (tp) cc_final: 0.5828 (mt) REVERT: M 54 PHE cc_start: 0.6207 (m-10) cc_final: 0.5136 (t80) REVERT: M 65 MET cc_start: 0.7890 (tpp) cc_final: 0.7592 (mmt) REVERT: N 16 MET cc_start: -0.1708 (tpp) cc_final: -0.2276 (tpp) REVERT: N 17 MET cc_start: 0.0280 (mpp) cc_final: -0.0892 (tpt) REVERT: O 17 MET cc_start: 0.6534 (mtp) cc_final: 0.4166 (tpt) REVERT: O 30 ILE cc_start: 0.7535 (tp) cc_final: 0.7158 (pt) REVERT: P 44 ASP cc_start: 0.8412 (m-30) cc_final: 0.7861 (p0) REVERT: P 65 MET cc_start: 0.2975 (mmp) cc_final: 0.2622 (mmp) REVERT: Q 16 MET cc_start: 0.4947 (ttt) cc_final: 0.4570 (tpp) REVERT: W 67 GLN cc_start: 0.9071 (mt0) cc_final: 0.8846 (tt0) REVERT: W 109 ASP cc_start: 0.8630 (t70) cc_final: 0.8377 (t0) REVERT: W 137 LYS cc_start: 0.8374 (tmtt) cc_final: 0.7705 (tmtt) REVERT: W 141 LYS cc_start: 0.8406 (mmtm) cc_final: 0.8154 (mmtm) REVERT: W 142 ILE cc_start: 0.8576 (pt) cc_final: 0.8221 (mp) REVERT: X 30 MET cc_start: 0.2063 (mmt) cc_final: 0.1828 (mmt) REVERT: X 98 ARG cc_start: 0.8752 (ttp80) cc_final: 0.8513 (ttt90) REVERT: Y 150 ASP cc_start: 0.8750 (t0) cc_final: 0.8533 (m-30) REVERT: a 6 MET cc_start: 0.1014 (ppp) cc_final: 0.0560 (ppp) REVERT: a 167 LYS cc_start: 0.6906 (tttt) cc_final: 0.6663 (tptt) REVERT: a 168 MET cc_start: 0.5866 (mmt) cc_final: 0.5539 (mmt) REVERT: a 177 GLU cc_start: 0.4929 (mt-10) cc_final: 0.4524 (tm-30) REVERT: a 257 MET cc_start: 0.7734 (ppp) cc_final: 0.7498 (ppp) REVERT: a 269 GLU cc_start: 0.5519 (OUTLIER) cc_final: 0.4832 (mm-30) outliers start: 67 outliers final: 37 residues processed: 363 average time/residue: 0.2146 time to fit residues: 130.7526 Evaluate side-chains 339 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 297 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL 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 A residue 504 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 56 HIS Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain M residue 57 MET Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 63 ILE Chi-restraints excluded: chain W residue 111 ILE Chi-restraints excluded: chain W residue 145 SER Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 216 TYR Chi-restraints excluded: chain a residue 269 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 358 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 377 optimal weight: 40.0000 chunk 184 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 314 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 367 optimal weight: 6.9990 chunk 252 optimal weight: 6.9990 chunk 386 optimal weight: 8.9990 chunk 468 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 GLN B 27 ASN ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 361 GLN ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 GLN a 185 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.087865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.051338 restraints weight = 123275.126| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.95 r_work: 0.2729 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 37231 Z= 0.270 Angle : 0.650 11.779 50399 Z= 0.334 Chirality : 0.044 0.229 5875 Planarity : 0.004 0.046 6501 Dihedral : 6.898 120.007 5330 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.22 % Favored : 97.76 % Rotamer: Outliers : 1.68 % Allowed : 12.09 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 1.23 (0.12), residues: 4770 helix: 1.55 (0.10), residues: 2665 sheet: 0.64 (0.22), residues: 540 loop : -0.32 (0.16), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 41 TYR 0.020 0.002 TYR A 236 PHE 0.032 0.002 PHE R 53 TRP 0.017 0.001 TRP G 203 HIS 0.006 0.001 HIS a 185 Details of bonding type rmsd covalent geometry : bond 0.00626 (37231) covalent geometry : angle 0.65021 (50399) hydrogen bonds : bond 0.05450 ( 2166) hydrogen bonds : angle 4.63320 ( 6342) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 311 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.8995 (mtt) cc_final: 0.8608 (mtt) REVERT: A 289 ASP cc_start: 0.8558 (t0) cc_final: 0.8073 (t0) REVERT: B 236 TYR cc_start: 0.9629 (OUTLIER) cc_final: 0.9388 (t80) REVERT: B 262 ASP cc_start: 0.8533 (m-30) cc_final: 0.8305 (m-30) REVERT: C 94 ILE cc_start: 0.9452 (OUTLIER) cc_final: 0.9206 (mm) REVERT: D 224 LEU cc_start: 0.9625 (OUTLIER) cc_final: 0.9315 (tt) REVERT: E 330 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8077 (mp) REVERT: G 38 MET cc_start: 0.8860 (ttm) cc_final: 0.8520 (ttm) REVERT: H 26 THR cc_start: 0.4166 (OUTLIER) cc_final: 0.3939 (p) REVERT: H 46 LYS cc_start: 0.8643 (mtmt) cc_final: 0.8364 (mtmm) REVERT: H 49 MET cc_start: 0.7664 (tpp) cc_final: 0.7334 (tpp) REVERT: H 70 GLU cc_start: 0.8201 (pt0) cc_final: 0.7460 (pp20) REVERT: H 76 VAL cc_start: 0.8162 (m) cc_final: 0.7858 (p) REVERT: H 93 ARG cc_start: 0.8668 (tpt170) cc_final: 0.8443 (tpt-90) REVERT: I 61 ASP cc_start: 0.5752 (m-30) cc_final: 0.5295 (t0) REVERT: I 65 MET cc_start: 0.3242 (mmp) cc_final: 0.2964 (mtp) REVERT: L 16 MET cc_start: 0.5009 (mtm) cc_final: 0.4742 (mtp) REVERT: L 54 PHE cc_start: 0.5954 (m-10) cc_final: 0.4673 (t80) REVERT: M 16 MET cc_start: 0.6409 (mmm) cc_final: 0.6170 (mmm) REVERT: M 17 MET cc_start: 0.3827 (mtm) cc_final: 0.3499 (tmm) REVERT: M 31 LEU cc_start: 0.5935 (tp) cc_final: 0.5642 (mt) REVERT: M 54 PHE cc_start: 0.6289 (m-10) cc_final: 0.5176 (t80) REVERT: M 65 MET cc_start: 0.7856 (tpp) cc_final: 0.7553 (mmt) REVERT: N 16 MET cc_start: -0.1703 (tpp) cc_final: -0.2067 (tpp) REVERT: O 17 MET cc_start: 0.6486 (mtp) cc_final: 0.4198 (tpt) REVERT: O 30 ILE cc_start: 0.7509 (tp) cc_final: 0.7124 (pt) REVERT: P 65 MET cc_start: 0.2826 (mmp) cc_final: 0.2568 (mmp) REVERT: Q 16 MET cc_start: 0.4795 (ttt) cc_final: 0.4480 (tpp) REVERT: R 35 PHE cc_start: 0.7704 (t80) cc_final: 0.7333 (t80) REVERT: S 17 MET cc_start: 0.5115 (mmm) cc_final: 0.3078 (ttt) REVERT: W 67 GLN cc_start: 0.9099 (mt0) cc_final: 0.8843 (tt0) REVERT: W 109 ASP cc_start: 0.8453 (t70) cc_final: 0.8113 (t0) REVERT: W 137 LYS cc_start: 0.8227 (tmtt) cc_final: 0.7574 (tmtt) REVERT: W 141 LYS cc_start: 0.8432 (mmtm) cc_final: 0.8150 (mmtm) REVERT: X 98 ARG cc_start: 0.8758 (ttp80) cc_final: 0.8548 (ttt90) REVERT: a 6 MET cc_start: 0.1084 (OUTLIER) cc_final: 0.0704 (tmm) REVERT: a 115 MET cc_start: 0.2789 (ptm) cc_final: 0.2522 (ptm) REVERT: a 167 LYS cc_start: 0.6992 (tttt) cc_final: 0.6735 (tptt) REVERT: a 168 MET cc_start: 0.6037 (mmt) cc_final: 0.5764 (mmt) REVERT: a 177 GLU cc_start: 0.4846 (mt-10) cc_final: 0.4486 (tm-30) REVERT: a 269 GLU cc_start: 0.5559 (OUTLIER) cc_final: 0.4854 (mm-30) outliers start: 64 outliers final: 41 residues processed: 364 average time/residue: 0.2123 time to fit residues: 130.3242 Evaluate side-chains 343 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 295 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL 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 A residue 504 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 56 HIS Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain M residue 57 MET Chi-restraints excluded: chain O residue 3 ASN Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 63 ILE Chi-restraints excluded: chain W residue 111 ILE Chi-restraints excluded: chain W residue 145 SER Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain a residue 6 MET Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 216 TYR Chi-restraints excluded: chain a residue 269 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 335 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 343 optimal weight: 5.9990 chunk 242 optimal weight: 2.9990 chunk 217 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 11 optimal weight: 0.0170 chunk 385 optimal weight: 7.9990 chunk 411 optimal weight: 0.0870 chunk 92 optimal weight: 0.9980 chunk 384 optimal weight: 8.9990 overall best weight: 0.8198 ------------------------------------------------------------------------------- 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 ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 ASN ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.089750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.053541 restraints weight = 122585.273| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.84 r_work: 0.2795 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 37231 Z= 0.126 Angle : 0.582 12.115 50399 Z= 0.296 Chirality : 0.041 0.216 5875 Planarity : 0.004 0.049 6501 Dihedral : 6.542 117.020 5328 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.45 % Allowed : 12.72 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 1.47 (0.12), residues: 4770 helix: 1.74 (0.10), residues: 2664 sheet: 0.78 (0.22), residues: 532 loop : -0.20 (0.16), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Y 36 TYR 0.023 0.001 TYR L 10 PHE 0.027 0.001 PHE R 53 TRP 0.018 0.001 TRP a 241 HIS 0.005 0.001 HIS C 479 Details of bonding type rmsd covalent geometry : bond 0.00265 (37231) covalent geometry : angle 0.58165 (50399) hydrogen bonds : bond 0.04758 ( 2166) hydrogen bonds : angle 4.41106 ( 6342) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 312 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.9034 (mtt) cc_final: 0.8632 (mtt) REVERT: A 289 ASP cc_start: 0.8369 (t0) cc_final: 0.7876 (t0) REVERT: B 236 TYR cc_start: 0.9567 (OUTLIER) cc_final: 0.9312 (t80) REVERT: C 48 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8655 (ptp) REVERT: C 94 ILE cc_start: 0.9413 (OUTLIER) cc_final: 0.9131 (mm) REVERT: D 224 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9224 (tt) REVERT: E 330 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8026 (mp) REVERT: G 38 MET cc_start: 0.8824 (ttm) cc_final: 0.8494 (ttm) REVERT: H 22 LYS cc_start: 0.8633 (tmtt) cc_final: 0.8398 (tptt) REVERT: H 26 THR cc_start: 0.4296 (OUTLIER) cc_final: 0.4083 (p) REVERT: H 46 LYS cc_start: 0.8662 (mtmt) cc_final: 0.8406 (mtmm) REVERT: H 49 MET cc_start: 0.7729 (tpp) cc_final: 0.7450 (tpp) REVERT: H 70 GLU cc_start: 0.8261 (pt0) cc_final: 0.7519 (pp20) REVERT: H 76 VAL cc_start: 0.8199 (m) cc_final: 0.7909 (p) REVERT: I 61 ASP cc_start: 0.5804 (m-30) cc_final: 0.5188 (t0) REVERT: I 65 MET cc_start: 0.3395 (mmp) cc_final: 0.2971 (mtm) REVERT: J 11 MET cc_start: 0.5607 (mmm) cc_final: 0.4291 (tpp) REVERT: J 54 PHE cc_start: 0.6670 (m-10) cc_final: 0.5681 (t80) REVERT: L 11 MET cc_start: 0.2791 (mpp) cc_final: 0.2401 (mpp) REVERT: L 16 MET cc_start: 0.4869 (mtm) cc_final: 0.4610 (mtp) REVERT: L 54 PHE cc_start: 0.6052 (m-10) cc_final: 0.4715 (t80) REVERT: M 31 LEU cc_start: 0.5821 (tp) cc_final: 0.5591 (mt) REVERT: N 16 MET cc_start: -0.1924 (tpp) cc_final: -0.2334 (tpp) REVERT: O 17 MET cc_start: 0.6432 (mtp) cc_final: 0.4099 (tpt) REVERT: O 30 ILE cc_start: 0.7522 (tp) cc_final: 0.7172 (pt) REVERT: Q 6 MET cc_start: 0.2685 (mpp) cc_final: 0.2479 (mmm) REVERT: R 28 ILE cc_start: 0.7846 (mm) cc_final: 0.7575 (tp) REVERT: R 53 PHE cc_start: 0.7577 (t80) cc_final: 0.7313 (t80) REVERT: R 57 MET cc_start: 0.6608 (ptp) cc_final: 0.5756 (mmt) REVERT: S 17 MET cc_start: 0.5154 (mmm) cc_final: 0.3014 (ttt) REVERT: W 67 GLN cc_start: 0.9072 (mt0) cc_final: 0.8858 (tt0) REVERT: W 109 ASP cc_start: 0.8617 (t70) cc_final: 0.8347 (t0) REVERT: W 137 LYS cc_start: 0.8429 (tmtt) cc_final: 0.7899 (tmtt) REVERT: X 98 ARG cc_start: 0.8797 (ttp80) cc_final: 0.8575 (ttt90) REVERT: a 6 MET cc_start: 0.0924 (ppp) cc_final: 0.0478 (ppp) REVERT: a 167 LYS cc_start: 0.6912 (tttt) cc_final: 0.6672 (tptt) REVERT: a 168 MET cc_start: 0.5973 (mmt) cc_final: 0.5716 (mmt) REVERT: a 177 GLU cc_start: 0.4998 (mt-10) cc_final: 0.4606 (tm-30) REVERT: a 203 LYS cc_start: 0.8959 (mmtt) cc_final: 0.8758 (mmmm) REVERT: a 269 GLU cc_start: 0.5557 (OUTLIER) cc_final: 0.4863 (mm-30) outliers start: 55 outliers final: 32 residues processed: 358 average time/residue: 0.2206 time to fit residues: 132.5279 Evaluate side-chains 336 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 297 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL 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 A residue 504 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain M residue 57 MET Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain O residue 3 ASN Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain S residue 63 ILE Chi-restraints excluded: chain W residue 145 SER Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 269 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 267 optimal weight: 3.9990 chunk 63 optimal weight: 0.3980 chunk 149 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 278 optimal weight: 4.9990 chunk 206 optimal weight: 0.9980 chunk 248 optimal weight: 4.9990 chunk 284 optimal weight: 8.9990 chunk 233 optimal weight: 9.9990 chunk 328 optimal weight: 10.0000 chunk 84 optimal weight: 0.7980 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.089316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.053123 restraints weight = 122797.638| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.80 r_work: 0.2785 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37231 Z= 0.150 Angle : 0.597 12.626 50399 Z= 0.302 Chirality : 0.042 0.216 5875 Planarity : 0.004 0.049 6501 Dihedral : 6.467 115.603 5328 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.10 % Allowed : 13.32 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 1.49 (0.12), residues: 4770 helix: 1.76 (0.10), residues: 2660 sheet: 0.82 (0.22), residues: 534 loop : -0.20 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Y 36 TYR 0.024 0.001 TYR L 10 PHE 0.032 0.001 PHE M 54 TRP 0.018 0.001 TRP a 241 HIS 0.005 0.001 HIS C 479 Details of bonding type rmsd covalent geometry : bond 0.00331 (37231) covalent geometry : angle 0.59680 (50399) hydrogen bonds : bond 0.04771 ( 2166) hydrogen bonds : angle 4.41928 ( 6342) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 307 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.9016 (mtt) cc_final: 0.8610 (mtt) REVERT: A 289 ASP cc_start: 0.8405 (t0) cc_final: 0.7943 (t0) REVERT: B 236 TYR cc_start: 0.9579 (OUTLIER) cc_final: 0.9248 (t80) REVERT: C 48 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8664 (ptp) REVERT: C 94 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.9126 (mm) REVERT: D 224 LEU cc_start: 0.9541 (OUTLIER) cc_final: 0.9231 (tt) REVERT: E 330 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8057 (mp) REVERT: E 445 MET cc_start: 0.8368 (mmm) cc_final: 0.8113 (mmm) REVERT: G 38 MET cc_start: 0.8837 (ttm) cc_final: 0.8500 (ttm) REVERT: H 26 THR cc_start: 0.4308 (OUTLIER) cc_final: 0.4078 (p) REVERT: H 46 LYS cc_start: 0.8633 (mtmt) cc_final: 0.8380 (mtmm) REVERT: H 49 MET cc_start: 0.7821 (tpp) cc_final: 0.7612 (tpp) REVERT: H 70 GLU cc_start: 0.8284 (pt0) cc_final: 0.7510 (pp20) REVERT: H 76 VAL cc_start: 0.8232 (m) cc_final: 0.7932 (p) REVERT: I 61 ASP cc_start: 0.5897 (m-30) cc_final: 0.5137 (t0) REVERT: I 65 MET cc_start: 0.3548 (mmp) cc_final: 0.3282 (mtm) REVERT: J 11 MET cc_start: 0.5521 (mmm) cc_final: 0.4108 (tpt) REVERT: J 54 PHE cc_start: 0.6607 (m-10) cc_final: 0.5626 (t80) REVERT: L 11 MET cc_start: 0.2902 (mpp) cc_final: 0.2499 (mpp) REVERT: L 16 MET cc_start: 0.4874 (mtm) cc_final: 0.4530 (mtp) REVERT: L 54 PHE cc_start: 0.5913 (m-10) cc_final: 0.4570 (t80) REVERT: M 16 MET cc_start: 0.6350 (mmm) cc_final: 0.5996 (mmm) REVERT: M 31 LEU cc_start: 0.5847 (tp) cc_final: 0.5636 (mt) REVERT: M 54 PHE cc_start: 0.6394 (m-10) cc_final: 0.4830 (t80) REVERT: N 16 MET cc_start: -0.1966 (tpp) cc_final: -0.2329 (tpp) REVERT: O 16 MET cc_start: 0.4608 (mmm) cc_final: 0.4020 (mmm) REVERT: O 17 MET cc_start: 0.6439 (mtp) cc_final: 0.4195 (tpt) REVERT: O 30 ILE cc_start: 0.7513 (tp) cc_final: 0.7143 (pt) REVERT: Q 6 MET cc_start: 0.2723 (mpp) cc_final: 0.2509 (mmm) REVERT: R 35 PHE cc_start: 0.7725 (t80) cc_final: 0.7401 (t80) REVERT: S 17 MET cc_start: 0.5171 (mmm) cc_final: 0.3273 (ttt) REVERT: W 137 LYS cc_start: 0.8408 (tmtt) cc_final: 0.7786 (tmtt) REVERT: X 98 ARG cc_start: 0.8815 (ttp80) cc_final: 0.8608 (ttt90) REVERT: a 6 MET cc_start: 0.0864 (ppp) cc_final: 0.0425 (ppp) REVERT: a 167 LYS cc_start: 0.6948 (tttt) cc_final: 0.6744 (tptt) REVERT: a 177 GLU cc_start: 0.5014 (mt-10) cc_final: 0.4622 (tm-30) REVERT: a 203 LYS cc_start: 0.8965 (mmtt) cc_final: 0.8739 (mmmm) outliers start: 42 outliers final: 32 residues processed: 343 average time/residue: 0.2176 time to fit residues: 126.1222 Evaluate side-chains 336 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 298 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 254 GLU 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 A residue 425 GLN Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain M residue 57 MET Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain O residue 3 ASN Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain S residue 63 ILE Chi-restraints excluded: chain W residue 145 SER Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain a residue 79 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 392 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 373 optimal weight: 0.8980 chunk 454 optimal weight: 7.9990 chunk 267 optimal weight: 5.9990 chunk 310 optimal weight: 6.9990 chunk 151 optimal weight: 0.8980 chunk 277 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 174 optimal weight: 0.9980 chunk 348 optimal weight: 0.0970 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 GLN ** C 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.090243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.054112 restraints weight = 122914.488| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.87 r_work: 0.2817 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 37231 Z= 0.121 Angle : 0.596 13.553 50399 Z= 0.300 Chirality : 0.041 0.226 5875 Planarity : 0.004 0.046 6501 Dihedral : 6.300 110.860 5328 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.05 % Allowed : 13.46 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 1.56 (0.12), residues: 4770 helix: 1.80 (0.10), residues: 2662 sheet: 0.85 (0.22), residues: 524 loop : -0.16 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Y 36 TYR 0.026 0.001 TYR L 10 PHE 0.040 0.001 PHE P 35 TRP 0.025 0.001 TRP a 241 HIS 0.010 0.001 HIS A 423 Details of bonding type rmsd covalent geometry : bond 0.00251 (37231) covalent geometry : angle 0.59598 (50399) hydrogen bonds : bond 0.04499 ( 2166) hydrogen bonds : angle 4.33529 ( 6342) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 316 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 ASP cc_start: 0.8304 (t0) cc_final: 0.7818 (t0) REVERT: B 236 TYR cc_start: 0.9537 (OUTLIER) cc_final: 0.9215 (t80) REVERT: B 415 ASP cc_start: 0.8029 (m-30) cc_final: 0.7548 (p0) REVERT: C 48 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8706 (ptp) REVERT: C 94 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.9087 (mm) REVERT: D 224 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9168 (tt) REVERT: E 445 MET cc_start: 0.8428 (mmm) cc_final: 0.8154 (mmm) REVERT: G 38 MET cc_start: 0.8806 (ttm) cc_final: 0.8482 (ttm) REVERT: H 46 LYS cc_start: 0.8504 (mtmt) cc_final: 0.8261 (mtmm) REVERT: H 49 MET cc_start: 0.7602 (tpp) cc_final: 0.7388 (tpp) REVERT: H 70 GLU cc_start: 0.8180 (pt0) cc_final: 0.7354 (pp20) REVERT: H 76 VAL cc_start: 0.8109 (m) cc_final: 0.7833 (p) REVERT: I 65 MET cc_start: 0.3373 (mmp) cc_final: 0.2565 (mtm) REVERT: J 11 MET cc_start: 0.4888 (mmm) cc_final: 0.3898 (tpt) REVERT: J 54 PHE cc_start: 0.6628 (m-10) cc_final: 0.5732 (t80) REVERT: L 11 MET cc_start: 0.3021 (mpp) cc_final: 0.2608 (mpp) REVERT: L 16 MET cc_start: 0.4912 (mtm) cc_final: 0.4705 (mtp) REVERT: L 54 PHE cc_start: 0.5934 (m-10) cc_final: 0.4548 (t80) REVERT: M 16 MET cc_start: 0.6488 (mmm) cc_final: 0.6145 (mmm) REVERT: M 17 MET cc_start: 0.5376 (tmm) cc_final: 0.3366 (ptp) REVERT: M 31 LEU cc_start: 0.5937 (tp) cc_final: 0.5726 (mt) REVERT: M 54 PHE cc_start: 0.6474 (m-10) cc_final: 0.4945 (t80) REVERT: N 16 MET cc_start: -0.2004 (tpp) cc_final: -0.2335 (tpp) REVERT: O 16 MET cc_start: 0.4517 (mmm) cc_final: 0.4109 (mmm) REVERT: O 17 MET cc_start: 0.6508 (mtp) cc_final: 0.4311 (tpt) REVERT: O 30 ILE cc_start: 0.7568 (tp) cc_final: 0.7184 (pt) REVERT: P 65 MET cc_start: 0.2614 (mmp) cc_final: 0.1796 (mmt) REVERT: R 53 PHE cc_start: 0.7590 (t80) cc_final: 0.7332 (t80) REVERT: S 17 MET cc_start: 0.5146 (mmm) cc_final: 0.3365 (ttt) REVERT: W 67 GLN cc_start: 0.8712 (tt0) cc_final: 0.8442 (tt0) REVERT: W 137 LYS cc_start: 0.8469 (tmtt) cc_final: 0.7857 (tmtt) REVERT: X 98 ARG cc_start: 0.8801 (ttp80) cc_final: 0.8596 (ttt90) REVERT: a 6 MET cc_start: 0.0892 (ppp) cc_final: 0.0417 (ppp) REVERT: a 167 LYS cc_start: 0.6848 (tttt) cc_final: 0.6575 (tptt) REVERT: a 177 GLU cc_start: 0.4993 (mt-10) cc_final: 0.4606 (tm-30) REVERT: a 269 GLU cc_start: 0.5588 (OUTLIER) cc_final: 0.4905 (mm-30) outliers start: 40 outliers final: 28 residues processed: 349 average time/residue: 0.2135 time to fit residues: 126.0755 Evaluate side-chains 332 residues out of total 3810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 299 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 504 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain O residue 3 ASN Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain S residue 63 ILE Chi-restraints excluded: chain W residue 145 SER Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 269 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 239 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 466 optimal weight: 7.9990 chunk 416 optimal weight: 7.9990 chunk 374 optimal weight: 10.0000 chunk 233 optimal weight: 8.9990 chunk 1 optimal weight: 0.7980 chunk 320 optimal weight: 0.3980 chunk 272 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 GLN ** C 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 GLN ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.090259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.054255 restraints weight = 122267.840| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.94 r_work: 0.2817 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 37231 Z= 0.121 Angle : 0.591 17.092 50399 Z= 0.295 Chirality : 0.041 0.228 5875 Planarity : 0.004 0.047 6501 Dihedral : 6.185 106.016 5328 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.00 % Allowed : 13.61 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.47 % 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: 1.63 (0.12), residues: 4770 helix: 1.85 (0.10), residues: 2664 sheet: 0.92 (0.22), residues: 522 loop : -0.12 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Y 36 TYR 0.027 0.001 TYR L 10 PHE 0.029 0.001 PHE R 53 TRP 0.023 0.001 TRP a 241 HIS 0.005 0.001 HIS C 479 Details of bonding type rmsd covalent geometry : bond 0.00256 (37231) covalent geometry : angle 0.59091 (50399) hydrogen bonds : bond 0.04423 ( 2166) hydrogen bonds : angle 4.30338 ( 6342) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12911.08 seconds wall clock time: 220 minutes 17.86 seconds (13217.86 seconds total)