Starting phenix.real_space_refine on Mon Jul 6 15:58:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dbu_27307/07_2026/8dbu_27307.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbu_27307/07_2026/8dbu_27307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dbu_27307/07_2026/8dbu_27307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbu_27307/07_2026/8dbu_27307.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dbu_27307/07_2026/8dbu_27307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbu_27307/07_2026/8dbu_27307.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8dbu_27307/07_2026/8dbu_27307.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dbu_27307/07_2026/8dbu_27307.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 179 5.16 5 C 23452 2.51 5 N 6307 2.21 5 O 6958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 36917 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3826 Classifications: {'peptide': 508} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 489} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 3877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3877 Classifications: {'peptide': 513} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 494} Chain: "C" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3849 Classifications: {'peptide': 510} Link IDs: {'PTRANS': 18, 'TRANS': 491} Chain: "D" Number of atoms: 3520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3520 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 437} Chain: "E" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "F" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "G" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2186 Classifications: {'peptide': 284} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 274} Chain: "H" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1021 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "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: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1190 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "Y" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "a" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2104 Classifications: {'peptide': 266} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 250} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.48, per 1000 atoms: 0.23 Number of scatterers: 36917 At special positions: 0 Unit cell: (181.272, 219.037, 135.954, 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 6958 8.00 N 6307 7.00 C 23452 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: 3.71 Conformation dependent library (CDL) restraints added in 2.1 seconds 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8806 Finding SS restraints... Secondary structure from input PDB file: 193 helices and 23 sheets defined 61.5% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 4 through 19 removed outlier: 3.595A pdb=" N ALA A 17 " --> pdb=" O LYS A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.509A 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: 3.897A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 Processing helix chain 'A' and resid 289 through 299 removed outlier: 3.551A pdb=" N HIS A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.689A 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 381 removed outlier: 3.970A pdb=" N ALA A 380 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA A 381 " --> pdb=" O GLY A 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 377 through 381' Processing helix chain 'A' and resid 383 through 391 removed outlier: 3.570A pdb=" N GLY A 391 " --> pdb=" O LYS A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 408 removed outlier: 3.581A 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 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: 3.682A pdb=" N ARG A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP A 478 " --> pdb=" O TYR A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 489 Processing helix chain 'A' and resid 493 through 510 Processing helix chain 'B' and resid 2 through 19 removed outlier: 3.545A pdb=" N THR B 6 " --> pdb=" O GLN B 2 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE B 16 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA B 17 " --> pdb=" O LYS B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.516A pdb=" N ALA B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 237 through 251 removed outlier: 3.787A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 287 through 288 No H-bonds generated for 'chain 'B' and resid 287 through 288' Processing helix chain 'B' and resid 289 through 299 Processing helix chain 'B' and resid 305 through 314 Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 377 through 382 removed outlier: 4.165A pdb=" N ALA B 380 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 408 removed outlier: 5.009A pdb=" N GLY B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG B 394 " --> pdb=" O SER B 390 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N THR B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 431 Processing helix chain 'B' and resid 440 through 453 Processing helix chain 'B' and resid 462 through 479 removed outlier: 4.477A pdb=" N SER B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 490 Processing helix chain 'B' and resid 493 through 511 Processing helix chain 'C' and resid 8 through 18 Processing helix chain 'C' and resid 20 through 24 Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 237 through 253 removed outlier: 3.799A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (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 287 through 288 No H-bonds generated for 'chain 'C' and resid 287 through 288' Processing helix chain 'C' and resid 289 through 299 removed outlier: 3.643A pdb=" N HIS C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 313 Processing helix chain 'C' and resid 339 through 349 Processing helix chain 'C' and resid 356 through 362 Processing helix chain 'C' and resid 377 through 382 removed outlier: 3.698A pdb=" N ALA C 380 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 404 removed outlier: 4.304A pdb=" N GLY C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU C 402 " --> pdb=" O ALA C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.173A pdb=" N GLN C 408 " --> pdb=" O ALA C 405 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA C 410 " --> pdb=" O SER C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 432 removed outlier: 3.957A pdb=" N LYS C 432 " --> pdb=" O THR C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 453 Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 463 through 479 Processing helix chain 'C' and resid 479 through 490 removed outlier: 3.520A pdb=" N MET C 483 " --> pdb=" O HIS C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 509 removed outlier: 3.858A 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: 3.833A pdb=" N ILE D 168 " --> pdb=" O ARG D 164 " (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: 3.666A pdb=" N ARG D 216 " --> pdb=" O PRO D 212 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 256 removed outlier: 3.837A pdb=" N THR D 248 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL D 254 " --> pdb=" O ALA D 250 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 280 removed outlier: 3.581A pdb=" N LEU D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 302 Processing helix chain 'D' and resid 305 through 313 removed outlier: 4.233A pdb=" N ALA D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 327 Processing helix chain 'D' and resid 345 through 350 Processing helix chain 'D' and resid 350 through 378 removed outlier: 4.286A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) removed outlier: 3.796A 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 383 through 400 removed outlier: 3.524A pdb=" N LEU D 388 " --> pdb=" O GLU D 384 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS D 395 " --> pdb=" O ALA D 391 " (cutoff:3.500A) 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 459 removed outlier: 3.779A 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: 3.690A 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: 3.883A pdb=" N ILE E 168 " --> pdb=" O ARG E 164 " (cutoff:3.500A) removed outlier: 3.687A 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 233 removed outlier: 3.567A pdb=" N ARG E 216 " --> pdb=" O PRO E 212 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 258 removed outlier: 3.680A pdb=" N THR E 248 " --> pdb=" O ILE E 244 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA E 256 " --> pdb=" O THR E 252 " (cutoff:3.500A) removed outlier: 4.505A 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: 7.759A pdb=" N GLN E 351 " --> pdb=" O LEU E 347 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N GLU E 352 " --> pdb=" O VAL E 348 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N HIS E 353 " --> pdb=" O VAL E 349 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE E 373 " --> pdb=" O GLU E 369 " (cutoff:3.500A) removed outlier: 3.912A 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: 3.623A pdb=" N ARG E 398 " --> pdb=" O ARG E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 412 Processing helix chain 'E' and resid 419 through 432 Processing helix chain 'E' and resid 433 through 436 Processing helix chain 'E' and resid 448 through 459 removed outlier: 3.800A pdb=" N VAL E 453 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLU E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 22 removed outlier: 4.448A pdb=" N VAL F 22 " --> pdb=" O GLN F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 Processing helix chain 'F' and resid 130 through 137 Processing helix chain 'F' and resid 154 through 169 Processing helix chain 'F' and resid 182 through 196 Processing helix chain 'F' and resid 198 through 200 No H-bonds generated for 'chain 'F' and resid 198 through 200' Processing helix chain 'F' and resid 212 through 233 removed outlier: 3.567A pdb=" N ARG F 216 " --> pdb=" O PRO F 212 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 259 Processing helix chain 'F' and resid 263 through 267 Processing helix chain 'F' and resid 270 through 280 Processing helix chain 'F' and resid 305 through 313 removed outlier: 3.751A pdb=" N ALA F 313 " --> pdb=" O ALA F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 328 removed outlier: 3.607A 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: 4.059A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 3.610A 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 383 through 400 removed outlier: 3.540A pdb=" N LEU F 388 " --> pdb=" O GLU F 384 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS F 395 " --> pdb=" O ALA F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 406 No H-bonds generated for 'chain 'F' and resid 404 through 406' Processing helix chain 'F' and resid 407 through 412 Processing helix chain 'F' and resid 419 through 432 Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 448 through 459 removed outlier: 3.822A pdb=" N GLU F 454 " --> pdb=" O GLU F 450 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS F 458 " --> pdb=" O GLU F 454 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 57 removed outlier: 4.079A pdb=" N GLU G 24 " --> pdb=" O THR G 20 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA G 27 " --> pdb=" O MET G 23 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG G 37 " --> pdb=" O LYS G 33 " (cutoff:3.500A) Proline residue: G 43 - end of helix removed outlier: 3.752A pdb=" N GLY G 53 " --> pdb=" O ARG G 49 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N HIS G 54 " --> pdb=" O LYS G 50 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU G 55 " --> pdb=" O VAL G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 108 removed outlier: 3.837A pdb=" N LYS G 97 " --> pdb=" O ASN G 93 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS G 108 " --> pdb=" O THR G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 129 removed outlier: 3.505A pdb=" N VAL G 122 " --> pdb=" O GLY G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 161 removed outlier: 4.462A pdb=" N VAL G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 283 Processing helix chain 'H' and resid 54 through 58 removed outlier: 3.778A pdb=" N HIS H 58 " --> pdb=" O GLN H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 108 removed outlier: 3.650A pdb=" N SER H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 134 removed outlier: 3.846A pdb=" N ALA H 119 " --> pdb=" O ALA H 115 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU H 132 " --> pdb=" O LEU H 128 " (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: 3.844A pdb=" N MET I 11 " --> pdb=" O ASP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 78 removed outlier: 4.254A pdb=" N LEU I 48 " --> pdb=" O ASP I 44 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU I 59 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ILE I 63 " --> pdb=" O LEU I 59 " (cutoff:3.500A) Proline residue: I 64 - end of helix Processing helix chain 'J' and resid 4 through 42 removed outlier: 4.031A pdb=" N LEU J 8 " --> pdb=" O LEU J 4 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA J 25 " --> pdb=" O ALA J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 61 removed outlier: 3.582A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 77 removed outlier: 3.870A pdb=" N ILE J 66 " --> pdb=" O ALA J 62 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA J 67 " --> pdb=" O ILE J 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 42 removed outlier: 4.092A pdb=" N LEU L 8 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU L 9 " --> pdb=" O ASN L 5 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR L 10 " --> pdb=" O MET L 6 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET L 11 " --> pdb=" O ASP L 7 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE L 28 " --> pdb=" O ALA L 24 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS L 34 " --> pdb=" O ILE L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 61 removed outlier: 3.738A pdb=" N THR L 51 " --> pdb=" O PRO L 47 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU L 59 " --> pdb=" O ILE L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 77 removed outlier: 3.571A pdb=" N ILE L 66 " --> pdb=" O ALA L 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 42 removed outlier: 3.622A pdb=" N MET M 11 " --> pdb=" O ASP M 7 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 61 removed outlier: 4.157A pdb=" N LEU M 59 " --> pdb=" O ILE M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 77 removed outlier: 3.501A pdb=" N MET M 65 " --> pdb=" O ASP M 61 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE M 66 " --> pdb=" O ALA M 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 42 removed outlier: 4.916A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET N 16 " --> pdb=" O ALA N 12 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA N 21 " --> pdb=" O MET N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 77 removed outlier: 3.696A pdb=" N THR N 51 " --> pdb=" O PRO N 47 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY N 58 " --> pdb=" O PHE N 54 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU N 59 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE N 63 " --> pdb=" O LEU N 59 " (cutoff:3.500A) Proline residue: N 64 - end of helix Processing helix chain 'O' and resid 5 through 42 removed outlier: 4.016A pdb=" N LEU O 9 " --> pdb=" O ASN O 5 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR O 10 " --> pdb=" O MET O 6 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE O 28 " --> pdb=" O ALA O 24 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG O 41 " --> pdb=" O GLU O 37 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN O 42 " --> pdb=" O GLY O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 61 removed outlier: 3.796A pdb=" N LEU O 59 " --> pdb=" O ILE O 55 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP O 61 " --> pdb=" O MET O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 77 Processing helix chain 'P' and resid 4 through 42 removed outlier: 3.923A pdb=" N LEU P 8 " --> pdb=" O LEU P 4 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA P 21 " --> pdb=" O MET P 17 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE P 28 " --> pdb=" O ALA P 24 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS P 34 " --> pdb=" O ILE P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 77 removed outlier: 3.855A pdb=" N LEU P 59 " --> pdb=" O ILE P 55 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) Proline residue: P 64 - end of helix removed outlier: 3.674A pdb=" N ALA P 67 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 42 removed outlier: 3.504A pdb=" N LEU Q 8 " --> pdb=" O LEU Q 4 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR Q 10 " --> pdb=" O MET Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 77 removed outlier: 3.790A pdb=" N THR Q 51 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE Q 55 " --> pdb=" O THR Q 51 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU Q 59 " --> pdb=" O ILE Q 55 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE Q 63 " --> pdb=" O LEU Q 59 " (cutoff:3.500A) Proline residue: Q 64 - end of helix Processing helix chain 'R' and resid 4 through 42 removed outlier: 3.677A pdb=" N LEU R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA R 21 " --> pdb=" O MET R 17 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE R 28 " --> pdb=" O ALA R 24 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS R 34 " --> pdb=" O ILE R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 77 removed outlier: 3.940A pdb=" N LEU R 59 " --> pdb=" O ILE R 55 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE R 63 " --> pdb=" O LEU R 59 " (cutoff:3.500A) Proline residue: R 64 - end of helix 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: 3.647A pdb=" N MET S 16 " --> pdb=" O ALA S 12 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 61 removed outlier: 3.710A pdb=" N GLY S 58 " --> pdb=" O PHE S 54 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU S 59 " --> pdb=" O ILE S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 78 removed outlier: 3.668A pdb=" N MET S 65 " --> pdb=" O ASP S 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 3 through 21 Proline residue: W 9 - end of helix Processing helix chain 'W' and resid 23 through 39 removed outlier: 3.550A pdb=" N PHE W 33 " --> pdb=" O ASP W 29 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR W 38 " --> pdb=" O ALA W 34 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 48 Processing helix chain 'W' and resid 52 through 64 Processing helix chain 'W' and resid 71 through 82 Processing helix chain 'W' and resid 84 through 86 No H-bonds generated for 'chain 'W' and resid 84 through 86' Processing helix chain 'W' and resid 87 through 92 Processing helix chain 'W' and resid 93 through 103 Processing helix chain 'W' and resid 118 through 132 Processing helix chain 'W' and resid 162 through 171 Processing helix chain 'X' and resid 5 through 24 Processing helix chain 'X' and resid 25 through 47 removed outlier: 3.852A pdb=" N ALA X 47 " --> pdb=" O GLY X 43 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 136 removed outlier: 3.781A pdb=" N LEU X 56 " --> pdb=" O LYS X 52 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS X 122 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN X 123 " --> pdb=" O GLU X 119 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) Processing helix chain 'X' and resid 144 through 155 removed outlier: 4.139A pdb=" N ILE X 148 " --> pdb=" O ALA X 144 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU X 155 " --> pdb=" O LYS X 151 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 25 removed outlier: 3.739A pdb=" N LYS Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 49 removed outlier: 3.768A pdb=" N LEU Y 29 " --> pdb=" O VAL Y 25 " (cutoff:3.500A) Processing helix chain 'Y' and resid 49 through 139 removed outlier: 3.960A pdb=" N ASP Y 53 " --> pdb=" O ARG Y 49 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN Y 73 " --> pdb=" O LYS Y 69 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS Y 114 " --> pdb=" O GLU Y 110 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU Y 119 " --> pdb=" O ARG Y 115 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU Y 120 " --> pdb=" O ALA Y 116 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS Y 134 " --> pdb=" O ALA Y 130 " (cutoff:3.500A) Processing helix chain 'Y' and resid 141 through 156 removed outlier: 3.520A pdb=" N ALA Y 154 " --> pdb=" O ASP Y 150 " (cutoff:3.500A) Processing helix chain 'a' and resid 7 through 16 Processing helix chain 'a' and resid 43 through 65 Processing helix chain 'a' and resid 73 through 94 removed outlier: 3.927A pdb=" N ALA a 78 " --> pdb=" O LYS a 74 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET a 93 " --> pdb=" O SER a 89 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 118 Processing helix chain 'a' and resid 119 through 121 No H-bonds generated for 'chain 'a' and resid 119 through 121' Processing helix chain 'a' and resid 124 through 133 Processing helix chain 'a' and resid 142 through 145 Processing helix chain 'a' and resid 146 through 181 removed outlier: 3.781A pdb=" N THR a 150 " --> pdb=" O ASP a 146 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE a 171 " --> pdb=" O LYS a 167 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N GLY a 172 " --> pdb=" O MET a 168 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY a 173 " --> pdb=" O LYS a 169 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE a 174 " --> pdb=" O GLY a 170 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR a 175 " --> pdb=" O ILE a 171 " (cutoff:3.500A) removed outlier: 3.823A 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: 4.109A pdb=" N ILE a 194 " --> pdb=" O PRO a 190 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 3.700A pdb=" N ALA a 217 " --> pdb=" O GLY a 213 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU a 229 " --> pdb=" O ILE a 225 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 269 removed outlier: 4.051A pdb=" N ILE a 236 " --> pdb=" O TRP a 232 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 4.070A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 66 removed outlier: 4.385A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ARG A 93 " --> pdb=" O MET A 52 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER A 54 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR A 91 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASP D 67 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N GLN D 32 " --> pdb=" O ASP D 67 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ARG D 52 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLN D 45 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ILE D 50 " --> pdb=" O GLN D 45 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.493A 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: 3.607A pdb=" N ILE A 198 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA A 256 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N LEU A 327 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ILE A 258 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ILE A 329 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR A 260 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N GLU A 331 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU A 166 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LEU A 355 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.759A 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: 4.341A 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: 6.515A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.793A 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: 5.847A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 3.668A 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: 6.640A pdb=" N ARG E 52 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N GLN E 45 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ILE E 50 " --> pdb=" O GLN E 45 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 50 through 55 current: chain 'W' and resid 135 through 138 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 135 through 138 current: chain 'W' and resid 157 through 160 Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA7, first strand: chain 'B' and resid 107 through 109 removed outlier: 6.426A pdb=" N LYS B 192 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ILE B 259 " --> pdb=" O LYS B 192 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE B 194 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ASP B 261 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL B 196 " --> pdb=" O ASP B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 329 through 331 removed outlier: 6.417A pdb=" N ILE B 167 " --> pdb=" O ILE B 330 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.424A 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: 4.286A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ARG C 93 " --> pdb=" O MET C 52 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER C 54 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR C 91 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ARG C 40 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL C 34 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ASP F 67 " --> pdb=" O GLN F 32 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLN F 32 " --> pdb=" O ASP F 67 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA F 28 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ARG F 52 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLN F 45 " --> pdb=" O ILE F 50 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE F 50 " --> pdb=" O GLN F 45 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.595A 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: 4.478A 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: 6.480A pdb=" N VAL D 145 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL D 296 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 6.108A 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: 4.745A 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 79 removed outlier: 4.815A pdb=" N GLU E 105 " --> pdb=" O VAL E 79 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 87 through 88 removed outlier: 6.188A pdb=" N MET E 88 " --> pdb=" O TYR E 206 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N GLN E 208 " --> pdb=" O MET E 88 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL E 145 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL E 296 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU E 147 " --> pdb=" O VAL E 296 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LYS E 144 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL E 319 " --> pdb=" O LYS E 144 " (cutoff:3.500A) removed outlier: 6.172A 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: 3.971A 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: 4.658A 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: 6.054A pdb=" N MET F 88 " --> pdb=" O TYR F 206 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N GLN F 208 " --> pdb=" O MET F 88 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL F 237 " --> pdb=" O THR F 291 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL F 293 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU F 239 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ALA F 295 " --> pdb=" O LEU F 239 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL F 241 " --> pdb=" O ALA F 295 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL F 145 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LYS F 144 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N VAL F 319 " --> pdb=" O LYS F 144 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY F 146 " --> pdb=" O VAL F 319 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 134 through 136 removed outlier: 4.218A pdb=" N ALA G 134 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS G 166 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ASN G 172 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU G 167 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE G 175 " --> pdb=" O SER G 179 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N SER G 179 " --> pdb=" O ILE G 175 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 206 through 207 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 206 through 207 current: chain 'H' and resid 14 through 20 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 14 through 20 current: chain 'H' and resid 32 through 34 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 32 through 34 current: chain 'H' and resid 61 through 70 removed outlier: 6.943A pdb=" N ILE H 62 " --> pdb=" O ARG H 85 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ARG H 85 " --> pdb=" O ILE H 62 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU H 64 " --> pdb=" O ALA H 83 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA H 83 " --> pdb=" O LEU H 64 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLY H 66 " --> pdb=" O ASP H 81 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'a' and resid 27 through 29 removed outlier: 3.566A pdb=" N SER a 27 " --> pdb=" O ASP a 22 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLN a 20 " --> pdb=" O VAL a 29 " (cutoff:3.500A) 2249 hydrogen bonds defined for protein. 6582 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: 9.96 Time building geometry restraints manager: 4.84 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: 6327 1.31 - 1.44: 8796 1.44 - 1.57: 21964 1.57 - 1.69: 27 1.69 - 1.82: 358 Bond restraints: 37472 Sorted by residual: bond pdb=" C PRO F 23 " pdb=" O PRO F 23 " ideal model delta sigma weight residual 1.234 1.187 0.046 1.14e-02 7.69e+03 1.63e+01 bond pdb=" CA SER B 375 " pdb=" CB SER B 375 " ideal model delta sigma weight residual 1.532 1.474 0.058 1.58e-02 4.01e+03 1.34e+01 bond pdb=" CA SER B 373 " pdb=" CB SER B 373 " ideal model delta sigma weight residual 1.530 1.477 0.053 1.48e-02 4.57e+03 1.29e+01 bond pdb=" C ILE Q 63 " pdb=" N PRO Q 64 " ideal model delta sigma weight residual 1.335 1.372 -0.037 1.19e-02 7.06e+03 9.88e+00 bond pdb=" N LEU O 45 " pdb=" CA LEU O 45 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.32e-02 5.74e+03 8.88e+00 ... (remaining 37467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 49415 2.26 - 4.52: 1138 4.52 - 6.78: 140 6.78 - 9.04: 21 9.04 - 11.30: 7 Bond angle restraints: 50721 Sorted by residual: angle pdb=" N THR A 148 " pdb=" CA THR A 148 " pdb=" C THR A 148 " ideal model delta sigma weight residual 109.96 101.16 8.80 1.68e+00 3.54e-01 2.75e+01 angle pdb=" N VAL E 198 " pdb=" CA VAL E 198 " pdb=" C VAL E 198 " ideal model delta sigma weight residual 113.20 108.20 5.00 9.60e-01 1.09e+00 2.71e+01 angle pdb=" C HIS A 479 " pdb=" N ALA A 480 " pdb=" CA ALA A 480 " ideal model delta sigma weight residual 120.58 126.21 -5.63 1.32e+00 5.74e-01 1.82e+01 angle pdb=" C VAL A 146 " pdb=" N GLN A 147 " pdb=" CA GLN A 147 " ideal model delta sigma weight residual 122.84 117.31 5.53 1.30e+00 5.92e-01 1.81e+01 angle pdb=" N ILE O 46 " pdb=" CA ILE O 46 " pdb=" CB ILE O 46 " ideal model delta sigma weight residual 110.50 112.94 -2.44 6.30e-01 2.52e+00 1.50e+01 ... (remaining 50716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.49: 22232 35.49 - 70.98: 373 70.98 - 106.47: 50 106.47 - 141.96: 3 141.96 - 177.45: 2 Dihedral angle restraints: 22660 sinusoidal: 8895 harmonic: 13765 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 300.00 122.55 177.45 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP F 500 " pdb=" O5' ADP F 500 " pdb=" PA ADP F 500 " pdb=" O2A ADP F 500 " ideal model delta sinusoidal sigma weight residual 300.00 125.32 174.69 1 2.00e+01 2.50e-03 4.79e+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 300.00 179.58 120.43 1 2.00e+01 2.50e-03 3.62e+01 ... (remaining 22657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 5503 0.099 - 0.197: 399 0.197 - 0.296: 7 0.296 - 0.394: 3 0.394 - 0.493: 2 Chirality restraints: 5914 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 2.15 0.49 2.00e-01 2.50e+01 6.07e+00 chirality pdb=" CA THR A 148 " pdb=" N THR A 148 " pdb=" C THR A 148 " pdb=" CB THR A 148 " both_signs ideal model delta sigma weight residual False 2.53 2.96 -0.43 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CA TYR F 26 " pdb=" N TYR F 26 " pdb=" C TYR F 26 " pdb=" CB TYR F 26 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.84e+00 ... (remaining 5911 not shown) Planarity restraints: 6540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG W 169 " -0.241 9.50e-02 1.11e+02 1.09e-01 9.44e+00 pdb=" NE ARG W 169 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG W 169 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG W 169 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG W 169 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 59 " 0.214 9.50e-02 1.11e+02 9.72e-02 8.76e+00 pdb=" NE ARG A 59 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 59 " 0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG A 59 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG A 59 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 296 " 0.015 2.00e-02 2.50e+03 2.88e-02 8.32e+00 pdb=" C ARG A 296 " -0.050 2.00e-02 2.50e+03 pdb=" O ARG A 296 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU A 297 " 0.017 2.00e-02 2.50e+03 ... (remaining 6537 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 63 2.50 - 3.10: 27767 3.10 - 3.70: 55379 3.70 - 4.30: 83326 4.30 - 4.90: 136635 Nonbonded interactions: 303170 Sorted by model distance: nonbonded pdb="MG MG D 501 " pdb=" O1G ATP D 502 " model vdw 1.900 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 601 " model vdw 2.006 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 601 " model vdw 2.062 2.170 nonbonded pdb=" O2G ATP C 600 " pdb="MG MG C 601 " model vdw 2.101 2.170 nonbonded pdb=" OG1 THR D 156 " pdb="MG MG D 501 " model vdw 2.115 2.170 ... (remaining 303165 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 47 or resid 50 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: 2.820 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: 0.650 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 39.230 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 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 : 0.004 0.072 37472 Z= 0.230 Angle : 0.833 11.300 50721 Z= 0.461 Chirality : 0.052 0.493 5914 Planarity : 0.009 0.109 6540 Dihedral : 14.177 177.445 13854 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.58 % Favored : 98.40 % Rotamer: Outliers : 0.76 % Allowed : 4.88 % Favored : 94.36 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.11), residues: 4799 helix: 0.28 (0.09), residues: 2614 sheet: 0.25 (0.21), residues: 528 loop : -0.42 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.004 ARG A 59 TYR 0.035 0.006 TYR G 205 PHE 0.042 0.003 PHE O 54 TRP 0.033 0.005 TRP G 203 HIS 0.009 0.002 HIS G 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.23 (37472) covalent geometry : angle 0.83345 / 0.46 (50721) hydrogen bonds : bond 0.12999 / 8.70 ( 2249) hydrogen bonds : angle 6.26370 / 4.51 ( 6582) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 517 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 386 MET cc_start: 0.8727 (mmm) cc_final: 0.8355 (mmt) REVERT: D 445 MET cc_start: 0.8889 (mmt) cc_final: 0.8677 (mmm) REVERT: E 56 MET cc_start: 0.9133 (mmm) cc_final: 0.8868 (mmp) REVERT: E 242 ASP cc_start: 0.7159 (t70) cc_final: 0.6163 (t70) REVERT: E 397 GLN cc_start: 0.8584 (tt0) cc_final: 0.8069 (tm-30) REVERT: F 136 MET cc_start: 0.8363 (mmm) cc_final: 0.8030 (mmm) REVERT: G 48 MET cc_start: 0.8608 (mmt) cc_final: 0.8213 (mmm) REVERT: H 53 VAL cc_start: 0.8848 (p) cc_final: 0.8578 (p) REVERT: H 63 TYR cc_start: 0.6661 (t80) cc_final: 0.6289 (t80) REVERT: H 127 GLN cc_start: 0.8194 (mt0) cc_final: 0.7871 (tt0) REVERT: J 11 MET cc_start: 0.5319 (tpp) cc_final: 0.5093 (tmm) REVERT: J 65 MET cc_start: 0.3343 (OUTLIER) cc_final: 0.3131 (mmp) REVERT: L 6 MET cc_start: 0.6287 (ttp) cc_final: 0.5968 (mtm) REVERT: L 17 MET cc_start: 0.7017 (mtm) cc_final: 0.6698 (tpp) REVERT: L 57 MET cc_start: 0.0866 (tmm) cc_final: 0.0394 (tpp) REVERT: M 17 MET cc_start: 0.6233 (mtm) cc_final: 0.3680 (tpt) REVERT: M 44 ASP cc_start: 0.6857 (m-30) cc_final: 0.5948 (t70) REVERT: M 75 MET cc_start: 0.3690 (ttp) cc_final: 0.3057 (tmm) REVERT: N 65 MET cc_start: 0.0914 (mtt) cc_final: 0.0644 (mtm) REVERT: O 37 GLU cc_start: 0.6882 (tt0) cc_final: 0.6577 (tp30) REVERT: O 65 MET cc_start: 0.4916 (mmt) cc_final: 0.4432 (mmm) REVERT: P 6 MET cc_start: 0.4010 (mmt) cc_final: 0.3586 (ptp) REVERT: P 11 MET cc_start: 0.5183 (tpp) cc_final: 0.4658 (mpp) REVERT: P 47 PRO cc_start: 0.5615 (Cg_endo) cc_final: 0.5050 (Cg_exo) REVERT: Q 11 MET cc_start: 0.7515 (tpt) cc_final: 0.6697 (mmp) REVERT: Q 17 MET cc_start: 0.7185 (mtm) cc_final: 0.6320 (tpt) REVERT: S 4 LEU cc_start: 0.3890 (tp) cc_final: 0.3626 (pt) REVERT: S 31 LEU cc_start: 0.6715 (tp) cc_final: 0.6093 (pp) REVERT: X 74 VAL cc_start: 0.8539 (m) cc_final: 0.8312 (m) REVERT: X 136 ILE cc_start: 0.6856 (OUTLIER) cc_final: 0.6651 (mm) REVERT: X 150 ASP cc_start: 0.8174 (t0) cc_final: 0.7763 (m-30) REVERT: Y 24 TYR cc_start: 0.2664 (m-80) cc_final: 0.1869 (t80) REVERT: Y 26 TRP cc_start: 0.4381 (t60) cc_final: 0.3085 (m100) REVERT: Y 37 GLN cc_start: 0.5105 (mt0) cc_final: 0.4798 (tp40) REVERT: Y 73 GLN cc_start: 0.7455 (tp40) cc_final: 0.6664 (pt0) REVERT: Y 113 ARG cc_start: 0.7593 (ttt180) cc_final: 0.7317 (ttt180) REVERT: Y 115 ARG cc_start: 0.8810 (ttp80) cc_final: 0.8590 (tpt90) REVERT: a 65 LYS cc_start: 0.2966 (tttt) cc_final: 0.2478 (pttt) REVERT: a 168 MET cc_start: 0.6152 (mmt) cc_final: 0.5500 (tpp) outliers start: 29 outliers final: 5 residues processed: 535 average time/residue: 0.2774 time to fit residues: 231.6674 Evaluate side-chains 314 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 307 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain J residue 65 MET Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 106 GLN Chi-restraints excluded: chain X residue 136 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 10.0000 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.0000 chunk 470 optimal weight: 4.9990 overall best weight: 3.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 272 GLN C 220 ASN C 358 ASN C 479 HIS E 365 GLN G 57 HIS ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 GLN O 42 GLN P 3 ASN R 52 GLN S 52 GLN Y 73 GLN Y 123 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.083349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.052123 restraints weight = 150792.423| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.04 r_work: 0.2870 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 37472 Z= 0.199 Angle : 0.649 8.132 50721 Z= 0.341 Chirality : 0.045 0.300 5914 Planarity : 0.005 0.079 6540 Dihedral : 7.179 165.761 5249 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.44 % Favored : 98.54 % Rotamer: Outliers : 1.31 % Allowed : 8.59 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.12), residues: 4799 helix: 0.86 (0.10), residues: 2700 sheet: 0.48 (0.21), residues: 548 loop : -0.22 (0.16), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG X 121 TYR 0.018 0.002 TYR P 10 PHE 0.021 0.002 PHE R 35 TRP 0.038 0.003 TRP G 203 HIS 0.006 0.001 HIS W 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 (37472) covalent geometry : angle 0.64892 / 0.34 (50721) hydrogen bonds : bond 0.06070 / 4.07 ( 2249) hydrogen bonds : angle 5.00585 / 3.59 ( 6582) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 324 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8148 (mm) REVERT: B 1 MET cc_start: 0.3952 (ttm) cc_final: 0.3156 (mmm) REVERT: B 10 GLU cc_start: 0.9334 (tm-30) cc_final: 0.8955 (mp0) REVERT: C 180 ILE cc_start: 0.9372 (pt) cc_final: 0.9145 (mm) REVERT: E 56 MET cc_start: 0.9467 (mmm) cc_final: 0.9082 (mmp) REVERT: E 397 GLN cc_start: 0.9002 (tt0) cc_final: 0.8317 (tm-30) REVERT: E 445 MET cc_start: 0.8959 (mmt) cc_final: 0.8455 (mmm) REVERT: F 0 MET cc_start: 0.7816 (pmm) cc_final: 0.7493 (pmm) REVERT: F 384 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8414 (tm-30) REVERT: H 49 MET cc_start: 0.6290 (ppp) cc_final: 0.6076 (ppp) REVERT: L 6 MET cc_start: 0.6564 (ttp) cc_final: 0.6328 (mtm) REVERT: L 65 MET cc_start: 0.0830 (mmm) cc_final: -0.0370 (ptm) REVERT: M 16 MET cc_start: 0.6883 (mtp) cc_final: 0.6559 (mmm) REVERT: M 17 MET cc_start: 0.5617 (mtm) cc_final: 0.3426 (tpt) REVERT: N 3 ASN cc_start: 0.7469 (t0) cc_final: 0.5974 (m-40) REVERT: N 16 MET cc_start: 0.5411 (mmm) cc_final: 0.4488 (tpp) REVERT: P 6 MET cc_start: 0.3846 (mmt) cc_final: 0.3330 (ptp) REVERT: P 11 MET cc_start: 0.5129 (tpp) cc_final: 0.4619 (mpp) REVERT: Q 11 MET cc_start: 0.7189 (tpt) cc_final: 0.6615 (mmm) REVERT: Q 17 MET cc_start: 0.7306 (mtm) cc_final: 0.6308 (tpt) REVERT: Q 37 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8311 (tm-30) REVERT: Y 24 TYR cc_start: 0.2588 (m-80) cc_final: 0.2136 (t80) REVERT: Y 26 TRP cc_start: 0.3801 (t60) cc_final: 0.2840 (m100) REVERT: Y 73 GLN cc_start: 0.7209 (tp-100) cc_final: 0.6494 (pt0) REVERT: Y 89 GLU cc_start: 0.8771 (tp30) cc_final: 0.8459 (tm-30) REVERT: Y 115 ARG cc_start: 0.8873 (ttp80) cc_final: 0.8640 (tpt90) REVERT: a 65 LYS cc_start: 0.2460 (tttt) cc_final: 0.2149 (pttt) REVERT: a 168 MET cc_start: 0.6115 (mmt) cc_final: 0.5515 (tpp) outliers start: 50 outliers final: 22 residues processed: 361 average time/residue: 0.2471 time to fit residues: 145.2940 Evaluate side-chains 296 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 273 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 30 ILE Chi-restraints excluded: chain Q residue 44 ASP Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain a residue 121 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 403 optimal weight: 4.9990 chunk 378 optimal weight: 6.9990 chunk 440 optimal weight: 6.9990 chunk 333 optimal weight: 30.0000 chunk 116 optimal weight: 1.9990 chunk 460 optimal weight: 0.6980 chunk 239 optimal weight: 1.9990 chunk 187 optimal weight: 0.6980 chunk 366 optimal weight: 8.9990 chunk 196 optimal weight: 9.9990 chunk 433 optimal weight: 6.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 484 GLN A 488 GLN F 243 ASN ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 64 GLN a 15 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.083378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.052374 restraints weight = 150333.960| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.03 r_work: 0.2880 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 37472 Z= 0.152 Angle : 0.586 9.017 50721 Z= 0.304 Chirality : 0.043 0.264 5914 Planarity : 0.004 0.092 6540 Dihedral : 6.511 155.883 5241 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.38 % Allowed : 9.42 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.12), residues: 4799 helix: 1.29 (0.10), residues: 2682 sheet: 0.59 (0.21), residues: 554 loop : -0.12 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 210 TYR 0.018 0.001 TYR H 63 PHE 0.020 0.001 PHE I 54 TRP 0.034 0.002 TRP G 203 HIS 0.005 0.001 HIS W 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (37472) covalent geometry : angle 0.58647 / 0.30 (50721) hydrogen bonds : bond 0.05345 / 3.58 ( 2249) hydrogen bonds : angle 4.70698 / 3.38 ( 6582) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 300 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 PHE cc_start: 0.7410 (OUTLIER) cc_final: 0.7208 (t80) REVERT: B 1 MET cc_start: 0.2855 (ttm) cc_final: 0.2337 (mmt) REVERT: B 10 GLU cc_start: 0.9308 (tm-30) cc_final: 0.8979 (mp0) REVERT: C 187 ARG cc_start: 0.9344 (OUTLIER) cc_final: 0.9072 (ptp-170) REVERT: E 46 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8975 (pp) REVERT: E 56 MET cc_start: 0.9417 (mmm) cc_final: 0.9088 (mmp) REVERT: E 397 GLN cc_start: 0.8969 (tt0) cc_final: 0.8300 (tm-30) REVERT: E 445 MET cc_start: 0.9005 (mmt) cc_final: 0.8533 (mmt) REVERT: F 243 ASN cc_start: 0.8051 (OUTLIER) cc_final: 0.7673 (m-40) REVERT: I 17 MET cc_start: 0.4468 (ppp) cc_final: 0.4229 (ppp) REVERT: L 6 MET cc_start: 0.6426 (ttp) cc_final: 0.6148 (mtm) REVERT: L 41 ARG cc_start: 0.6864 (mmm160) cc_final: 0.6488 (tpp-160) REVERT: L 65 MET cc_start: 0.1011 (mmm) cc_final: 0.0546 (ptt) REVERT: L 75 MET cc_start: 0.4030 (tmm) cc_final: 0.3793 (tmm) REVERT: N 3 ASN cc_start: 0.7550 (t0) cc_final: 0.6037 (m110) REVERT: N 16 MET cc_start: 0.5393 (mmm) cc_final: 0.4823 (tpp) REVERT: N 17 MET cc_start: 0.4866 (tpt) cc_final: 0.3601 (mtt) REVERT: P 6 MET cc_start: 0.3563 (mmt) cc_final: 0.3282 (ptp) REVERT: P 11 MET cc_start: 0.4823 (tpp) cc_final: 0.4263 (mpp) REVERT: Q 11 MET cc_start: 0.6998 (tpt) cc_final: 0.6510 (mmt) REVERT: Q 17 MET cc_start: 0.7333 (mtm) cc_final: 0.6347 (tpt) REVERT: X 147 ASP cc_start: 0.7413 (m-30) cc_final: 0.6834 (t70) REVERT: Y 26 TRP cc_start: 0.3731 (t60) cc_final: 0.2851 (m100) REVERT: Y 73 GLN cc_start: 0.6988 (tp-100) cc_final: 0.6359 (pt0) REVERT: Y 82 ARG cc_start: 0.7186 (mmm160) cc_final: 0.6706 (mmm160) REVERT: Y 115 ARG cc_start: 0.8892 (ttp80) cc_final: 0.8615 (tpt90) REVERT: a 65 LYS cc_start: 0.2392 (tttt) cc_final: 0.2135 (pttt) REVERT: a 168 MET cc_start: 0.6502 (mmt) cc_final: 0.5494 (tpp) outliers start: 53 outliers final: 26 residues processed: 340 average time/residue: 0.2275 time to fit residues: 127.2101 Evaluate side-chains 297 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 267 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain F residue 243 ASN Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain Y residue 18 VAL Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 228 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 5 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 326 optimal weight: 8.9990 chunk 255 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 chunk 371 optimal weight: 8.9990 chunk 352 optimal weight: 7.9990 chunk 110 optimal weight: 0.0270 chunk 120 optimal weight: 3.9990 chunk 199 optimal weight: 0.0670 chunk 253 optimal weight: 9.9990 overall best weight: 1.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.083760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.053643 restraints weight = 150916.303| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.15 r_work: 0.2876 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 37472 Z= 0.130 Angle : 0.558 11.058 50721 Z= 0.287 Chirality : 0.041 0.282 5914 Planarity : 0.004 0.058 6540 Dihedral : 6.220 155.420 5241 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.54 % Allowed : 10.08 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.12), residues: 4799 helix: 1.54 (0.10), residues: 2677 sheet: 0.64 (0.21), residues: 567 loop : -0.08 (0.16), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Y 83 TYR 0.013 0.001 TYR a 11 PHE 0.029 0.001 PHE F 189 TRP 0.017 0.001 TRP G 203 HIS 0.004 0.001 HIS H 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (37472) covalent geometry : angle 0.55809 / 0.29 (50721) hydrogen bonds : bond 0.04898 / 3.28 ( 2249) hydrogen bonds : angle 4.52013 / 3.24 ( 6582) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 284 time to evaluate : 1.343 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: B 10 GLU cc_start: 0.9320 (tm-30) cc_final: 0.9048 (mp0) REVERT: B 236 TYR cc_start: 0.9441 (OUTLIER) cc_final: 0.8648 (t80) REVERT: C 187 ARG cc_start: 0.9327 (OUTLIER) cc_final: 0.9037 (ptp-170) REVERT: D 445 MET cc_start: 0.9286 (mmt) cc_final: 0.9029 (mmm) REVERT: E 46 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8881 (pp) REVERT: E 445 MET cc_start: 0.9029 (mmt) cc_final: 0.8561 (mmt) REVERT: F 379 MET cc_start: 0.8268 (tpp) cc_final: 0.7977 (tpt) REVERT: I 11 MET cc_start: -0.0491 (ttt) cc_final: -0.0810 (ttt) REVERT: L 6 MET cc_start: 0.6550 (ttp) cc_final: 0.6173 (mtm) REVERT: L 65 MET cc_start: 0.1975 (mmm) cc_final: 0.1580 (ptm) REVERT: N 16 MET cc_start: 0.5721 (mmm) cc_final: 0.4908 (tpp) REVERT: P 6 MET cc_start: 0.3806 (mmt) cc_final: 0.3515 (ptp) REVERT: P 11 MET cc_start: 0.4790 (tpp) cc_final: 0.4223 (mpp) REVERT: Q 17 MET cc_start: 0.7300 (mtm) cc_final: 0.6327 (tpt) REVERT: S 31 LEU cc_start: 0.6555 (tp) cc_final: 0.6332 (mm) REVERT: X 115 ARG cc_start: 0.8648 (ptp-110) cc_final: 0.8399 (ptt-90) REVERT: X 147 ASP cc_start: 0.7533 (m-30) cc_final: 0.7013 (t70) REVERT: Y 26 TRP cc_start: 0.3928 (t60) cc_final: 0.2872 (m100) REVERT: Y 73 GLN cc_start: 0.7141 (tp-100) cc_final: 0.6514 (pt0) REVERT: Y 115 ARG cc_start: 0.8924 (ttp80) cc_final: 0.8708 (tpt90) REVERT: a 65 LYS cc_start: 0.2560 (tttt) cc_final: 0.2259 (pttt) REVERT: a 168 MET cc_start: 0.6490 (mmt) cc_final: 0.5405 (tpp) outliers start: 59 outliers final: 31 residues processed: 324 average time/residue: 0.2058 time to fit residues: 111.7665 Evaluate side-chains 296 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 262 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 17 MET Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 106 GLN Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 228 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 321 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 395 optimal weight: 30.0000 chunk 210 optimal weight: 0.8980 chunk 351 optimal weight: 8.9990 chunk 89 optimal weight: 8.9990 chunk 298 optimal weight: 1.9990 chunk 374 optimal weight: 7.9990 chunk 106 optimal weight: 0.0980 chunk 223 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 368 GLN ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 67 GLN a 20 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.083653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.054121 restraints weight = 149881.958| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.22 r_work: 0.2869 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 37472 Z= 0.132 Angle : 0.555 12.862 50721 Z= 0.283 Chirality : 0.041 0.262 5914 Planarity : 0.004 0.093 6540 Dihedral : 6.014 154.252 5241 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.23 % Allowed : 10.81 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.12), residues: 4799 helix: 1.71 (0.10), residues: 2670 sheet: 0.58 (0.21), residues: 575 loop : -0.02 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 51 TYR 0.014 0.001 TYR H 63 PHE 0.021 0.001 PHE F 189 TRP 0.013 0.001 TRP a 235 HIS 0.005 0.001 HIS H 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (37472) covalent geometry : angle 0.55494 / 0.28 (50721) hydrogen bonds : bond 0.04670 / 3.14 ( 2249) hydrogen bonds : angle 4.40220 / 3.16 ( 6582) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 282 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 GLU cc_start: 0.9275 (tm-30) cc_final: 0.9052 (mp0) REVERT: B 236 TYR cc_start: 0.9426 (OUTLIER) cc_final: 0.8438 (t80) REVERT: C 187 ARG cc_start: 0.9341 (OUTLIER) cc_final: 0.9050 (ptp-170) REVERT: D 445 MET cc_start: 0.9295 (mmt) cc_final: 0.9013 (mmm) REVERT: E 46 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8860 (pp) REVERT: E 445 MET cc_start: 0.9010 (mmt) cc_final: 0.8528 (mmt) REVERT: F 0 MET cc_start: 0.7846 (pmm) cc_final: 0.7638 (pmm) REVERT: F 379 MET cc_start: 0.8226 (tpp) cc_final: 0.7937 (tpt) REVERT: F 445 MET cc_start: 0.8758 (mmm) cc_final: 0.8446 (mmm) REVERT: H 52 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8132 (pt) REVERT: I 11 MET cc_start: -0.0799 (ttt) cc_final: -0.1118 (ttt) REVERT: I 17 MET cc_start: 0.4528 (ppp) cc_final: 0.4273 (ppp) REVERT: J 66 ILE cc_start: 0.6603 (tp) cc_final: 0.6263 (pt) REVERT: L 6 MET cc_start: 0.6516 (ttp) cc_final: 0.6153 (mtm) REVERT: L 11 MET cc_start: 0.5326 (mmm) cc_final: 0.5119 (mmm) REVERT: L 41 ARG cc_start: 0.6677 (mmm160) cc_final: 0.6336 (tpp-160) REVERT: L 65 MET cc_start: 0.1950 (mmm) cc_final: 0.1699 (ptm) REVERT: P 6 MET cc_start: 0.3836 (mmt) cc_final: 0.3551 (ptp) REVERT: P 11 MET cc_start: 0.4976 (tpp) cc_final: 0.4227 (mpp) REVERT: Q 11 MET cc_start: 0.6783 (tpt) cc_final: 0.6332 (mmt) REVERT: Q 17 MET cc_start: 0.7261 (mtm) cc_final: 0.6268 (tpt) REVERT: S 75 MET cc_start: 0.3969 (ttt) cc_final: 0.3745 (tmm) REVERT: W 109 ASP cc_start: 0.8230 (t0) cc_final: 0.7668 (t0) REVERT: X 115 ARG cc_start: 0.8642 (ptp-110) cc_final: 0.8402 (ptt-90) REVERT: X 147 ASP cc_start: 0.7625 (m-30) cc_final: 0.7116 (t70) REVERT: Y 26 TRP cc_start: 0.3943 (t60) cc_final: 0.2903 (m100) REVERT: Y 73 GLN cc_start: 0.7106 (tp-100) cc_final: 0.6497 (pt0) REVERT: Y 115 ARG cc_start: 0.8956 (ttp80) cc_final: 0.8708 (tpt90) REVERT: a 65 LYS cc_start: 0.2578 (tttt) cc_final: 0.2252 (pttt) REVERT: a 168 MET cc_start: 0.6486 (mmt) cc_final: 0.5434 (tpp) outliers start: 47 outliers final: 31 residues processed: 317 average time/residue: 0.2239 time to fit residues: 119.0458 Evaluate side-chains 297 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 262 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 395 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 17 MET Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 228 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 449 optimal weight: 40.0000 chunk 54 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 412 optimal weight: 5.9990 chunk 306 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 238 optimal weight: 0.2980 chunk 40 optimal weight: 8.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 479 HIS ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN O 42 GLN W 67 GLN a 15 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.082734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.053354 restraints weight = 153273.171| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.58 r_work: 0.2844 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 37472 Z= 0.177 Angle : 0.581 11.549 50721 Z= 0.296 Chirality : 0.042 0.287 5914 Planarity : 0.004 0.047 6540 Dihedral : 5.980 154.109 5241 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.59 % Allowed : 11.62 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.12), residues: 4799 helix: 1.77 (0.10), residues: 2668 sheet: 0.58 (0.21), residues: 580 loop : -0.05 (0.16), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Y 82 TYR 0.015 0.001 TYR E 247 PHE 0.033 0.001 PHE a 56 TRP 0.013 0.001 TRP a 235 HIS 0.005 0.001 HIS H 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (37472) covalent geometry : angle 0.58116 / 0.30 (50721) hydrogen bonds : bond 0.04784 / 3.21 ( 2249) hydrogen bonds : angle 4.44216 / 3.19 ( 6582) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 269 time to evaluate : 1.500 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: B 236 TYR cc_start: 0.9482 (OUTLIER) cc_final: 0.8892 (t80) REVERT: C 187 ARG cc_start: 0.9368 (OUTLIER) cc_final: 0.9087 (ptp-170) REVERT: E 46 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8891 (pp) REVERT: E 408 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7878 (tp30) REVERT: E 445 MET cc_start: 0.8927 (mmt) cc_final: 0.8469 (mmt) REVERT: F 0 MET cc_start: 0.7856 (pmm) cc_final: 0.7647 (pmm) REVERT: F 379 MET cc_start: 0.8214 (tpp) cc_final: 0.7923 (tpt) REVERT: F 445 MET cc_start: 0.8863 (mmm) cc_final: 0.8486 (mmm) REVERT: H 95 MET cc_start: 0.7170 (mmm) cc_final: 0.6894 (mmm) REVERT: I 11 MET cc_start: -0.0807 (ttt) cc_final: -0.1241 (ttt) REVERT: L 6 MET cc_start: 0.6201 (ttp) cc_final: 0.5941 (mtm) REVERT: L 8 LEU cc_start: 0.6275 (OUTLIER) cc_final: 0.5982 (mp) REVERT: L 65 MET cc_start: 0.1987 (mmm) cc_final: 0.1691 (ptm) REVERT: M 17 MET cc_start: 0.3982 (mtt) cc_final: 0.1715 (tpp) REVERT: N 3 ASN cc_start: 0.7380 (t0) cc_final: 0.5798 (m110) REVERT: N 16 MET cc_start: 0.5535 (mmm) cc_final: 0.4380 (tpp) REVERT: P 6 MET cc_start: 0.3832 (mmt) cc_final: 0.3551 (ptp) REVERT: P 11 MET cc_start: 0.5049 (tpp) cc_final: 0.4237 (mpp) REVERT: Q 17 MET cc_start: 0.7233 (mtm) cc_final: 0.6255 (tpt) REVERT: Q 65 MET cc_start: 0.5638 (tpt) cc_final: 0.5406 (tpt) REVERT: S 31 LEU cc_start: 0.6455 (tp) cc_final: 0.5901 (mt) REVERT: X 104 GLN cc_start: 0.8563 (pp30) cc_final: 0.8209 (pt0) REVERT: X 147 ASP cc_start: 0.7457 (m-30) cc_final: 0.7010 (t70) REVERT: Y 26 TRP cc_start: 0.3898 (t60) cc_final: 0.2882 (m100) REVERT: Y 73 GLN cc_start: 0.7094 (tp-100) cc_final: 0.6551 (pt0) REVERT: Y 82 ARG cc_start: 0.6365 (mmm160) cc_final: 0.5825 (mmm160) REVERT: Y 115 ARG cc_start: 0.8959 (ttp80) cc_final: 0.8691 (tpt90) REVERT: a 65 LYS cc_start: 0.2649 (tttt) cc_final: 0.2307 (pttt) REVERT: a 168 MET cc_start: 0.6488 (mmt) cc_final: 0.5439 (tpp) outliers start: 61 outliers final: 41 residues processed: 313 average time/residue: 0.2302 time to fit residues: 121.3867 Evaluate side-chains 301 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 255 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 17 MET Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 228 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 150 optimal weight: 3.9990 chunk 241 optimal weight: 7.9990 chunk 163 optimal weight: 0.2980 chunk 171 optimal weight: 0.0020 chunk 126 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 386 optimal weight: 20.0000 chunk 344 optimal weight: 4.9990 chunk 210 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 chunk 288 optimal weight: 6.9990 overall best weight: 1.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 14 HIS a 15 HIS 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 = 0.083589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.054494 restraints weight = 152299.514| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.64 r_work: 0.2877 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 37472 Z= 0.120 Angle : 0.554 13.351 50721 Z= 0.280 Chirality : 0.041 0.292 5914 Planarity : 0.004 0.048 6540 Dihedral : 5.790 153.365 5241 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.44 % Allowed : 11.96 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.12), residues: 4799 helix: 1.83 (0.10), residues: 2680 sheet: 0.68 (0.21), residues: 563 loop : 0.00 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 477 TYR 0.012 0.001 TYR E 247 PHE 0.017 0.001 PHE L 76 TRP 0.012 0.001 TRP a 235 HIS 0.005 0.001 HIS H 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (37472) covalent geometry : angle 0.55368 / 0.28 (50721) hydrogen bonds : bond 0.04403 / 2.96 ( 2249) hydrogen bonds : angle 4.31263 / 3.09 ( 6582) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 267 time to evaluate : 1.564 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: B 12 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7824 (pt) REVERT: B 236 TYR cc_start: 0.9411 (OUTLIER) cc_final: 0.8532 (t80) REVERT: B 504 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9034 (mm) REVERT: C 187 ARG cc_start: 0.9336 (OUTLIER) cc_final: 0.9050 (ptp-170) REVERT: E 46 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8801 (pp) REVERT: E 408 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7946 (tp30) REVERT: E 445 MET cc_start: 0.8929 (mmt) cc_final: 0.8491 (mmt) REVERT: F 379 MET cc_start: 0.8202 (tpp) cc_final: 0.7925 (tpt) REVERT: G 155 MET cc_start: 0.8228 (tpp) cc_final: 0.7999 (tpp) REVERT: H 95 MET cc_start: 0.7209 (mmm) cc_final: 0.6922 (mmm) REVERT: I 11 MET cc_start: -0.0658 (ttt) cc_final: -0.1030 (ttt) REVERT: L 6 MET cc_start: 0.6125 (ttp) cc_final: 0.5728 (mtm) REVERT: L 8 LEU cc_start: 0.6315 (OUTLIER) cc_final: 0.6046 (mp) REVERT: L 41 ARG cc_start: 0.6686 (mmm160) cc_final: 0.6343 (tpp-160) REVERT: L 65 MET cc_start: 0.1913 (mmm) cc_final: 0.1705 (ptm) REVERT: N 16 MET cc_start: 0.5403 (mmm) cc_final: 0.4617 (tpp) REVERT: P 6 MET cc_start: 0.3861 (mmt) cc_final: 0.3597 (ptp) REVERT: P 11 MET cc_start: 0.5084 (tpp) cc_final: 0.4257 (mpp) REVERT: P 34 LYS cc_start: 0.3416 (tppt) cc_final: 0.2854 (mttp) REVERT: Q 11 MET cc_start: 0.6694 (tpt) cc_final: 0.6351 (mmm) REVERT: Q 17 MET cc_start: 0.7259 (mtm) cc_final: 0.6157 (tpt) REVERT: Q 65 MET cc_start: 0.5704 (tpt) cc_final: 0.5441 (tpt) REVERT: Q 72 LEU cc_start: 0.6045 (OUTLIER) cc_final: 0.5599 (mm) REVERT: S 17 MET cc_start: -0.0461 (mtt) cc_final: -0.0734 (mtt) REVERT: S 31 LEU cc_start: 0.6382 (tp) cc_final: 0.5929 (mt) REVERT: X 104 GLN cc_start: 0.8527 (pp30) cc_final: 0.8181 (pt0) REVERT: X 147 ASP cc_start: 0.7590 (m-30) cc_final: 0.7251 (t70) REVERT: Y 26 TRP cc_start: 0.3934 (t60) cc_final: 0.2822 (m100) REVERT: Y 73 GLN cc_start: 0.7069 (tp-100) cc_final: 0.6492 (pt0) REVERT: Y 82 ARG cc_start: 0.6629 (mmm160) cc_final: 0.6028 (mmm160) REVERT: Y 115 ARG cc_start: 0.8962 (ttp80) cc_final: 0.8699 (tpt90) REVERT: a 168 MET cc_start: 0.6577 (mmt) cc_final: 0.5531 (tpp) REVERT: a 215 MET cc_start: 0.3261 (mmp) cc_final: 0.2355 (mmp) outliers start: 55 outliers final: 34 residues processed: 309 average time/residue: 0.2284 time to fit residues: 119.0294 Evaluate side-chains 299 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 257 time to evaluate : 1.475 ------------------------------------------------------------------------------- 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 395 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 17 MET Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain a residue 118 MET Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 228 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 244 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 445 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 286 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 377 optimal weight: 8.9990 chunk 153 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 15 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.083071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.052335 restraints weight = 153417.953| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.99 r_work: 0.2894 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 37472 Z= 0.153 Angle : 0.580 14.756 50721 Z= 0.291 Chirality : 0.041 0.256 5914 Planarity : 0.004 0.065 6540 Dihedral : 5.768 155.056 5241 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.44 % Allowed : 12.40 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.12), residues: 4799 helix: 1.85 (0.10), residues: 2689 sheet: 0.67 (0.22), residues: 551 loop : 0.02 (0.16), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 51 TYR 0.013 0.001 TYR E 247 PHE 0.016 0.001 PHE O 53 TRP 0.013 0.001 TRP a 235 HIS 0.005 0.001 HIS H 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (37472) covalent geometry : angle 0.57961 / 0.29 (50721) hydrogen bonds : bond 0.04488 / 3.02 ( 2249) hydrogen bonds : angle 4.32974 / 3.10 ( 6582) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 265 time to evaluate : 1.557 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: B 236 TYR cc_start: 0.9452 (OUTLIER) cc_final: 0.8464 (t80) REVERT: B 504 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9010 (mm) REVERT: D 445 MET cc_start: 0.9239 (mmt) cc_final: 0.8949 (mmm) REVERT: E 46 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8819 (pp) REVERT: E 408 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7963 (tp30) REVERT: E 445 MET cc_start: 0.8910 (mmt) cc_final: 0.8448 (mmt) REVERT: G 155 MET cc_start: 0.8276 (tpp) cc_final: 0.8001 (tpp) REVERT: H 95 MET cc_start: 0.7275 (mmm) cc_final: 0.7006 (mmm) REVERT: I 11 MET cc_start: -0.0762 (ttt) cc_final: -0.1177 (ttt) REVERT: J 6 MET cc_start: 0.0102 (mmp) cc_final: -0.0936 (ptt) REVERT: L 8 LEU cc_start: 0.6212 (OUTLIER) cc_final: 0.5943 (mp) REVERT: L 65 MET cc_start: 0.1687 (mmm) cc_final: 0.1476 (ptm) REVERT: M 17 MET cc_start: 0.4057 (mtt) cc_final: 0.1764 (tpp) REVERT: N 16 MET cc_start: 0.5560 (mmm) cc_final: 0.4821 (tpp) REVERT: O 75 MET cc_start: 0.2007 (tmm) cc_final: 0.1744 (tmm) REVERT: P 6 MET cc_start: 0.4111 (mmt) cc_final: 0.3677 (ptp) REVERT: P 11 MET cc_start: 0.5003 (tpp) cc_final: 0.4286 (mpp) REVERT: Q 17 MET cc_start: 0.7103 (mtm) cc_final: 0.5957 (tpt) REVERT: Q 54 PHE cc_start: 0.5905 (m-80) cc_final: 0.5682 (m-80) REVERT: Q 65 MET cc_start: 0.5641 (tpt) cc_final: 0.5360 (tpt) REVERT: S 31 LEU cc_start: 0.6481 (tp) cc_final: 0.6014 (mt) REVERT: X 104 GLN cc_start: 0.8535 (pp30) cc_final: 0.8211 (pt0) REVERT: X 147 ASP cc_start: 0.7507 (m-30) cc_final: 0.7160 (t70) REVERT: Y 26 TRP cc_start: 0.3746 (t60) cc_final: 0.2807 (m100) REVERT: Y 73 GLN cc_start: 0.7128 (tp-100) cc_final: 0.6559 (pt0) REVERT: Y 115 ARG cc_start: 0.8943 (ttp80) cc_final: 0.8694 (tpt90) REVERT: a 168 MET cc_start: 0.6534 (mmt) cc_final: 0.5539 (tpp) REVERT: a 215 MET cc_start: 0.3255 (mmp) cc_final: 0.2832 (mmp) outliers start: 55 outliers final: 39 residues processed: 308 average time/residue: 0.2345 time to fit residues: 120.6974 Evaluate side-chains 300 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 256 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 228 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 270 optimal weight: 6.9990 chunk 428 optimal weight: 7.9990 chunk 401 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 202 optimal weight: 0.1980 chunk 203 optimal weight: 4.9990 chunk 301 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 429 optimal weight: 10.0000 chunk 351 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 135 GLN a 15 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.083122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.053308 restraints weight = 154867.505| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.26 r_work: 0.2879 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 37472 Z= 0.145 Angle : 0.584 13.967 50721 Z= 0.293 Chirality : 0.041 0.317 5914 Planarity : 0.004 0.054 6540 Dihedral : 5.735 153.568 5241 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.46 % Allowed : 12.48 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.12), residues: 4799 helix: 1.88 (0.10), residues: 2687 sheet: 0.66 (0.22), residues: 551 loop : 0.02 (0.16), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 477 TYR 0.013 0.001 TYR E 247 PHE 0.016 0.001 PHE O 53 TRP 0.013 0.001 TRP a 235 HIS 0.005 0.001 HIS H 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (37472) covalent geometry : angle 0.58384 / 0.29 (50721) hydrogen bonds : bond 0.04439 / 2.99 ( 2249) hydrogen bonds : angle 4.33720 / 3.11 ( 6582) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 267 time to evaluate : 1.506 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: B 236 TYR cc_start: 0.9450 (OUTLIER) cc_final: 0.8568 (t80) REVERT: B 504 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9053 (mm) REVERT: D 445 MET cc_start: 0.9314 (mmt) cc_final: 0.9024 (mmm) REVERT: E 46 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8814 (pp) REVERT: E 408 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7955 (tp30) REVERT: E 434 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.8019 (mp0) REVERT: E 445 MET cc_start: 0.8957 (mmt) cc_final: 0.8453 (mmt) REVERT: F 386 ASP cc_start: 0.8511 (m-30) cc_final: 0.8219 (m-30) REVERT: G 31 MET cc_start: 0.8786 (ttp) cc_final: 0.8550 (ttp) REVERT: G 155 MET cc_start: 0.8159 (tpp) cc_final: 0.7930 (tpp) REVERT: H 95 MET cc_start: 0.7251 (mmm) cc_final: 0.7012 (mmm) REVERT: I 11 MET cc_start: -0.0709 (ttt) cc_final: -0.1100 (ttt) REVERT: J 6 MET cc_start: -0.0157 (mmp) cc_final: -0.1010 (ptt) REVERT: L 6 MET cc_start: 0.5940 (mtm) cc_final: 0.5051 (ttm) REVERT: L 8 LEU cc_start: 0.6122 (OUTLIER) cc_final: 0.5842 (mp) REVERT: L 65 MET cc_start: 0.1682 (mmm) cc_final: 0.1435 (ptm) REVERT: M 17 MET cc_start: 0.3774 (mtt) cc_final: 0.1611 (tpp) REVERT: N 16 MET cc_start: 0.5621 (mmm) cc_final: 0.4875 (tpp) REVERT: P 6 MET cc_start: 0.4207 (mmt) cc_final: 0.3812 (ptp) REVERT: P 11 MET cc_start: 0.5003 (tpp) cc_final: 0.4330 (mpp) REVERT: Q 17 MET cc_start: 0.7110 (mtm) cc_final: 0.5981 (tpt) REVERT: Q 54 PHE cc_start: 0.5903 (m-80) cc_final: 0.5615 (m-80) REVERT: Q 65 MET cc_start: 0.5666 (tpt) cc_final: 0.5392 (tpt) REVERT: Q 72 LEU cc_start: 0.5898 (OUTLIER) cc_final: 0.5648 (mm) REVERT: R 17 MET cc_start: 0.2336 (ttp) cc_final: 0.2024 (tmm) REVERT: S 31 LEU cc_start: 0.6453 (tp) cc_final: 0.5942 (mt) REVERT: W 109 ASP cc_start: 0.8132 (t0) cc_final: 0.7833 (t0) REVERT: X 104 GLN cc_start: 0.8565 (pp30) cc_final: 0.8236 (pt0) REVERT: X 147 ASP cc_start: 0.7557 (m-30) cc_final: 0.7354 (t70) REVERT: X 150 ASP cc_start: 0.7934 (t0) cc_final: 0.7428 (m-30) REVERT: Y 26 TRP cc_start: 0.3805 (t60) cc_final: 0.2740 (m100) REVERT: Y 73 GLN cc_start: 0.7007 (tp-100) cc_final: 0.6510 (pt0) REVERT: Y 115 ARG cc_start: 0.8949 (ttp80) cc_final: 0.8697 (tpt90) REVERT: a 168 MET cc_start: 0.6529 (mmt) cc_final: 0.5519 (tpp) REVERT: a 215 MET cc_start: 0.3077 (mmp) cc_final: 0.2679 (mmp) outliers start: 56 outliers final: 42 residues processed: 310 average time/residue: 0.2302 time to fit residues: 119.7366 Evaluate side-chains 308 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 259 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 178 MET Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 228 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 229 optimal weight: 8.9990 chunk 366 optimal weight: 5.9990 chunk 443 optimal weight: 8.9990 chunk 462 optimal weight: 7.9990 chunk 421 optimal weight: 20.0000 chunk 214 optimal weight: 9.9990 chunk 399 optimal weight: 0.5980 chunk 370 optimal weight: 8.9990 chunk 258 optimal weight: 8.9990 chunk 92 optimal weight: 0.8980 chunk 224 optimal weight: 4.9990 overall best weight: 4.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 15 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.081943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.052038 restraints weight = 154620.758| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 3.18 r_work: 0.2841 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 37472 Z= 0.223 Angle : 0.649 13.540 50721 Z= 0.325 Chirality : 0.043 0.301 5914 Planarity : 0.004 0.060 6540 Dihedral : 5.862 151.455 5241 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.31 % Favored : 97.67 % Rotamer: Outliers : 1.38 % Allowed : 12.66 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.12), residues: 4799 helix: 1.77 (0.10), residues: 2690 sheet: 0.49 (0.22), residues: 553 loop : -0.08 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 129 TYR 0.017 0.001 TYR E 247 PHE 0.019 0.001 PHE O 53 TRP 0.014 0.001 TRP a 235 HIS 0.009 0.001 HIS H 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 (37472) covalent geometry : angle 0.64922 / 0.32 (50721) hydrogen bonds : bond 0.04803 / 3.25 ( 2249) hydrogen bonds : angle 4.48109 / 3.21 ( 6582) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9598 Ramachandran restraints generated. 4799 Oldfield, 0 Emsley, 4799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 261 time to evaluate : 1.521 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: B 236 TYR cc_start: 0.9495 (OUTLIER) cc_final: 0.9185 (t80) REVERT: B 504 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9027 (mm) REVERT: C 86 MET cc_start: 0.9039 (ptp) cc_final: 0.8833 (ptp) REVERT: E 46 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8805 (pp) REVERT: E 408 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7982 (tp30) REVERT: E 434 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: E 445 MET cc_start: 0.8963 (mmt) cc_final: 0.8485 (mmm) REVERT: G 31 MET cc_start: 0.8789 (ttp) cc_final: 0.8474 (ttp) REVERT: G 155 MET cc_start: 0.8182 (tpp) cc_final: 0.7869 (tpp) REVERT: H 95 MET cc_start: 0.7289 (mmm) cc_final: 0.7077 (mmm) REVERT: I 11 MET cc_start: -0.0405 (ttt) cc_final: -0.0779 (ttt) REVERT: J 6 MET cc_start: -0.0368 (mmp) cc_final: -0.1192 (ptt) REVERT: L 8 LEU cc_start: 0.6119 (OUTLIER) cc_final: 0.5893 (mp) REVERT: L 65 MET cc_start: 0.2191 (mmm) cc_final: 0.1718 (ptm) REVERT: M 17 MET cc_start: 0.3664 (mtt) cc_final: 0.1569 (tpp) REVERT: N 16 MET cc_start: 0.5494 (mmm) cc_final: 0.4780 (tpp) REVERT: O 75 MET cc_start: 0.1401 (tmm) cc_final: 0.1175 (tmm) REVERT: P 6 MET cc_start: 0.4312 (mmt) cc_final: 0.3771 (ptp) REVERT: P 11 MET cc_start: 0.4602 (tpp) cc_final: 0.4023 (mpp) REVERT: Q 11 MET cc_start: 0.6934 (tpt) cc_final: 0.6247 (mmp) REVERT: Q 17 MET cc_start: 0.7084 (mtm) cc_final: 0.5893 (tpt) REVERT: Q 54 PHE cc_start: 0.5685 (m-80) cc_final: 0.5482 (m-80) REVERT: Q 65 MET cc_start: 0.5796 (tpt) cc_final: 0.5529 (tpt) REVERT: R 17 MET cc_start: 0.2462 (ttp) cc_final: 0.1924 (tmm) REVERT: X 104 GLN cc_start: 0.8604 (pp30) cc_final: 0.8246 (pt0) REVERT: X 150 ASP cc_start: 0.7961 (t0) cc_final: 0.7441 (m-30) REVERT: Y 26 TRP cc_start: 0.3665 (t60) cc_final: 0.2800 (m100) REVERT: Y 73 GLN cc_start: 0.7068 (tp-100) cc_final: 0.6571 (pt0) REVERT: Y 115 ARG cc_start: 0.8982 (ttp80) cc_final: 0.8744 (tpt90) REVERT: a 168 MET cc_start: 0.6489 (mmt) cc_final: 0.5526 (tpp) outliers start: 53 outliers final: 44 residues processed: 300 average time/residue: 0.2304 time to fit residues: 116.0487 Evaluate side-chains 302 residues out of total 3834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 252 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 170 HIS Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 178 MET Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain H residue 4 TYR Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 58 HIS Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain O residue 11 MET Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain a residue 121 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 344 optimal weight: 0.0070 chunk 435 optimal weight: 20.0000 chunk 357 optimal weight: 8.9990 chunk 324 optimal weight: 0.0980 chunk 135 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 379 optimal weight: 50.0000 chunk 5 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 208 optimal weight: 0.9980 overall best weight: 1.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 294 HIS G 157 GLN ** O 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 15 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.083494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.053902 restraints weight = 153929.614| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.24 r_work: 0.2892 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37472 Z= 0.120 Angle : 0.594 13.007 50721 Z= 0.295 Chirality : 0.041 0.305 5914 Planarity : 0.004 0.066 6540 Dihedral : 5.679 147.000 5241 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.88 % Favored : 98.10 % Rotamer: Outliers : 1.23 % Allowed : 13.03 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.12), residues: 4799 helix: 1.89 (0.10), residues: 2688 sheet: 0.62 (0.22), residues: 550 loop : -0.00 (0.16), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 51 TYR 0.016 0.001 TYR a 94 PHE 0.037 0.001 PHE Q 76 TRP 0.014 0.001 TRP a 235 HIS 0.004 0.001 HIS H 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (37472) covalent geometry : angle 0.59402 / 0.30 (50721) hydrogen bonds : bond 0.04318 / 2.92 ( 2249) hydrogen bonds : angle 4.33129 / 3.10 ( 6582) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10715.35 seconds wall clock time: 184 minutes 0.59 seconds (11040.59 seconds total)